Genetic variation and population structure in native Americans

We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians--signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.     

Using ancient mtDNA to reconstruct the population history of northeastern North America

Mitochondrial DNA (mtDNA) was extracted and analyzed from the skeletal remains of 44 individuals, representing four prehistoric populations, and compared to that from two other prehistoric and several contemporary Native American populations to investigate biological relationships and demographic history in northeastern North America. The mtDNA haplogroup frequencies of ancient human remains from the Morse (Red Ocher tradition, 2,700 BP) and Orendorf (Mississippian tradition, 800 BP) sites from the Central Illinois River Valley, and the Great Western Park (Western Basin tradition, 800 BP) and Glacial Kame (2,900 BP) populations from southwestern Ontario, change over time while maintaining a regional continuity between localities. Haplotype patterns suggest that some ancestors of present day Native Americans in northeastern North America have been in that region for at least 3,000 years but have experienced extensive gene flow throughout time, resulting, at least in part, from a demic expansion of ancestors of modern Algonquian-speaking people. However, genetic drift has also been a significant force, and together with a major population crash after European contact, has altered haplogroup frequencies and caused the loss of many haplotypes.     

The Uto‐Aztecan premolar among North and South Amerindians: Geographic variation and genetics

The Uto‐Aztecan premolar (UAP) is a dental polymorphism characterized by an exaggerated distobuccal rotation of the paracone in combination with the presence of a fossa at the intersection of the distal occlusal ridge and distal marginal ridge of upper first premolars. This trait is important because, unlike other dental variants, it has been found exclusively in Native American populations. However, the trait's temporal and geographic variation has never been fully documented. The discovery of a Uto‐Aztecan premolar in a prehistoric skeletal series from northern South America calls into question the presumed linguistic and geographic limits of this trait. We examined published and unpublished data for this rare but highly distinctive trait in samples representing over 5,000 Native Americans from North and South America. Our findings in living Southwest Amerindian populations corroborate the notion that the variable goes beyond the bounds of the Uto‐Aztecan language family. It is found in prehistoric Native Americans from South America, eastern North America, Northern and Central Mexico, and in living and prehistoric populations in the American Southwest that are not members of the Uto‐Aztecan language stock. The chronology of samples, its geographic distribution, and trait frequencies suggests a North American origin (Southwest) for UAP perhaps between 15,000 BP and 4,000 BP and a rapid and widespread dispersal into South America during the late Holocene. Family data indicate that it may represent an autosomal recessive mutation that occurred after the peopling of the Americas as its geographic range appears to be limited to North and South Amerindian populations. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Native American mtDNA prehistory in the American Southwest

This study examines the mtDNA diversity of the proposed descendants of the multiethnic Hohokam and Anasazi cultural traditions, as well as Uto-Aztecan and Southern-Athapaskan groups, to investigate hypothesized migrations associated with the Southwest region. The mtDNA haplogroups of 117 Native Americans from southwestern North America were determined. The hypervariable segment I (HVSI) portion of the control region of 53 of these individuals was sequenced, and the within-haplogroup diversity of 18 Native American populations from North, Central, and South America was analyzed. Within North America, populations in the West contain higher amounts of diversity than in other regions, probably due to a population expansion and high levels of gene flow among subpopulations in this region throughout prehistory. The distribution of haplogroups in the Southwest is structured more by archaeological tradition than by language. Yumans and Pimans exhibit substantially greater genetic diversity than the Jemez and Zuni, probably due to admixture and genetic isolation, respectively. We find no evidence of a movement of mtDNA lineages northward into the Southwest from Central Mexico, which, in combination with evidence from nuclear markers, suggests that the spread of Uto-Aztecan was facilitated by predominantly male migration. Southern Athapaskans probably experienced a bottleneck followed by extensive admixture during the migration to their current homeland in the Southwest.     

