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Using Population Genetics of Human Head and Clothing Lice to Elucidate Human Evolution

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Title:
Using Population Genetics of Human Head and Clothing Lice to Elucidate Human Evolution
Creator:
Toups, Melissa
Place of Publication:
[Gainesville, Fla.]
Publisher:
University of Florida
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Language:
english
Physical Description:
1 online resource (49 p.)

Thesis/Dissertation Information

Degree:
Master's ( M.S.)
Degree Grantor:
University of Florida
Degree Disciplines:
Zoology
Committee Chair:
Reed, David L.
Committee Members:
Soltis, Pamela S.
Miyamoto, Michael M.
Graduation Date:
8/9/2008

Subjects

Subjects / Keywords:
Clothing ( jstor )
Genomes ( jstor )
Hair ( jstor )
Head ( jstor )
Humans ( jstor )
Lice ( jstor )
Parasite hosts ( jstor )
Population estimates ( jstor )
Roux ( jstor )
Typhus ( jstor )
Zoology -- Dissertations, Academic -- UF
humanus, pediculus
Genre:
Electronic Thesis or Dissertation
born-digital ( sobekcm )
Zoology thesis, M.S.

Notes

Abstract:
Parasites are often used as proxies for investigating their host evolution. This is particularly common in the study of human evolution. In this study, I use the genetics of human head and clothing lice to address the origin of clothing use in humans and develop new microsatellite loci to further the study of louse population genetics. Parasitic head and clothing use may be used to address the origin of clothing use because the divergence between these taxa is indicative of a minimum age of clothing use. When humans lost their body hair 1.2 million years ago, lice that once roamed the entire body were isolated on the head, and recolonized the body with the advent of clothing use. Coalescent analyses of multilocus data indicate that head and clothing lice diverged between 650,000 and 700,000 years ago, indicating that clothing was an innovation of archaic hominids, not modern humans as previously thought. This is consistent with several other lines of evidence for an archaic origin of clothing, such as the presence of archaic hominids in high latitudes during this time period and the appearance of tools used to scrape hide 300,000 years ago. Furthermore, our analyses indicate that only a small proportion of head lice initially colonized clothing. Finally, I developed eleven polymorphic microsatellite loci for head and clothing lice. All loci were tested on eighteen head louse individuals, and the number of alleles ranged from three to seven. These loci will be valuable for further study of louse population genetics. ( en )
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In the series University of Florida Digital Collections.
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Includes vita.
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Includes bibliographical references.
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This bibliographic record is available under the Creative Commons CC0 public domain dedication. The University of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
Thesis:
Thesis (M.S.)--University of Florida, 2008.
Local:
Adviser: Reed, David L.
Electronic Access:
RESTRICTED TO UF STUDENTS, STAFF, FACULTY, AND ON-CAMPUS USE UNTIL 2010-08-31
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by Melissa Toups.

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Copyright Toups, Melissa. Permission granted to the University of Florida to digitize, archive and distribute this item for non-profit research and educational purposes. Any reuse of this item in excess of fair use or other copyright exemptions requires permission of the copyright holder.
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8/31/2010
Resource Identifier:
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Classification:
LD1780 2008 ( lcc )

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Finally, I developed eleven polymorphic microsatellite loci for head and clothing lice. All

loci were tested on eighteen head louse individuals, and the number of alleles ranged from three

to seven. These loci will be valuable for further study of louse population genetics.









because the only known nonhuman reservoir, the flying squirrel (Glaucomys volans volans), is

native to Mexico (Bozeman et al. 1975). Historically, this has been challenged by the lack of

evidence that clothing lice successfully accompanied the Amerindians in the migration to the

New World. However, a recent ancient DNA study by Raoult et al. (2008) demonstrated that

head lice belonging to a pre-Columbian Peruvian mummy belonged to the same clade of lice that

contains clothing lice, suggesting that clothing lice likely colonized the New World along with

the Amerindians. This finding weakens the argument that clothing lice did not exist in the pre-

Columbian New World. However, the first definitive evidence of typhus occurred in the

fifteenth century in Spain and sixteenth century in Mexico (Raoult et al. 2004).

Rickettsiaprowazekii is a pathogen to the louse as well as its human host. Clothing lice

contract typhus through feeding on an infected person, though transmission rate is not 100%

(Wolbach et al. 1922). Once ingested, R. prowazekii infects the midgut epithelial cells of the

louse and multiplies (Raoult and Roux 1999). These cells become enlarged and burst, which

releases the bacteria into the gut lumen (Raoult and Roux 1999). R. prowazekii is then excreted

from the louse in large quantities in the feces (Raoult and Roux 1999). Since the ruptured

epithelial cells of the gut are not replaced, infection with R. prowazekii eventually kills the louse

(Raoult and Roux 1999). After the cells rupture, the ingested blood will flow freely through the

intestine and occasionally cause the louse to turn red (Bozeman et al. 1975). Interestingly, R.

prowazekii cannot be transmitted vertically from mother to egg (Buxton 1940; Houhamdi et al.

2002).

The salivary glands of the louse do not contain R. prowazekii (Arkwright and Bacot 1923),

and therefore R. prowazekii is not transmitted to the human host through the louse bite. R.

prowazekii is transmitted to the human host when infective feces are rubbed into open sores









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10,000,000 generations with samples taken every 1,000 generations and the first 1,000,000

generations were discarded as bum-in.

Isolation with Migration Analysis

A Bayesian isolation-with-migration coalescent analysis (Hey and Nielsen 2004; Nielsen

and Wakeley 2001) was performed on the multilocus louse dataset using the program IM (Hey

2005). The isolation-with-migration coalescent model assumes that an ancestral population of

effective size NA diverges at some time t into two daughter populations of initial size sNA and (1-

s)NA, both of which then experience independent exponential growth and migration between

populations (with rates mi and m2). All IM analyses were performed with a Hasegawa-Kishino-

Yano (HKY) nucleotide substitution model for all four loci, and the upper bound of the prior

distribution for the time of divergence was set to 5.5MYA, following best estimates for the

human-chimpanzee divergence (see above). Estimates of i from the evolutionary rate calculation

above were used to convert population mutation parameter estimates (i.e. t) from mutational

units into absolute units. All other priors were conservatively estimated from preliminary runs

with very broad uniform prior distributions to facilitate adequate Markov chain mixing. All

Markov chains were run for 600 million generations and sampled every 600 generations. Ten

replicate runs with unique seed values were performed to ensure Markov chain convergence.

Results

Independent runs of IM analyses converged on similar posterior distributions

(summarized in Figure 1). Peaks in the distribution were taken as point estimates of population

genetic parameters. At the time of completion, all estimates of effective sample size exceeded

400. Estimates of 0 and t were converted to effective population size and absolute time-since-









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Busvine, J. R., 1948. The 'head' and 'body' races ofPediculus humanus L. Parasitology 39:1-
16.

Busvine, J. R. 1978. Evidence from double infestations for the specific status of human head and
body lice (Anoplura). Syst. Entomol. 3:1-8.

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that occur among three lineages ofP. humanus are potentially informative about the relationships

between archaic hominids and modern humans (Reed et al. 2004).

Currently, evolutionary biologists and anthropologists studying lice rely on three nuclear

markers, EF1-alpha, RPII, and 18S, four mitochondrial markers, COI, CytB, ND4, and control

region, and five microsatellite loci (Leo and Barker 2005) to draw inferences about the

population genetics of head and clothing lice. With the release of the P. humanus genome, a

variety of new molecular tools will soon be available, such as a variety of nuclear genes, SNPs,

microsatellites, and oligonucleotide arrays. These new tools will allow researchers to address

biological and anthropological questions whose answers have been elusive thus far.









primates and confirmed the date of the human-chimp divergence to be 5-7 million years ago.

Another study by Reed et al. (2007) dated the divergence between two sister taxa of lice, the

gorilla louse, Pthirus gorillae, and the human pubic louse, Pthiruspubis, to be three million

years. This date is significantly earlier than the human-chimp ancestor and gorilla divergence of

7-8 million years ago (Reed et al. 2007), suggesting a host switch from gorillas to humans.

Sucking lice, particularly P. humanus, has also provided insights into the population

genetics of archaic and modern humans. Reed et al. (2004) confirmed that head and clothing lice

went through a population bottleneck and subsequent expansion out of Africa with modern

humans. Reed et al. (2004) also determined that there are three mitochondrial lineages of P.

humanus, one that contains head and clothing lice and two that contain only head lice. Also,

ancient DNA from P. humanus of a 1000 year-old Peruvian mummy indicates that the clade

containing head and clothing lice was in the New World prior to European colonization (Raoult

et al. 2008). This discovery supports the hypothesis that the bacterial agent of typhus, Rickettsia

prowazekii, may be the result of a New World origin that involves a host switch of the bacterium

from its reservoir host, the flying squirrel, Glaucomys volans volans (Raoult et al. 2008).

Population genetics of P. humanus has the potential to address several other questions

relating to human evolutionary history. In order to address the origin of clothing use, Kittler et

al. (2003, 2004) used unspecified phylogenetic methods to date the age of the clade that

contained both head and clothing lice to 107,000 years ago. Though the phylogenetic methods

used by Kittler et al. (2003, 2004) may have been inappropriate for a population-level question,

lice may provide insight into the origin of the clothing use through coalescent methods to date

the population divergence between head and clothing lice. Also, the taxonomic status of head

and clothing lice may be addressed using molecular techniques. Further, the deep divergences









USING POPULATION GENETICS OF HUMAN HEAD AND CLOTHING LICE TO
ELUCIDATE HUMAN EVOLUTION





















By

MELISSA ANNE TOUPS


A THESIS PRESENTED TO THE GRADUATE SCHOOL
OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT
OF THE REQUIREMENTS FOR THE DEGREE OF
MASTER OF SCIENCE

UNIVERSITY OF FLORIDA

2008









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11:201-220.

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humanus and Phthiruspubis. Parasitology 11:329-346.

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Pediculus. Parasitology 12:136-153.

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Genom. Hum. G. 6:165-183.

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the primary endosymbiont of human head and body lice. FASEB J. 21:1058-1066.

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2008. Molecular identification of lice from pre-Columbian mummies. J. Infect. Dis.
197:535-543.

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Clin. N. Am. 18:127-+.

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TABLE OF CONTENTS

page

A C K N O W L E D G M E N T S ..............................................................................................................4

LIST OF TABLES ......... ..... .... ........... ....................................6

LIST OF FIGURES .................................. .. ..... ...................... .7

ABSTRAC T ............................................ ...............................................

CHAPTER

1 THE NATURAL HISTORY OF THE HUMAN HEAD AND CLOTHING LOUSE,
P ediculus hum anus ..................................................................... .................... 10

Introduction ........... ....... ....................................10
Ecology of P hum anus ......... ................ ...... .......... ..................... 11
Taxonomic Debate ................................................ ..................... ......... 12
M medical Im portance of P. hum anus................................................ ............................ 14
L house Transm ission.......... ............ .. ... ............ .. ............ .. .15
Clothing Lice as Vectors of Bacterial Pathogens............. .............................................16
Rickettsia prowazekii ......... .. .......................... ............ .......... .... 16
Borrelia recurrentis ....................................................... .............. .. 18
Bartonella quintana......... ......................._................ .. ........ .. ........ 19
Sequencing of the Clothing Louse Genome................................................................. 20
Lice as Markers of Human Evolutionary History..................................... ...............22

2 POPULATION GENETIC ANALYSIS OF Pediculus humanus PROVIDES INSIGHT
INTO THE ORIGIN OF HUMAN CLOTHING....................................... ............... 25

Intro du action ................... .......................................................... ................ 2 5
M materials and M methods ...................................... .. ......... ......... .....28
M molecular D ata ...........................................................................................28
E volutionaryR ate C alculation .............................................................. .....................28
Isolation w ith M igration A analysis ........................................................ ............... 29
R e su lts ................... ...................2...................9..........
D iscu ssio n ................... ...................3...................0..........

3 CHARACTERIZATION OF ELEVEN POLYMORPHIC MICROSATELLITE LOCI
FROM THE HUMAN HEAD AND CLOTHING LOUSE, Pediculus humanus..................37

R E F E R E N C E S ........................................................ ...................................4 1

B IO G R A PH IC A L SK E T C H .............................................................................. .....................49









(1946) presented an argument that head and clothing lice are probably too similar to be

considered distinct species, but may represent "species in the making." Fahrenholz (1915,

1916), Busvine (1944, 1978), and Schaefer (1978), on the other hand, argued that the differences

observed between head and clothing lice were more than sufficient to recognize these taxa as

distinct species. This taxonomic confusion regarding the species status of head and clothing lice

continues today, primarily because of the ecological differences.

In recent years, the specific status of head and clothing lice has also been addressed in

studies examining louse isozymes (Amevigbe et al. 2000), louse primary endosymbionts (Allen

et al. 2007; Perotti et al. 2007; Sasaki-Fukatsu et al. 2006), and louse bacterial pathogens (Sasaki

et al. 2006; but see Parola et al. 2006). While the results of the endosymbiont and bacteria work

indicate that head and clothing lice are conspecific, the results of the isozyme work indicate that

genetic differentiation may exist between these louse forms. There also has been a series of

DNA-based studies that have directly addressed the specific status of head and clothing lice

(Kittler et al. 2003; Leo and Barker 2005; Leo et al. 2002; Reed et al. 2004; Yong et al. 2003).

The majority of these molecular-based studies have concluded that head and clothing lice are not

distinct species because of the lack of reciprocal monophyly between head and clothing lice.

Reed et al. (2004) found three deeply divergent mitochondrial clades of lice, all of which

contained head lice, whereas only one of which contained clothing lice. Furthermore, all three

clades had unique geographic distributions: 1) one clade was composed of a worldwide

distribution of both head and clothing lice, 2) one clade consisted only of head lice from North

America, Central America, Australia, and Europe, and 3) a second clade that contained only head

lice from Africa and Nepal (further sampling is necessary to determine the geographic range of

lice belonging to this third mitochondrial lineage). These mitochondrial results, the presence of









CHAPTER 2
POPULATION GENETIC ANALYSIS OF Pediculus humanus PROVIDES INSIGHT INTO
THE ORIGIN OF HUMAN CLOTHING

Introduction

Biologists studying organisms with reduced genetic variation have begun to regularly

exploit host parasites and pathogens to track events in the evolutionary history of the host. This

is particularly true in the fields of conservation (Whiteman and Parker 2005), invasive species

(Meusnier et al. 2001), and human evolution research (reviewed in Wirth et al. 2005), where host

genetic variation is greatly reduced. In such scenarios, the parasite may generate more genetic

diversity than the host due to its generally shorter generation time, which increases its

evolutionary rate. Additionally, parasites often have larger effective population sizes, and

therefore maintain more genetic variation through bottleneck events. The faster evolutionary

rate of the parasite and increased genetic variation may therefore capture evolutionary events that

are not coded in host DNA, allowing biologists to study the evolutionary history of the host

through analysis of parasite DNA. This has been used most often in studies of human history

(reviewed in Wirth et al. 2005), where JC virus, herpes simplex virus 1, human papillomaviruses,

and Helicobacterpylori have been used to track human evolution.

