David Glenn Smith

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 intial 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.

Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas

It is well accepted that the Americas were the last continents reached by modern humans, most likely through Beringia. However, the precise time and mode of the colonization of the New World remain hotly disputed issues. Native American populations exhibit almost exclusively five mitochondrial DNA (mtDNA) haplogroups (A-D and X). Haplogroups A-D are also frequent in Asia, suggesting a northeastern Asian origin of these lineages. However, the differential pattern of distribution and frequency of haplogroup X led some to suggest that it may represent an independent migration to the Americas. Here we show, by using 86 complete mitochondrial genomes, that all Native American haplogroups, including haplogroup X, were part of a single founding population, thereby refuting multiple-migration models. A detailed demographic history of the mtDNA sequences estimated with a Bayesian coalescent method indicates a complex model for the peopling of the Americas, in which the initial differentiation from Asian populations ended with a moderate bottleneck in Beringia during the last glacial maximum (LGM), around approximately 23,000 to approximately 19,000 years ago. Toward the end of the LGM, a strong population expansion started approximately 18,000 and finished approximately 15,000 years ago. These results support a pre-Clovis occupation of the New World, suggesting a rapid settlement of the continent along a Pacific coastal route.

Genomic evidence for the Pleistocene and recent population history of Native Americans

Genetic history of Native Americans Several theories have been put forth as to the origin and timing of when Native American ancestors entered the Americas. To clarify this controversy, Raghavan et al. examined the genomic variation among ancient and modern individuals from Asia and the Americas. There is no evidence for multiple waves of entry or recurrent gene flow with Asians in northern populations. The earliest migrations occurred no earlier than 23,000 years ago from Siberian ancestors. Amerindians and Athabascans originated from a single population, splitting approximately 13,000 years ago. Science, this issue 10.1126/science.aab3884 Genetic variation within ancient and extant Native American populations informs on their migration into the Americas. INTRODUCTION The consensus view on the peopling of the Americas is that ancestors of modern Native Americans entered the Americas from Siberia via the Bering Land Bridge and that this occurred at least ~14.6 thousand years ago (ka). However, the number and timing of migrations into the Americas remain controversial, with conflicting interpretations based on anatomical and genetic evidence. RATIONALE In this study, we address four major unresolved issues regarding the Pleistocene and recent population history of Native Americans: (i) the timing of their divergence from their ancestral group, (ii) the number of migrations into the Americas, (iii) whether there was ~15,000 years of isolation of ancestral Native Americans in Beringia (Beringian Incubation Model), and (iv) whether there was post-Pleistocene survival of relict populations in the Americas related to Australo-Melanesians, as suggested by apparent differences in cranial morphologies between some early (“Paleoamerican”) remains and those of more recent Native Americans. We generated 31 high-coverage modern genomes from the Americas, Siberia, and Oceania; 23 ancient genomic sequences from the Americas dating between ~0.2 and 6 ka; and SNP chip genotype data from 79 present-day individuals belonging to 28 populations from the Americas and Siberia. The above data sets were analyzed together with published modern and ancient genomic data from worldwide populations, after masking some present-day Native Americans for recent European admixture. RESULTS Using three different methods, we determined the divergence time for all Native Americans (Athabascans and Amerindians) from their Siberian ancestors to be ~20 ka, and no earlier than ~23 ka. Furthermore, we dated the divergence between Athabascans (northern Native American branch, together with northern North American Amerindians) and southern North Americans and South and Central Americans (southern Native American branch) to be ~13 ka. Similar divergence times from East Asian populations and a divergence time between the two branches that is close in age to the earliest well-established archaeological sites in the Americas suggest that the split between the branches occurred within the Americas. We additionally found that several sequenced Holocene individuals from the Americas are related to present-day populations from the same geographical regions, implying genetic continuity of ancient and modern populations in some parts of the Americas over at least the past 8500 years. Moreover, our results suggest that there has been gene flow between some Native Americans from both North and South America and groups related to East Asians and Australo-Melanesians, the latter possibly through an East Asian route that might have included ancestors of modern Aleutian Islanders. Last, using both genomic and morphometric analyses, we found that historical Native American groups such as the Pericúes and Fuego-Patagonians were not “relicts” of Paleoamericans, and hence, our results do not support an early migration of populations directly related to Australo-Melanesians into the Americas. CONCLUSION Our results provide an upper bound of ~23 ka on the initial divergence of ancestral Native Americans from their East Asian ancestors, followed by a short isolation period of no more than ~8000 years, and subsequent entrance and spread across the Americas. The data presented are consistent with a single-migration model for all Native Americans, with later gene flow from sources related to East Asians and, indirectly, Australo-Melanesians. The single wave diversified ~13 ka, likely within the Americas, giving rise to the northern and southern branches of present-day Native Americans. Population history of present-day Native Americans. The ancestors of all Native Americans entered the Americas as a single migration wave from Siberia (purple) no earlier than ~23 ka, separate from the Inuit (green), and diversified into “northern” and “southern” Native American branches ~13 ka. There is evidence of post-divergence gene flow between some Native Americans and groups related to East Asians/Inuit and Australo-Melanesians (yellow). How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative “Paleoamerican” relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Distribution of mtDNA haplogroup X among Native North Americans.