Hierarchical modeling of genome‐wide Short Tandem Repeat (STR) markers infers native American prehistory

This study examines a genome‐wide dataset of 678 Short Tandem Repeat loci characterized in 444 individuals representing 29 Native American populations as well as the Tundra Netsi and Yakut populations from Siberia. Using these data, the study tests four current hypotheses regarding the hierarchical distribution of neutral genetic variation in native South American populations: (1) the western region of South America harbors more variation than the eastern region of South America, (2) Central American and western South American populations cluster exclusively, (3) populations speaking the Chibchan‐Paezan and Equatorial‐Tucanoan language stock emerge as a group within an otherwise South American clade, (4) Chibchan‐Paezan populations in Central America emerge together at the tips of the Chibchan‐Paezan cluster. This study finds that hierarchical models with the best fit place Central American populations, and populations speaking the Chibchan‐Paezan language stock, at a basal position or separated from the South American group, which is more consistent with a serial founder effect into South America than that previously described. Western (Andean) South America is found to harbor similar levels of variation as eastern (Equatorial‐Tucanoan and Ge‐Pano‐Carib) South America, which is inconsistent with an initial west coast migration into South America. Moreover, in all relevant models, the estimates of genetic diversity within geographic regions suggest a major bottleneck or founder effect occurring within the North American subcontinent, before the peopling of Central and South America. Am J Phys Anthropol 2010. © 2009 Wiley‐Liss, Inc.     

Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas

The genetic characterization of Native Mexicans is important to understand multiethnic based features influencing the medical genetics of present Mexican populations, as well as to the reconstruct the peopling of the Americas. We describe the Y-chromosome genetic diversity of 197 Native Mexicans from 11 populations and 1,044 individuals from 44 Native American populations after combining with publicly available data. We found extensive heterogeneity among Native Mexican populations and ample segregation of Q-M242* (46%) and Q-M3 (54%) haplogroups within Mexico. The northernmost sampled populations falling outside Mesoamerica (Pima and Tarahumara) showed a clear differentiation with respect to the other populations, which is in agreement with previous results from mtDNA lineages. However, our results point toward a complex genetic makeup of Native Mexicans whose maternal and paternal lineages reveal different narratives of their population history, with sex-biased continental contributions and different admixture proportions. At a continental scale, we found that Arctic populations and the northernmost groups from North America cluster together, but we did not find a clear differentiation within Mesoamerica and the rest of the continent, which coupled with the fact that the majority of individuals from Central and South American samples are restricted to the Q-M3 branch, supports the notion that most Native Americans from Mesoamerica southwards are descendants from a single wave of migration. This observation is compatible with the idea that present day Mexico might have constituted an area of transition in the diversification of paternal lineages during the colonization of the Americas.     

Y-chromosome evidence for differing ancient demographic histories in the Americas

To scrutinize the male ancestry of extant Native American populations, we examined eight biallelic and six microsatellite polymorphisms from the nonrecombining portion of the Y chromosome, in 438 individuals from 24 Native American populations (1 Na Dené and 23 South Amerinds) and in 404 Mongolians. One of the biallelic markers typed is a recently identified mutation (M242) characterizing a novel founder Native American haplogroup. The distribution, relatedness, and diversity of Y lineages in Native Americans indicate a differentiated male ancestry for populations from North and South America, strongly supporting a diverse demographic history for populations from these areas. These data are consistent with the occurrence of two major male migrations from southern/central Siberia to the Americas (with the second migration being restricted to North America) and a shared ancestry in central Asia for some of the initial migrants to Europe and the Americas. The microsatellite diversity and distribution of a Y lineage specific to South America (Q-M19) indicates that certain Amerind populations have been isolated since the initial colonization of the region, suggesting an early onset for tribalization of Native Americans. Age estimates based on Y-chromosome microsatellite diversity place the initial settlement of the American continent at approximately 14,000 years ago, in relative agreement with the age of well-established archaeological evidence.     

Mitochondrial diversity in human head louse populations across the Americas

Anthropological studies suggest that the genetic makeup of human populations in the Americas is the result of diverse processes including the initial colonization of the continent by the first people plus post‐1492 European migrations. Because of the recent nature of some of these events, understanding the geographical origin of American human diversity is challenging. However, human parasites have faster evolutionary rates and larger population sizes allowing them to maintain greater levels of genetic diversity than their hosts. Thus, we can use human parasites to provide insights into some aspects of human evolution that may be unclear from direct evidence. In this study, we analyzed mitochondrial DNA (mtDNA) sequences from 450 head lice in the Americas. Haplotypes clustered into two well‐supported haplogroups, known as A and B. Haplogroup frequencies differ significantly among North, Central and South America. Within each haplogroup, we found evidence of demographic expansions around 16,000 and 20,000 years ago, which correspond broadly with those estimated for Native Americans. The parallel timing of demographic expansions of human lice and Native Americans plus the contrasting pattern between the distribution of haplogroups A and B through the Americas suggests that human lice can provide additional evidence about the human colonization of the New World. Am J Phys Anthropol 152:118–129, 2013. © 2013 Wiley Periodicals, Inc.     

