Title: Three-stage colonization model for the peopling of the Americas
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Title: Three-stage colonization model for the peopling of the Americas
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Language: English
Creator: Kitchen, Andrew
Miyamoto, Michael M.
Mulligan, Connie J.
Publisher: Andrw Kitchen et al.
Place of Publication: Gainesville, Fla.
Publication Date: February, 2008
Copyright Date: 2008
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General Note: PLoS ONE ; February 2008 ; volume 3, issue 2, e1596
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A Three-Stage Colonization Model for the Peopling of

the Americas

Andrew Kitchen1, Michael M. Miyamoto2, Connie J. Mulligan'*
1 Department of Anthropology, University of Florida, Gainesville, Florida, United States of America, 2 Department of Zoology, University of Florida, Gainesville, Florida,
United States of America


Abstract

Background: We evaluate the process by which the Americas were originally colonized and propose a three-stage model
that integrates current genetic, archaeological, geological, and paleoecological data. Specifically, we analyze mitochondrial
and nuclear genetic data by using complementary coalescent models of demographic history and incorporating non-
genetic data to enhance the anthropological relevance of the analysis.

Methodology/Findings: Bayesian skyline plots, which provide dynamic representations of population size changes over time,
indicate that Amerinds went through two stages of growth 40,000 and 15,000 years ago separated by a long period of
population stability. Isolation-with-migration coalescent analyses, which utilize data from sister populations to estimate a
divergence date and founder population sizes, suggest an Amerind population expansion starting 15,000 years ago.

Conclusions/Significance: These results support a model for the peopling of the New World in which Amerind ancestors
diverged from the Asian gene pool prior to 40,000 years ago and experienced a gradual population expansion as they
moved into Beringia. After a long period of little change in population size in greater Beringia, Amerinds rapidly expanded
into the Americas 15,000 years ago either through an interior ice-free corridor or along the coast. This rapid colonization
of the New World was achieved by a founder group with an effective population size of 21,000-5,400 individuals. Our
model presents a detailed scenario for the timing and scale of the initial migration to the Americas, substantially refines the
estimate of New World founders, and provides a unified theory for testing with future datasets and analytic methods.

Citation: Kitchen A, Miyamoto MM, Mulligan CJ (2008) A Three-Stage Colonization Model for the Peopling of the Americas. PLoS ONE 3(2): e1596. doi:10.1371/
journal.pone.0001596
Editor: Henry Harpending, University of Utah, United States of America
Received January 8, 2008; Accepted January 16, 2008; Published February 13, 2008
Copyright: 2008 Kitchen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This study was supported by a grant from the National Science Foundation to CJM (BSR-0518530) and by funds from the Department of Zoology,
University of Florida to MMM.
Competing Interests: The authors have declared that no competing interests exist.
*E-mail: mulligan@anthro.ufl.edu


Introduction

For decades, intense and interdisciplinary attention has focused
on the colonization of the last habitable landmass on the planet-
the peopling of the Americas. The first comprehensive, interdis-
ciplinary model for New World colonization incorporated
linguistic, ] ,1.... il...... .1..;. ,1 and genetic data and generated
great controversy, which was due at least in part, to the uniquely
broad scope of the research [1]. Since that time, more focused
studies have resulted in agreement on the general parameters of
the colonization process, such as a single migration in contrast to
the original three-migration model that distinguished Amerinds,
Na-Dene, and Eskimo-Aleuts [1]. However, a full understanding
of the complex and dynamic nature of the timing and magnitude
of the colonization process remains elusive.
The majority of the genetic literature supports a single
migration of Paleoindians into the New World from an East
Asian source population [2]. Specifically, the reduced variation
and ubiquitous distribution of mitochondrial and Y chromosome
haplogroups and microsatellite diversity 1i..i 1.....,I the New
World relative to Asia argue strongly for a single migration [3,4].
However, a great many models have been proposed that differ
1 ,.1 ;, the timing and size of this migration event [2,5-15].


