Does Mitochondrial Haplogroup X Indicate Ancient Trans-Atlantic Migration to the Americas? A Critical Re-Evaluation

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Does Mitochondrial Haplogroup X Indicate
Ancient Trans-Atlantic Migration to the
Americas? A Critical Re-Evaluation
Jennifer A. Raff
University of Kansas, Lawrence
Deborah A. Bolnick
University of Texas, Austin
It might seem strange for an article to focus largely on the
history of a single mitochondrial haplogroup in an era
when complete genome sequencing is becoming more
common. But as recent publications and film documen-
taries have shown (Meldrum 2009; Oppenheimer et al.
2014; Smoot et al. 2010; Stanford and Bradley 2012),
there is still considerable confusion about what the struc-
ture of mitochondrial genetic diversity in the Americas
means for Native American population history.
Specifically, there are persistent claims that the presence
of mitochondrial haplogroup X2a in Native American
populations is evidence for ancient trans-Atlantic gene
flow from Europe or the Middle East into North
America (Meldrum 2009; Oppenheimer et al. 2014;
Smoot et al. 2010; Stanford and Bradley 2012). If true,
this genetic evidence would lend considerable support to
the Solutrean hypothesis, which suggests that the North
American Clovis culture (13,300–12,800 cal yr BP) is
directly descended from the Solutrean culture of south-
western Europe (23,500–18,000 cal yr BP). The current
iteration of the Solutrean hypothesis was developed by
Bruce Bradley and Dennis Stanford (Bradley and
Stanford 2004; Stanford and Bradley 2012; see Abbott
1877, Greenman 1963 and Hibben 1941 for previous iter-
ations of the hypothesis), and it has been heavily critiqued
by many archaeologists (Eren et al. 2013, 2015; O’Brien
et al. 2014; Philips 2014; Sellet 1998; Straus et al. 2005).
The idea that haplogroup X2a is derived from an
ancient trans-Atlantic migration to the Americas has
been repeatedly considered —and rejected —by
anthropological geneticists over the last two decades
(Brown et al. 1998; Fagundes et al. 2008; Reidla
et al. 2003; Smith et al. 1999, 2005). However, we
revisit it here because it continues to be discussed
and because recently published genomic data from
ancient and contemporary North Americans help
clarify the population history of North America and
the likely history of this haplogroup.
1. The current model
Several decades of studies analyzing classical genetic
markers, DNA sequences from single loci, and, very
recently, genome wide variants have cumulatively
shown that all Native Americans derive ancestry
from a fairly small founder population that likely occu-
pied Beringia during the Last Glacial Maximum
(LGM; ∼28,000 and 18,000 cal yr BP) (reviewed in
Hoffecker et al. 2014; Kemp and Schurr 2010; Raff
and Bolnick 2014). There is still a great deal that is
unknown about this founder population, but current
genetic evidence shows that it was descended from
peoples in eastern Siberia who were related to the
ancestors of both contemporary East Asians and con-
temporary West Eurasians (Kemp and Schurr 2010;
O’Rourke and Raff 2010; Raghavan et al. 2014b).
Some Native Americans also share ancestry with con-
temporary Austro-Melanesians, although it is debated
whether these affinities reflect (a) gene flow from the
Asian ancestors of Austro-Melanesians into Beringia
before people moved into the Americas (Skoglund
et al. 2015), or (b) gene flow after the founder popu-
lation had entered and dispersed through the
Americas (Raghavan et al. 2015). Either way, this
founder population likely inhabited northeastern
Siberia (Madsen 2015) or Beringia (Hoffecker et al.
2014) for an extended period of time (∼7000–15,000
years), possibly in isolated refugia (Hoffecker et al.
2014; Kitchen et al. 2008; Mulligan et al. 2008;
Raghavan et al. 2015). During that time, a number
of genetic variants evolved through mutation and
genetic drift, and many of those variants are found
only (or primarily) in the Americas today (Tamm
et al. 2007).
