Vilar Labs
Published Papers
Vanessa Forbes-Pateman, Aram Yardumian, Miguel Vilar, Tanya M. Simms, Michael P. Pateman, William Keegan
American Journal of Biological Anthropology, 2022
Abstract
Abstract Objectives: The Bahamas is an archipelago in the western Atlantic Ocean that stretches over 1000 km, just north of Cuba and east of the Florida Peninsula. Modern DNA studies show that contemporary Bahamians are genetic descendants of European and African ancestors, unlike Cuba, Dominican Republic, and Puerto Rico, where Indigenous descendancy is well documented. For The Bahamas little was known about the genetic ancestry of the Indigenous Lucayans (AD 700–1600) and their relationship to other Indigenous Caribbean populations. In this study, we investigated genetic diversity in Indigenous Lucayans from the Bahamas Archipelago to better understand the phylogeography of their genetic lineages, and to determine their relationship with other Indigenous Caribbean populations. Materials and methods: We characterized genetic diversity across two uniparental markers in 31 ancient individuals from burial sites on seven Bahamian islands. Results: We observed significant homogeneity in Lucayan paternal lineages, with only two haplogroups (Q-M902 and Q-Z781) found among them. Mitochondrial lineages were more diverse, with individuals belonging to haplogroup A2, B2, C1b, and C1d1. Four were assigned to a previously unidentified C1d lineage. Of the B2 samples, 7 of 11 belonged to the rare South America/Caribbean haplogroup B2e. This haplogroup was the most prevalent in the Northwest Bahamas while C1, particularly C1d, was more prevalent in the Central and Southern Bahamas. Discussion: These findings document a complex genetic history with an initial migration from Hispaniola beginning 1300 years ago, and possible gene flow from Cuba to Andros in late Bahamian prehistory.
Paul A. Maier, Göran Runfeldt, Roberta J. Estes & Miguel G. Vilar
Scientific Reports 2022
Abstract
Archaeological and genomic evidence suggest that modern Homo sapiens have roamed the planet for some 300–500 thousand years. In contrast, global human mitochondrial (mtDNA) diversity coalesces to one African female ancestor (“Mitochondrial Eve”) some 145 thousand years ago, owing to the ¼ gene pool size of our matrilineally inherited haploid genome. Therefore, most of human prehistory was spent in Africa where early ancestors of Southern African Khoisan and Central African rainforest hunter-gatherers (RFHGs) segregated into smaller groups. Their subdivisions followed climatic oscillations, new modes of subsistence, local adaptations, and cultural-linguistic differences, all prior to their exodus out of Africa. Seven African mtDNA haplogroups (L0–L6) traditionally captured this ancient structure—these L haplogroups have formed the backbone of the mtDNA tree for nearly two decades. Here we describe L7, an eighth haplogroup that we estimate to be ~ 100 thousand years old and which has been previously misclassified in the literature. In addition, L7 has a phylogenetic sublineage L7a*, the oldest singleton branch in the human mtDNA tree (~ 80 thousand years). We found that L7 and its sister group L5 are both low-frequency relics centered around East Africa, but in different populations (L7: Sandawe; L5: Mbuti). Although three small subclades of African foragers hint at the population origins of L5'7, the majority of subclades are divided into Afro-Asiatic and eastern Bantu groups, indicative of more recent admixture. A regular re-estimation of the entire mtDNA haplotype tree is needed to ensure correct cladistic placement of new samples in the future.
Rocío Gómez, Miguel G. Vilar, Marco Antonio Meraz-Ríos, David Véliz, Gerardo Zúñiga, Esther Alhelí Hernández-Tobías, Maria del Pilar Figueroa-Corona, Amanda C. Owings, Jill B. Gaieski, Theodore G. Schurr, The Genographic Consortium
Cell 2021
Summary
Native Mexican populations are crucial for understanding the genetic ancestry of Aztec descendants and coexisting ethnolinguistic groups in the Valley of Mexico and elucidating the population dynamics of the prehistoric colonization of the Americas. Mesoamerican societies were multicultural in nature and also experienced significant admixture during Spanish colonization of the region. Despite these facts, Native Mexican Y chromosome diversity has been greatly understudied. To further elucidate their genetic history, we conducted a high-resolution Y chromosome analysis with Chichimecas, Nahuas, Otomies, Popolocas, Tepehuas, and Totonacas using 19 Y-short tandem repeat and 21 single nucleotide polymorphism loci. We detected enormous paternal genetic diversity in these groups, with haplogroups Q-MEH2, Q-M3, Q-Z768, Q-L663, Q-Z780, and Q-PV3 being identified. These data affirmed the southward colonization of the Americas via Beringia and connected Native Mexicans with indigenous populations from South-Central Siberia and Canada. They also suggested that multiple population dispersals gave rise to Y chromosome diversity in these populations.