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Different migration dates have been proposed ranging from 13
thousand years ago (kya) to 30-40 kya [2,5-15]. Numerical
estimates of the founder effective population size (Ne) are
infrequent in the literature but vary substantially, from a high of
5000 [6] to a low of 70 Paleoindian founders [16]. These dates
and population sizes have been proposed to accommodate a
wealth of scenarios including ancient, recent, and/or additional
migrations responsible for the peopling of the Americas.
Archaeological data provide clear support for a widespread
human presence in the Americas by 13 kya (all calendar dates
are recalibrated radiocarbon dates as reported in the cited
literature), the time by which the Clovis complex was established
across the interior of North America [17,18]. Older archaeological
sites, e.g. the Nenana Complex in Alaska [18], the Monte Verde
site in Chile [19], and the Schaefer, Hebior and Mud Lake sites in
Wisconsin [20,21], document an earlier chronology possibly
2,400 years before Clovis [18,20,21]. Additionally, very old
radiocarbon dates have been obtained from sites in Asian Beringia
suggesting that human populations had reached the north of
western Beringia by 30 kya [22,23].
The geological and paleoecological records for Beringia and
northwestern North America provide further constraints on the
timing for the peopling of the Americas. Beringia was a continuous


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Peopling of the Americas


landmass that connected Asia and North America roughly 60 kya
until 11-10 kya [23-25]. However, Beringia was isolated from
continental North America until 14 kya when an intraconti-
nental ice-free corridor opened up between the Laurentide and
Cordilleran Ice Sheets [26]. Paleoecological data indicate that
Beringia was able to sustain at least small human populations.
Fossil pollen and plant macrofossils from ancient eastern Beringia
are indicative of a productive, dry grassland ecosystem [27] and
paleontological evidence from Alaska and Siberia demonstrates
that large mammals roamed Beringia [28].
After 11-10 kya, Late Pleistocene sea levels rose sufficiently to
re-inundate Beringia [24,25], creating the Bering strait that now
separates the New World from Siberia by at least 100 kilometers
(km) of open frigid water. Studies of human settlement 1 .. .1 ...1
the Pacific Islands indicate that open water distances of >100 km
constitute significant barriers to human migration, possibly
because ancient people were unlikely to travel further than one
day out of sight of land [29]. Similar constraints (if not worse)
would apply to early humans in Alaska and Siberia, thereby
severely reducing the migration rate between the New and Old
World once Beringia was re-inundated. Reduced migration due to
the Bering Strait remains valid even as recent rates of short-range
migration have increased between Siberia and Alaska [13]. In
effect, the two continents were essentially geographically isolated
from 11-10 kya until modern times.
No detailed, unified theory of New World colonization currently
exists that can account for the breadth and complexity of these
interdisciplinary data. We analyze Native American mitochondrial
DNA (mtDNA) coding genomes plus non-coding control region
sequences as well as a combined nuclear and mitochondrial coding
DNA dataset from New World and Asian populations. Mitochondrial
DNA data represent the 'gold standard' of genetic data types and
provide the most extensive comparative database for human
populations worldwide [30]. Furthermore, it has been proposed that
mtDNA may be more sensitive to demographic changes, such as
population bottlenecks, due to its smaller effective population size
[31]. The combined nuclear and mtDNA dataset was recently used to
propose an unusually small N, for the Amerind founders [16], and
thus investigation of this dataset is of much interest when i.i. ii. i;1.
to reconcile the existing genetic evidence. We use two complementary
coalescent methods to develop a comprehensive scenario of New
World colonization, with a focus on the timing and scale of the
migration process. Bayesian skyline plot analyses use data from a
single population to provide an unbiased estimate of changes in N,
1,...._ 1 time, and thus are a powerful means for estimating past
population _1.. 11i patterns when the nature of the _1., 11. (e.g.
exponential or constant) is unknown [32]. The isolation-by-migration
(IM) structured coalescent model uses data from sister populations to
jointly estimate population divergence time, migration rates and a
founder N,, with an assumption of exponential _1.. 1, [16].
Importantly, we explicitly incorporate archaeological, geological,
and paleoecological constraints into both analyses. Our goal is to
provide a comprehensive model for the initial settlement of the
Americas that generates new testable hypotheses and has high
predictive power for the inclusion of new datasets. In light of our
results, we propose a three-stage model in which a recent, rapid
expansion into the Americas was preceded by a long period of
population stability in greater Beringia by the Paleoindian population
after divergence and expansion from their ancestral Asian population.