Microparasites (bacteria and viruses) often reproduce clonally, and are thus highly

susceptible to selective sweeps at a few loci producing patterns of genomic diversity that do not

reflect the history of the host (Grenfell et al. 2004; Nieberding et al. 2006; Rich et al. 1998).

Conversely, macroparasites (such as parasitic arthropods) often reproduce sexually and may

therefore track host evolutionary history more accurately because selective sweeps affect only

closely linked loci in their genomes (Grenfell et al. 2004). For this reason, the use of

macroparasites, such as pinworms (Araujo et al. 2008) and lice (Raoult et al. 2008; Reed et al.

2004), has become increasingly common in the study of human evolution.









the homeless populations in developed countries in the United States and Western Europe

(Brouqui et al. 1996; Drancourt et al. 1995; Koehler et al. 1997; Raoult and Roux 1999).

As their names imply, head and clothing lice are spatially segregated on their human hosts.

Head lice are found on the head and attach their eggs to the base of hair shafts, most often behind

the ears, whereas clothing lice are found on the body and in clothing and prefer to attach their

eggs to the pleats and seams of clothing, particularly the undergarments, rather than body hair

(Burgess 1995; Buxton 1946; Maunder 1982; Nuttall 1917). In the absence of clothing, clothing

lice will infest beads and necklaces (Buxton 1946; Busvine 1978). Clothing lice are believed to

have evolved from head lice, invading the body region only recently with the advent of clothing

use in modern humans (Burgess 1995; Kittler et al. 2003; Kittler et al. 2004). Head lice require

more frequent blood meals than do clothing lice (Alpatov and Nastjukova 1955). Head and

clothing lice tend to return to their preferred ecological habitat when displaced, and clothing lice

are known to be especially attracted to areas that are occupied by other clothing lice or clothing

louse feces (Wigglesworth 1941; Mumcuoglu et al. 1986). Morphologically, clothing lice (and

their eggs) are generally larger than head lice, most notably in the length of the tibia on the

second pair of legs (Scholl, 1955; Busvine 1978; Reed et al. 2004). However, these

morphological differences are small, and were apparent to Reed et al. (2004) only when assessed

with discriminant function analysis.

Taxonomic Debate

The species status of human Pediculus has been a topic for debate for over a century.

Ferris (1951) and Burgess (1995) provide detailed accounts of this taxonomic confusion. Nuttall

(1917, 1919a, 1919b, 1920) and Ferris (1935) strongly argued that head and clothing lice

represented, at most, subspecies, and that the morphological, behavioral, and ecological

differences between these two louse groups represented natural intraspecific variation. Buxton









Sucking lice (Phthiraptera: Anoplura) have cospeciated with their primate hosts for at

least the last 22.5 million years (Reed et al. 2004). These lice are permanent, obligate

ectoparasites that require direct contact between their primate hosts for transmission (Burgess

2004; Canyon et al. 2002). Molecular examination of these lice has confirmed events known

from primate history, such as the human-chimp divergence 5-7 million years ago (Reed et al.

2004). Additionally, the study of human lice (Pediculus humanus) has confirmed events in

human demographic history, such as the population expansion of anatomically modern humans

100,000 years ago (Reed et al. 2004). These findings indicate that human lice have great utility

for the study of human population history.

Two varieties of human lice, head and clothing lice (both P. humanus; see Light et al.

2008), may also provide insights into human evolution not recorded in human genetic data,

specifically the origin of clothing use. Determining the origin of clothing use has been primarily

inferential in anthropological literature as most materials used for clothing (furs, skin, cloth)

degrade rapidly and are thus unknown in the archaeological record of the Late Pleistocene.

Archaeological evidence for the use of tailored clothing, such as needles, first appears -40,000

years ago (Delson et al. 2000). Earlier evidence for tools used to scrape hide appears -300,000

years ago (Toth and Schick 1993); however, there is no definitive evidence that these tools were

used to make even rudimentary clothing. The inability of the archaeological record to answer this

question suggests that an innovative approach is necessary.

The biology of human head and clothing lice makes them potentially useful markers to

infer the origin of clothing use in humans. Molecular data suggest that humans lost their body

hair approximately 1.2 million years ago (Rogers et al. 2004). Prior to body hair loss, lice in the

genus Pediculus likely occurred more uniformly across the body, but upon body hair loss









Cutler, S. J., J. Moss, M. Fukunaga, D. J. Wright, D. Fekade, and D. Warrell. 1997. Borrelia
recurrentis characterization and comparison with relapsing-fever, Lyme-associated, and
other Borrelia spp. Int. J. Syst. Bacteriol. 47:958-968.

Delson, E., Tattersall, I., Van Couvering, J., and Brooks, A. (2000). Encyclopedia of Human
Evolution and Prehistory. Garland, New York, NY.

Dennell, R. 2003. Dispersal and colonisation, long and short chronologies: how continuous is
the Early Pleistocene record for hominids outside East Africa? J. Hum. Evol. 45:421-440.

Dieringer, D. and C. Schlotterer. 2003. Microsatellite analyser (MSA): a platform independent
analysis tool for large microsatellite data sets. Mol. Ecol. Notes 3:167-169.

Drancourt, M., J. L. Mainardi, P. Brouqui, F. Vandenesch, a. Carta, F. Lehnert, J. Etienne, F.
Goldstein, J. Acar, and D. Raoult. 1995. Bartonella (Rochalimaea) Quintana
Endocarditis in 3 Homeless Men. New Engl. J. Med. 332:419-423.

Drummond, A. J., S. Y. Ho, M. J. Phillips, and A. Rambaut. 2006. Relaxed phylogenetics and
dating with confidence. PLoS Biol. 4:e88.

Drummond, A. J., and A. Rambaut. 2007. BEAST: Bayesian evolutionary analysis by sampling
trees. BMC Evol. Biol. 7:214.

Edwards, S. V., and P. Beerli. 2000. Perspective: gene divergence, population divergence, and
the variance in coalescence time in phylogeographic studies. Evolution 54:1839-1854.

Fahrenholz, H. 1915. Lause verschiedener Menschenrassen. Z. Morphol. Anthropol. 17:591-
602.

Fahrenholz, H. 1916. Zur Nomenklatur einiger Anopluren-Arten. Zool. Anz. 47:269-272.

Farrell, B. D. 1998. "Inordinate fondness" explained: Why are there so many beetles? Science
281:555-559.

Ferris, G. F. 1951. The sucking lice. Mem. Pacif. Cst. Ent. Soc. 1:1-320.

Ferris, G. F. 1935. Contribution towards a monograph of the sucking lice. Part VIII. Stanford
Univ. Publs. Biol. Sci. 2:527-634.

Finlayson, C. 2005. Biogeography and evolution of the genus Homo. Trends Ecol. Evol.
20:457-463

Foucault, C., P. Brouqui, and D. Raoult. 2006. Bartonella quintana characteristics and clinical
management. Emerg. Infect. Dis. 12:217-223.









there is no evidence to suggest that clothing lice can successfully colonize the head louse niche,

which provides further support for unidirectional gene flow.

Coalescent methods that use multiple loci for population genetic inference reduce

uncertainty in estimates of divergence time related to genealogical stochasticity (Edwards and

Beerli 2000). This allows us to estimate the divergence of head and clothing lice, as opposed to

dating the origin of the clade of head and clothing lice using phylogenetic methods (Kittler et al.

2003; Kittler et al. 2004). By using population genetic methods to date the divergence, we are

able to obtain a more precise estimate of when populations of P. humanus began to colonize the

clothing niche. Furthermore, our analyses uncovered a high rate of migration (m = 1.16) from

head to clothing lice, further indicating that the divergence between head and clothing lice is a

population genetic process.

Our point estimate of 650,000 years ago (90% HPD 225kya-6mya) indicates that head

and clothing lice diverged significantly earlier than previously thought and suggests that the use

of rudimentary clothing originated with archaic hominids, not anatomically modern humans,

which arose only within the last 120,000 years (Pakendorf and Stoneking 2005). Also, it is

important to note that the divergence of human head and clothing lice provides a minimum date

for the origin of clothing use; it is possible that the clothing niche existed for some time before

parasitic lice successfully colonized clothing.

There are both adaptive and neutral explanations for why and how clothing use arose.

Clothing may have arisen in Africa because it conferred an advantage to archaic hominids living

in high altitudes. Alternatively, clothing use may have arisen for decorative purposes. Though

our study cannot disentangle these alternatives, it can provide some insight as to where clothing

use arose.



































2008 Melissa Toups









experience bacteremia (Foucault et al. 2006). Infection with B. quintana is the least fatal of the

known louse borne diseases, with a mortality rate of <1% (Raoult and Roux 1999). Little is

known about the effectiveness of antibiotic treatment of trench fever, since most data from

infections occurred prior to the use of antibiotics (Raoult and Roux 1999). However, a

combination of doxycyline and gentamicin has been shown to be effective (Raoult and Roux

1999).

Sequencing of the Clothing Louse Genome

The sequencing and annotation of the clothing louse genome was recently completed,

although its final publication has not occurred. The completed genome will provide important

genetic information for the biomedical community. The bacterial genomes for pathogens carried

by clothing lice, R. prowezii, (Anderson et al. 1998), B. quintana (Alsmark et al. 2004), and two

species of Borrelia (Fraser et al. 1997; Glockner et al. 2004) have already been sequenced. The

sequenced genome of P. humanus will provide insights into host-vector-pathogen interactions

(Pittendrigh et al. 2006). The discovery of genes that are involved in vitellogenin production or

olfactory receptors involved in locating potential hosts may provide targets for louse-specific

pesticides (Pittendrigh et al. 2006). The development of oligonucleotide arrays and RNAi may

aid in gene discovery. Further, oligonucleotide arrays may aid in determining which genes are

induced or repressed during changes in louse behavior and environment, such as between head

lice and clothing lice (Pittendrigh et al. 2006). Finally, sequencing of the P. humanus genome

has the potential to determine if head lice are able to serve as vectors for bacterial pathogens

(Pittendrigh et al. 2006).

In addition to the importance of the P. humanus genome to the biomedical community,

the genome will also provide insights to the evolutionary biology community. P. humanus will

be the first genome sequenced of a hemimetabolous insect. Already, the small size (105MB) of









Materials and Methods


Molecular Data

All available DNA sequence data for the following genes were downloaded from

GenBank (see Supplemental Table 1): mitochondrial gene COI (166 sequences) and the nuclear

genes 18S rRNA (22 sequences), EF-la (40 sequences; not including any of the sequences from

(Yong et al. 2003), which were shown by Light et al. (2008) to be contaminants, and RPII (53

sequences). Sequences for the outgroup taxon Pediculus schaeffi (parasitic on chimpanzees)

were downloaded from GenBank for each of the four genes (Supplemental Table 1). All COI,

EF-la and RPII sequences were aligned by hand using MacClade (Maddison and Maddison

2005) and manually edited to maintain proper reading frames using Se-Al v2.01al 1. All 18S

rDNA sequences were aligned manually in reference to secondary structure (Gillespie et al.

2004; Gillespie et al. 2005); alignment available at the jRNA web site) and ambiguously aligned

sites were removed before analysis.

EvolutionaryRate Calculation

Phylogenies and evolutionary rates (ti) for each of the four genes were co-estimated

under a "relaxed" (uncorrelated lognormal distribution) molecular clock using BEAST v.1.4.6

(Drummond et al. 2006; Drummond and Rambaut 2007). Estimates of [t were calibrated under

an assumption of host-louse cospeciation, which has been demonstrated by Reed et al. (2004) for

Hominidae. Specifically, an exponential prior distribution with a lower bound of 5MYA and

mean of 5.5MYA was placed on the divergence of P. humanus and P. schaeffi that reflects

current estimates for the divergence of their human and chimpanzee hosts (Kumar and Hedges

1998), respectively. All analyses were performed with a GTR + I + F nucleotide substitution

model and a Yule birth-death prior on the tree topology. All Markov chains were run for









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regained: the evolutionary history of anthropoid primate lice. BMC Biol. 5:-.

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analysis of lice supports direct contact between modem and archaic humans. PLoS Biol.
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recent population bottleneck throughout the world populations of Plasmodiumfalciparum.
Proc. Natl. Acad. Sci. USA 95:4425-4430.

Robinson, D., N. Leo, P. Prociv, and S. C. Barker. 2003. Potential role of head lice, Pediculus
humanus capitis, as vectors of Rickettsiaprowazekii. Parasitol. Res. 90:209-211.

Rogers, A. R., D. Iltis and S. Wooding. 2004. Genetic variation at the MC1R locus and the time
since loss of human body hair. Curr. Anthropol. 4: 105-108.

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programmers. Methods. Mol. Biol. 132:365-386.

Sasaki, T., S. K. S. Poudel, H. Isawa, T. Hayashi, N. Seki, T. Tomita, K. Sawabe, and M.
Kobayashi. 2006. First molecular evidence of Bartonella quintana in Pediculus humanus
capitis (Phthiraptera: Pediculidae) collected from Nepalese children. J. Med. Entomol.
43:788-788.

Sasaki-Fukatsu, K., R. Koga, N. Nikoh, K. Yoshizawa, S. Kasai, M. Mihara, M. Kobayashi, T.
Tomita, and T. Fukatsu. 2006. Symbiotic bacteria associated with stomach discs of
human lice. Appl. Environ. Microbiol. 72:7349-7352.

Schaefer, C.W., 1978. Ecological separation of the human head lice and body lice (Anoplura:
Pediculidae). T. R. Soc. Trop. Med. H. 72:669-670.

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microbiological review. Medicine 48:129-149.

Takano-Lee, M., J. D. Edman, B. A. Mullens, and J. M. Clark. 2005. Transmission potential of
the human head louse, Pediculus capitis (Anoplura: Pediculidae). Int. J. Dermatol. 44:811-
816.

Toth, N., and K. Schick. 1993. Early stone industries and inferences regarding language and
cognition. Pp. 346-362 in K. R. Gibson and T. Ingold eds. Tools, Language and Cognition
in Human Evolution. Cambridge University Press, Cambridge.

Whiteman, N. K., and P. G. Parker. 2005. Using parasites to infer host population history: a
new rationale for parasite conservation. Anim. Conserv. 8:175-181.

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Annu. Rev. Entomol. 43:129-151.









parasitic louse to a single host species (Price et al. 2003). This often results in cospeciation

between louse and host, such as the twenty-five million year coevolution between primates and

their sucking lice (Reed et al. 2007; Reed et al. 2004).

Members of two louse families parasitize humans. The family Phthiridae includes the

human pubic louse, Pthiruspubis, and its sister taxon, the gorilla louse, Pthirus gorillae. P.

pubis likely switched from a gorilla-like host to an archaic hominid approximately 3 million

years ago (Reed et al. 2007). The family Pediculidae includes the species Pediculus humanus,

which exists as two morphotypes, the human head louse and human clothing louse, Pediculus

humanus capitis and P. humanus humanus, respectively. Pediculus humanus is thought to have

diverged from chimpanzee lice, Pediculus schaeffi, at the chimp-human divergence 5-7 million

years ago.

