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Brief communication The Thule migration Rejecting population histories using computer simulation.

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AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 134:281–284 (2007)
Brief Communication: The Thule Migration: Rejecting
Population Histories Using Computer Simulation
E.E. Marchani,* A.R. Rogers, and D.H. O’Rourke
Department of Anthropology, University of Utah, Salt Lake City, UT 84112
KEY WORDS
coalescent theory; computer simulation; Thule migration; mitochondrial haplogroups
ABSTRACT
Locked within our genetic code are the
histories of our genes and the genes of our ancestors.
Deciphering a population’s history from genetic data often involves lengthy investigations of many loci for
many individuals. We test hypothetical population histories of the Thule expansion using a new coalescent
The Thule, an ancient arctic population defined by
their association with a sophisticated toolkit and focus
on whaling, expanded eastward *1,100 years ago from
northwest Alaska to Greenland, possibly following bowhead whale that were increasing their migratory range
as a result of the Medieval warm period (Savelle and
McCartney, 1999; Dyke and Savelle, 2001; Coltrain
et al., 2004; Le Mouël and Le Mouël, 2002). The Thule
reached Greenland in one to two centuries, colonizing
territory occupied previously by Dorset Paleo-Eskimo
populations (Jordan, 1984; Park, 1993; Hayes et al.,
2003; Hayes et al., Genetic signature of population
replacement coincident with paleoclimatic change, submitted, 2007).
The rapid nature of this colonization event is supported both by archaeological evidence and an observed
distinct genetic signature of reduced variation among
the Inuit, the Thule’s modern descendants. Reduced
genetic diversity within a population is often a signature
of a population bottleneck or founder effect, when a population is founded by a subset of a larger population and
therefore begins with a reduced level of genetic diversity.
This can be exaggerated by genetic drift, where small
populations are more prone to lose genetic variation
through stochastic processes.
Craniometric analyses show that modern Eastern
Inuit exhibit a range of variations that is a subset of the
variation observed among the Birnirk, one of the Thule’s
possible ancestral cultures (Ousley, 2004). Many studies
of genetic diversity confirm this reduced level of variation among Inuit populations. Analyses of 90 mtDNA
sequences from the circumarctic region revealed low
mean pairwise sequence differences among the five circumarctic populations studied, a sign of a recent population expansion (Shields et al., 1993). Similar results
were obtained by Dugoujon et al. (2004) when they analyzed immunoglobulin GM haplotype diversity among
arctic populations, concluding that isolation by distance
best explained the pattern of genetic variation.
Figure 1 illustrates the distribution of mitochondrial
haplogroup diversity in the American arctic (Lorenz &
Smith, 1996; Starikovskaya et al., 1998; Schurr et al.,
1999). The most dramatic sign of reduced biological diC 2007
V
WILEY-LISS, INC.
simulation method that uses little more than mitochondrial haplogroup data. This new methodology rejects a
severe bottleneck at expansion and reveals the range of
probable population histories on which to focus future research. Am J Phys Anthropol 134:281–284, 2007. V 2007
C
Wiley-Liss, Inc.
versity among the Thule and their modern descendents,
the Eastern Inuit, is their essential monomorphism for
mitochondrial haplogroup A (Saillard et al., 2000; Hayes
et al., 2003; Helgason et al., 2006). Furthermore, the
sequence diversity associated with haplogroup A among
arctic populations is reduced when compared with that
observed in other Native American groups (Saillard
et al., 2000).
While modern humans have a long history of colonizing unoccupied territory, such as the colonization of Australia or the Americas, mitochondrial haplogroup monomorphism has only been observed among the Thule and
their Eastern Inuit descendents. What was it about this
colonization event that resulted in this unique phenomenon? Did this population undergo a severe bottleneck,
or can this monomorphism be explained in another way?
In this study, we investigate this event using a new coalescent-based methodology that tests the female effective
size of and migration rate between the Eastern Inuit
and their Siberian Eskimo sister population in an effort
to expose the population conditions that could lead to mitochondrial haplogroup monomorphism among both the
Eastern Inuit and their ancestors, the Thule.
We develop this new method in an effort to maximize
the information gained from minimal input data and
time. Other simulation methods require extensive
genetic data or the identification of several specific parameters, such as population size and growth rates,
prior to simulation (Fix, 1999, 2002; Hey, 2005). When
parameter values are unknown and must be varied, it
radically increases the number of simulations that must
be performed and does not necessarily reveal which val-
*Correspondence to: Elizabeth Marchani, Department of Anthropology, University of Utah, 270 S 1400 E, Rm 102, Salt Lake City,
UT 84112. E-mail: liz.marchani@anthro.utah.edu
Received 27 March 2006; accepted 8 August 2006
DOI 10.1002/ajpa.20650
Published online 13 June 2007 in Wiley InterScience
(www.interscience.wiley.com).
282
E.E. MARCHANI ET AL.
