A global analysis of matches and mismatches between human genetic and linguistic histories.

Human history is written in both our genes and our languages. The extent to which our biological and linguistic histories are congruent has been the subject of considerable debate, with clear examples of both matches and mismatches. To disentangle the patterns of demographic and cultural transmission, we need a global systematic assessment of matches and mismatches. Here, we assemble a genomic database (GeLaTo, or Genes and Languages Together) specifically curated to investigate genetic and linguistic diversity worldwide. We find that most populations in GeLaTo that speak languages of the same language family (i.e., that descend from the same ancestor language) are also genetically highly similar. However, we also identify nearly 20% mismatches in populations genetically close to linguistically unrelated groups. These mismatches, which occur within the time depth of known linguistic relatedness up to about 10,000 y, are scattered around the world, suggesting that they are a regular outcome in human history. Most mismatches result from populations shifting to the language of a neighboring population that is genetically different because of independent demographic histories. In line with the regularity of such shifts, we find that only half of the language families in GeLaTo are genetically more cohesive than expected under spatial autocorrelations. Moreover, the genetic and linguistic divergence times of population pairs match only rarely, with Indo-European standing out as the family with most matches in our sample. Together, our database and findings pave the way for systematically disentangling demographic and cultural history and for quantifying processes of shifts in language and social identities on a global scale.

A Customized Human Mitochondrial DNA Database (hMITO DB v1.0) for Rapid Sequence Analysis, Haplotyping and Geo-Mapping.

The field of mitochondrial genomics has advanced rapidly and has revolutionized disciplines such as molecular anthropology, population genetics, and medical genetics/oncogenetics. However, mtDNA next-generation sequencing (NGS) analysis for matrilineal haplotyping and phylogeographic inference remains hindered by the lack of a consolidated mitogenome database and an efficient bioinformatics pipeline. To address this, we developed a customized human mitogenome database (hMITO DB) embedded in a CLC Genomics workflow for read mapping, variant analysis, haplotyping, and geo-mapping. The database was constructed from 4286 mitogenomes. The macro-haplogroup (A to Z) distribution and representative phylogenetic tree were found to be consistent with published literature. The hMITO DB automated workflow was tested using mtDNA-NGS sequences derived from Pap smears and cervical cancer cell lines. The auto-generated read mapping, variants track, and table of haplotypes and geo-origins were completed in 15 min for 47 samples. The mtDNA workflow proved to be a rapid, efficient, and accurate means of sequence analysis for translational mitogenomics.

Archaic hominin introgression into modern human genomes.

Ancient genomes from multiple Neanderthal and the Denisovan individuals, along with DNA sequence data from diverse contemporary human populations strongly support the prevalence of gene flow among different hominins. Recent studies now provide evidence for multiple gene flow events that leave genetic signatures in extant and ancient human populations. These events include older gene flow from an unknown hominin in Africa predating out-of-Africa migrations, and in the last 50,000-100,000 years, multiple gene flow events from Neanderthals into ancestral Eurasian human populations, and at least three distinct introgression events from a lineage close to Denisovans into ancestors of extant Southeast Asian and Oceanic populations. Some of these introgression events may have happened as late as 20,000 years before present and reshaped the way in which we think about human evolution. In this review, I aim to answer anthropologically relevant questions with regard to recent research on ancient hominin introgression in the human lineage. How have genomic data from archaic hominins changed our view of human evolution? Is there any doubt about whether introgression from ancient hominins to the ancestors of present-day humans occurred? What is the current view of human evolutionary history from the genomics perspective? What is the impact of introgression on human phenotypes?

The Multiple Histories of Western Asia: Perspectives from Ancient and Modern Genomes.

Western Asia lies at the heart of the Old World, in the midst of Africa, Asia, and Europe. As such, this region has been populated and repopulated by myriad peoples, starting with the first migrants from Africa. All evidence points to Western Asia for the beginnings of sedentary life, and indeed, first the villages and later the cities of this land remain as archaeological wonders, revealing complex histories of multiple peoples and their interactions. With the wondrous breakthroughs in genomic studies, we now have the power to look at these histories with a truly quantitative lens. Here, we review the recent anthropological genomics literature pertaining to this region, with an outlook for the future challenges and exciting possibilities for the field.

Exercises in ethically engaged work in biological anthropology.