Reich, et al
Nature 2021
Abstract
Humans settled the Caribbean ~6,000 years ago, with ceramic use and intensified agriculture marking a shift from the Archaic to the Ceramic Age ~2,500 years ago1–3. We report genomewide data from 174 individuals from The Bahamas, Hispaniola, Puerto Rico, Curaçao, and Venezuela co-analyzed with published data. Archaic Age Caribbean people derive from a deeply divergent population closest to Central and northern South Americans; contrary to previous work4, we find no support for ancestry contributed by a population related to North Americans. Archaic lineages were >98% replaced by a genetically homogeneous ceramic-using population related to Arawak-speakers from northeast South America who moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools reflecting small effective population sizes which we estimate to be a minimum of Ne=500–1500 and a maximum of Ne=1530–8150 on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the analyzed individuals lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous estimates of hundreds of thousands of people are too large5–6. Confirming a small, interconnected Ceramic Age population7, we detect 19 pairs of cross-island cousins, close relatives ~75 kilometers apart in Hispaniola, and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland but instead reflected interactions within an interconnected Caribbean world.
Miguel G. Vilar, Carlalynne Melendez, Akiva B. Sanders, Akshay Walia, Jill B. Gaieski, Amanda C. Owings, Theodore G. Schurr, The Genographic Consortium
American Journal of Physical Anthropology 2014
Abstract
Puerto Rico and the surrounding islands rest on the eastern fringe of the Caribbean's Greater Antilles, located less than 100 miles northwest of the Lesser Antilles. Puerto Ricans are genetic descendants of pre-Columbian peoples, as well as peoples of European and African descent through 500 years of migration to the island. To infer these patterns of pre-Columbian and historic peopling of the Caribbean, we characterized genetic diversity in 326 individuals from the southeastern region of Puerto Rico and the island municipality of Vieques. We sequenced the mitochondrial DNA (mtDNA) control region of all of the samples and the complete mitogenomes of 12 of them to infer their putative place of origin. In addition, we genotyped 121 male samples for 25 Y-chromosome single nucleotide polymorphism and 17 STR loci. Approximately 60% of the participants had indigenous mtDNA haplotypes (mostly from haplogroups A2 and C1), while 25% had African and 15% European haplotypes. Three A2 sublineages were unique to the Greater Antilles, one of which was similar to Mesoamerican types, while C1b haplogroups showed links to South America, suggesting that people reached the island from the two distinct continental source areas. However, none of the male participants had indigenous Y-chromosomes, with 85% of them instead being European/Mediterranean and 15% sub-Saharan African in origin. West Eurasian Y-chromosome short tandem repeat haplotypes were quite diverse and showed similarities to those observed in southern Europe, North Africa and the Middle East. These results attest to the distinct, yet equally complex, pasts for the male and female ancestors of modern day Puerto Ricans.
Kelsey Needham Dancause ,Miguel G. Vilar,Rlene Steffy,J. Koji Lum
PLoS ONE 2011
Abstract
Background
Mitochondrial DNA (mtDNA) hypervariable region (HVR) sequences of prehistoric Polynesian chicken samples reflect dispersal of two haplogroups—D and E—by the settlers of the Pacific. The distribution of these chicken haplogroups has been used as an indicator of human movement. Recent analyses suggested similarities between prehistoric Pacific and South American chicken samples, perhaps reflecting prehistoric Polynesian introduction of the chicken into South America. These analyses have been heavily debated. The current distribution of the D and E lineages among contemporary chicken populations in the Western Pacific is unclear, but might ultimately help to inform debates about the movements of humans that carried them.
Objectives
We sought to characterize contemporary mtDNA diversity among chickens in two of the earliest settled archipelagoes of Remote Oceania, the Marianas and Vanuatu.
Methods
We generated HVR sequences for 43 chickens from four islands in Vanuatu, and for 5 chickens from Guam in the Marianas.
Results
Forty samples from Vanuatu and three from Guam were assigned to haplogroup D, supporting this as a Pacific chicken haplogroup that persists in the Western Pacific. Two haplogroup E lineages were observed in Guam and two in Vanuatu. Of the E lineages in Vanuatu, one was identical to prehistoric Vanuatu and Polynesian samples and the other differed by one polymorphism. Contrary to our expectations, we observed few globally distributed domesticate lineages not associated with Pacific chicken dispersal. This might suggest less European introgression of chickens into Vanuatu than expected. If so, the E lineages might represent lineages maintained from ancient Pacific chicken introductions. The Vanuatu sample might thus provide an opportunity to distinguish between maintained ancestral Pacific chicken lineages and replacement by global domesticates through genomic analyses, which could resolve questions of contemporary haplogroup E chicken relationships and inform interpretations of debated sequences from archaeological samples
Graduate Research Papers
Pending
Coming soon!
Undergraduate Capstone Papers
Mia Tomeo
Mia completed a Capstone Project under Dr. Vilar’s guidance. She authored a comprehensive 30-page systematic literature review that analyzed and synthesized research findings from multiple academic sources to assess the impact of cerebellar development on cognitive functions and social behaviors. The purpose of this project was to investigate the evolutionary significance of the cerebellum and compare Neanderthal brain structure to that of Homo Sapiens, aiming to describe possible ways the cerebellum may have provided Homo Sapiens an evolutionary advantage. Through conducting this literature review, she found that there are asymmetries in the cerebellar lobe unique to homo sapiens. She further connected these findings to other studies that found the cerebellum is implicated in cognitive and social development, using these separate studies to draw evolutionary connections.
Phuong Nguyen
Phuong's capstone paper integrates genetic evidence with environmental and cultural context to provide a more comprehensive understanding of Vietnamese ancestry and population history.