Fig. 1. Mitochondrial haplogroup variation in the American
Far North (Lorenz and Smith, 1996; Starikovskaya et al., 1998;
Saillard et al., 2000).
ues are most appropriate given the data. Our method is
designed to identify the most appropriate values for
effective population size and migration rates, while
rejecting those values that are inconsistent with the
genetic data. The genetic data required for our method
are limited to the distribution of haplotypes between sister populations and their common ancestral population.
This is more easily obtained from the literature or ancient DNA studies than are the sequence data required
for some other methods, making it ideal for pilot studies
(Hey, 2005).
METHODS
For the purposes of this study, a population’s history
consists of a series of time periods, or epochs, during
which population size was constant. Each population history contains the female effective population size of the
modern Eastern Inuit, modern Siberian Eskimo, and
their shared common ancestor for both the epoch before
and after the Thule expansion, as well as the date of
divergence between the Inuit and Siberian Eskimo.
Siberian Eskimos are used here as a sister population
to the modern Inuit. The ancient Thule culture, though
associated with the American arctic, has Siberian roots
in the prehistoric Old Bering Sea, Okvik, Punuk, and
Birnirk cultures (Ackerman, 1984; Dumond, 1984;
Hughes, 1984; McGhee, 1984). Genetic evidence from mitochondrial DNA (Saillard et al., 2000), the Y chromosome (Lell et al., 2002), and JC viral polymorphism
(Sugimoto et al., 2002) corroborate this archaeological inference.
The Inuit and Siberian Eskimo sister populations are
set to diverge 1,100 years BP, as the archaeological record suggests that the Thule left northwestern Alaska to
head east, colonizing the North American high arctic
near this date (Park, 1993; Bosch et al., 2003; Coltrain
et al., 2004). Though this divergence process may have
taken up to 200 years, as inferred from the archaeological record, this is nearly instantaneous on the time scale
of the coalescent process, and is modeled as such.
We have tested migration rates of 0, 0.5, 1, 5, and 10
individuals per generation between the Siberian Eskimo
and Inuit populations. Although great geographical distance existed between these two populations, the mobile
nature of the subsistence strategy of the Thule may
have allowed regular mate exchange between the Thule
and the Siberian Eskimo. The lowest values approximate
complete isolation, while the highest values approach
random mixing. This allows for the modeling of an
incomplete separation between the Siberian Eskimo and
Eastern Inuit populations, where genes are able to flow
between the two populations.
The female effective population sizes for the Inuit and
Siberian Eskimo populations tested in these simulations
are as follows: 5, 25, 50, 250, 500, 2,500, and 5,000
females. These values range from that of a very small
and bottlenecked population to one-half the estimate of
the female effective population size of modern humans
(Nei and Graur, 1984; Takahata, 1993; Zhao et al., 2000).
The distribution of mtDNA haplogroups among 82 modern Eastern Inuit and 79 modern Siberian Eskimos (Starikovskaya et al., 1998; Saillard et al., 2000) was used for
hypothesis formation and sample sizes for the Inuit and
Siberian Eskimo populations in the simulations.
Our computer program uses coalescent simulations to
generate gene genealogies. It is freely available from the
authors and is based on GTree, a library of C functions
for gene genealogies (http://www.anthro.utah.edu/*rogers/
src/index.html).
Each simulation produces a gene tree with X leaves in
sister population A and Y leaves in sister population B.
We wish to estimate a tail probability: the probability of
an outcome \at least as extreme" as the one observed. In
our example case, the Eastern Inuit population exhibits
just one allele (haplogroup), whereas the Siberian
Eskimo population exhibits not only that allele but also
the remaining two alleles. Mitochondrial or Y-chromosomal haplogroups represent monophyletic clades in a
tree of mitochondrial or Y-chromosomal diversity ascertained using several restriction sites (Richards and Macaulay, 2001). Thus, we counted the number of simulated
gene trees out of the 1,000 generated in which descendants of all three of the deepest clades are found in the
Siberian Eskimo population, but only one cladistic lineage is found in the Eastern Inuit population. The result
is a P value, the probability of each population history
given the observed distribution of haplogroups in the
genetic data. A population history was rejected if the
Eastern Inuits were monomorphic for one of the three
mitochondrial haplogroups present in the Siberian
Eskimo in 50 or fewer gene genealogies out of the thousand simulated for each population history. This approximates a P value of 0.05 or lower.