An ethical paradigm shift currently taking place within biological anthropology is pushing scholars to envisage and develop paths toward more ethical futures. Drawing from case studies in our own teaching, research, and fieldwork experience, we reflect on the complex, diverse, and dynamic nature of ethical considerations in our field. We discuss the acquisition and institutional narrative of a human osteological teaching collection at the University of Louisville as an embodiment of structural apathy turned structural violence, and the need for professional guidance in the potential retirement of deceased individuals from our classrooms. In documented collections (i.e., the Robert J. Terry Collection), we share our process and scholarly reemphasis of the humanity of a deceased individual through contextualized analysis (i.e., osteobiography and archival history) and postmortem agentive acts. Lastly, we present an archeological site in the U.S. Virgin Islands, which poses ethical concerns as biocultural bioarcheologists and archeologists attempt to negotiate the possible wishes of the deceased with the cultural value of reconstructing the community's otherwise undocumented past, all amidst the immediate threat of anthropogenic climate change. We offer these exercises and discussion in ethically engaged projects transparently and with an overarching admission that none are models for replication. Rather, at various stages in our careers and engagement with ethics, we acknowledge that progress is worthwhile, albeit challenging, and that proceeding forward collectively as biological anthropologists should be deliberate, reflexive, and compassionate for deceased individuals and their descendant communities, as well as among and between colleagues.

Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa.

The population dynamics that followed the Out of Africa (OoA) expansion and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macropopulations have long been debated. Shedding light on these events may, in turn, provide clues to better understand the cultural evolution in Eurasia between 50 and 35 ka. Here, we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust'Ishim, Bacho Kiro, and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 ka, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 ka, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones, whereas moving through Siberia (Yana, Mal'ta). Before these events, we also confirm Zlatý Kun as the most basal human lineage sequenced to date OoA, potentially representing an earlier wave of expansion out of the Hub.

The congruence between matrilineal genetic (mtDNA) and geographic diversity of Iranians and the territorial populations.

OBJECTIVES: From the ancient era, emergence of Agriculture in the connecting region of Mesopotamia and the Iranian plateau at the foothills of the Zagros Mountains, made Iranian gene pool as an important source of populating the region. It has differentiated the population spread and different language groups. In order to trace the maternal genetic affinity between Iranians and other populations of the area and to establish the place of Iranians in a broad framework of ethnically and linguistically diverse groups of Middle Eastern and South Asian populations, a comparative study of territorial groups was designed and used in the population statistical analysis. MATERIALS AND METHODS: Mix of 616 samples was sequenced for complete mtDNA or hyper variable regions in this study. A published dataset of neighboring populations was used as a comparison in the Iranian matrilineal lineage study based on mtDNA haplogroups. RESULTS: Statistical analyses data, demonstrate a close genetic structure of all Iranian populations, thus suggesting their origin from a common maternal ancestral gene pool and show that the diverse maternal genetic structure does not reflect population differentiation in the region in their language. CONCLUSION: In the aggregate of the eastward spreads of proto-Elamo-Dravidian language from the Southwest region of Iran, the Elam province, a reasonable degree of homogeneity has been observed among Iranians in this study. The approach will facilitate our perception of the more detailed relationship of the ethnic groups living in Iran with the other ancient peoples of the area, testing linguistic hypothesis and population movements.

Genetic relationship among twenty-six populations using Y-STR polymorphism information / 解剖学报

Objective To study the genetic relationship of the Y chromosomal short tandem repeat gene loci in Lanzhou Han population and other 25 populations .Methods The frequency of alleles of Y-STRloci was obtained from a sample of 500 unrelated individuals living in Lanzhou City , and other 25 populations in different areas collected from the published data were used to calculate the genetic similarity coefficient and genetic distance .Phylogenetic trees based on the genetic distance were established .Results Populations of Lanzhou , Beijing, Shanxi and Inner Mongolia were in an identical cluster .Compared with minorities , the genetic distance between Lanzhou Han population and Inner Mongolia Mongolian population was dramatically smaller from other subpopulations .The populations in Malays and Indians were far from the other groups .Conclusion The Y-STR gene frequency distribution in 26 populations has identified differentiation in race, clime and evolution, and it is basically identical with the classification of human races which is similar to or according with other molecular anthropology research conclusions .

GENETIC EVIDENCE FOR A PLEISTOCENE POPULATION EXPLOSION.

Expansions of population size leave characteristic signatures in mitochondrial "mismatch distributions." Consequently, these distributions can inform us about the history of changes in population size. Here, I study a simple model of population history that assumes that, t generations before the present, a population grows (or shrinks) suddenly from female size N0 to female size N1 . Although this model is simple, it often provides an accurate description of data generated by complex population histories. I develop statistical methods that estimate θ0 = 2uN0 , θ1 = 2uN1 , and τ = 2ut (where u is the mutation rate), and place a confidence region around these estimates. These estimators are well behaved, and insensitive to simplifying assumptions. Finally, I apply these methods to published mitochondrial data, and infer that a major expansion of the human population occurred during the late Pleistocene.