Ecology of P. humanus

Human head and clothing lice are found on every continent. Head lice are common

worldwide, infesting millions of school children every year. This resistance is due, in part, to the

evolution of resistance to insecticidal shampoos that are used to treat pediculosis (Burgess 1995).

Clothing lice are less prevalent, but are potentially more harmful because they are known vectors

of at least three bacterial pathogens in humans: Rickettsiaprowazekii (epidemic or louse- borne

typhus; but see Robinson et al. 2003), Borrelia recurrentis (louse-borne relapsing fever) and

Bartonella quintana (trench fever; Buxton 1946; but see Sasaki et al. 2006). The incidence of

clothing lice is determined by weather, humidity, poverty, and a lack of hygienic conditions

(Raoult and Roux 1999). Clothing lice, and consequently their bacterial pathogens, are most

common in areas with cold weather, where people wear multiple layers of clothes, and in areas

stricken by poverty or political and social unrest that prevent inhabitants from having multiple

sets of clothes (Raoult and Roux 1999). They are also becoming increasingly common among









the P. humanus genome relative to other insect genomes, such as Drosophila (175MB) and

Anopheles gambiae (260MB), is raising important evolutionary questions, particularly because

most other hemimetabolous insects are generally estimated to have large genomes (2000MB-

16,300MB) (Pittendrigh et al. 2006). In order to explain such a small genome size, several

questions related to genome composition are raised, such as the number and size of noncoding

regions and the number and types of repetitive elements (Pittendrigh et al. 2006). Further, is the

reduction in genome size a result of human parasitism, and if so, is it a result of selection for

metabolic or replication efficiency or ecological specialization for the human host (Pittendrigh et

al. 2006)? In addition to interesting biological questions raised by the small genome size,

evolutionary biologists can also use the P. humanus genome to search for genes that help resolve

relationships within Phthiraptera. Further, genes involved in parasitism of vertebrate hosts will

be identified (Pittendrigh et al. 2006).

The P. humanus genome project has achieved 8x coverage. Preliminary analyses indicate

that the genome is AT rich, with a GC content of only 27.5%. However, 56% of genes of P.

humanus occur in GC rich regions, indicating a slight bias for genes to occur in GC rich areas.

Currently, 11,214 genes have been identified, and 90% of those (10,187) share sequence

similarity to genes in other insects. Of the 11,214 genes, 9698 contain introns, of which the

average length is 303 base pairs and the average exon length is 238 base pairs. Only 1% of the

P. humanus genome consists of transposable elements, and both class I and class II elements are

present. When compared with other insect genomes, such as Apis mellifera, Drosphila

melanogaster, Anopheles gambiae, and Tribolium castaneum, P. humanus shows a reduction in

gene families associated with detoxification, such as the p450, GST, and esterase gene

superfamilies. The reduction in detoxification mechanisms is consistent with the life-history of










Table 3-1. Characteristics of eleven microsatellite loci for the human head and clothing louse, P.
humanus, including locus name, primer sequence, repeat motif, allele size range,
number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (HE),
and probability associated with Hardy-Weinberg equilibrium.
Repeat Allele Size
Locus Primer Sequence Motif (bp) Na Ho HE P
M2 2 F: TCTTGCAGTGTGTCTCTTTGC GA 392-412 4 0.056 0.678 0.000
R: CTATCGGAAATGTGCAGAGC
M2 3 F: TGATATTTTAGGCGCACAACC GA 364-370 4 0.059 0.497 0.000
R: GTCTCAATTCGGCCACTTCT
M2 4 F: TTCAGGATCTTCTGCCCAAC GA 308-316 4 0.056 0.662 0.000
R: GGGTTCGCAAAAAGGTGAC
M2 16 F: TAACGACCGCTTTTCGAGTT GA 242-266 6 0.111 0.697 0.000
R: GGGGTGAACTGGATGTTTCA
M2 17 F: GCCTAGCGAAAGCTCTGAAA TA 235-253 6 0.188 0.714 0.000
R: GAAGTATCATTTCGGCGTGA
M2 19 F: GGTGGCAAAAACCACTAATGA TA 182-198 4 0.278 0.486 0.050
R: TCCGTTAAAAATGGCAAAGG
M3 3 F: TGTTCCTGCTGGTAAACTTGC TAA 238-295 7 0.176 0.820 0.000
R: GAACGATCAATCTGCTTCTGC
M3 9 F: CCCGTAAAATATCCACGCTGT TTA 284-302 3 0.278 0.332 0.507
R: CTGGTCGGCTATGTTTTGCT
M3 11 F: CTCCTAACGGGAGCAAAGAA TTA 299-357 6 0.167 0.749 0.000
R: CCATACATATTAGTCGCCTTCCA
M3 18 F: CGTCGGAGGAATGTATAGGG GAC 275-299 4 0.111 0.303 0.011
R:GACAGTGACGGATCGAACG
M3 19 F: TTAAGAGCTGATGCCACGTC CAT 346-358 4 0.118 0.405 0.000
R: TCTGGAAAAGGACGAAAGGA









The mitochondrial clade of P. humanus that contains both head and clothing lice has the

genetic signature of a population expansion that occurred 100,000 years ago (Reed et al. 2004)

suggesting that these lice accompanied modern humans out of Africa. Because the date of

divergence of head and clothing lice only provides a minimum estimate for the origin of clothing

use, the technology to make clothing may have existed for some time prior to 650,000 years ago.

Anthropologists recognize multiple dispersals of hominid species out of Africa (Anton

and Swisher 2004; Dennell 2003; Finlayson 2005), with the first dispersal ofH. erectus

occurring approximately 2 million years ago (Anton and Swisher 2004; Dennell 2003; Finlayson

2005). Most of the evidence suggests that H. erectus populations outside of Africa were largely

confined to Southeast Asia, though there is some evidence ofH. erectus in northern Asia around

this time (Anton and Swisher 2004; Dennell 2003; Finlayson 2005). The permanence of these

earliest dispersals into northern latitudes has been questioned (Dennell 2003). Interestingly, our

estimate approximately coincides with the first evidence of permanent archaic hominid

settlements into high latitude regions of Europe and Central Asia between 800,000 and 500,000

years ago (Ascenzi et al. 1996; Carbonell et al. 1995; Dennell 2003; Ranov 1995). It is possible

that the archaic hominids that dispersed and successfully colonized colder climates 800,000 to

500,000 years ago may have possessed the knowledge to use furs and skins as rudimentary

clothing, which would have allowed them to survive and persist in the temperate climates of

Europe and Central Asia. Alternatively, it is conceivable that clothing use originated with

archaic hominids in Europe and Central Asia, and spread to archaic hominid populations in

Africa via intermittent contact. However, this is less likely, considering that archaic hominid

populations in Central Asia and Europe were likely spatially and temporally discontinuous




























To my family.









and exhibit heterozygote deficiency,it is likely the population tested that is out of Hardy-

Weinberg equilibrium, and not the loci.

Our results indicate that these microsatellites are clearly polymorphic in this population,

though not in Hardy-Weinberg equilibrium. Several possible explanations exist for why the

population may be out of Hardy-Weinberg equilibrium, such as high population substructure or

nonrandom mating. Additional populations should be screened to determine if this is specific to

the population of head lice in West Palm Beach, Florida, or if it is characteristic of the species in

general. Alternatively, further sampling of the population in West Palm may reveal a high level

of population substructure. The polymorphic microsatellites identified in this study may be

useful in examining differences between head and clothing lice, in examining fine-scale host

migrations, and characterizing local populations worldwide.









during this time period (Dennell 2003), making transfer of technology between populations

difficult.

The natural history of clothing lice suggests that they are ecologically distinct from head

lice, and therefore it is assumed that clothing lice only arose with the advent of clothing use

(Burgess 1995; Busvine 1978; Kittler et al. 2003; Kittler et al. 2004). Our analyses indicate that

only a small proportion of lice initially colonized clothing, but that migration from head to

clothing has been considerable (m = 1.16) since. Further, our analyses suggest that clothing use

originated with archaic hominids in Africa 650,000 years ago, not modern humans, and may

have played a role in the archaic hominid colonization of Central Asia and Europe.









membranes (Houhamdi and Raoult 2005).

Humans are the only host of B. recurrentis. Infection of B. recurrentis is characterized by

an initial stage of fever, chills, and headaches, which is often the most severe, followed by a

period of recovery, and a less severe relapse approximately a week later. This cycle continues

and is caused by the cyclic antigenic response of the bacteria. Gene rearrangements within the

bacterium allow new serotypes to be serially expressed. After several relapses, the genetic

variation within the bacterium is often exhausted, and the immune system is able to prevent

further relapses (Raoult and Roux 1999). In the absence of antibiotic treatment, 10-40% of

relapsing fever cases are fatal. However, treatment with antibiotics reduces fatality to 2-4%

(Southern and Sanford 1969).

Bartonella quintana

Members of the genus Bartonella are specialized to infect mammalian hosts and are

transmitted through a variety of arthropod vectors (Raoult and Roux 1999). Infection with B.

quintana is known as trench fever because the first records of infection with B. quintana

occurred in both Allied and German forces during WWI (Raoult and Roux 1999). Currently, the

only identified reservoir host is humans, and the only known vector for B. quintana is the

clothing louse (Raoult and Roux 1999).

Bartonella quintana does not cause illness in the louse host. A louse becomes infected

with B. quintana through feeding on an infected host (Raoult and Roux 1999). B. quintana then

multiples within the louse intestine and is transmitted to the human host through infective louse

feces rubbed into broken skin or conjunctivae or mucus membranes (Raoult and Roux 1999).

Once infected, a person experiences severe fever, headache, shin pain, and dizziness

(Foucault et al. 2006). Infection with B. quintana also occurs in cycles, with the first cycle being

the most severe. A small proportion of infected patients are asymptomatic, though some










Table 2-1: Estimates of evolutionary rate (i) in substitutions/locus/year for each locus.
Locus I
EF1-alpha 0.00000285
COI 0.0000163
18S 0.0000118
RPII 0.000041









Abstract of Thesis Presented to the Graduate School
of the University of Florida in Partial Fulfillment of the
Requirements for the Master of Science

USING POPULATION GENETICS OF HUMAN HEAD AND CLOTHING LICE TO
ELUCIDATE HUMAN EVOLUTION

By

Melissa Toups

August 2008

Chair: David Reed
Major: Zoology

Parasites are often used as proxies for investigating their host evolution. This is

particularly common in the study of human evolution. In this study, I use the genetics of human

head and clothing lice to address the origin of clothing use in humans and develop new

microsatellite loci to further the study of louse population genetics.

Parasitic head and clothing use may be used to address the origin of clothing use because

the divergence between these taxa is indicative of a minimum age of clothing use. When

humans lost their body hair 1.2 million years ago, lice that once roamed the entire body were

isolated on the head, and recolonized the body with the advent of clothing use. Coalescent

analyses of multilocus data indicate that head and clothing lice diverged between 650,000 and

700,000 years ago, indicating that clothing was an innovation of archaic hominids, not modem

humans as previously thought. This is consistent with several other lines of evidence for an

archaic origin of clothing, such as the presence of archaic hominids in high latitudes during this

time period and the appearance of tools used to scrape hide 300,000 years ago. Furthermore,

our analyses indicate that only a small proportion of head lice initially colonized clothing.









became restricted to the head. As humans started wearing clothing, a portion of head lice

colonized this new habitat and became the ancestors of clothing lice (Burgess 1995; Kittler et al.

2003; Kittler et al. 2004). These lice then became specialized for the clothing niche, and at

present spend more time in clothing than on the body, only returning to the body to feed once or

twice per day. Of the three mitochondrial lineages of P. humanus (Leo et al. 2002; Raoult et al.

2008; Reed et al. 2004), two lineages contain only head lice and the third contains both head and

clothing lice. Kittler et al. (2003, 2004) used phylogenetic methods to date the age of the lineage

that contained both head and clothing lice and determined the origin of clothing use to be

107,000 years ago.

Kittler et al.'s date of 107,000 years (2003, 2004) suggests a recent origin of human

clothing use. However, phylogenetic methods are inappropriate for answering this population-

level question since several researchers have shown that head and clothing lice do not form

reciprocally monophyletic clades (Leo et al. 2002; Reed et al. 2004; Yong et al. 2003).

Furthermore, a recent study has demonstrated significant gene flow between head and clothing

lice (Light et al. 2008), suggesting that recent head and clothing lice evolution is best understood

as a population genetic process.

In this study, we exploit recent advances in coalescent methodology using multiple loci to

analyze louse genetic data and address the origin of clothing use in humans. We first use a

relaxed clock method (Drummond et al. 2006) to estimate mutation rates for our multilocus

dataset. We then employ an isolation-with-migration coalescent method that jointly estimates

divergence times, population sizes and migration rates from our multilocus dataset (Hey 2005;

Nielsen and Wakeley 2001) to date the divergence of, and migration rates between, human head

and clothing louse populations.









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Press, Cambridge, MA.

Yong, Z., P. E. Fournier, E. Rydkina, and D. Raoult. 2003. The geographical segregation of
human lice preceded that of Pediculus humanus capitis and Pediculus humanus humanus.
C. R. Biol. 326:565-574.

Zinsser, H. 1935. Rats, lice, and history. Broadway House, London.













0.01

0.009

0.008 Head
Clothing
0.007

0.006

0.005 A

0.004

0.003

0.002

0.001

0
0 2 4 6 8
Population Size (millions)




0.035

0.03
head to clothing

0.025 clothing to head

0.02 B

0.015

0.01

0.005



0 2 4 6 8
Migration


0.007

0.006

0.005

0.004
C
0.003

0.002

0.001


0 1 2 3 4 5 6
Time (million years)


Figure 2-1: Marginal posterior probability distributions for model IM parameters in demographic
units. (A) Effective population size. (B) Migration rates (m). (C) Time since
divergence.









argue that these findings are evidence for fomite transmission. However, how dislodged lice

reattach to their host is not addressed by these studies. Given the findings of Canyon et al.

(2002), it seems that such specific requirements for louse transmission are unlikely to be met

during the 24-36 hour period that a louse can survive off the host.

Clothing Lice as Vectors of Bacterial Pathogens

The clothing louse vectors three deadly bacterial pathogens. It is generally assumed that

head lice cannot vector diseases (Burgess 2004), though head lice can vector these pathogens in a

laboratory setting (Goldberger and Anderson 1912). Both R. prowazekii, which causes epidemic

typhus, and B. quintana, which causes trench fever, are members of the ac subgroup of

Proteobacteria, and B. recurrentis, which causes relapsing fever, is a spirochete (Raoult and

Roux 1999).