Correspondence to: Jennifer Raff. Email: jennifer.raff@ku.edu
©2015W.S.Maney&SonLtd
and the Center for the Study of the First Americans
DOI 10.1179/2055556315Z.00000000040 PaleoAmerica 2015 VOL. 1NO. 4297

The precise history of migration out of Siberia/
Beringia following the LGM is currently the focus of
active research and debate in anthropological genetics,
archaeology, and geology. It is clear that people
reached Monte Verde in Chile by 14,600 cal yr BP
via a coastal route (Dillehay et al. 2008). By
13,000 cal yr BP, descendants of the Beringian
founder population had differentiated into two major
genetic groups (clades) in the Americas —one con-
taining individuals from both North and South
America (including the 12,600 cal yr BP Anzick-1
infant from Montana and the 8690–8400 cal yr BP
Kennewick Man from Washington), and one restricted
to North America (Raghavan et al. 2015). It has also
been suggested based on mitochondrial DNA that
some individuals from the ancestral Siberian/
Beringian population moved into the Americas via a
second interior route when an ice-free corridor
opened between the Cordilleran and Laurentide ice
sheets, after 13,500 cal yr BP (Perego et al. 2009).
This migration might help account for the observed
genetic structure in North and South America, but
more genomic data from North American populations
is needed to test this hypothesis (Achilli et al. 2013;
Raghavan et al. 2015). Additional population move-
ments from Siberia, including migrations at approxi-
mately 4000 cal yr BP and 1000–800 cal yr BP, also
contributed to the contemporary gene pool
in northern North America (Raff et al. 2015;
Raghavan et al. 2014b; Reich et al. 2012). Other
regions of the Americas saw more localized migration,
gene flow, and genetic drift over the millennia, with the
region-specific genetic structure of the Americas
largely in place by 4000 cal yr BP (Raff et al. 2011).
However, it is important to remember that the compo-
sition of these regional Native American gene pools
may have been dramatically reshaped by post-1492
contact with Europeans, which brought warfare,
disease, enslavement, removals and relocations, and
extensive admixture (Bolnick et al. 2006; Crawford
1998; Dobyns 1983; Livi-Bacci 2006; Malhi et al.
2008; Reich et al. 2012; Smith 1987; Ubelaker 2006;
Zlojutro et al. 2009). Thus, contemporary Native
American populations are genetically diverse, deriving
varying proportions of their ancestry from ancient
Siberia/Beringia, Europe, Asia, Africa, and elsewhere
(Bolnick et al. 2006; Hunley and Healy 2011; Moreno-
Estrada et al. 2013; Reich et al. 2012; Smith et al.
2014; Verdu et al. 2014; Zegura et al. 2004).
A small number of scholars contend that in addition
to having ancient Beringian ancestry, North American
populations also derived some genetic ancestry from a
trans-Atlantic migration in prehistoric times.
Proponents of the Solutrean hypothesis suggest that a
trans-Atlantic migration brought individuals inhab-
iting southwestern Europe between 23,500 and
18,000 cal yr BP to the Americas (Oppenheimer et al.
2014; Stanford and Bradley 2012), while others have
proposed a trans-Atlantic migration of ancient
Hebrews from the Middle East a few thousand years
ago (Meldrum 2009; Smoot et al. 2010). For the sake
of clarity and brevity, we focus our discussion here on
the validity of the two main lines of evidence presented
as supporting an ancient trans-Atlantic migration: the
presence of mitochondrial haplogroup X2a on the
North American continent and a signal of “West
Eurasian ancestry”within Native American genomes.
2. Haplogroup X2a
X2a (and the related, rare haplogroup X2g) is a
uniquely North American haplogroup, found at the
highest frequencies in Great Lakes populations and
at lower frequencies in the Plains and Pacific
Northwest. It appears to be completely absent in
populations from Central and South America
(Perego et al. 2009). Its presence in pre-European
contact skeletal remains confirms that it was not the
result of post-1492 admixture (Bolnick and Smith
2007; Malhi and Smith 2002; Rasmussen et al. 2015).
However, unlike the other American mitochondrial
haplogroups (A–D), which have clear parental haplo-
types persisting in contemporary Siberian populations,
there is no clear record of the evolutionary history of
X2a in any population (Fernandes et al. 2012;
Reidla et al. 2003). X2a’s“grand-parental”hap-
logroup, X2, is found throughout, at low levels today
throughout much of the world, including in the Near
East (where X is more common and therefore
thought to have initially evolved), South Caucasus,
Europe, Siberia, Central Asia, and North Africa
(Reidla et al. 2003). It is important to note that
while the Altai people in southern Siberia exhibit X2
(Derenko et al. 2001), their lineages are not ancestral
to those of North Americans, and the presence of
X2 there today appears to be the result of recent
gene flow from the west (Reidla et al. 2003).