Results
Skyline Plot Analyses
Our alignment of 77 full mitochondrial coding genomes is one
of the largest published alignments of Native American mtDNA


coding genomes (Figure Sl). It includes genomes from the four
major mtDNA haplogroups in the Americas i i i. 1_ i,. A, B, C,
and D are each represented by 17-31% of the entire sample), as
well as the minor haplogroup X (2%). Correspondingly, this set of
77 complete coding mtDNA genomes represents geographically
and linguistically diverse populations distributed 1, ..1 ....i the
New World [3]. Bayesian skyline plots [32] were used to visually
illustrate changes in Amerind female effective population size (Nef)
over time. Bayesian skyline plots assume a single migration event,
which makes the approach ideal for questions concerning the
peopling of the Americas since it is generally agreed that there was
a single migration [3]. Our skyline plot of the coding genomes
describes a three-stage process in which there are two distinct
increases in Nf at "40 kya and 15 kya that are separated by a
long period of little to no -,.1 11, (Figure 1). Specifically, Nf
increases from 640 [95% credible interval (CI) = 148-9,969] to
4,400 individuals (95% CI= 235-18,708) at the first inflection
point, and from u4,000 (95% CI=911-13,006) to u64,000
individuals (95% CI=15,871-202,990) at the second inflection
point. There is also an apparent decrease in Nf prior to the second
inflection point in which median Nf drops to "2700 (95%
CI= 404-36,628). We define a significant change in population
size as the occurrence of non-overlapping 95% CIs at the
beginning and end of an increase (see shading in Figure 1). Thus,
we interpret the recent 16-fold increase in Nf over the interval
"16-9 kya as significant. The earlier "7-fold increase at 43-
36 kya is suggestive but not significant, ,l.... J1, the increase is
significant when compared over a much longer time period, e.g.
from "25 kya to the coalescent. Overall, the recent increase is
consistent with a rapid, large-scale expansion into the Americas
while the older increase is suggestive of a gradual expansion within
Asia or Beringia.
The dataset of 812 concatenated mtDNA hypervariable region
(HVR) I and II sequences is one of the largest published
alignments of Native American HVRI+II sequences (Figure S2).
It includes all major New World haplogroups, and represents
geographically and linguistically diverse populations distributed


1.000,000
if

S100,000
0

S10000


I
, 1,000


u. 100


Oc(upaion of Be lgia


[43,210-69.8701


10 20 30 40 50
Thousands of years before present (kya)


0


Figure 1. Bayesian skyline plot for the mtDNA coding genome
sequences. The curve plots median Nef with its 95% CI indicated by
the light gray lines. The calculated Nef assumes a generation time of
20 years following Hey [16]; alternatively, using a generation time of
25 years [55] would uniformly decrease all estimates of Nef by 20%. "X"
marks the median coalescent time with its 95% CI given in brackets. The
shaded regions highlight two periods of substantial population growth.
This skyline plot provides the principal evidence for our three-stage
model of New World colonization, i.e. the three stages that are depicted
and labeled here.
doi:1 0.1371/journal.pone.0001596.g001


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Peopling of the Americas


......l....i the Americas. The HVRI+II dataset was randomly
divided into ten non-overlapping alignments of 81 HVRI+II
sequences, which allowed for ten independent trials for parameter
estimation with a sample size similar to the coding genome
alignment. The HVRI+II skyline plot analyses (Figure 2) produce
estimates for median time to coalescence (55.5 kya, 95%
CI= 33.5-87.2 kya) and Nf at coalescence (820, 95% CI= 26
3,979) and the present (66,200, 95% CI = 9,839-346,289) that are
similar to the coding genome analyses (Figure 1). However, in
contrast to the coding genome skyline plot, the HVRI+II skyline
plot traces a very gradual increase in N,f over 40,000 years with
no clear inflection points. The HVRI+II plot does show a
significant increase in N,f but only when measured over the past
35,000 years. The fine detail evidenced in the coding genome
skyline plot likely reflects the greater phylogenetic signal in the
mitochondrial coding genome relative to the HVR [33]. In
general, estimates of the time to the most recent common ancestor
are less sensitive to reductions in the historical signal in mtDNA
sequence data than phylogenetic estimation [33], a result
consistent with our ability to recover similar coalescence times
but not the changes in N,f seen when comparing the coding vs.
HVRI+II skyline plots.

