Inference of sex-specific expansion patterns in human populations from Y-chromosome polymorphism

Genetic analysis of a bronze age individual from Ulug-depe (Turkmenistan)

The Oxus Civilisation (or Bactrio-Margian Archaeological Complex, BMAC) was the main archaeological culture of the Bronze Age in southern Central Asia. Paleogenetic analyses were previously conducted mainly on samples from the eastern part of BMAC. The population associated with BMAC descends from local Chalcolithic populations, with some outliers of steppe or South-Asian descent. Here, we present new genome-wide data for one individual from Ulug-depe (Turkmenistan), one of the main BMAC sites, located at the southwestern edge of the BMAC. We demonstrate that this individual genetically belongs to the BMAC cluster. Using this genome, we confirm that modern Indo-Iranian–speaking populations from Central Asia derive their ancestry from BMAC populations, with additional gene flow from the western and the Altai steppes in higher proportions among the Tajiks than the Yagnobi ethnic group.

Genetic Diversity on the Sex Chromosomes

Levels and patterns of genetic diversity can provide insights into a population’s history. In species with sex chromosomes, differences between genomic regions with unique inheritance patterns can be used to distinguish between different sets of possible demographic and selective events. This review introduces the differences in population history for sex chromosomes and autosomes, provides the expectations for genetic diversity across the genome under different evolutionary scenarios, and gives an introductory description for how deviations in these expectations are calculated and can be interpreted. Predominantly, diversity on the sex chromosomes has been used to explore and address three research areas: 1) Mating patterns and sex-biased variance in reproductive success, 2) signatures of selection, and 3) evidence for modes of speciation and introgression. After introducing the theory, this review catalogs recent studies of genetic diversity on the sex chromosomes across species within the major research areas that sex chromosomes are typically applied to, arguing that there are broad similarities not only between male-heterogametic (XX/XY) and female-heterogametic (ZZ/ZW) sex determination systems but also any mating system with reduced recombination in a sex-determining region. Further, general patterns of reduced diversity in nonrecombining regions are shared across plants and animals. There are unique patterns across populations with vastly different patterns of mating and speciation, but these do not tend to cluster by taxa or sex determination system.

The association between mid-facial morphology and climate in northeast Europe differs from that in north Asia: Implications for understanding the morphology of Late Pleistocene Homo sapiens

The climate of northeastern Europe is likely to resemble in many ways Late Pleistocene periglacial conditions in Europe, but there have been relatively few studies exploring the association between climate and morphology in the mid-face of modern northeastern European populations. To fill this gap, we sampled 540 male skulls from 22 European and Near Eastern groups, including 314 skulls from 11 populations from northeastern Europe, to test for possible climate-morphology association at the continental scale. Our results found a moderate and highly significant association (R = 0.48, p = 0.0013, Mantel test) between sets of 23 mid-facial measurements and eight climatic variables. A partial least squares analysis revealed this association to be mostly driven by differences between groups from northeastern Europe and populations from the Mediterranean and the Caucasus. Matrices of between-group genetic distances based on Y-chromosome and mtDNA markers, as well as cranial non-metric and geographic distance matrices, were used to control for the possible influence of shared population history. Irrespective of which measure of neutral between-population distances is taken into account, the association between cranial variables and climate remains significant. The pattern of association between climate and morphology of the mid-face in western Eurasia was then compared to that in east and north Asia. Although differences between the two were found, there were also similarities that support existing functional interpretations of morphology for the bony parts of the upper airways. Last, in a preliminary analysis using a reduced set of measurements, mid-facial morphology of several Upper Paleolithic European Homo sapiens specimens was found to be more similar to groups from northern and northeastern Europe than to southern European populations. Thus, the population of northeastern Europe rather than east and north Asian groups should be used as a model when studying climate-mediated mid-facial morphology of Upper Paleolithic European H. sapiens.

Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans

Recent population genetic studies have provided valuable insights on the demographic history of our species. However, some issues such as the dating of the first demographic expansions in human populations remain puzzling. Indeed, although a few genetic studies argued that the first human expansions were concomitant with the Neolithic transition, many others found signals of expansion events starting during the Palaeolithic. Here we performed a simulation study to show that these contradictory findings may result from the differences in the genetic markers used, especially if two successive expansion events occurred. For a large majority of replicates for each scenario tested, microsatellite data allow only detecting the recent expansion event in that case, whereas sequence data allow only detecting the ancient expansion. Combined with previous real data analyses, our results bring support to the ideas that (i) a first human expansions started during the Palaeolithic period, (ii) a second expansion event occurred later, concomitantly with the Neolithic transition.

Worldwide genetic and cultural change in human evolution

Both genetic variation and certain culturally transmitted phenotypes show geographic signatures of human demographic history. As a result of the human cultural predisposition to migrate to new areas, humans have adapted to a large number of different environments. Migration to new environments alters genetic selection pressures, and comparative genetic studies have pinpointed numerous likely targets of this selection. However, humans also exhibit many cultural adaptations to new environments, such as practices related to clothing, shelter, and food. Human culture interacts with genes and the environment in complex ways, and studying genes and culture together can deepen our understanding of human evolution.

Genomic signatures of sex-biased demography: progress and prospects

Sex-biased demographic events have played a crucial role in shaping human history. Many of these processes affect genetic variation and can therefore leave detectable signatures in the genome because autosomal, X-linked, Y-linked, and mitochondrial DNA inheritance differ between sexes. Here, we discuss how sex-biased processes shape patterns of genetic diversity across the genome, review recent genomic evidence for sex-biased demography in modern human populations, and suggest directions for future research.