Thus, the intermediate lineages linking X2 and X2a
appear to have been lost in contemporary populations,
or are so rare that they have not yet been well studied.
We might expect to find them in ancient populations,
but our temporal and spatial coverage of ancient
populations is still quite sparse.
Despite —or perhaps because of —this gap in the
phylogeographic record for haplogroup X2, the pres-
ence of X2a in North America has been cited as evi-
dence for two different trans-Atlantic migrations
before European contact. First, Meldrum (2009) and
Smoot et al. (2010) suggested that X2a is the result of
an ancient Hebrew migration from the Middle East to
North America approximately 2500 cal yr BP. This
hypothesis is undermined, though, by four key findings:
X2a is not found in the Middle East, none of the X2
Raff and Bolnick Does Mitochondrial Haplogroup X Indicate Ancient Trans-Atlantic Migration to the Americas?
PaleoAmerica 2015 VOL. 1NO. 4298

lineages present in the Middle East are immediately
ancestral to X2a, the date of coalescence for X2a
(14,200–17,000 cal yr BP) significantly precedes the
hypothesized migration from the Middle East (Perego
et al. 2009), and haplogroup X2a was present in
North America far earlier than the hypothesized
Hebrew migration, having been found in the
8690–8400 cal yr BP Kennewick Man remains from
Washington state (Rasmussen et al. 2015). Thus, X2a
does not provide any evidence for an ancient Hebrew
migration from the Middle East to North America.
Second, Stanford and Bradley (2012) and
Oppenheimer et al. (2014) have hypothesized that hap-
logroup X2a was brought to North America via a
Pleistocene migration of Solutreans from western
Europe. Stanford and Bradley (2012) specifically cite
the high frequency of haplogroup X2 in the Orkney
Islands near Scotland (in 7.24% of the sampled individ-
uals; Helgason et al. 2001) as supporting the trans-
Atlantic migration of X2a. Madsen (2015) also notes
that it is interesting that “a modern population with
one of the highest percentages of the X2 clade, higher
even than Native American populations, is found in
the Orkney Islands off the coast of Scotland”(Madsen
2015, 213). However, the X2 haplotypes found in the
Orkney Islands was not ancestral to X2a, so this particu-
lar observation is irrelevant to the genetic prehistory of
the Americas. We therefore focus instead on Stanford
and Bradley’s (2012) and Oppenheimer et al.’s(2014)
other arguments in support of the idea that X2a
derives from a Solutrean migration.
They base this hypothesis on two main lines of
reasoning: (1) lineages ancestral to X2a have not been
found in Siberia, in contrast to the other American hap-
logroups, and (2) the phylogeographic distribution of
X2a in North America places “the oldest and deepest
X2a branch ancestry”in northeast Canada, supporting
an “ultimately eastern introduction of X2a and X2g to
the Americas consistent with an additional trans-
Atlantic migration suggested by archaeological evi-
dence”(Stanford and Bradley 2012, 763).
First, it seems to us a very large leap to go from the
observation that haplogroup X2a’s ancestors have not
been observed in Siberia to the conclusion that the
Solutrean hypothesis “offers the only credible route-
explanation for the unique, substantial presence of
West Eurasian-derived X2g and X2a in the Great
Lakes region of north-east America, and their anti-
quity”(Oppenheimer et al. 2014, 769). Although
X2a’s ancestor (X2) is thought to have evolved in the
Near East ( part of “West Eurasia”), characterizing
X2a as a “West Eurasian”haplogroup is inaccurate
because X2a is found only in people with indigenous
North American ancestry. Associating X2a with
“West Eurasia”is like saying “Solutreans evolved in
Africa”: each statement refers to a location where the
ancestral population is thought to have lived long
ago, but that location is not relevant to the question
under consideration. In particular, because X2 dis-
persed from the Near East and became widely distrib-
uted throughout the world, its descendent lineage X2a
need not have evolved in the same place.
To differentiate between a Solutrean and Beringian
source for X2a, one must look instead at the phylogeo-
graphy of the most recent ancestors of X2a (Figure 1).