Isolation-with-Migration Coalescent Analyses
Bayesian IM coalescent analyses were performed on a set of
nine coding nuclear and mitochondrial loci that had been
previously analyzed by Hey [16] in support of an extremely small
New World founder N, of 70 individuals. Thus, we performed
our analysis on his identical dataset and used the same coalescent
and substitution models and model parameters with the exception
of new priors on the divergence time and on migration rates
between Asian and Amerind populations (mAsia-NW and
mNw-Asia). The lower bound on divergence time was set to15 kya,
which corresponds to the period immediately preceding the
earliest archaeological evidence for human habitation in the
Americas [18-21]. We also instituted serial constraints on m in
order to gauge the effect of changing migration rates on founder
N, estimates. We interpret the various m values in comparison to
an empirical estimate of m for modern Europe (m= 4.3; see


1,000.000
i

* 100,000
0
J 10,000
0.

, 1.000


" 100
E
- 10


0 10 20 30 40 50
Thousands of years before present (kya)


Figure 2. Bayesian skyline plot for the mtDNA HVR 1+11
datasets. This plot follows the conventions of Figure 1. Its estimates
of coalescent time and Nef at the coalescence and today are in
agreement with the coding mtDNA skyline plot (Figure 1). In contrast,
this HVRI+II plot provides little resolution for other population size
changes, most likely because of mutational saturation in the non-
coding control region (see text).
doi:1 0.1371/journal.pone.0001596.g002


Materials and Methods). In contrast to modern Europe, migration
between the New World and Siberia from 15 kya to more recent
times would have become increasingly limited as Late Pleistocene
sea levels rose sufficiently to inundate the Bering land bridge
[24,25]. Thus, we expect m for modern Europe to be much higher
than ancient migration rates between Asia and the Americas,
especially after the inundation of Beringia.
Constraining divergence time by applying a lower bound of
15 kya results in an estimate of 200 for the Amerind founding
N,. Serially constraining mAsiaNW and mNW-Asia, in conjunction
with the constrained divergence time, produces increasingly larger
estimates of N, (Figure 3). Specifically, as both m parameters are
simultaneously forced to lower and more biologically realistic
values, estimates of N, steadily increase from 200 to 31,200,
especially after their priors are constrained to be <5. Regardless of
the specific priors on the m parameters, estimates for the Amerind
divergence/expansion event are consistently 15 kya (data not
shown), which is very close to the lower bound of our prior
established with known archaeological sites in the New World.
Our results demonstrate that smaller estimates of N, depend upon
a substantial level of migration from Asia to account for present-
day levels of Amerind genetic diversity, e.g. Hey's [16] estimate of
70 founders is associated with a mAsia-NW>9.0, which is twice
the migration rate for contemporary Europe (m = 4.3). Fli;N; ,;..
all migration between Asia and the New World (m = 0) results in
the largest estimate of N, for the Amerind founding population of
S1,200 individuals.

Discussion

When studying complex colonization scenarios, the interpreta-
tion of genetic data can benefit substantially from the incorpora-
tion of non-genetic material evidence. In our study, we do this in
three ways. First, we interpret the skyline plot (see Figure 1) to
reflect archaeological evidence that places Amerinds in the
Americas by 15 kya and human populations in Beringia
30 kya, as well as geological and paleoecological evidence that


- 1400
z
1200

* 1000
i o I
S800-

S600 I
aII
* 400

S200
S0
0 2 4 6 8
Upper bound for the priors on m,..,


10 50
Iw and mNw-A.a


Figure 3. Graph of IM results for the combined nuclear and
mitochondrial coding DNA dataset. The plot depicts mean N. for
the Amerind founder population (y-axis) as a product of increasing the
constraint on the upper bound of the priors for the migration rates (x-
axis). In these analyses, the prior on the lower bound of the divergence
time was uniformly set to 15 kya on the basis of known archaeological
materials for human occupation in the New World (see text). Each point
is based on the average of the estimated medians for ten independent
replicate analyses, with the bars corresponding to 1 standard
deviation. These standard deviations are often small (with coefficients
of variation less than 0.01), since their Markov chains were run for 100
million generations each.
doi:1 0.1371/journal.pone.0001596.g003