Beringian standstill and spread of Native American founders

Native Americans derive from a small number of Asian founders who likely arrived to the Americas via Beringia. However, additional details about the initial colonization of the Americas remain unclear. To investigate the pioneering phase in the Americas we analyzed a total of 623 complete mtDNAs from the Americas and Asia, including 20 new complete mtDNAs from the Americas and seven from Asia. This sequence data was used to direct high-resolution genotyping from 20 American and 26 Asian populations. Here we describe more genetic diversity within the founder population than was previously reported. The newly resolved phylogenetic structure suggests that ancestors of Native Americans paused when they reached Beringia, during which time New World founder lineages differentiated from their Asian sister-clades. This pause in movement was followed by a swift migration southward that distributed the founder types all the way to South America. The data also suggest more recent bi-directional gene flow between Siberia and the North American Arctic.     

Possible migration routes into South America deduced from mitochondrial DNA studies in Colombian Amerindian populations

Mitochondrial DNA haplotype studies have been useful in unraveling the origins of Native Americans. Such studies are based on restriction site and intergenic deletion/insertion polymorphisms, which define four main haplotype groups common to Asian and American populations. Several studies have characterized these lineages in North, Central, and South American Amerindian, as well as Na Dene and Aleutian populations. Siberian, Central Asian, and Southeast Asian populations have also been analyzed, in the hope of fully depicting the route(s) of migration between Asia and America. Colombia, a key route of migration between North and South America, has until now not been studied. To resolve the current lack of information about Colombian Amerindian populations, we have investigated the presence of the founder haplogroups in 25 different ethnic groups from all over the country. The present research is part of an interdisciplinary program, Expedición Humana, fostered by the Universidad Javeriana and Dr. J. E. Bernal V. The results show the presence of the four founder A-D Amerindian lineages, with varied distributions in the different populations, as well as the presence of other haplotypes in frequencies ranging from 3% to 26%. These include some unique or private polymorphisms, and also indicate the probable presence of other Asian and a few non-Amerindian lineages. A spatial structure is apparent for haplogroups A and D, and to a lesser extent for haplogroup C. While haplogroup A and D frequencies in Colombian populations from the northwestern side of the Andes resemble those seen in Central American Amerindians more than those seen in South American populations, their frequencies on the southeastern side more closely resemble the bulk of South American frequencies so far reported, raising the question as to whether they reflect more than one migration route into South America. High frequencies of the B lineage are also characteristic of some populations. Our observations may be explained by historical events during the pre-Columbian dispersion of the first settlers and, later, by disruptions caused by the European colonization.     

American Indian prehistory as written in the mitochondrial DNA: a review.

Native Americans have been divided into three linguistic groups: the reasonably well-defined Eskaleut and Nadene of northern North America and the highly heterogeneous Amerind of North, Central, and South America. The heterogeneity of the Amerinds has been proposed to be the result of either multiple independent migrations or a single ancient migration with extensive in situ radiation. To investigate the origin and interrelationship of the American Indians, we examined the mitochondrial DNA (mtDNA) variation in 87 Amerinds (Pima, Maya, and Ticuna of North, Central, and South America, respectively), 80 Nadene (Dogrib and Tlingit of northwest North America and Navajo of the southwest North America), and 153 Asians from 7 diverse populations. American Indian mtDNAs were found to be directly descended from five founding Asian mtDNAs and to cluster into four lineages, each characterized by a different rare Asian mtDNA marker. Lineage A is defined by a HaeIII site gain at np 663, lineage B by a 9-bp deletion between the COII and tRNA(Lys) genes, lineage C by a HincII site loss at np 13259, and lineage D by an AluI site loss at np 5176. The North, Central, and South America Amerinds were found to harbor all four lineages, demonstrating that the Amerinds originated from a common ancestral genetic stock. The genetic variation of three of the four Amerind lineages (A, C, and D) was similar with a mean value of 0.084%, whereas the sequence variation in the fourth lineage (B) was much lower, raising the possibility of an independent arrival. By contrast, the Nadene mtDNAs were predominantly from lineage A, with 27% of them having a Nadene-specific RsaI site loss at np 16329. The accumulated Nadene variation was only 0.021%. These results demonstrate that the Amerind mtDNAs arose from one or maybe two Asian migrations that were distinct from the migration of the Nadene and that the Amerind populations are about four times older than the Nadene.     