X2a’j is the clade that unites X2a and its nearest sister
clade, X2j (Fernandes et al. 2012; Reidla et al. 2003).
The geographic distribution of X2a’j haplotypes —
especially those with some of the defining mutations
for X2a (indicating that they belong to the lineage
that led to X2a) —would be informative to this ques-
tion, but no contemporary or ancient individuals
belonging to these lineages have been identified, with
the possible exception of one individual from Iran
with the X2a’j defining transition at mitochondrial
nucleotide position 12397. However, because this tran-
sition has been observed in other haplogroups and is
known to occur recurrently, it is unclear if this
Iranian individual belongs to the X2a’j lineage or
not (Reidla et al. 2003). X2a’s sister clade, X2j, is
also extremely rare, being found in just a few contem-
porary individuals from Iran and Egypt (Fernandes
et al. 2012). It is possible that the common ancestor
of X2a and X2j originated there, but without identify-
ing more individuals bearing X2j or X2a’j lineages,
any inferences about the geographic origins of X2a’j
or X2a are very tenuous.
Thus, at this time, there is simply no evidence that X2a
evolved in the Near East, Europe, or anywhere in West
Eurasia. Stanford and Bradley (2012) and
Oppenheimer et al. (2014) argue that the absence of evi-
dence for X2a in West Eurasia is not evidence of absence,
but of course, the same holds for Siberia. There is no
compelling reason to think that X2a is more likely to
have come from Europe than Siberia.
Where does this leave us? Until we have better geo-
graphic sampling of ancient DNA from the relevant
time periods, the only way we can deduce anything
about X2a’s history is by studying it within North
America or by making inferences based on the geo-
graphic distribution of other haplogroups or the pat-
terns at other genetic loci. This indirect approach has
been used in numerous studies, which have looked at
the geographic distribution of X2a within North
America to try to infer a migration route, compared
the coalescence date of X2a to that of other founder
haplogroups in the Americas, and examined the demo-
graphic histories of each haplogroup to see if they
underwent similar evolutionary pressures (such as
population bottlenecks and expansions) (Achilli
et al. 2008; Fagundes et al. 2008; Kashani et al.
2012; Perego et al. 2009; Smith et al. 1999, 2005;
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Tamm et al. 2007). These studies have all reached the
same conclusion and suggest that haplogroup X2a is
likely to have originated in the same population(s) as
the other American founder haplogroups, by virtue
of having comparable coalescence dates and demo-
graphic histories.
Stanford and Bradley (2012) and Oppenheimer
et al. (2014) have also argued in support of the
Solutrean hypothesis by suggesting that the phylogeo-
graphic distribution of X2a in North America places
the oldest (most basal) X2a lineages in northeastern
Canada, which would be more consistent with an
eastern introduction (and trans-Atlantic migration)
of this haplogroup to the Americas. However, the
newly published findings from the genome of
Kennewick Man of Washington state are clearly at
odds with this assessment. Kennewick Man’s
remains were directly dated to 8690–8400 cal yr BP,
and the question of his affiliation with European
(and Polynesian) populations was explicitly tested
with genome-wide data —and rejected (Rasmussen
et al. 2015). He is closely related to other ancient
and contemporary Native Americans and shows
clear Siberian affinities, with no recent European
ancestry. Significantly, Kennewick Man’s mitochon-
drial DNA belongs to haplogroup X2a, and he exhi-
bits the most basal X2a lineage yet found
(Rasmussen et al. 2015). Because this study places
the oldest and most basal X2a lineage in the Pacific
Northwest, it deals a serious blow to claims of
genetic support for the Solutrean hypothesis. By
Oppenheimer et al.’s own logic, this finding supports
a Beringian, not Solutrean, origin for X2a. Thus,
Kennewick Man’s genome strongly suggests that X2a
was not the result of trans-Atlantic gene flow.
3. “West Eurasian Ancestry”in Native Americans
What about evidence elsewhere in the genome for West
Eurasian ancestry in Native Americans, which
Oppenheimer et al. (2014) also cite as supporting the
Solutrean hypothesis? If the Solutrean hypothesis is
correct, there ought to be ancient European ancestry
in at least some Native American populations, reflect-
ing the genetic contributions of the ancient Solutrean
mariners who would have populated the East Coast.