Mitochondrial DNA (mtDNA) samples of 70 Native Americans, most of whom had been found not to belong to any of the four common Native American haplogroups (A, B, C, and D), were analyzed for the presence of Dde I site losses at np 1715 and np 10394. These two mutations are characteristic of haplogroup X which might be of European origin. The first hypervariable segment (HVSI) of the non-coding control region (CR) of mtDNA of a representative selection of samples exhibiting these mutations was sequenced to confirm their assignment to haplogroup X. Thirty-two of the samples exhibited the restriction site losses characteristic of haplogroup X and, when sequenced, a representative selection (n = 11) of these exhibited the CR mutations commonly associated with haplogroup X, C --> T transitions at np 16278 and 16223, in addition to as many as three other HVSI mutations. The wide distribution of this haplogroup throughout North America, and its prehistoric presence there, are consistent with its being a fifth founding haplogroup exhibited by about 3% of modern Native Americans. Its markedly nonrandom distribution with high frequency in certain regions, as for the other four major mtDNA haplogroups, should facilitate establishing ancestor/descendant relationships between modern and prehistoric groups of Native Americans. The low frequency of haplogroups other than A, B, C, D, and X among the samples studied suggests a paucity of both recent non-Native American maternal admixture in alleged fullblood Native Americans and mutations at the restriction sites that characterize the five haplogroups as well as the absence of additional (undiscovered) founding haplogroups.

Distribution of four founding mtDNA haplogroups among Native North Americans

The mtDNA of most Native Americans has been shown to cluster into four lineages, or haplogroups. This study provides data on the haplogroup affiliation of nearly 500 Native North Americans including members of many tribal groups not previously studied. Phenetic cluster analysis shows a fundamental difference among 1) Eskimos and northern Na-Dene groups, which are almost exclusively mtDNA haplogroup A, 2) tribes of the Southwest and adjacent regions, predominantly Hokan and Uto-Aztecan speakers, which lack haplogroup A but exhibit high frequencies of haplogroup B, 3) tribes of the Southwest and Mexico lacking only haplogroup D, and 4) a geographically heterogeneous group of tribes which exhibit varying frequencies of all four haplogroups. There is some correspondence between language group affiliations and the frequencies of the mtDNA haplogroups in certain tribes, while geographic proximity appears responsible for the genetic similarity among other tribes. Other instances of similarity among tribes suggest hypotheses for testing with more detailed studies. This study also provides a context for understanding the relationships between ancient and modern populations of Native Americans.