Linguistic and maternal genetic diversity are not correlated in Native Mexicans

Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.     

The Phylogeographic History of the New World Screwworm Fly,Inferred by Approximate Bayesian Computation Analysis

Insect pest phylogeography might be shaped both by biogeographic events and by human influence. Here, we conducted an approximate Bayesian computation (ABC) analysis to investigate the phylogeography of the New World screwworm fly, Cochliomyia hominivorax, with the aim of understanding its population history and its order and time of divergence. Our ABC analysis supports that populations spread from North to South in the Americas, in at least two different moments. The first split occurred between the North/Central American and South American populations in the end of the Last Glacial Maximum (15,300-19,000 YBP). The second split occurred between the North and South Amazonian populations in the transition between the Pleistocene and the Holocene eras (9,100-11,000 YBP). The species also experienced population expansion. Phylogenetic analysis likewise suggests this north to south colonization and Maxent models suggest an increase in the number of suitable areas in South America from the past to present. We found that the phylogeographic patterns observed in C. hominivorax cannot be explained only by climatic oscillations and can be connected to host population histories. Interestingly we found these patterns are very coincident with general patterns of ancient human movements in the Americas, suggesting that humans might have played a crucial role in shaping the distribution and population structure of this insect pest. This work presents the first hypothesis test regarding the processes that shaped the current phylogeographic structure of C. hominivorax and represents an alternate perspective on investigating the problem of insect pests.     

A formal test of linguistic and genetic coevolution in native Central and South America

This paper investigates a mechanism of linguistic and genetic coevolution in Native Central and South America. This mechanism proposes that a process of population fissions, expansions into new territories, and isolation of ancestral and descendant groups will produce congruent language and gene trees. To evaluate this population fissions mechanism, we collected published mtDNA sequences for 1,381 individuals from 17 Native Central and South American populations. We then tested the hypothesis that three well-known language classifications also represented the genetic structure of these populations. We rejected the hypothesis for each language classification. Our tests revealed linguistic and genetic correspondence in several shallow branches common to each classification, but no linguistic and genetic correspondence in the deeper branches contained in two of the language classifications. We discuss the possible causes for the lack of congruence between linguistic and genetic structure in the region, and describe alternative mechanisms of linguistic and genetic correspondence and their predictions.     

Contrasting mitochondrial diversity of European starlings (Sturnus vulgaris) across three invasive continental distributions

European starlings (Sturnus vulgaris) represent one of the most widespread and problematic avian invasive species in the world. Understanding their unique population history and current population dynamics can contribute to conservation efforts and clarify evolutionary processes over short timescales. European starlings were introduced to Central Park, New York in 1890, and from a founding group of about 100 birds, they have expanded across North America with a current population of approximately 200 million. There were also multiple introductions in Australia in the mid‐19th century and at least one introduction in South Africa in the late 19th century. Independent introductions on these three continents provide a robust system to investigate invasion genetics. In this study, we compare mitochondrial diversity in European starlings from North America, Australia, and South Africa, and a portion of the native range in the United Kingdom. Of the three invasive ranges, the North American population shows the highest haplotype diversity and evidence of both sudden demographic and spatial expansion. Comparatively, the Australian population shows the lowest haplotype diversity, but also shows evidence for sudden demographic and spatial expansion. South Africa is intermediate to the other invasive populations in genetic diversity but does not show evidence of demographic expansion. In previous studies, population genetic structure was found in Australia, but not in South Africa. Here we find no evidence of population structure in North America. Although all invasive populations share haplotypes with the native range, only one haplotype is shared between invasive populations. This suggests these three invasive populations represent independent subsamples of the native range. The structure of the haplotype network implies that the native‐range sampling does not comprehensively characterize the genetic diversity there. This study represents the most geographically widespread analysis of European starling population genetics to date.     