Rickettsia prowazekii

Zinsser (1935) argued that epidemic typhus is likely responsible for more deaths of soldiers

than all wars in history. During the twentieth century alone, typhus outbreaks were associated

with both world wars, and more recently, outbreaks of typhus have occurred in Burundi, Peru,

and Russia in the 1990s (Raoult and Roux 1999). Charles Nicolle demonstrated that the clothing

louse was the typhus vector in 1909 and was awarded the Nobel Prize in 1928 for this pioneering

work (Gross 1996).

There are two competing hypotheses for the origin of epidemic typhus. Some researchers

contend that typhus has an Old World origin (Zinsser 1935) and became established in Spain in

the fifteenth century. Zinsser (1935) speculated that a number of historical epidemics, including

the Athens plague, were possibly caused by typhus. However, given the generality of the

recorded symptoms of these events, it impossible to definitively know if R. prowazekii was the

responsible agent (Raoult et al. 2004). Others argue that typhus has a New World origin,









Louse Transmission

The transmission of head and clothing lice has been studied extensively (Burkhart and

Burkhart 2007; Canyon et al. 2002; Takano-Lee et al. 2005). Though lice can disperse at any

stage, adults are most likely to transfer from one head to another (Takano-Lee et al. 2005).

Canyon et al. (2002) explored the spatial and kinetic factors of direct head-to-head contact in

transmitting head lice. A variety of factors were explored, including the angle of the hairs, the

directionality of hair movement in relation to the louse, and the speed at which the hair moved

relative to the louse. Of the 240 lice that Canyon et al. (2002) tested, zero transferred to hairs

that were placed in a 900 angle to their body. However, when lice were presented with a hair

parallel to their bodies, a small proportion transferred to the new hair. The exact proportion of

lice that transferred was determined by the direction the hair was moving in and the speed at

which the hair was moving. Canyon et al. (2002) demonstrated that lice prefer hair that is

moving laterally (as opposed to dorsal-ventral or reverse) from slow-moving (-4m/min) tail

towards the head (as opposed to head to tail). Canyon et al. (2002) also observed that all lice that

successfully transferred hairs first grasped it with their tarsal claw on their first leg. The precise

kinetics required for lice to transfer from one hair to another indicates that transferring of lice

between hosts through brief head-to-head contact is likely rare (Canyon et al. 2002). The authors

also suggest that because such precise kinetics is necessary, the role of fomites (objects that may

indirectly move louse from one individual to another, such as towels, brushes, etc.) in

transmission may be overestimated (Canyon et al. 2002).

Takano-Lee et al. (2005) investigated the role of fomites in louse transmission. They

demonstrated that air movements, combing, or toweling easily dislodges lice, and lice also

passively transfer to fabric. Both Takano-Lee et al. (2005) and Burkhart and Burkhart (2007)









CHAPTER 1
THE NATURAL HISTORY OF THE HUMAN HEAD AND CLOTHING LOUSE, Pediculus
humanus

Introduction

At least half of the organisms that exist today are parasitic (Price 1980). The parasitic

lifestyle has been hypothesized to be a key innovation leading to the diversification of insects

within several different orders (Farrell 1998; Johnson et al. 2004; Whitfield 1998). The insect

order Phthiraptera consists of parasitic lice, which are permanent, obligate ectoparasites of

vertebrates. Phylogenetic analysis of Phthiraptera demonstrates that this order is polyphyletic

and indicates that there are two origins of parasitic lice (Johnson et al. 2004). One origin of

parasitism unites all members of one suborder of chewing lice, Amblycera, and the second origin

of parasitism unites two suborders of chewing lice, Ischnocera and Rhynchophthirina, with the

suborder of sucking lice, Anoplura.

Anoplurans spend their entire life cycle on their mammalian hosts and cannot survive

without their host for more than 24 to 36 hours. Fertilized eggs of sucking lice are referred to as

nits, which subsequently develop through three nymph stages (1st, 2nd, and 3rd instar) before

achieving adulthood. Sucking lice are hematophagous and contain endosymbiotic bacteria in

specialized mycetome cells (Allen et al. 2007; Perotti et al. 2007; Sasaki-Fukatsu et al. 2006) that

supplement the louse's diet with essential vitamins (Buchner 1965). Removal of endosymbionts

from a louse or from louse eggs results in louse and larval mortality (Aschner 1932).

Parasitism of vertebrates requires a variety of adaptations to meet the challenges of

remaining attached to the host, feeding on the host, and escaping the host defenses (Clayton and

Johnson 2003). For example, lice have a single tarsal claw on each leg that clings to host hair.

Anoplurans also have specialized mouthparts to suck blood from their mammalian hosts. Such

morphological, behavioral, and physiological specializations often restrict each species of









divergence, respectively, using estimates of [t obtained with BEAST v.1.4.6 (Drummond et al.

2006; Drummond and Rambaut 2007).

The distributions of current effective population sizes of head and clothing lice were

contained within the priors. Point estimates were 2.5 million individuals for head lice and

1.8 million individuals for clothing lice. Estimates of the splitting parameter s indicate that only

a small proportion of the ancestral population (<1%) initially colonized clothing, whereas the

majority (>99%) remained head lice, which is thought to be the ancestral condition. Estimates of

bidirectional migration (m) showed very high migration from head lice to clothing lice (m =

1.16), but virtually no migration in the opposite direction (m = 0.0040).

The posterior distribution for the time of population divergence peaks between 650,000-

700,000 years ago in all IM replicates. The effective population size for the common ancestor of

head and clothing louse peaked at the lowest bin and decreased thereafter. There are two

potential explanations for this. First, the effective population size of the common ancestor was

smaller than our analysis could detect. Alternatively, because head and clothing lice diverged

long ago and have likely been through the same population bottlenecks as their human host, there

may be too little information in the data to effectively estimate this parameter.

Discussion

Pediculus humanus diverged from its sister taxon, the chimpanzee louse P. schaeffi, at

the human-chimp divergence roughly 5.5 million years ago (Reed et al. 2007; Reed et al. 2004).

It is likely that lice in the genus Pediculus parasitized all subsequent hominid lineages given their

history of cospeciation. Because P. schaeffi is found throughout the body of their chimpanzee

hosts it is likely that the human parasite species of Pediculus also utilized much of the human

body prior to the general loss of body hair in humans. At the time humans lost their body hair,









three deeply divergent clades and the finding that clothing lice arose from only a subset of head

lice, were novel compared to previous studies based on both mitochondrial and nuclear data

(Kittler et al. 2003; Leo et al. 2002; Yong et al. 2003) and resulted in several follow-up studies

examining these results (Leo and Barker 2005; Light et al. 2008).

Light et al. (2008) assessed the taxonomic status of head and clothing lice using both

phylogenetic and population genetic methods and the most diverse geographic and molecular

sampling available. The analyses resulted in reticulated networks, gene flow, and a lack of

reciprocal monophyly, all of which indicate that head and clothing lice do not represent

genetically distinct evolutionary units. Based on these findings, as well as inconsistencies of

morphological, behavioral, and ecological variability between head and clothing lice, Light et al.

(2008) state that no known species concept would recognize head and clothing lice as separate

species.

Medical Importance of P. humanus

Parasitism by lice is a recognized medical condition known as pediculosis. Most patients

are infested by only a few individuals (Raoult and Roux 1999), however, some patients can be

infested with up to hundreds or thousands of lice (Raoult and Roux 1999). When the louse

punctures the host's skin to feed, it injects the host with an anticoagulant and an anesthetic

(Burgess 1995). After three to four weeks of infection, the host begins to have an allergic

reaction, which leads to pruritis. In a clothing louse infestation, areas of the host that are heavily

parasitized may darken, which is referred to as vagabond's disease (Burgess 1995). Heavy

infestation of lice can also cause dull headache, drowsiness, joint pain, rash, and a mild fever

(Buxton 1946).









Johnston, J. S., K. S. Yoon, J. P. Strycharz, B. R. Pittendrigh, and J. M. Clark. 2007. Body lice
and head lice (Anoplura: Pediculidae) have the smallest genomes of any hemimetabolous
insect reported to date. J. Med. Entomol. 44:1009-1012.

Kittler, R., M. Kayser, and M. Stoneking. 2003. Molecular evolution of Pediculus humanus and
the origin of clothing. Curr. Biol. 13:1414-1417.

Kittler, R., M. Kaysar, and M. Stoneking. 2004. Molecular evolution of Pediculus
humanus and the origin of clothing. Curr. Biol. 14: 2309 (vol 13, pg 1414, 2003).

Koehler, J. E., M. A. Sanchez, C. S. Garrido, M. J. Whitfeld, F. M. Chen, T. G. Berger, M. C.
Rodriguez-Barradas, P. E. LeBoit, and J. W. Tappero. 1997. Molecular epidemiology of
Bartonella infections in patients with bacillary angiomatosis-peliosis. New Engl. J. Med.
337:1876-1883.

Kumar, S., and S. B. Hedges. 1998. A molecular timescale for vertebrate evolution. Nature
392:917-920.

Leo, N. P., and S. C. Barker. 2005. Unravelling the evolution of the head lice and body lice of
humans. Parasitol. Res. 98:44-47.

Leo, N. P., N. J. H. Campbell, X. Yang, K. Mumcuoglu, and S. C. Barker. 2002. Evidence from
mitochondrial DNA that head lice and body lice of humans (Phthiraptera: Pediculidae) are
conspecific. J. Med. Entomol. 39:662-666.

Levene, H., and T. Dobzhansky. 1959. Possible genetic difference between the head louse and
the body louse (Pediculus humanus L.). Am. Nat. 93: 347-353.

Light, J. E., M. A. Toups, and D. L. Reed. 2008. What's in a name? The taxonomic status
of human head and clothing lice. Mol. Phyl. Evol. 47: 1203-1216.

Maddison, W. P., and D. R. Maddison. 2005. MacClade: Analysis of phylogeny and character
evolution, version 4.08. Sinauer Associates, Sunderland, MA.

Maunder, J. W. 1982. Pediculosis capitis in a zoological context. R. Soc. Health J. 102:255-
257.

Meusnier, I., J. L. Olsen, W. T. Stam, C. Destombe, and M. Valero. 2001. Phylogenetic
analyses of Caulerpa taxifolia (Chlorophyta) and of its associated bacterial microflora
provide clues to the origin of the Mediterranean introduction. Mol. Ecol. 10:931-946.

Mumcuoglu, K. Y., R. Galun, and R. Ikan. 1986. The aggregation response of human body
louse, Pediculus humanus (Insecta: Anoplura) to its excretory products. Insect Sci. Appl.
7:629-632.

Nieberding, C., and I. Olivieri. 2006. Parasites: proxies for host genealogy and ecology? Trends
Ecol. Evol. 22:156-165.









LIST OF TABLES


Table page

2-1 Estimates of evolutionary rate (i) in substitutions/locus/year for each locus .................36

3-1 Characteristics of eleven microsatellite loci for the human head and clothing louse,
P. hum anus .................. ................. .......................................40









CHAPTER 3
CHARACTERIZATION OF ELEVEN POLYMORPHIC MICRO SATELLITE LOCI FROM
THE HUMAN HEAD AND CLOTHING LOUSE, Pediculus humanus

Human head and clothing lice, Pediculus humanus capitis and Pediculus humanus

humanus, respectively, have parasitized humans for thousands of years (Araujo et al. 2000).

Currently, head lice are pandemic, infesting millions of schoolchildren worldwide. Clothing lice,

though less prevalent, are common among areas stricken by poverty or political and social unrest

that prevent inhabitants from having multiple sets of clothes (Raoult and Roux 1999). Clothing

lice (also called body lice) are also becoming increasingly common among the homeless

populations in developed countries such as the United States and Western Europe (Brouqui et al.

1996; Drancourt et al. 1995; Koehler et al. 1997). Clothing lice are more harmful parasites

because they can vector three bacterial pathogens: Rickettsiaprowazekii (epidemic or louse-

borne typhus; but see (Robinson et al. 2003), Borrelia recurrentis (louse-borne relapsing fever)

and Bartonella quintana (trench fever; Buxton 1946; but see Sasaki et al. 2006).

In addition to their importance in the biomedical field, human head and clothing lice are

of interest to evolutionary biologists and anthropologists. Head and clothing lice are part of a

group of anoplurans that have cospeciated with primates for 22.5 million years (Reed et al.

2004), and therefore have been used to provide insights into human evolutionary history (Kittler

et al. 2003; Kittler et al. 2004, Raoult et al. 2008; Reed et al. 2007; Reed et al. 2004). For

example, head and clothing lice have been used to estimate the origin of clothing use in humans

(Kittler et al. 2003; Kittler et al. 2004). The use of population level markers, such as

microsatellites, may provide insights into the epidemiology and evolutionary history of one of

the oldest human parasites.

Microsatellite loci were mined from the Human Body Louse Genome Project (Johnston

et al. 2007) using Tandem Repeat Finder (Benson 1999). Of the initial microsatellite search, loci









were selected that contained a minimum of eight repeats and at least 200 base pair flanking

regions on each side that was free of other repetitive elements. These loci were further screened

when designing primer pairs using PRIMER3 (Rozen and Skaletsky 2000) for formation of

hairpins, self-dimers, hetero-dimers, and optimal primer GC content of 40-60%. Primer pairs

were designed for a total of 48 loci, of which 11 have been assessed for polymorphism using 18

head louse individuals, each from a separate host individual, from West Palm Beach, Florida.

DNA amplifications were carried out in 25[tL reactions containing 11.5[tL of distilled

water, 10[tL of 5Prime HotMaster Mix (Eppendorf), 11tL of 1CtM M13 labeled forward primer,

1ltL of 10M reverse primer, and 1ltL of 10M FAM label, and 0.5 ptL of DNA template.

Thermocycling conditions for all loci were identical and are as follows: 940 for 3 min, followed

by 10 cycles of 940 for 30 s, 520 for 30 s, 650 for 45 s, then 30 cycles of 940 for 30 s, 480 for 30

s, 650 for 45 s, and a final extension of 650 for 10 min. Fragment lengths of PCR products were

detected using ABI 3730 Automated Sequencer and scored using GENEMAPPER 3.0 software

(Applied Biosystems).

Data for loci analyzed are available in Table 1. The number of alleles ranged from 3-7

per locus. Observed and expected heterozygosities were calculated using MICROSATELLITE

ANALYSER 4.05 (Dieringer and Schlotterer 2003) and ranged from 0.056-0.278 and 0.303-

0.820, respectively. Linkage disequilibrium with a Bonferroni correction was tested using

GENEPOP version 3.4 (Raymond and Rousset 1995) and no linkage disequilibrium was

identified. Deviations from Hardy-Weinberg equilibrium were tested using GENEPOP version

3.4 (Raymond and Rousset 1995). Only two loci, M2_19 and M3_9 are in Hardy-Weinberg

equilibrium, and M2_19 is only marginally so (p=0.050). Because 9 of 11 loci are polymorphic









BIOGRAPHICAL SKETCH

Melissa Toups was born and raised in New Orleans, Louisiana. After graduating from

Archbishop Chapelle High School in 2000, she attended Tulane University and majored in

ecology and evolutionary biology. While at Tulane, she participated in the Junior Year Abroad

program and attended the University of Bristol. She graduated Tulane in the Spring 2004 magna

cum laude. She began her graduate career in August 2005 in the Zoology Department at the

University of Florida and received her M.S. in August 2008.