However, if their contribution to the Native
American gene pool was small, it may only be detect-
able through high resolution analysis of Native
American genomes —not through analyses of mito-
chondrial DNA alone. Accordingly, Oppenheimer
et al. (2014) have cited the 12,600 cal yr BP Anzick-1
genome from Montana (Rasmussen et al. 2014) and
the 24,000 cal yr BP Mal’ta (MA-1) genome from
south-central Siberia (Raghavan et al. 2014a) as
Figure 1 Phylogenetic relationships of the X haplogroups mentioned in the text. Tree structure and diagnostic mutations from
PhyloTree (van Oven and Kayser 2009). Dates (in cal yr BP) for the coalescence of haplogroup X2 and subclades are maximum
likelihood estimates using the complete mitochondrial genome (Fagundes et al. 2012). Geographic distribution of clades from
Fagundes et al. (2012) and Reidla et al. (2003). Note the considerable independent evolution that has occurred on the X2g, X2a,
and X2j lineages. X2g’s mutational motif and phylogenetic position is noted to be “preliminary”and “likely to be further refined as
additional sequences become available”on PhyloTree.
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showing “Pleistocene West Eurasian autosomal
admixture in the Americas, which would be predicted
by the SH [Solutrean Hypothesis]”(Oppenheimer
et al. 2014, 766). Madsen (2015, 228) has also
suggested that “the genetic relationship of Native
Americans to early west Eurasian populations makes
it difficult to rule out a pre-glacial entry point in
eastern North America.”
Raghavan et al. (2014b) did estimate, based on the
Mal’ta genome, that 14–38% of Native American
ancestry is derived from a population ancestral to con-
temporary western Eurasians, and Rasmussen et al.
(2014) concluded that the Anzick-1 individual had
ancestry from the same ancient population.
However, it is important to parse these statements
carefully, and we note that these studies did not find
that the Pleistocene ancestors of Native Americans
lived in West Eurasia. Rather, as Raghavan et al.
(2014b) suggested, it appears that the relevant ances-
tral population lived farther to the east 24,000 years
ago, extending into south-central Siberia, and the des-
cendants of this ancient population contributed to
both the contemporary West Eurasian gene pool and
the Native American gene pool.
Furthermore, a suite of genomic studies has recently
shown that the contemporary European gene pool
emerged only in the last 8000 years or so, following
large-scale migrations from the east and extensive
admixture and population replacements in western
Eurasia (Allentoft et al. 2015; Gamba et al. 2014;
Haak et al. 2015; Lazaridis et al. 2014). We are
unable to make direct genetic comparisons between
Native Americans and the Solutrean peoples of south-
western Europe because no ancient DNA studies have
included samples from Solutrean-associated skeletal
remains, but the genomic data that are available from
pre-Neolithic hunter–gatherers in Europe suggest that
they were not closely related to Native Americans
(Allentoft et al. 2015; Haak et al. 2015; Lazaridis
et al. 2014). In other words, changes in the European
gene pool over the last 8000 years have resulted in con-
temporary West Eurasians being more genetically
similar to Native Americans than earlier Europeans
were. Consequently, the genetic connections we see
between Native Americans and West Eurasians today
do not indicate connections between Native
Americans and western Europeans in Pleistocene times.
Oppenheimer et al. (2014) noted that few studies have
formally tested the trans-Atlantic migration hypothesis
alongside other models, and we agree that it is indeed
important to do so. Rasmussen et al. (2014) did evalu-
ate the genetic affinities of the Anzick-1 individual with
143 contemporary populations in Eurasia, and deter-
mined that this ancient Native American was only dis-
tantly related to western Eurasian populations.
Likewise, Rasmussen et al. (2015) explicitly assessed
the degree of shared genetic history between
Kennewick Man and contemporary Europeans, and
found no evidence for European ancestry in
Kennewick Man’s genome. Perhaps the best test to
date, though, comes from Lazaridis et al.’s (2014)
study, which used ancient and modern genomes to
model the ancestral relationships between Eurasian,
African, and Native American populations. The
model that best fits their data was one in which the
population ancestral to Native Americans was
derived from ancient North Eurasian and East Asian
sources, while contemporary Europeans were derived
from ancient North Eurasian and West Eurasian
sources (Lazaridis et al. 2014). In other words, gene
flow was from the ancestral North Eurasian population
into both the ancestral Native American and ancestral
European populations. Lazaridis et al. (2014) did not
find any evidence of Pleistocene gene flow directly
from West Eurasians into Native Americans. Their
model is also consistent with other studies, which
have shown that 62–86% of Native American ancestry
derives from East Asia (Raghavan et al. 2014b).