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55,450
t33,540-87,210


,.* ', PLoS ONE I www.plosone.org







Peopling of the Americas


Beringia was habitable yet isolated from the Americas from
30 kya to 17 kya. Second, we use archaeological radiocarbon
dates to constrain the divergence time prior in our IM analyses to
15 kya as the latest possible date for both the divergence of the
Amerind and Asian gene pools and the Amerind expansion into
North America (Figure 3). Since the IM model assumes that
divergence and expansion occur simultaneously, constraining the
time of the expansion also requires identical constraint of the
divergence date. Third, in our IM analyses we serially constrain
the migration rate parameters to smaller values and deduce likely
migration rates between Asia and the New World based on
empirical estimates of current migration rates within Europe
versus the_1 11 reduced migration rates of ancient people across
the Bering Strait starting 11-10 kya.
Based on our results, we propose a three-stage colonization
process for the peopling of the New World, with a specific focus on
the dating and magnitude of the Amerind population expansions
(Figure 4). We propose that the first stage was a period of gradual
population ., 11. as Amerind ancestors diverged from the central
Asian gene pool and moved to the northeast. This was followed by
an extended period of population stability in greater Beringia. The
final stage was a single, rapid population expansion as Amerinds
colonized the New World from Beringia.
The initial stage of the colonization process involved the
divergence of Amerind ancestors from the East Central Asian gene
pool (Figure 4A). Based on previous studies that included Asian
mtDNA sequences, this divergence likely occurred prior to
"50 kya [5,6]. Our coding skyline plot (Figure 1) indicates that
the divergence was followed by a period of gradual _,.. 11 during
which the proto-Amerind population experienced a 7-fold increase
from "640 to "4,400 females over 7,000 years, from "43-
36 kya. The migrating founder population (N --. 1 11 was a small
subset of the ancestral Asian population, as evidenced by the low
levels of variation in New World populations relative to Asians
(e.g. [3]) as well as the larger effective size of the ancestral Asian
population [16]. Thus, divergence from the Asian gene pool was
the time at which a severe population bottleneck occurred that
reduced the genetic variation in Amerind populations. The lack of
archaeological sites in Siberia and Beringia that date to 43-
36 kya [34] suggests that this first stage of slow population .- 1. i1,
left a light "footprint" on the landscape because of relatively rapid
and continuous movement. Consistent with this hypothesis are the
younger coalescent dates for modern Siberian populations relative
to modern New World populations [15,35], which indicate that
the New World migrants passed 11. ..1 1 Siberia before other East
Central Asian populations) settled permanently in this region at a
later date. Such relatively rapid and continuous movement would
leave few archaeological sites, which have not yet been discovered
due to the vast expanse and harsh conditions of Siberia and the
current inundation of Beringia. Thus, an important prediction of
the first stage of our model is that older archaeological sites dating
to "43-36 kya await discovery in these regions.
The proposed second stage (Figure 4B) consisted of an extended
period of little change in population size from "36-16 kya
(Figure 1). It is difficult to assign a precise geographic location to
this population, but it may have occupied the large region from
Siberia to Alaska, most of which is currently underwater. Our Nf
estimates of 4,000-5,000 (equivalent to N, of 8,000-10,000,
assuming an equal sex ratio) indicate that the proposed human
presence would have been minor when compared to the size of
greater Beringia. Nevertheless, the presence of this population in
Beringia for "20,000 years would have afforded sufficient time for
the generation of new mutations. Indeed, the existence of New
World-specific variants that are distributed 1.i. .. .ni the


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1400 1600 1800 1600 140"
SA Expansion out of East Central Asia. 43-36kya
_. im-1 1 I


50'orth Amer can he sheets
Br Occupation of Beringiiia. 36-16ky
... ....... ................... .. "..... "




















growth for 20,000 years. (C) Rapid colonization of the New World by a
founder group migrating southward through the ice free, inland
































Sheets (green arrow) and/or along the Pacific coast (red arrow). In (B),
50glacial maximum at kya [25]. In (A) and (C), the exposed
C.s Expansion into the Americas. 16kya






60...