LIST OF FIGURES


Figure


2-1 Marginal posterior probability distributions for model IM parameters in demographic
u n its ................... ............................................................. ................ 3 5


page









ACKNOWLEDGMENTS

I would like to thank my advisor, Dr. David Reed, and my committee members Dr.

Pamela Soltis and Dr. Mike Miyamoto. I would also like to thank the Zoology department

faculty for all their support, particularly Dr. Marta Wayne, Dr. Charlie Baer, and Dr. Colette St.

Mary. I would like to acknowledge my coauthors Dr. Andrew Kitchen and Dr. Jessica Light, as

well as my labmates Angelo Soto and Julie Allen. Finally, I would like to thank my friends Ondi

Crino and Matt Salomon.









P. humanus. Because P. humanus is so closely ecologically tied to its human host, it is not

exposed to secondary compounds produced by plants. Similarly, the P. humanus genome also

has a reduction of gene families involved in sensory functions, such as opsin and chemoreceptor

genes.

In addition to the clothing louse genome, the primary endosymbiont and mitochondrial

genomes of P. humanus have also been sequenced. The reduced size of the primary

endosymbiont, Candidatus Riesiapediculicola, is consistent with the genome reduction that

occurs when a bacterium is sequestered as an endosymbiont. Phylogenetic analysis of the

Candidates Riesiapediculicola sequence indicates that it is placed among the basal gamma-

proteobacteria.

The mitochondrial genome of P. humanus displays a unique organization. Unlike the

other >1000 bilaterian animals with sequenced mitochondrial genomes, the P. humanus genome

does not consist of a single circular 16kb chromosome. Rather, it consists of 18 minicircular

chromosomes, each of which has a length of 3kb and 1-3 genes. Analysis of the mitochondria of

the pubic louse (Pthiruspubis), chimp louse (Pediculus schaeffi), and the langur louse

(Pedicinus ancoratus) indicates that these also have minicircular mitochondrial genomes, and

that the most recent common ancestor of these lice that parasitize primates likely had a similar

mitochondrial genome organization 22.5 million years ago.

Lice as Markers of Human Evolutionary History

Sucking lice complete their entire life cycle on their mammalian host, which selects for

high host specificity and leads to cospeciation between parasite and host. Primates and their

parasitic sucking lice have been cospeciating for the last 22.5 million years (Reed et al. 2004).

Researchers have exploited this property to learn more about primate evolution (Reed et al. 2004,

Reed et al. 2007). Reed et al. (2004) analyzed molecular data from sucking lice of anthropoid









(often caused by louse bites) in the host's skin or into conjunctivae or mucus membranes (Raoult

and Roux 1999). Infective bacteria can persist in the louse excrement for over 100 days (Raoult

and Roux 1999).

Once a person is infected with R. prowazekii, the bacterium spreads throughout the host's

body through the bloodstream and damages the endothelial cells, compromising the host's

vascular system and causing hemorrhages (Raoult and Roux 1999). During this time, the patient

will likely experience fever and headaches, and may also experience a variety of other

symptoms, including cough, nausea, a rash on the trunk of the body, and myalgias (Raoult and

Roux 1999). Many patients develop some abnormalities of the central nervous system (Raoult

and Roux 1999). Without antibiotic treatment, 10-30% of all R. prowazekii infections are fatal

(Raoult and Roux 1999). However, a single dose of 200mg of doxycycline often cures the

patient of epidemic typhus (Raoult and Roux 1999).

Borrelia recurrentis

B. recurrentis, the agent of louse-borne relapsing fever, is closely related to B. duttonii, the

agent of East African tick-borne relapsing fever (Cutler et al. 1997; Raoult and Roux 1999). It is

suspected that the ancestor of B. recurrentis diverged from its tick-borne relatives after it became

associated with clothing lice (Raoult and Roux 1999).

Unlike R. prowazekii, B. recurrentis does not cause illness in its louse host. However,

similar to R. prowazekii, B. recurrentis is not transmitted to the human host through the louse

bite (Raoult and Roux 1999). Until recently, it was thought that B. recurrentis was only to

transmitted to its human host through louse crushing. However, a recent experiment by

Houhamdi and Raoult (2005) showed evidence of B. recurrentis in louse feces, suggesting an

additional route of infection. Like R. prowazekii, B. recurrentis may infect its human host

through infective louse feces rubbed into open sores of the host or into conjunctivae or mucus









Pediculus likely became restricted to head hair, and only invaded the body niche recently with

the advent of clothing use (Busvine 1978; Burgess 1995; Kittler et al. 2003; Kittler et al. 2004).

This is inferred primarily from the current natural history of clothing lice. At present, clothing

lice spend the majority of their time in clothing, and only return to the body to feed. Clothing lice

prefer to attach their eggs to the pleats and seams of clothing, particularly the undergarments,

rather than body hair (Burgess 1995; Buxton 1946; Nuttall 1917). In the absence of clothing,

clothing lice will infest beads and necklaces (Busvine 1978; Buxton 1946). When displaced,

clothing lice tend to return to the clothing and are particularly attracted to areas that are occupied

by other clothing lice or clothing louse feces (Mumcuoglu et al. 1986; Wigglesworth, 1941).

Our results support the assertion that the head was likely the ancestral habitat for P.

humanus. The splitting parameter s indicates that a large proportion of the ancestral louse

population (>99%) was of the head lice type at the time of divergence, and that only a small

proportion (<1%) moved to the clothing niche as a founder population. Furthermore, our results

indicate a lack of migration from clothing louse to head louse populations, suggesting that

clothing lice are ecologically distinct and possibly unable to survive under head louse conditions.

This finding is consistent with empirical transplantation experiments. When head lice are reared

as clothing lice in the laboratory (in pill boxes worn upon the skin), morphological and

behavioral changes take place such that the head lice gain the morphological and natural history

characteristics of clothing lice within a few generations (Alpatov and Nastjukova 1955; Bacot,

1917; Levene and Dobzhansky 1959; see Busvine, 1948 for a single known exception). Further,

when clothing lice are displaced, they return to clothing, particularly areas occupied by other

clothing lice and clothing louse feces (Mumcuoglu et al. 1986; Wigglesworth 1941). However,




Full Text

PAGE 1

1 USING POPULATION GENETICS OF HUMAN HEAD AND CLOTHING LICE TO ELUCIDATE HUMAN EVOLUTION By MELISSA ANNE TOUPS A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLOR IDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE UNIVERSITY OF FLORIDA 2008

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2 2008 Melissa Toups

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3 To my family.

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4 ACKNOWLEDGMENTS I would like to thank my advisor, Dr. David Reed, and my committee members Dr. Pamela Soltis and Dr. Mike Miyamoto. I woul d also like to thank the Zoology department faculty for all their support, pa rticularly Dr. Marta Wayne, Dr. Ch arlie Baer, and Dr. Colette St. Mary. I would like to acknowledge my coauthor s Dr. Andrew Kitchen and Dr. Jessica Light, as well as my labmates Angelo Soto and Julie Allen. Finally, I would like to thank my friends Ondi Crino and Matt Salomon.

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5 TABLE OF CONTENTS page ACKNOWLEDGMENTS...............................................................................................................4 LIST OF TABLES................................................................................................................. ..........6 LIST OF FIGURES.........................................................................................................................7 ABSTRACT.....................................................................................................................................8 CHAP TER 1 THE NATURAL HISTORY OF THE HUMAN HEAD AND CLOTHING LOUSE, Pediculus humanus .................................................................................................................10 Introduction................................................................................................................... ..........10 Ecology of P. humanus ...........................................................................................................11 Taxonomic Debate............................................................................................................... ...12 Medical Importance of P. humanus ........................................................................................14 Louse Transmission.........................................................................................................15 Clothing Lice as Vectors of Bacterial Pathogens ............................................................16 Rickettsia prowazekii ................................................................................................16 Borrelia recurrentis ..................................................................................................18 Bartonella quintana ..................................................................................................19 Sequencing of the Cl othing Louse Genom e........................................................................... 20 Lice as Markers of Human Evolutionary History................................................................... 22 2 POPULATION GENETIC ANALYSIS OF Pediculus humanus PROVIDES INSIGHT INTO THE ORIGIN OF HUMAN CLOTHING ...................................................................25 Introduction................................................................................................................... ..........25 Materials and Methods...........................................................................................................28 Molecular Data................................................................................................................ 28 EvolutionaryRate Calculation.........................................................................................28 Isolation with Migration Analysis................................................................................... 29 Results.....................................................................................................................................29 Discussion...............................................................................................................................30 3 CHARACTERIZATION OF ELEVEN POLYM ORPHIC MICROSATELLITE LOCI FROM THE HUMAN HEAD A ND CLOTHING LOUSE, Pediculus humanus ..................37 REFERENCES..............................................................................................................................41 BIOGRAPHICAL SKETCH.........................................................................................................49

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6 LIST OF TABLES Table page 2-1 Estimates of evolutionary rate () in substitutions/locus/year for each locu s................... 36 3-1 Characteristics of eleven microsatellite loci for the hum an head and clothing louse, P. humanus .........................................................................................................................40

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7 LIST OF FIGURES Figure page 2-1 Marginal posterior probability distributi ons for model IM param eters in demographic units.......................................................................................................................... ..........35

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8 Abstract of Thesis Presen ted to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Master of Science USING POPULATION GENETICS OF HUMAN HEAD AND CLOTHING LICE TO ELUCIDATE HUMAN EVOLUTION By Melissa Toups August 2008 Chair: David Reed Major: Zoology Parasites are often used as proxies for i nvestigating their host evolution. This is particularly common in the study of human evolu tion. In this study, I use the genetics of human head and clothing lice to addr ess the origin of clothing use in humans and develop new microsatellite loci to further the study of louse population genetics. Parasitic head and clothing use may be used to address the origin of clothing use because the divergence between these taxa is indicative of a minimum age of clothing use. When humans lost their body hair 1.2 million years ago, lice that once roamed the entire body were isolated on the head, and recolonized the body with the advent of clothing use. Coalescent analyses of multilocus data indicate that head and clothing lice diverged between 650,000 and 700,000 years ago, indicating that clothing was an innovation of archaic hominids, not modern humans as previously thought. This is consiste nt with several other lines of evidence for an archaic origin of clothing, such as the presence of archaic hominids in hi gh latitudes during this time period and the appearance of tools used to scrape hide 300,000 years ago. Furthermore, our analyses indicate that only a small proportion of head lic e initially colonized clothing.

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9 Finally, I developed eleven polym orphic microsatellite loci for head and clothing lice. All loci were tested on eighteen head louse individua ls, and the number of alleles ranged from three to seven. These loci will be valuable for further study of louse population genetics.

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10 CHAPTER 1 THE NATURAL HISTORY OF THE HUMAN HEAD AND CLOTHING LOUSE, Pediculus humanus Introduction At least half of the organisms that exist today are parasitic (Pri ce 1980). The parasitic lifestyle has been hypothesized to be a key innovation leading to the diversification of insects within several different orders (Farrell 1998; Johnson et al. 2004; Whitfield 1998). The insect order Phthiraptera consists of parasitic lice, which are permanent, obligate ectoparasites of vertebrates. Phylogenetic analysis of Phthiraptera demonstrates that this order is polyphyletic and indicates that there are two origins of parasitic lice (Johnson et al. 2004). One origin of parasitism unites all members of one suborder of chewing lice, Amblycera, and the second origin of parasitism unites two suborders of chewing lice, Ischnocera and Rhynchophthirina, with the suborder of sucking lice, Anoplura. Anoplurans spend their entire life cycle on their mammalian hosts and cannot survive without their host for more than 24 to 36 hours. Fe rtilized eggs of sucki ng lice are referred to as nits, which subsequently devel op through three nymph stages (1st, 2nd, and 3rd instar) before achieving adulthood. Sucking lice are hematophagous and contain endosymbiotic bacteria in specialized mycetome cells (Allen et al. 2007; Perotti et al. 2007; Sasaki-Fukatsu et al. 2006) that supplement the louses diet with essential vita mins (Buchner 1965). Removal of endosymbionts from a louse or from louse eggs results in louse and larval mortality (Aschner 1932). Parasitism of vertebrates requires a variety of adaptations to meet the challenges of remaining attached to the host, feeding on the host, and escaping the host defenses (Clayton and Johnson 2003). For example, lice have a single tars al claw on each leg that clings to host hair. Anoplurans also have specialized mouthparts to suck blood from their mammalian hosts. Such morphological, behavioral, and physiological spec ializations often rest rict each species of

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11 parasitic louse to a single host species (Price et al. 2003). This often results in cospeciation between louse and host, such as the twenty-fiv e million year coevolution between primates and their sucking lice (Reed et al. 2007; Reed et al. 2004). Members of two louse families parasitize humans. The family Phthiridae includes the human pubic louse, Pthirus pubis, and its sister taxon, the gorilla louse, Pthirus gorillae P. pubis likely switched from a gorilla-like host to an archaic hominid approximately 3 million years ago (Reed et al. 2007). The fa mily Pediculidae includes the species Pediculus humanus, which exists as two morphotypes, the human head louse and human clothing louse, Pediculus humanus capitis and P. humanus humanus respectively. Pediculus humanus is thought to have diverged from chimpanzee lice, Pediculus schaeffi, at the chimp-human divergence 5-7 million years ago. Ecology of P. humanus Human head and clothing lice are found on every continent. Head lice are common worldwide, infesting millions of school children ever y year. This resistance is due, in part, to the evolution of resistance to insec ticidal shampoos that are used to treat pediculosis (Burgess 1995). Clothing lice are less prevalent, but are potentially more harmful because they are known vectors of at least three bacter ial pathogens in humans: Rickettsia prowazekii (epidemic or louseborne typhus; but see Robins on et al. 2003), Borrelia recurrentis (louse-borne relapsing fever) and Bartonella quintana (trench fever; Buxton 1946; but see Sa saki et al. 2006). The incidence of clothing lice is determined by weather, humid ity, poverty, and a lack of hygienic conditions (Raoult and Roux 1999). Clothing lice, and conse quently their bacterial pathogens, are most common in areas with cold weather, where people wear multiple layers of clothes, and in areas stricken by poverty or political and social unrest that prevent inhabitants from having multiple sets of clothes (Raoult and Roux 1999). They are also becoming increasingly common among