Sexual behaviour and paternity in three captive groups of rhesus monkeys (Macaca mulatta)

Abstract Each offspring born into three captive groups of rhesus monkeys (Macaca mulatta) during the spring of 1981 was assigned (1) a most probable behavioural father and (2) a subset of all possible behavioural fathers, on the basis of intensive observations of sexual activity during the 1980 fall breeding season. These predictions were then compared with true paternity determined by electrophoretic and serological analyses of polymorphic blood proteins of mothers, infants, and all adult and subadult males. Coincidence between the assignments of paternity based upon behavioural and biochemical data occurred no more frequently than chance would allow. Furthermore, there were no significant relationships between biochemical and behavioural rankings of overall reproductive success. It was concluded that conventional estimates of sexual activity during the breeding season are not a reliable indicator of true paternity and relative reproductive success in rhesus macaques.

The Structure of Diversity within New World Mitochondrial DNA Haplogroups: Implications for the Prehistory of North America

The mitochondrial DNA haplogroups and hypervariable segment I (HVSI) sequences of 1,612 and 395 Native North Americans, respectively, were analyzed to identify major prehistoric population events in North America. Gene maps and spatial autocorrelation analyses suggest that populations with high frequencies of haplogroups A, B, and X experienced prehistoric population expansions in the North, Southwest, and Great Lakes region, respectively. Haplotype networks showing high levels of reticulation and high frequencies of nodal haplotypes support these results. The haplotype networks suggest the existence of additional founding lineages within haplogroups B and C; however, because of the hypervariability exhibited by the HVSI data set, similar haplotypes exhibited in Asia and America could be due to convergence rather than common ancestry. The hypervariability and reticulation preclude the use of estimates of genetic diversity within haplogroups to argue for the number of migrations to the Americas.

A private allele ubiquitous in the Americas

The three-wave migration hypothesis of Greenberg et al. has permeated the genetic literature on the peopling of the Americas. Greenberg et al. proposed that Na-Dene, Aleut-Eskimo and Amerind are language phyla which represent separate migrations from Asia to the Americas. We show that a unique allele at autosomal microsatellite locus D9S1120 is present in all sampled North and South American populations, including the Na-Dene and Aleut-Eskimo, and in related Western Beringian groups, at an average frequency of 31.7%. This allele was not observed in any sampled putative Asian source populations or in other worldwide populations. Neither selection nor admixture explains the distribution of this regionally specific marker. The simplest explanation for the ubiquity of this allele across the Americas is that the same founding population contributed a large fraction of ancestry to all modern Native American populations.

Simple sequence repeat (SSR) polymorphisms for colony management and population genetics in rhesus macaques (Macaca mulatta)

Cross‐species amplification of 72 SSR (predominantly tetranucleotide) loci from the DNA of six rhesus macaques of diverse regional origins was conducted using human primers for the polymerase chain reaction (PCR). Thirteen of these primer pairs, which consistently and unambiguously amplified polymorphic fragments from these six samples and which exhibited Mendelian properties, were also used to amplify SSR loci for 176 male rhesus macaques that are founders of six different captive breeding colonies. These include four groups of macaques originating in India and one group of macaques each that originated in China and Thailand. Gene diversity based on the SSR loci provided a reliable estimate of average heterozygosity but was between two and four times higher than that for 9 protein coding loci. Based on the SSR loci, Chinese rhesus were more genetically diverse and unique than were rhesus from India or Thailand, a conclusion not consistent with data based on protein coding loci. The six most informative SSR loci are unlinked and provide probabilities of single parent exclusion and genetic identity exceeding 0.99 and one in one million, respectively, both of which are reasonable standards for colony management purposes. Am. J. Primatol. 42:199–213, 1997.

Distribution of Mitochondrial DNA Lineages among Native American Tribes of Northeastern North America

The mtDNA haplogroups of 185 individuals from Native American tribes in Northeast North America were determined. A subset of these individuals was analyzed by sequencing hypervariable segments I and II of the control region. The haplogroup frequency distributions of populations in the Northeast exhibit regional continuity that predates European contact. A large amount of gene flow has occurred between Siouan- and Algonquian-speaking groups, probably due to an Algonquian intrusion into the Northeast. The data also support both the Macro-Siouan hypothesis and a relatively recent intrusion of Northern Iroquoians into the Northeast. These conclusions are consistent with archaeological and linguistic evidence.