doi:1 i0.1371Current O Epo/jred
s North American ice sheets
after 36kya

-3000 Km


Figure 4. Maps depicting each phase of our three-step
colonization model for the peopling of the Americas. (A)
Divergence, then gradual population expansion of the Amerind
ancestors from their East Central Asian gene pool (blue arrow). (B)
Proto-Amerind occupation of Beringia with little to no population
growth for 20,000 years. (C) Rapid colonization of the New World by a
founder group migrating southward through the ice free, inland
corridor between the eastern Laurentide and western Cordilleran Ice
Sheets (green arrow) and/or along the Pacific coast (red arrow). In (B),
the exposed seafloor is shown at its greatest extent during the last
glacial maximum at -20-18 kya [25]. In (A) and (C), the exposed
seafloor is depicted at -40 kya and -16 kya, when prehistoric sea
levels were comparable [24,25]. Because of the earth's curvature, the km
scale (which is based on the straight line distance at the equator)
provides only an approximation of the same distance between two
points on these maps. In addition, a scaled-down version of Beringia
today (60% reduction of A-C) is presented in the lower left corner. This
smaller map highlights the Bering Strait that has geographically
separated the New World from Asia since -11-10 kya.
doi:l 0.1371/journal.pone.0001596.g004

Americas indicate that substantial genetic diversification occurred
during the Beringian occupation (e.g. [13-15,36,37]). The
proposed period of Beringian occupation coincides with archae-
ological evidence for the first Arctic inhabitation of western
Beringia ( 30 kya) [23] and pre-dates archaeological evidence for
occupation of the New World [18-21]. This period also coincides
with geological evidence for restricted access to North America


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Peopling of the Americas


because of the impenetrability of the Cordilleran and Laurentide
ice sheets ( 17-30 kya) [38,39]. Botanical remains, such as
macrofossils and ancient pollen, indicate that Beringia was a
productive grassland ecosystem rather than an exceedingly harsh
Arctic desert environment [27]. Paleontological evidence from
Alaska and Siberia demonstrates that large mammals such as
steppe bison, mammoth, horse, lion, musk-oxen, sheep, wholly
rhinoceros, and caribou inhabited this area [28].Thus, the
paleoecological data are consistent with a human presence in
Beringia ,l..... 1. the carrying capacity of Beringia and
technological limitations of the human population may have
restricted ,-.. i 1 until the population could expand into new and
fertile lands in the Americas. The rapid expansion of the
population only after an ice-free corridor into North America
opened (see below) suggests that the population may have
departed Beringia as soon as a viable alternative presented.
The final colonization stage (Figure 4C) was a rapid geographic
expansion into the New World resulting in a significant population
increase ( 16-fold; Figure 1). The rapid population increase
occurred over the period 16-9 kya according to the coding
skyline plot or over the past 15,000 years based on the IM analyses
(the latter results supported only the most recent and largest
expansion, most likely because IM analyses assume a single,
simultaneous divergence/expansion event). The geological record
indicates that North America became accessible from Beringia
between 17-14 kya, when the ice sheets covering what is now
Canada began to retreat [26,39]. The coincident timing of an ice-
free corridor into North America and the rapid expansion of the
Amerind population suggests that a land route may have been the
preferred entry into the New World. However, the northwest
Pacific coast of North America also may have been deglaciated by
S17 kya, thus presenting a viable coastal route to continental
North America [4,39]. This period also coincides with the initial
inundation of the Bering land bridge, after which migration with
Asia would have been severely limited. The first unequivocal
evidence for human occupation of the New World occurs in the form
of Clovis sites dating to 13 kya [18] and pre-Clovis sites in both
North and South America dating to 14-15 kya [19-21]. Our
datasets do not include typings from the Na-Dene or Esk-Aleut, so
we limit our scope to the largest, initial migration of Amerinds into
the New World. However, Na-Dene and Esk-Aleut genetic diversity
represents a subset of Amerind diversity (e.g. [40-42]) i i., ;_ l1, I
Na-Dene and Esk-Aleuts are derived from the same Beringian
source population as Amerinds. As stated above, extensive
archaeological evidence supports the presence of multiple distinct
Native American material cultures by 13 kya (e.g. Clovis, Nenana
and pre-Clovis lithic technologies [18]). Our r, ., .... 1 i. ii..
distinct cultures derive from a single New World founder population
and are most likely the product of an extensive and complex process
of post-peopling migrations within the Americas, possibly 1.,..11 _1. a
combination of coastal and/or riverine routes [4,43].
Determination of the size of the Amerind founding population
has received considerable attention. Based on the coding Bayesian
skyline plot (Figure 1), there is a slight decrease in population size
]. .... U,,_ 1,. increase seen at 15 kya. This decrease is consistent
with a secondary founder effect in which a subset of the Beringian
population seeded the proto-Amerind expansion into the Amer-
icas. Assuming the apparent decrease in N,f is the result of such a
founder effect, the upper bound on the founder population size is
5,400 individuals (N -- ',700). Our IM analyses suggest that the
founder population size could be lower depending on prior
assumptions about the over water migration rates between the
Americas and Asia (see Figure 3). Migration rates (m) within
Europe today based on census data have been determined to be