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12 the homeless populations in developed countries in the United States and Western Europe (Brouqui et al. 1996; Drancour t et al. 1995; Koehler et al. 1997; Raoult and Roux 1999). As their names imply, head and clothing lice ar e spatially segregated on their human hosts. Head lice are found on the head and a ttach their eggs to the base of hair shafts, most often behind the ears, whereas clothing lice are found on the body and in clothi ng and prefer to attach their eggs to the pleats and seams of clothing, particularly the undergarments, rather than body hair (Burgess 1995; Buxton 1946; Maun der 1982; Nuttall 1917). In the absence of clothing, clothing lice will infest beads and necklaces (Buxton 1946; Busvine 1978). Clothing lice are believed to have evolved from head lice, invading the body region only recently with the advent of clothing use in modern humans (Burgess 1995; Kittler et al. 2003; Kittler et al. 2004). Head lice require more frequent blood meals than do clothing lice (Alpatov and Nastjukova 1955). Head and clothing lice tend to return to their preferred ecological habitat when displaced, and clothing lice are known to be especially attract ed to areas that are occupied by other clothing lice or clothing louse feces (Wigglesworth 1941; Mumcuoglu et al. 1986). Morphologically, clothing lice (and their eggs) are generally larger th an head lice, most notably in the length of the tibia on the second pair of legs (Schll, 1955; Busvin e 1978; Reed et al. 2004). However, these morphological differences are small, and were apparent to Reed et al. (2004) only when assessed with discriminant function analysis. Taxonomic Debate The species status of human Pediculus has been a topic for debate for over a century. Ferris (1951) and Burgess (1995) provide detailed accounts of this taxonomic confusion. Nuttall (1917, 1919a, 1919b, 1920) and Ferris (1935) strongl y argued that head and clothing lice represented, at most, subspecies, and that th e morphological, behavi oral, and ecological differences between these two louse groups repres ented natural intraspeci fic variation. Buxton

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13 (1946) presented an argument that head and clothing lice are probabl y too similar to be considered distinct species, but may represent species in the making. Fahrenholz (1915, 1916), Busvine (1944, 1978), and Schaefer (1978), on the other hand, argued that the differences observed between head and clothing lice were more than sufficient to recognize these taxa as distinct species. This taxonomi c confusion regarding th e species status of head and clothing lice continues today, primarily because of the ecological differences. In recent years, the specific status of h ead and clothing lice has al so been addressed in studies examining louse isozymes (Amevigbe et al. 2000), louse primary endosymbionts (Allen et al. 2007; Perotti et al. 2007; Sasaki-Fukatsu et al. 2006), and l ouse bacterial pathogens (Sasaki et al. 2006; but see Parola et al 2006). While the results of the endosymbiont and bacteria work indicate that head and clothing lice are conspecifi c, the results of the is ozyme work indicate that genetic differentiation may exist be tween these louse forms. Ther e also has been a series of DNA-based studies that ha ve directly addressed the specific status of head and clothing lice (Kittler et al. 2003; Leo and Bark er 2005; Leo et al. 2002; Reed et al. 2004; Yong et al. 2003). The majority of these molecular-based studies have concluded that head a nd clothing lice are not distinct species becaus e of the lack of reciprocal monophyl y between head and clothing lice. Reed et al. (2004) found three deeply divergen t mitochondrial clades of lice, all of which contained head lice, whereas only one of which c ontained clothing lice. Furthermore, all three clades had unique geographic distributions: 1) one clade was composed of a worldwide distribution of both head and clot hing lice, 2) one clade consisted only of head lice from North America, Central America, Australia, and Europe and 3) a second clade th at contained only head lice from Africa and Nepal (furth er sampling is necessary to de termine the geographic range of lice belonging to this third mitochondrial lineage) These mitochondrial results, the presence of

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14 three deeply divergent clades and the finding that clothing lice arose from only a subset of head lice, were novel compared to previous studies based on both mitochondrial and nuclear data (Kittler et al. 2003; Leo et al. 2002; Yong et al. 2003) and resulted in several follow-up studies examining these results (Leo and Barker 2005; Light et al. 2008). Light et al. (2008) assessed the taxonomic status of head and cl othing lice using both phylogenetic and population genetic methods and the most diverse geographic and molecular sampling available. The analyses resulted in re ticulated networks, gene flow, and a lack of reciprocal monophyly, all of which indicate th at head and clothing lice do not represent genetically distinct evol utionary units. Based on these findings, as well as inconsistencies of morphological, behavioral, and ecological variability between head and clothing lice, Light et al. (2008) state that no known species concept would recognize head and clothing lice as separate species. Medical Importance of P. humanus Parasitism by lice is a recognized medical condi tion known as pediculosis. Most patients are infested by only a few indi viduals (Raoult and Roux 1999), how ever, some patients can be infested with up to hundreds or thousands of lice (Raoult and Roux 1999). When the louse punctures the hosts skin to feed, it injects the host with an anticoagul ant and an anesthetic (Burgess 1995). After three to f our weeks of infection, the host begins to have an allergic reaction, which leads to pruritis. In a clothing louse infestation, ar eas of the host th at are heavily parasitized may darken, which is referred to as vagabonds disease (Burgess 1995). Heavy infestation of lice can also cause dull headache, drowsiness, joint pain, rash, and a mild fever (Buxton 1946).

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15 Louse Transmission The transmission of head and clothing lice has been studied exte nsively (Burkhart and Burkhart 2007; Canyon et al. 2002 ; Takano-Lee et al. 2005). T hough lice can disperse at any stage, adults are most likely to transfer from one head to an other (Takano-Lee et al. 2005). Canyon et al. (2002) explored the sp atial and kinetic factors of di rect head-to-head contact in transmitting head lice. A variety of factors were explored, including the angle of the hairs, the directionality of hair movement in relation to the louse, and the speed at which the hair moved relative to the louse. Of the 240 lice that Canyon et al. (2002) te sted, zero transferred to hairs that were placed in a 90 angle to their body. However, when lice were presented with a hair parallel to their bodies, a sm all proportion transferred to the new hair. The exact proportion of lice that transferred was determined by the dir ection the hair was movi ng in and the speed at which the hair was moving. Canyon et al. (2002) demonstrated that lice prefer hair that is moving laterally (as opposed to dorsal-ventral or reverse) fr om slow-moving (~4m/min) tail towards the head (as opposed to h ead to tail). Canyon et al. (2002) also observed that all lice that successfully transferred hairs first grasped it with their tarsal claw on their first leg. The precise kinetics required for lice to tran sfer from one hair to another i ndicates that transferring of lice between hosts through brief head-to-head contact is likely rare (Canyon et al. 2002). The authors also suggest that because such pr ecise kinetics is necessary, the ro le of fomites (objects that may indirectly move louse from one individual to another, such as towels, brushes, etc.) in transmission may be overest imated (Canyon et al. 2002). Takano-Lee et al. (2005) investigated the ro le of fomites in louse transmission. They demonstrated that air movements, combing, or toweling easily dislodge s lice, and lice also passively transfer to fabric. Both Takano-Lee et al. (2005) and Burkha rt and Burkhart (2007)

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16 argue that these findings are ev idence for fomite transmission. However, how dislodged lice reattach to their host is not addressed by these studies. Give n the findings of Canyon et al. (2002), it seems that such specific requirements for louse transmission are unlikely to be met during the 24-36 hour period that a louse can survive off the host. Clothing Lice as Vectors of Bacterial Pathogens The clothing louse vectors three deadly bact erial pathogens. It is generally assumed that head lice cannot vector diseases (Burgess 2004), though head lice can vector these pathogens in a laboratory setting (Goldberge r and Anderson 1912). Both R. prowazekii which causes epidemic typhus, and B. quintana which causes trench fever, are members of the subgroup of Proteobacteria, and B. recurrentis which causes relapsing fever, is a spirochete (Raoult and Roux 1999). Rickettsia prowazekii Zinsser (1935) argued that epid emic typhus is likely responsible for more deaths of soldiers than all wars in history. During the twentieth century alone, typhus outbreaks were associated with both world wars, and more recently, outbreaks of typhus have occurred in Burundi, Peru, and Russia in the 1990s (Raoult and Roux 1999). Ch arles Nicolle demonstrated that the clothing louse was the typhus vector in 1909 and was awarde d the Nobel Prize in 1 928 for this pioneering work (Gross 1996). There are two competing hypotheses for the orig in of epidemic typhus. Some researchers contend that typhus has an Old World origin (Z insser 1935) and became established in Spain in the fifteenth century. Zinsser (1935) speculated th at a number of historical epidemics, including the Athens plague, were possibly caused by t yphus. However, given the generality of the recorded symptoms of these events, it impossible to definitively know if R. prowazekii was the responsible agent (Raoult et al 2004). Others argue that ty phus has a New World origin,

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17 because the only known nonhuman reservoir, the flying squirrel ( Glaucomys volans volans ), is native to Mexico (Bozeman et al. 1975). Histori cally, this has been challenged by the lack of evidence that clothing lice successfully accompan ied the Amerindians in the migration to the New World. However, a recent ancient DNA st udy by Raoult et al. (2008) demonstrated that head lice belonging to a pre-Columbian Peruvian mummy belonged to the same clade of lice that contains clothing lice, suggesti ng that clothing lice likely colo nized the New World along with the Amerindians. This finding weakens the argume nt that clothing lice did not exist in the preColumbian New World. However, the first de finitive evidence of typhus occurred in the fifteenth century in Spain and sixteenth cen tury in Mexico (Raoult et al. 2004). Rickettsia prowazekii is a pathogen to the louse as we ll as its human host. Clothing lice contract typhus through feedi ng on an infected person, though transmission rate is not 100% (Wolbach et al. 1922). Once ingested, R. prowazekii infects the midgut ep ithelial cells of the louse and multiplies (Raoult and Roux 1999). These cells become enlarged and burst, which releases the bacteria into the gut lumen (Raoult and Roux 1999). R. prowazekii is then excreted from the louse in large quantities in the f eces (Raoult and Roux 1999). Since the ruptured epithelial cells of the gut are not replaced, infection with R. prowazekii eventually kills the louse (Raoult and Roux 1999). After the cells rupture, the ingested blood will flow freely through the intestine and occasionally cause the louse to tu rn red (Bozeman et al. 1975). Interestingly, R. prowazekii cannot be transmitted vertically from mo ther to egg (Buxton 1940; Houhamdi et al. 2002). The salivary glands of the louse do not contain R. prowazekii (Arkwright and Bacot 1923), and therefore R. prowazekii is not transmitted to the human host through the louse bite. R. prowazekii is transmitted to the human host when infective feces are rubbed into open sores

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18 (often caused by louse bites) in the hosts skin or into conjunctivae or mucus membranes (Raoult and Roux 1999). Infective bacteria can persist in the louse excrement for over 100 days (Raoult and Roux 1999). Once a person is infected with R. prowazekii the bacterium spread s throughout the hosts body through the bloodstream and damages the endothelial cells, compromising the hosts vascular system and causing hemorrhages (Raou lt and Roux 1999). During this time, the patient will likely experience fever and headaches, and may also experience a variety of other symptoms, including cough, nausea, a rash on the trunk of the body, and myalgias (Raoult and Roux 1999). Many patients develop some abnorma lities of the central nervous system (Raoult and Roux 1999). Without antibiot ic treatment, 10-30% of all R. prowazekii infections are fatal (Raoult and Roux 1999). However, a single dose of 200mg of doxycycline often cures the patient of epidemic typhus (Raoult and Roux 1999). Borrelia recurrentis B. recurrentis the agent of louse-borne relapsi ng fever, is closely related to B. duttonii, the agent of East African tick-borne relapsing feve r (Cutler et al. 1997; Raoul t and Roux 1999). It is suspected th at the ancestor of B. recurrentis diverged from its tick-borne relatives after it became associated with clothing lice (Raoult and Roux 1999). Unlike R. prowazekii B. recurrentis does not cause illness in its louse host. However, similar to R. prowazekii, B. recurrentis is not transmitted to the human host through the louse bite (Raoult and Roux 1999). Un til recently, it was thought that B. recurrentis was only to transmitted to its human host through louse crushing. However, a recent experiment by Houhamdi and Raoult (2005) showed evidence of B. recurrentis in louse feces, suggesting an additional route of infection. Like R. prowazekii, B. recurrentis may infect its human host through infective louse feces rubbed into open sores of the host or into conjunctivae or mucus

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19 membranes (Houhamdi and Raoult 2005). Humans are the only host of B. recurrentis. Infection of B. recurrentis is characterized by an initial stage of fever, chills, and headaches, which is often the most severe, followed by a period of recovery, and a less seve re relapse approximately a week later. This cycle continues and is caused by the cyclic antigen ic response of the bacteria. Gene rearrangements within the bacterium allow new serotypes to be serially expressed. After severa l relapses, the genetic variation within the bacterium is often exhauste d, and the immune system is able to prevent further relapses (Raoult and Roux 1999). In th e absence of antibiotic treatment, 10-40% of relapsing fever cases are fatal. However, treatm ent with antibiotics redu ces fatality to 2-4% (Southern and Sanford 1969). Bartonella quintana Members of the genus Bartonella are specialized to infect mammalian hosts and are transmitted through a variety of arthropod vect ors (Raoult and Roux 1999). Infection with B. quintana is known as trench fever because th e first records of infection with B. quintana occurred in both Allied and German forces during WWI (Raoult and Ro ux 1999). Currently, the only identified reservoir host is humans, and the only known vector for B. quintana is the clothing louse (Raoult and Roux 1999). Bartonella quintana does not cause illness in the louse host. A louse becomes infected with B. quintana through feeding on an infected host (Raoult and Roux 1999). B. quintana then multiples within the louse intes tine and is transmitted to the human host through infective louse feces rubbed into broken skin or conjunctivae or mucus membranes (Raoult and Roux 1999). Once infected, a person experiences severe fever, headache, shin pain, and dizziness (Foucault et al. 2006). Infection with B. quintana also occurs in cycles, with the first cycle being the most severe. A small proportion of inf ected patients are asymptomatic, though some

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20 experience bacteremia (Foucault et al. 2006). Infection with B. quintana is the least fatal of the known louse borne diseases, with a mortality ra te of <1% (Raoult and Roux 1999). Little is known about the effectiveness of antibiotic treatment of trench fever, since most data from infections occurred prior to the use of antibiotics (Ra oult and Roux 1999). However, a combination of doxycyline and gentamicin has b een shown to be effective (Raoult and Roux 1999). Sequencing of the Clothing Louse Genome The sequencing and ann otation of the clothing louse genome was recently completed, although its final publication has not occurred. The completed genome will provide important genetic information for the biomedical community. The bacterial genomes for pathogens carried by clothing lice, R. prowezii (Anderson et al. 1998), B. quintana (Alsmark et al. 2004), and two species of Borrelia (Fraser et al. 1997; Gloc kner et al. 2004) have alr eady been sequenced. The sequenced genome of P. humanus will provide insights into host -vector-pathogen interactions (Pittendrigh et al. 2006). The di scovery of genes that are involve d in vitellogenin production or olfactory receptors involved in locating potential hosts may provi de targets for louse-specific pesticides (Pittendrigh et al. 2006). The development of oligonuc leotide arrays and RNAi may aid in gene discovery. Further, oligonucleotide arrays may aid in determining which genes are induced or repressed during change s in louse behavior and envir onment, such as between head lice and clothing lice (Pittendrigh et al. 2006). Finally, sequencing of the P. humanus genome has the potential to determine if head lice are ab le to serve as vectors for bacterial pathogens (Pittendrigh et al. 2006). In addition to the importance of the P. humanus genome to the biomedical community, the genome will also provide insights to the evolutionary biology community. P. humanus will be the first genome sequenced of a hemimetabolous insect. Already, the small size (105MB) of