Altogether, these results seem more consistent with
migration to the Americas through East Asia and
Siberia, as they are most parsimoniously explained by
admixture between groups in Siberia (rather than in
the Americas following separate migrations through
Beringia and across the Atlantic). If West Eurasian
alleles instead reached the Americas via a Solutrean
migration after the initial movement into the Americas
from Beringia, as Oppenheimer et al. (2014) suggest,
we would not expect to see their signature present uni-
formly across all Native American populations, but
rather distributed in a gradient, with the highest levels
around the presumed landing point of the Solutreans.
Instead, the signature of West Eurasian ancestry is
found equally in all Native American genomes tested
to date, and therefore predates the evolution of regional
genetic structure within North and South America
(Raghavan et al. 2014a).
4. Concluding thoughts
We remain unconvinced by the arguments advanced
thus far in favor of a trans-Atlantic migration prior
to 1500 cal yr BP or so. As we have discussed, X2a
has not been found anywhere in Eurasia, and phylo-
geography gives us no compelling reason to think it
is more likely to come from Europe than from
Siberia. Furthermore, analysis of the complete
genome of Kennewick Man, who belongs to the
most basal lineage of X2a yet identified, gives no indi-
cation of recent European ancestry and moves the
location of the deepest branch of X2a to the West
Coast, consistent with X2a belonging to the same
ancestral population as the other founder mitochon-
drial haplogroups. Nor have any high-resolution
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studies of genome-wide data from Native American
populations yielded any evidence of Pleistocene
European ancestry or trans-Atlantic gene flow.
It is of course possible that genetic evidence of an
ancient trans-Atlantic migration event simply has not
been found yet. Should credible evidence of direct
gene flow from an ancient Solutrean (or Middle
Eastern) population be found within ancient Native
American genomes, it would require the field to reas-
sess the “Beringian only”model of prehistoric
Native American migration. However, no such evi-
dence has been found, and the Beringian migration
model remains the best interpretation of the genetic,
archaeological, and paleoclimate data to date.
Acknowledgements
We thank Dennis O’Rourke, Metin Eren, Michael
Waters, Kelly Graf, Rick Smith, Lauren Springs, and
Aida Miró-Herrans for helpful comments on earlier
versions of this manuscript.
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Author Biographies
Jennifer Raff is an Assistant Professor in the Department of Anthropology at the University of Kansas. She
trained in a dual program in Genetics, Molecular, Cell, Developmental Biology and Biological Anthropology
at Indiana University, and conducted subsequent postdoctoral research at the University of Utah,
Northwestern University, and the University of Texas. Her research focuses on the genetics of Native
Americans in both ancient and contemporary populations, and encompasses questions about the initial peopling
of the Americas, as well as region-specific histories in the North American Arctic and Midcontinental United
States. She is also actively engaged in public outreach on issues pertaining to physical anthropology, genetics,
and scientific literacy through writing (primarily at www.violentmetaphors.com), public speaking, and social
media (primarily at https://twitter.com/JenniferRaff).
Deborah Bolnick is an Associate Professor of Anthropology and affiliated with the Population Research Center
at the University of Texas at Austin. She received her Ph.D. in Anthropology from the University of California at
Davis. Her research examines genetic variation in Native American populations and how it has been shaped by
culture, history, and geography. As part of this research, she collaborates with indigenous individuals in the
southern US, and analyzes DNA from both ancient and contemporary populations to track changes in genetic
diversity over time and to help reconstruct population history in the Americas. She is also interested in the
ethical, legal, social, and political implications of genetic research, including the ways in which genetic ancestry
studies intersect with Euro-American and indigenous ideas about race, ethnicity, and identity.
Raff and Bolnick Does Mitochondrial Haplogroup X Indicate Ancient Trans-Atlantic Migration to the Americas?
PaleoAmerica 2015 VOL. 1NO. 4304