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4.3, which can be taken as an extreme upper bound of possible
ancient migration rates between the Americas and Asia, especially
after the appearance of the Bering Strait 11-10 kya. Restricting
migration rates to <1 results in founder N, estimates between
S1,000 and 1,200, with 1,200 serving as an asymptotic upper
bound (see Figure 3). Taken -.._. 1., our Bayesian skyline plot
and IM analyses suggest that a founder population with
N,= 1,000-5,400 colonized the New World in a process
characterized by a rapid geographic and population expansion.
The range of N, values can be translated into an approximate
census population size by applying a scale factor estimated from
large mammal populations (scale factor = 5) [44], which suggests
that the founder population consisted of 5,000-27,000 people.
Our three-stage model now awaits further critical. ,. ;. ii.
datasets of independent nuclear loci and more sophisticated methods
of coalescent analysis. The extensive dataset of 700 autosomal
microsatellites, compiled by Wang et al. [4] for both Native
American and worldwide populations, offers the opportunity to
evaluate critically the size, timing, and duration of each step in our
model at essentially a population genomics level. Future versions of
BEAST will incorporate a structured coalescent where migration as
well as population _,.. 11. will be allowed to occur among
populations from both the New World and Asia (http://evolve.
zoo.ox.ac.uk/beast/manual.html). In these BEAST analyses, the
microsatellites can be modeled under a stepwise "ladder process,"
whereby alleles are inter-related according to their repeat 1 I. 11
One can then summarize over these microsatellite loci by assuming
independence, which thereby allows for the multiplication of their
separate posterior distributions and final estimations of their
combined Bayesian skyline plot. In these ways, we fully anticipate
that such critical testing will lead to many important refinements of
our three-step model, including a fi ,il. I ,1 ,.. ,_ of our proposed
range for the size of the founding population as well as new details
about post-peopling expansions within the New World.

Materials and Methods
Datasets
Three datasets were collected for analysis including: (z) 77 mtDNA
coding genomes; (iz) 812 mtDNA HVRI+II sequences; and (iiz)
combined nuclear and mitochondrial coding DNA dataset. The 77
mtDNA coding genomes were collected from publicly available
resources [45-48] and aligned using ClustalX [49]. The resultant
15,500 base pair (bp) multiple alignment was edited by hand to
minimize the number of unique gaps and to ensure the integrity of
the reading frame (available online as Figure Sl). A total of 812
combined HVRI+II sequences were collected from HVRbase
(http://www.hvrbase.org) [50]. These sequences were aligned
following the coding mtDNAs, resulting in a multiple alignment of
771 bps (available online as Supplemental Figure S2). The complete
dataset of 812 HVRI+II sequences was randomly divided into ten
non-overlapping alignments of 81 sequences that approximate the
sample size for the coding mtDNA dataset. Skyline plot analyses of
larger datasets (up to 200 HVRI+II sequences) gave the same results
as the 81 sequence datasets (data not shown). Thus, the smaller
datasets of 81 sequences each were emphasized here since they
avoided the likelihood rounding errors that can occur when using
large, heterogeneous datasets in Bayesian skyline plot analyses. The
coding nuclear and mtDNA dataset from Asian and Native
American populations of Hey (available at http:// i; ; in_.,
edu/~heylab/) [16] consisted of two autosomal coding loci, five X-
chromosome coding loci, one Y-chromosome coding locus, and the
complete mtDNA coding genome I .. '.1 .;_ 28,454 aligned bps). The
sample sizes for these nuclear loci and mitochondrial genome varied
from 12-108 sequences.