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21 the P. humanus genome relative to other in sect genomes, such as Drosophila (175MB) and Anopheles gambiae (260MB), is raising important evoluti onary questions, particularly because most other hemimetabolous insects are generally estimated to have large genomes (2000MB16,300MB) (Pittendrigh et al. 2006). In order to explain such a small genome size, several questions related to genome composition are ra ised, such as the number and size of noncoding regions and the number and types of repetitive elem ents (Pittendrigh et al. 2006). Further, is the reduction in genome size a result of human parasitism, and if so, is it a result of selection for metabolic or replication efficien cy or ecological specialization for the human host (Pittendrigh et al. 2006)? In addition to inte resting biological questions ra ised by the small genome size, evolutionary biologist s can also use the P. humanus genome to search for genes that help resolve relationships within Phthir aptera. Further, genes involved in pa rasitism of vertebrate hosts will be identified (Pitte ndrigh et al. 2006). The P. humanus genome project has achieved 8x covera ge. Preliminary analyses indicate that the genome is AT rich, with a GC cont ent of only 27.5%. However, 56% of genes of P. humanus occur in GC rich regions, indi cating a slight bias for genes to occur in GC rich areas. Currently, 11,214 genes have b een identified, and 90% of those (10,187) share sequence similarity to genes in other insects. Of the 11,214 genes, 969 8 contain introns, of which the average length is 303 base pairs and the average exon length is 238 base pairs. Only 1% of the P. humanus genome consists of transposable elements, and both class I and class II elements are present. When compared with ot her insect genomes, such as Apis mellifera, Drosphila melanogaster, Anopheles gambiae and Tribolium castaneum, P. humanus shows a reduction in gene families associated with detoxification, such as the p450, GST, and esterase gene superfamilies. The reduction in detoxification mech anisms is consistent with the life-history of

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22 P. humanus Because P. humanus is so closely ecologically tied to its human host, it is not exposed to secondary compounds produced by plants. Similarly, the P. humanus genome also has a reduction of gene families involved in sensory functions, such as opsin and chemoreceptor genes. In addition to the clothing louse genome the primary endosymbiont and mitochondrial genomes of P. humanus have also been sequenced. The reduced size of the primary endosymbiont, Candidatus Riesia pediculicola, is consistent with th e genome reduction that occurs when a bacterium is sequestered as an endosymbiont. Phylogenetic analysis of the Candidatus Riesia pediculicola sequence indicates that it is placed among the basal gammaproteobacteria. The mitochondrial genome of P. humanus displays a unique organization. Unlike the other >1000 bilaterian animals with sequenced mitochondrial genomes, the P. humanus genome does not consist of a single circ ular 16kb chromosome. Rather, it consists of 18 minicircular chromosomes, each of which has a length of 3kb and 1-3 genes. Analysis of the mitochondria of the pubic louse ( Pthirus pubis ), chimp louse (Pediculus schaeffi ), and the langur louse ( Pedicinus ancoratus ) indicates that these also have mi nicircular mitochondrial genomes, and that the most recent common ancestor of these li ce that parasitize primates likely had a similar mitochondrial genome organization 22.5 million years ago. Lice as Markers of Human Evolutionary History Sucking lice complete their entire life cy cle on their mammalian host, which selects for high host specificity and leads to cospeciation be tween parasite and host. Primates and their parasitic sucking lice have been cospeciating fo r the last 22.5 million ye ars (Reed et al. 2004). Researchers have exploited this property to learn more about pr imate evolution (Reed et al. 2004, Reed et al. 2007). Reed et al (2004) analyzed molecular data from sucking lice of anthropoid

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23 primates and confirmed the date of the human-chimp divergence to be 5-7 million years ago. Another study by Reed et al. ( 2007) dated the divergence between two sister taxa of lice, the gorilla louse, Pthirus gorillae and the human pubic louse, Pthirus pubis to be three million years. This date is significantly earlier than the human-chimp ancestor an d gorilla divergence of 7-8 million years ago (Reed et al. 2007), sugges ting a host switch from gorillas to humans. Sucking lice, particularly P. humanus has also provided insights into the population genetics of archaic and modern hum ans. Reed et al. (2004) confir med that head and clothing lice went through a population bottleneck and subse quent expansion out of Africa with modern humans. Reed et al. (2004) also determined that there are three mitochondrial lineages of P. humanus one that contains head and clothing lice and two that c ontain only head lice. Also, ancient DNA from P. humanus of a 1000 year-old Peruvian mu mmy indicates that the clade containing head and clothing lice was in the New World prior to European colonization (Raoult et al. 2008). This discover y supports the hypothesis that th e bacterial agent of typhus, Rickettsia prowazekii may be the result of a New World origin th at involves a host sw itch of the bacterium from its reservoir host, the flying squirrel, Glaucomys volans volans (Raoult et al. 2008). Population genetics of P. humanus has the potential to address several other questions relating to human evolutionary history. In order to address the origin of clothing use, Kittler et al. (2003, 2004) used unspecified phylogenetic me thods to date the age of the clade that contained both head and clothing lice to 107,000 years ago. Though the phylogenetic methods used by Kittler et al. (2003, 2004) may have been inappropriate for a population-level question, lice may provide insight into th e origin of the clothing use through coalescent methods to date the population divergence between head and clothing lice. Also, the taxonomic status of head and clothing lice may be addressed using molecula r techniques. Further, the deep divergences

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24 that occur among three lineages of P. humanus are potentially informative about the relationships between archaic hominids and modern humans (Reed et al. 2004). Currently, evolutionary biologists and anthr opologists studying lice re ly on three nuclear markers, EF1-alpha, RPII, and 18S, four mitochondrial markers, COI, CytB, ND4, and control region, and five microsatellite loci (Leo a nd Barker 2005) to draw inferences about the population genetics of head and clothi ng lice. With th e release of the P. humanus genome, a variety of new molecular tools will soon be available, such as a variety of nuclear genes, SNPs, microsatellites, and oligonucleotide arrays. Th ese new tools will allow researchers to address biological and anthropological questions whose answers have been elusive thus far.

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25 CHAPTER 2 POPULATION GENETIC ANALYSIS OF Pediculus humanus PROVIDES INSIGHT INTO THE ORIGIN OF HUM AN CLOTHING Introduction Biologists studying organisms with reduced genetic variation have begun to regularly exploit host parasites and pathogens to track events in the evolutio nary history of the host. This is particularly true in the fi elds of conservation (Whiteman a nd Parker 2005), invasive species (Meusnier et al. 2001), and human evolution resear ch (reviewed in Wirth et al. 2005), where host genetic variation is greatly reduced. In such scen arios, the parasite may generate more genetic diversity than the host due to its generally shorter generation time, which increases its evolutionary rate. Additionally, parasites often have larger effective population sizes, and therefore maintain more genetic variation through bottleneck even ts. The faster evolutionary rate of the parasite and increased genetic variation may therefore cap ture evolutionary events that are not coded in host DNA, allowing biologists to study the evolutionary history of the host through analysis of parasite DNA. This has been used most often in studies of human history (reviewed in Wirth et al. 2005), where JC virus, herpes simplex virus 1, human papillomaviruses, and Helicobacter pylori have been used to tr ack human evolution. Microparasites (bacteria a nd viruses) often reproduce clonally, and are thus highly susceptible to selective sweeps at a few loci prod ucing patterns of genomi c diversity that do not reflect the history of the host (G renfell et al. 2004; Nieberding et al. 2006; Rich et al. 1998). Conversely, macroparasites (such as parasitic arthropods) often reproduce sexually and may therefore track host evolutionary history more accurately because selective sweeps affect only closely linked loci in their genomes (Grenfe ll et al. 2004). For this reason, the use of macroparasites, such as pinworms (Araujo et al 2008) and lice (Raoult et al. 2008; Reed et al. 2004), has become increasingly common in the study of human evolution.

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26 Sucking lice (Phthiraptera: Anoplura) have cospeciated with their primate hosts for at least the last 22.5 million years (Reed et al. 2004). These lice are permanent, obligate ectoparasites that require direct contact between their primate hosts for transmission (Burgess 2004; Canyon et al. 2002). Molecular examinatio n of these lice has confirmed events known from primate history, such as the human-chim p divergence 5-7 million years ago (Reed et al. 2004). Additionally, the study of human lice ( Pediculus humanus ) has confirmed events in human demographic history, such as the population expansion of anatomically modern humans 100,000 years ago (Reed et al. 2004). These findings indicate that human lice have great utility for the study of human population history. Two varieties of human lice, head and clothing lice (both P. humanus; see Light et al. 2008), may also provide insights into human evol ution not recorded in human genetic data, specifically the origin of clothing use. Determini ng the origin of clothing use has been primarily inferential in anthropological literature as most materials used for clothi ng (furs, skin, cloth) degrade rapidly and are thus unknown in the arch aeological record of the Late Pleistocene. Archaeological evidence for the use of tailored clothing, such as needles, first appears ~40,000 years ago (Delson et al. 2000). Earlier evidence for tools used to scrape hide appears ~300,000 years ago (Toth and Schick 1993); however, there is no definitive evidence that these tools were used to make even rudimentary clothing. The inabil ity of the archaeological record to answer this question suggests that an innovative approach is necessary. The biology of human head and clothing lice makes them potentially useful markers to infer the origin of clothing use in humans. Mol ecular data suggest that humans lost their body hair approximately 1.2 million years ago (Rogers et al. 2004). Prior to body hair loss, lice in the genus Pediculus likely occurred more uniformly across the body, but upon body hair loss

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27 became restricted to the head. As humans st arted wearing clothing, a portion of head lice colonized this new habitat and became the ancesto rs of clothing lice (Burgess 1995; Kittler et al. 2003; Kittler et al. 2004). These lice then became specialized for the clothing niche, and at present spend more time in clothing than on the body, only returning to the body to feed once or twice per day. Of the thr ee mitochondrial lineages of P. humanus (Leo et al. 2002; Raoult et al. 2008; Reed et al. 2004), tw o lineages contain only head lice a nd the third contains both head and clothing lice. Kittler et al. (2003, 2004) used phylogenetic methods to date the age of the lineage that contained both head and clothing lice and determined the origin of clothing use to be 107,000 years ago. Kittler et al.s date of 107,000 years ( 2003, 2004) suggests a recent origin of human clothing use. However, phylogenetic methods are inappropriate for answering this populationlevel question since several researchers have shown that head and clothing lice do not form reciprocally monophyletic clades (Leo et al. 2002; Reed et al. 2004; Yong et al. 2003). Furthermore, a recent study has demonstrated si gnificant gene flow between head and clothing lice (Light et al. 2008), suggesti ng that recent head and clothing lice evolution is best understood as a population genetic process. In this study, we exploit recent advances in coalescent methodology using multiple loci to analyze louse genetic data and address the orig in of clothing use in humans. We first use a relaxed clock method (Drummond et al. 2006) to estimate mutation rates for our multilocus dataset. We then employ an isolation-with-mig ration coalescent method that jointly estimates divergence times, population sizes and migration rates from our multilocus dataset (Hey 2005; Nielsen and Wakeley 2001) to date the divergen ce of, and migration rates between, human head and clothing louse populations.

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28 Materials and Methods Molecular Data All available DNA sequence data for the following genes were downloaded from GenBank (see Supplemental Table 1): mitochondria l gene COI (166 sequences) and the nuclear genes 18S rRNA (22 sequences), EF-1 (40 sequences; not including any of the sequences from (Yong et al. 2003), which were shown by Light et al. (2008) to be contaminants, and RPII (53 sequences). Sequences for the outgroup taxon Pediculus schaeffi (parasitic on chimpanzees) were downloaded from GenBank for each of the four genes (Supplemental Table 1). All COI, EF-1 and RPII sequences were aligned by hand using MacClade (Maddison and Maddison 2005) and manually edited to maintain prope r reading frames using Se-Al v2.01a11. All 18S rDNA sequences were aligned manually in refere nce to secondary structure (Gillespie et al. 2004; Gillespie et al. 20 05); alignment available at the jRNA web site) and ambiguously aligned sites were removed before analysis. EvolutionaryRate Calculation Phylogenies and evolutionary rates () for each of the four genes were co-estimated under a relaxed (uncorrelated lognormal distribution) molecular clock using BEAST v.1.4.6 (Drummond et al. 2006; Drumm ond and Rambaut 2007). Estimates of were calibrated under an assumption of host-louse cosp eciation, which has been demonstr ated by Reed et al. (2004) for Hominidae. Specifically, an exponential prior distribution with a lower bound of 5MYA and mean of 5.5MYA was placed on the divergence of P. humanus and P. schaeffi that reflects current estimates for the divergence of thei r human and chimpanzee hosts (Kumar and Hedges 1998), respectively. All analyses we re performed with a GTR + I + nucleotide substitution model and a Yule birth-death prior on the tree topology. All Markov chains were run for

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29 10,000,000 generations with samples taken ev ery 1,000 generations and the first 1,000,000 generations were discarded as burn-in. Isolation with Migration Analysis A Bayesian isolation-with-migration coales cent analysis (Hey a nd Nielsen 2004; Nielsen and Wakeley 2001) was performed on the multilocus louse dataset using the program IM (Hey 2005). The isolation-with-migration coalescent m odel assumes that an an cestral population of effective size NA diverges at some time t into two daughter populations of initial size s NA and (1s )NA, both of which then experience independent exponential growth and migration between populations (with rates m1 and m2). All IM analyses were perf ormed with a Hasegawa-KishinoYano (HKY) nucleotide substitution model for al l four loci, and the upper bound of the prior distribution for the time of divergence was se t to 5.5MYA, following best estimates for the human-chimpanzee divergence (see above). Estimates of from the evolutionary rate calculation above were used to convert population mutation parameter estimates (i.e. t ) from mutational units into absolute units. All other priors were conservatively estimated from preliminary runs with very broad uniform prior distributions to facilitate adequate Markov chain mixing. All Markov chains were run for 600 million generations and sampled every 600 generations. Ten replicate runs with unique seed values were performed to ensure Markov chain convergence. Results Independent runs of IM an alyses converged on sim ila r posterior distributions (summarized in Figure 1). Peaks in the distribut ion were taken as point estimates of population genetic parameters. At the time of completion, all estimates of effec tive sample size exceeded 400. Estimates of and t were converted to effective populat ion size and absolute time-since-