Continent-Wide Decoupling of Y-Chromosomal Genetic Variation from Language and Geography in Native South Americans

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans.     

Patterns of genetic variation in Native America.

Allele frequencies from seven polymorphic red cell antigen loci (ABO, Rh, MN, S, P, Duffy, and Diego) were examined in 144 Native American populations. Mean genetic distances (Nei's D) and the fixation index FST are approximately equal for the North and South American samples but are reduced in the Central American geographic area. The relationship between genetic distance and geographic distance differs markedly across geographic areas. The correlation between geographic distance and genetic distance for the North and Central American data is twice as large as that observed for the South American samples. This geographic difference is confirmed in spatial autocorrelation analyses; no geographic structure is apparent in the South American data but geographic structure is prominent in North and Central American samples. These results confirm earlier observations regarding differences between North and South American gene frequency patterns.     

Molecular population genetics of the malaria vector Anopheles darlingi in Central and South America

To analyze the genetic relatedness and phylogeographic structure of Anopheles darlingi from 19 localities throughout Central and South America, we used a minimum spanning network, diversity measures, differentiation, neutrality tests, and mismatch distribution with mitochondrial cytochrome oxidase subunit I (COI) sequences. All the Central American haplotypes were separated by seven mutational steps from the South American haplotypes and the FST distance-based neighbor-joining tree showed a primary division between Central and South America, evidence for a putative gene pool division. More ancestral and diverse haplotypes were found in Amazonian and southern Brazil populations, suggesting that Central American populations may have originated in South America. The patterns of the mtDNA haplotype diversity and five of six tests for equilibrium implicate demographic expansion in the South American populations as the historical structure, but mismatch distribution depicts populations at mutation drift equilibrium (MDE). In South America, the departure from equilibrium was consistent with an expansion that occurred during the Pleistocene.     

Colonization models and initial genetic diversity in the Americas

The mode and tempo of colonization of the Americas established the initial pattern of continental genetic diversity. Despite a long history of study, the process of settlement remains controversial in terms of date, rate, and pattern. While there is agreement that Asia was the source population, several different models have been proposed for the colonization process. A classic model postulates a rapid spread of population ("blitzkrieg") from a small band of hunters entering through the corridor between the continental ice sheets circa 11,000 years B.P. Colonization occurred as a wave of expansion across the land masses of North and South America. An alternative model envisions the original colonists initially limiting settlement to the coastline, using boats, and entering the Americas at an earlier date, circa 13,500 B.P. Range expansion along this linear habitat from North to South America could be rapid without requiring population saturation of entire continental regions. These models have markedly different implications for genetic variation among Native Americans. The blitzkrieg colonization process would have generated multiple founder effects leading to extreme loss of genetic variation. Computer simulation of this model shows nearly complete fixation in 30 generations. Simulation of the coastal model, on the other hand, requires less extreme demographic assumptions and maintains substantial genetic variability after 100 generations. Although with the coastal model continental interiors are occupied less rapidly than with the blitzkrieg model, the coastal model allows earlier entry and rapid expansion to the southern limits of the hemisphere.     

Contrasting the ancestry patterns of three distinct population groups from the northernmost region of South America

Colombia, located in the north of the South American subcontinent is a country of great interest for population genetic studies given its high ethnic and cultural diversity represented by the admixed population, 102 indigenous peoples and African descent populations. In this study, an analysis of the genetic structure and ancestry was performed based on 46 ancestry informative INDEL markers (AIM-INDELs) and considering the genealogical and demographic variables of 451 unrelated individuals belonging to nine Native American, two African American, and four multiple ancestry populations. Measures of genetic diversity, ancestry components, and genetic substructure were analyzed to build a population model typical of the northernmost part of the South American continent. The model suggests three types of populations: Native American, African American, and multiple ancestry. The results support hypotheses posed by other authors about issues like the peopling of South America and the existence of two types of Native American ancestry. This last finding could be crucial for future research on the peopling of Colombia and South America in that a single origin of all indigenous communities should not be assumed. It then would be necessary to consider other events that could explain their genetic variability and complexity throughout the continent.