February 2008 | Volume 3 | Issue 2 e1596







Peopling of the Americas


Bayesian Skyline Plot Analyses
Bayesian skyline plots [32] were used to estimate changes in
Amerind Nf over time by providing highly parametric, piecewise
estimates of Nf. This approach produces serial estimates of
effective population size from the time intervals between
coalescent events in a genealogy of sampled individuals, and
utilizes a Markov chain Monte Carlo simulation approach to
integrate over all credible genealogies and other model parame-
ters. It thereby differs from previous approaches (e.g., [51]) in that
Bayesian skyline plots fully parameterize both the mutation model
(including relaxed clock models) and the genealogical process,
whereas prior methods relied on generating estimates from
summary statistics (e.g. the use of pairwise differences by [51]).
In these analyses, estimates of (Nfxgeneration time) were
converted to Nf by dividing by a generation time of 20 years,
following convention [16]. Skyline plots were generated for the 77
mtDNA coding genome sequences and the ten datasets of
HVRI+II sequences using the program BEAST vl.4 (http://
beast.bio.ed.ac.uk). These BEAST analyses relied on the same
coalescent and substitution models and run conditions of Kitchen
et al. [52] except as noted below. Plots were generated using the
established mutation rates (p) for coding mtDNA (p= 1.7 x10-8
substitutions/site/year) [46] and HVRI+II mtDNA
(p =4.7x10-7) [53]. Markov chains were run for 100,000,000
generations and sampled every 2,500 generations with the first
10,000,000 generations discarded as burn-in. Three independent
runs were performed for all coding and HVRI+II Bayesian skyline
plot analyses. Markov chain samples from the three independent
mtDNA coding replicates and from the 30 HVRI+II analyses were
separately combined using the LogCompiler program (distributed
with BEAST) and analyzed using Tracer v1.3 to produce the final
Bayesian skyline plots.

Isolation-with-Migration Coalescent Analyses
Bayesian IM coalescent analyses were performed using the
program IM [16] to estimate N, for the Amerind founder
population (males+females) and the divergence time for Amerind
and Asian populations. We used the same combined nuclear and
mtDNA dataset, same coalescent and substitution models, and
same model parameters as Hey [16] with the exception of new
priors on the divergence time and on the migration rates between
Asian and Amerind populations. All IM analyses were performed
using a flat uniform prior for the divergence time of Amerind and
Asian populations set to the interval 15-40 kya. The lower bound
of this prior is based on accepted archaeological and climatological
evidence for the first presence of humans in the Americas [18-21].
The upper bound of the flat uniform priors on the migration rates
per mutation per generation between the Amerindian and Asian

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PLoS ONE | www.plosone.org


populations (mAsiaNW and mNWAsia) was set to 12 different
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Supporting Information

Figure Sl Multiple sequence alignment for the 77 Amerind
mtDNA coding genomes used in this study. Here, "coding" refers
to both protein and structural RNA genes following Pakendorf and
Stoneking [30]. Gaps are represented by "-." Position 1 of this
alignment corresponds to site 546 of the Anderson Reference
Sequence (ARS; [56]). The final position of this alignment (15,500)
corresponds to site 16,042 of the ARS. Sequences starting with
"Herrn," 11. "Kiv", and "Mis" follow the naming conventions
of Herrnstadt et al. [45], Ingman et al. [46], Kivisild et al. [47],
and Mishmar et al. [48], respectively.
Found at: doi:10.1371/journal.pone.0001596.s001 (1.19 MB
TXT)

Figure S2 Multiple sequence alignments for the ten, randomly
selected, non-overlapping sets of 81 HVRI+II sequences used in
this study. In these alignments, positions 1-403 correspond to
HVRI, whereas sites 404-781 refer to HVRII. In turn, these
alignment positions correspond to sites 16003-16400 and 30-399
of the ARS, respectively. Gaps are represented by "-." The
HVRI+II sequences follow the naming conventions of HRVBase
[50].
Found at: doi:10.1371/journal.pone.0001596.s002 (0.64 MB
TXT)

Author Contributions
Conceived and designed the experiments: CM MM AK. Performed the
experiments: MM AK. Wrote the paper: CM MM AK.



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