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30 divergence, respectively, using estimates of obtained with BEAST v.1.4.6 (Drummond et al. 2006; Drummond and Rambaut 2007). The distributions of current effective popul ation sizes of head and clothing lice were contained within the priors. Point estimates were 2.5 million individuals for head lice and 1.8 million individuals for clothing lice. Estimates of the splitting parameter s indicate that only a small proportion of the ancestral population (< 1%) initially colonize d clothing, whereas the majority (>99%) remained head lice, which is th ought to be the ancestral condition. Estimates of bidirectional migration ( m ) showed very high migration from head lice to clothing lice ( m = 1.16), but virtually no migrati on in the opposite direction ( m = 0.0040). The posterior distribution for the time of population divergence peaks between 650,000700,000 years ago in all IM replicates. The eff ective population size for the common ancestor of head and clothing louse peaked at the lowest bin and decreased thereafter. There are two potential explanations for this. First, the e ffective population size of the common ancestor was smaller than our analysis could detect. Altern atively, because head and clothing lice diverged long ago and have likely been through the same population bottlenecks as their human host, there may be too little information in the data to effectively estimate this parameter. Discussion Pediculus humanus diverged from its sister taxon, the chimpanzee louse P. schaeffi at the human-chimp divergence roughly 5.5 million years ago (Reed et al. 2007; Reed et al. 2004). It is likely that lice in the genus Pediculus parasitized all subsequent hominid lineages given their history of cospeciation. Because P. schaeffi is found throughout the body of their chimpanzee hosts it is likely that the human parasite species of Pediculus also utilized much of the human body prior to the general loss of body hair in humans. At the time humans lost their body hair,

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31 Pediculus likely became restricted to head hair, a nd only invaded the body niche recently with the advent of clothing use (Busvine 1978; Burges s 1995; Kittler et al. 2003; Kittler et al. 2004). This is inferred primarily from the current natura l history of clothing lice At present, clothing lice spend the majority of their time in clothing, and only return to the bod y to feed. Clothing lice prefer to attach their eggs to the pleats and seams of clothing, particularly the undergarments, rather than body hair (Burgess 1995; Buxton 1946; Nuttall 1917). In th e absence of clothing, clothing lice will infest beads and necklaces (Busvine 1978; Buxton 1946). When displaced, clothing lice tend to return to th e clothing and are partic ularly attracted to areas that are occupied by other clothing lice or clothing louse feces (Mumcuoglu et al. 1986; Wigglesworth, 1941). Our results support the assert ion that the head was likel y the ancestral habitat for P. humanus The splitting parameter s indicates that a large pro portion of the ancestral louse population (>99%) was of the head lice type at th e time of divergence, and that only a small proportion (<1%) moved to the clothing niche as a founder population. Furthermore, our results indicate a lack of mi gration from clothing louse to head louse populations, suggesting that clothing lice are ecologically distinct and possibl y unable to survive under head louse conditions. This finding is consistent with empirical transpla ntation experiments. When head lice are reared as clothing lice in the laboratory (in pill boxes worn upon the skin), morphological and behavioral changes take place such that the head lice gain the morphological and natural history characteristics of clothing lice within a few generations (Alpatov and Nastjukova 1955; Bacot, 1917; Levene and Dobzhansky 1959; see Busvine, 1948 for a single known exception). Further, when clothing lice are displaced, they return to clothing, particularly areas occupied by other clothing lice and clothing louse feces (Mumcuoglu et al. 1986; Wigglesworth 1941). However,

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32 there is no evidence to suggest th at clothing lice can su ccessfully colonize th e head louse niche, which provides further support for unidirectional gene flow. Coalescent methods that use multiple loci for population genetic inference reduce uncertainty in estimates of divergence time rela ted to genealogical stoc hasticity (Edwards and Beerli 2000). This allows us to estimate the divergence of head and clothing lice, as opposed to dating the origin of the clade of head and clothi ng lice using phylogenetic methods (Kittler et al. 2003; Kittler et al. 2004). By using population gene tic methods to date the divergence, we are able to obtain a more precise estimate of when populations of P. humanus began to colonize the clothing niche. Furthermore, our analyses uncovered a high rate of migration ( m = 1.16) from head to clothing lice, further indicating that th e divergence between head and clothing lice is a population genetic process. Our point estimate of 650,000 years ago (90% HPD 225kya-6mya) indicates that head and clothing lice diverged signi ficantly earlier than pr eviously thought and suggests that the use of rudimentary clothing originated with archai c hominids, not anatomically modern humans, which arose only within the last 120,000 years (Pakendorf and Stoneking 2005). Also, it is important to note that the diverg ence of human head and clothing lice provides a minimum date for the origin of clothing use; it is possible that the clothing ni che existed for some time before parasitic lice successfully colonized clothing. There are both adaptive and neutral explanations for why a nd how clothing use arose. Clothing may have arisen in Africa because it co nferred an advantage to archaic hominids living in high altitudes. A lternatively, clothing use may have ar isen for decorative purposes. Though our study cannot disentangle these alternatives, it can provide some insight as to where clothing use arose.

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33 The mitochondrial clade of P. humanus that contains both head and clothing lice has the genetic signature of a populati on expansion that occurred 100, 000 years ago (Reed et al. 2004) suggesting that these lice accompanied modern humans out of Africa. Because the date of divergence of head and clothing lice only provides a minimum estim ate for the origin of clothing use, the technology to make clothing may have ex isted for some time prior to 650,000 years ago. Anthropologists recognize multiple dispersa ls of hominid species out of Africa (Anton and Swisher 2004; Dennell 2003; Finlayson 2005), with the fi rst dispersal of H. erectus occurring approximately 2 million years ago (Anton and Swisher 2004; Dennell 2003; Finlayson 2005). Most of the evidence suggests that H. erectus populations outside of Africa were largely confined to Southeast Asia, though there is some evidence of H. erectus in northern Asia around this time (Anton and Swisher 2004; Dennell 2003; Finlayson 2005). The permanence of these earliest dispersals into northern latitudes has been questioned (D ennell 2003). Interestingly, our estimate approximately coincides with the fi rst evidence of permanent archaic hominid settlements into high latitude regions of Europe and Central Asia between 800,000 and 500,000 years ago (Ascenzi et al. 1996; Carbonell et al. 1995; Dennell 2003; Ranov 1995). It is possible that the archaic hominids that dispersed and su ccessfully colonized co lder climates 800,000 to 500,000 years ago may have possessed the knowledge to use furs and skins as rudimentary clothing, which would have allowed them to survive and persist in the temperate climates of Europe and Central Asia. Altern atively, it is conceivable that clothing use originated with archaic hominids in Europe and Central Asia, and spread to archaic hominid populations in Africa via intermittent contact. However, this is less likely, considering that archaic hominid populations in Central Asia and Europe were li kely spatially and temporally discontinuous

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34 during this time period (Dennell 2003), making transfer of technol ogy between populations difficult. The natural history of clothi ng lice suggests that they are ecologically distinct from head lice, and therefore it is assume d that clothing lice only arose w ith the advent of clothing use (Burgess 1995; Busvine 1978; Kittler et al. 2003; K ittler et al. 2004). Our analyses indicate that only a small proportion of lice initi ally colonized clothing, but that migration from head to clothing has been considerable (m = 1.16) since. Further, our an alyses suggest that clothing use originated with archaic hominids in Afri ca 650,000 years ago, not modern humans, and may have played a role in the archaic hominid colonization of Central Asia and Europe.

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35 0 0.001 0.002 0.003 0.004 0.005 0.006 0.007 0.008 0.009 0.01 02468 Population Size (millions) Head Clothing 0 0.005 0.01 0.015 0.02 0.025 0.03 0.035 02468 Migration head to clothing clothing to head 0 0.001 0.002 0.003 0.004 0.005 0.006 0.007 0123456 Time (million years) Figure 2-1: Marginal posterior pr obability distributions for model IM parameters in demographic units. (A) Effective population size. (B) Migration rates ( m ). (C) Time since divergence. A B C

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36 Table 2-1: Estimates of evolutionary rate () in substitutions/locus/year for each locus. Locus EF1-alpha 0.00000285 COI 0.0000163 18S 0.0000118 RPII 0.000041

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37 CHAPTER 3 CHARACTERIZATION OF ELEVEN POLY M ORPHIC MICROSATELLITE LOCI FROM THE HUMAN HEAD AND CLOTHING LOUSE, Pediculus humanus Human head and clothing lice, Pediculus humanus capitis and Pediculus humanus humanus, respectively, have parasitized humans for t housands of years (Araujo et al. 2000). Currently, head lice are pandemic, infesting millions of schoolchildren worldwide. Clothing lice, though less prevalent, are common am ong areas stricken by poverty or political and social unrest that prevent inhabitants from having multiple se ts of clothes (Raoult and Roux 1999). Clothing lice (also called body lice) are also becomi ng increasingly common among the homeless populations in developed countries such as the Un ited States and Western Europe (Brouqui et al. 1996; Drancourt et al. 1995; Koehler et al. 1997). Clothing lice are more harmful parasites because they can vector three bacterial pathogens: Rickettsia prowazekii (epidemic or louseborne typhus; but see (Robinson et al. 2003), Borrelia recurrentis (louse-borne relapsing fever) and Bartonella quintana (trench fever; Buxton 1946; but see Sasaki et al. 2006). In addition to their importance in the biom edical field, human head and clothing lice are of interest to evolutionary biol ogists and anthropologists. Head and clothing lice are part of a group of anoplurans that have cospeciated with primates for 22.5 million years (Reed et al. 2004), and therefore have been used to provide in sights into human evolut ionary history (Kittler et al. 2003; Kittler et al. 2004, Ra oult et al. 2008; Reed et al. 2007; Reed et al. 2004). For example, head and clothing lice have been used to estimate the origin of clothing use in humans (Kittler et al. 2003; Kittler et al. 2004). The use of popula tion level markers, such as microsatellites, may provide insights into the ep idemiology and evolutionary history of one of the oldest human parasites. Microsatellite loci were mined from the Human Body L ouse Genome Project (Johnston et al. 2007) using Tandem Repeat Finder (Benson 1999). Of the initial microsat ellite search, loci

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38 were selected that contained a minimum of ei ght repeats and at leas t 200 base pair flanking regions on each side that was free of other repetitive elements. These loci were further screened when designing primer pairs using PRIMER3 (Rozen and Skaletsky 2000) for formation of hairpins, self-dimers, hetero-dimers, and optimal primer GC content of 40-60%. Primer pairs were designed for a total of 48 loci, of whic h 11 have been assessed for polymorphism using 18 head louse individuals, each from a separate hos t individual, from West Palm Beach, Florida. DNA amplifications were carried out in 25 L reactions containing 11.5 L of distilled water, 10 L of 5Prime HotMaster Mix (Eppendorf), 1 L of 1 M M13 labeled forward primer, 1 L of 10 M reverse primer, and 1 L of 10 M FAM label, and 0.5 L of DNA template. Thermocycling conditions for all loci were identical and are as follows: 94 for 3 min, followed by 10 cycles of 94 for 30 s, 52 for 30 s, 65 for 45 s, then 30 cycles of 94 for 30 s, 48 for 30 s, 65 for 45 s, and a final extension of 65 for 10 min. Fragment leng ths of PCR products were detected using ABI 3730 Automated Sequencer and scored using GENE MAPPER 3.0 software (Applied Biosystems). Data for loci analyzed are available in Ta ble 1. The number of alleles ranged from 3-7 per locus. Observed and expected hetero zygosities were calcul ated using MICROSATELLITE ANALYSER 4.05 (Dieringer and Schlotterer 2003) and ranged from 0.056-0.278 and 0.3030.820, respectively. Linkage disequilibrium with a Bonferroni correction was tested using GENEPOP version 3.4 (Raymond and Rousset 1995) and no linkage disequilibrium was identified. Deviations from Ha rdy-Weinberg equilibrium were tested using GENEPOP version 3.4 (Raymond and Rousset 1995). Only two lo ci, M2_19 and M3_9 are in Hardy-Weinberg equilibrium, and M2_19 is only marginally so (p=0.050). Because 9 of 11 loci are polymorphic

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39 and exhibit heterozygote deficien cy,it is likely the population tested that is out of HardyWeinberg equilibrium, and not the loci. Our results indicate that these microsatelli tes are clearly polymor phic in this population, though not in Hardy-Weinberg equilibrium. Seve ral possible explanati ons exist for why the population may be out of Hardy-We inberg equilibrium, such as hi gh population substructure or nonrandom mating. Additional populations should be screened to determine if this is specific to the population of head lice in West Palm Beach, Florid a, or if it is character istic of the species in general. Alternatively, further sampling of the population in West Palm may reveal a high level of population substructure. The polymorphic microsatellites identified in this study may be useful in examining differences between head and clothing lice, in examining fine-scale host migrations, and characterizing local populations worldwide.

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40 Table 3-1. Characteristics of elev en microsatellite loci for the human head and clothing louse, P. humanus including locus name, primer sequence, repeat motif, allele size range, number of alleles (Na), observed heterozygosity (HO), expected heterozygosity (HE), and probability associated with Hardy-Weinberg equilibrium. Locus Primer Sequence Repeat Motif Allele Size (bp) Na HO HE P M2_2 F: TCTTGCAGTGTGTCTCTTTGC GA 392-412 4 0.05 6 0.678 0.000 R: CTATCGGAAATGTG CAGAGC M2_3 F: TGATATTTTAGGCGCACAACC GA 364-370 4 0.059 0.497 0.000 R: GTCTCAATTCGGCCACTTCT M2_4 F: TTCAGGATCTTCTGCCCAAC GA 308-316 4 0.056 0.662 0.000 R: GGGTTCGCAAAAAGGTGAC M2_16 F: TAACGACCGCTTTTCGAGTT GA 242-266 6 0.11 1 0.697 0.000 R: GGGGTGAACTGGATGTTTCA M2_17 F: GCCTAGCGAAAGCTCTGAAA TA 235-253 6 0.188 0.714 0.000 R: GAAGTATCATTTCGGCGTGA M2_19 F: GGTGGCAAAAACCACTAATGA TA 182-198 4 0.278 0.486 0.050 R: TCCGTTAAAAATGGCAAAGG M3_3 F: TGTTCCTGCTGGTAAACTTGC TAA 238-295 7 0.176 0.820 0.000 R: GAACGATCAATCTGCTTCTGC M3_9 F: CCCGTAAAATATCCACGCTGT TTA 284-302 3 0.278 0.332 0.507 R: CTGGTCGGCTATGTTTTGCT M3_11 F: CTCCTAACGGGAGCAAAGAA TTA 299-357 6 0.167 0.749 0.000 R: CCATACATATTAGTCGCCTTCCA M3_18 F: CGTCGGAGGAATGTATAGGG GAC 275-299 4 0.111 0.303 0.011 R: GACAGTGACGGATCGAACG M3_19 F: TTAAGAGCTGATGCCACGTC CAT 346-358 4 0.118 0.405 0.000 R: TCTGGAAAAGGACGAAAGGA

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49 BIOGRAPHICAL SKETCH Melissa Toups was born and raised in New Or leans, Louisian a. After graduating from Archbishop Chapelle High School in 2000, she at tended Tulane University and majored in ecology and evolutionary biology. Wh ile at Tulane, she participated in the Junior Year Abroad program and attended the University of Bristol. She graduated Tulane in the Spring 2004 magna cum laude. She began her graduate career in August 2005 in the Zoology Department at the University of Florida and received her M.S. in August 2008.