RESULTS
Table 1 presents the maximum Inuit female effective
population size for every combination of Siberian Eskimo
female effective size and number of migrants per generation between the Siberian Eskimo and Eastern Inuit
populations (M) tested below which the population history cannot be rejected. Figures 2 and 3 provide a graphical summary of the results presented in Table 1. Each
circle within Figures 2 and 3 represents a single population history and 1 thousand simulations. If the circle is
filled, then we were able to reject the population history,
while empty circles represent those population histories
that we were unable to reject at the P ¼ 0.05 significance level. This means that we reject a population history when fewer than 50 of the 1000 simulations using
that population history as input result in monomorphism
among the Inuit with respect to the three haplogroups
American Journal of Physical Anthropology—DOI 10.1002/ajpa
283
THE THULE MIGRATION
TABLE I. Maximum Inuit female effective population size that cannot be rejected
Siberian Eskimo female
effective population size
5
25
50
250
500
2,500
5,000
Inuit female effective population size
M¼0
M ¼ 0.1
M ¼ 0.5
M¼1
M¼5
M ¼ 10
5
5
250
250
250
250
250
5
5
250
250
250
250
250
25
50
250
250
250
250
250
50
50
250
250
250
250
250
50
50
50
250
250
250
250
50
50
50
50
50
50
50
Fig. 2. Population histories which can and cannot be
rejected when migration rate is low.
Fig. 3. Population histories which can and cannot be
rejected when migration rate is high.
observed among the Siberian Eskimos. Empty circles
graphically represent the confidence interval of population histories consistent with our model of the Thule
expansion.
A visual comparison of Figures 2 and 3 illustrates that
the minimum female effective size of the Siberian
Eskimo decreases from 50 in Figure 2 to 5 in Figure 3 as
the migration rate increases from 0 to 10 individuals per
generation. Furthermore, the maximum female effective
size of the Inuit decreases from 50 in Figure 2 to 25 in
Figure 3 as the migration rate increases from 0 to 10
individuals per generation. Increasing levels of migration increase the range of acceptable Siberian Eskimo
female effective population sizes, but decrease the range
of Inuit female effective population sizes that cannot be
rejected from 50 to 25 females.
Given the negative relationship between Inuit female
effective population size and the probability of mitochondrial haplogroup monomorphism among the Inuit, it is
most likely that the Thule colonization event involved a
bottleneck, at least with respect to the female population
as inferred from mitochondrial data. If the ratio of the
length of the bottleneck in generations to the size of the
population during the bottleneck falls between 0.25 and
4.0, the bottleneck is said to have been moderate (Fay
and Wu, 1999; Marth et al., 2004).
If we assume that the bottleneck has lasted since the
onset of the Thule colonization event (900 AD), and that
the Inuit effective population size was no larger than
100, twice the largest female effective population size
above which monomorphism is not observed when the
migration rate is low, the bottleneck severity index is 44
generations/100 individuals, or 0.44. If instead, we
assume that the bottleneck lasted only 200 years, the
estimated time it took the Thule to reach Greenland, the
bottleneck severity index is 10 generations/100 individuals, or 0.10.
This indicates that the Inuits have not necessarily
gone through a severe bottleneck. However, the most
probable bottleneck severity indices are those indicating
at least a moderate bottleneck where t/N is greater than
or equal to 0.25. These values are lower limits of the
range of possible bottleneck indices, as it is the upper
limit of Inuit effective population size as estimated in
these simulations. Future work to provide a finer resolution of the length of the bottleneck, as well as the effective size of the Inuit during that period may well
increase the level of bottleneck severity that can not be
rejected for this population.
DISCUSSION
Our study has identified a confidence interval of population histories consistent with the mitochondrial haplogroup monomorphism observed among the Eastern
Inuits. We have found that the migration rate between
the Eastern Inuit and the hypothesized sister population
of the Siberian Eskimo can influence the population histories rejected by our method. We were able to reject all
population histories with Eastern Inuit female effective
sizes greater than 50 when the Eastern Inuits were completely isolated and Eastern Inuit female effective sizes
greater than 25 when the Eastern Inuit exchanged 10
mates per generation with the Siberian Eskimo.
We have been able to reject all population histories
with Eastern Inuit female effective population sizes
greater than 50 individuals, and cannot reject many histories where the female effective population size of the
Thule is less than or equal to 25. The range of female
effective sizes for other Arctic populations is *175–350,
assuming a mutation rate of 0.015 (Shields et al., 1993).
This suggests that the Thule have undergone a more
severe bottleneck or founding event than other Arctic
populations in Siberia and the American Far North, pro-
American Journal of Physical Anthropology—DOI 10.1002/ajpa
284
E.E. MARCHANI ET AL.
ducing mitochondrial haplogroup monomorphism among
the Eastern Inuit.
The population histories that fall within our confidence interval are consistent with a number of colonization scenarios. It is possible that the Thule expansion
involved sequential founding events, moving eastward.
It is also possible that the Thule did not settle into a
permanent location until they reached Greenland, and
then expanded westward from that point (cf. Collins,
1951). The discovery of additional archaeological sites in
the region may help resolve this question. Until that
occurs, the results of this study provide statistically significant female effective population sizes, migration
rates, and relative sizes between the Eastern Inuits and
Siberian Eskimos that emphasize the narrow conditions
under which the unique phenomenon of mitochondrial
haplogroup monomorphism can occur.
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American Journal of Physical Anthropology—DOI 10.1002/ajpa
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