Bantu distinguished from Khoe by uniparental markers, not genome-wide autosomal admixture

The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola, by Oliveira et al. bioRxiv (2018).

Interesting excerpts (emphasis mine):

The origins of NRY diversity in SW Angola

In accordance with our previous mtDNA study⁹, the present NRY analysis reveals a major division between the Kx’a-speaking !Xun and the Bantu-speaking groups, whose paternal genetic ancestry does not display any old remnant lineages, or a clear link to pre-Bantu eastern African migrants introducing Khoe-Kwadi languages and pastoralism into southern Africa (cf. 15). This is especially evident in the distribution of the

… Read the rest

Native American genetic continuity and oldest mtDNA hg A2ah in the Andean region

Native American gene continuity to the modern admixed population from the Colombian Andes: Implication for biomedical, population and forensic studies by Criollo-Rayo et al., Forensic Sci Int Genet (2018), in press, corrected proof.

Abstract (emphasis mine):

Andean populations have variable degrees of Native American and European ancestry, representing an opportunity to study admixture dynamics in the populations from Latin America (also known as Hispanics). We characterized the genetic structure of two indigenous (Nasa and Pijao) and three admixed (Ibagué, Ortega and Planadas) groups from Tolima, in the Colombian Andes. DNA samples from 348 individuals were genotyped for six mitochondrial DNA

… Read the rest

Domesticated horse population structure, selection, and mtDNA geographic patterns

Open access Detecting the Population Structure and Scanning for Signatures of Selection in Horses (Equus caballus) From Whole-Genome Sequencing Data, by Zhang et al, Evolutionary Bioinformatics (2018) 14:1–9.

Abstract (emphasis mine):

Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native

… Read the rest

Bayesian estimation of partial population continuity by using ancient DNA and spatially explicit simulations

Open access Bayesian estimation of partial population continuity by using ancient DNA and spatially explicit simulations, by Silva et al., Evolutionary Applications (2018).

Abstract (emphasis mine):

The retrieval of ancient DNA from osteological material provides direct evidence of human genetic diversity in the past. Ancient DNA samples are often used to investigate whether there was population continuity in the settlement history of an area. Methods based on the serial coalescent algorithm have been developed to test whether the population continuity hypothesis can be statistically rejected by analysing DNA samples from the same region but of different ages. Rejection of

… Read the rest

Contrastive principal component analysis (cPCA) to explore patterns specific to a dataset

Interesting open access paper Exploring patterns enriched in a dataset with contrastive principal component analysis, by Abid, Zhang, Bagaria & Zou, Nature Communications (2018) 9:2134.

Abstract (emphasis mine):

Visualization and exploration of high-dimensional data is a ubiquitous challenge across disciplines. Widely used techniques such as principal component analysis (PCA) aim to identify dominant trends in one dataset. However, in many settings we have datasets collected under different conditions, e.g., a treatment and a control experiment, and we are interested in visualizing and exploring patterns that are specific to one dataset. This paper proposes a method, contrastive principal component analysis

… Read the rest

Tales of Human Migration, Admixture, and Selection in Africa

Comprehensive review (behind paywall) Tales of Human Migration, Admixture, and Selection in Africa, by Carina M. Schlebusch & Mattias Jakobsson, Annual Review of Genomics and Human Genetics (2018), Vol. 9.

Abstract (emphasis mine):

In the last three decades, genetic studies have played an increasingly important role in exploring human history. They have helped to conclusively establish that anatomically modern humans first appeared in Africa roughly 250,000–350,000 years before present and subsequently migrated to other parts of the world. The history of humans in Africa is complex and includes demographic events that influenced patterns of genetic variation across the continent.

… Read the rest

Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations

Open access Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations, by Wang, Lu, Chung, and Xu, Hereditas (2018) 155:19.

Abstract (emphasis mine):

Background
Han Chinese, Japanese and Korean, the three major ethnic groups of East Asia, share many similarities in appearance, language and culture etc., but their genetic relationships, divergence times and subsequent genetic exchanges have not been well studied.

Results
We conducted a genome-wide study and evaluated the population structure of 182 Han Chinese, 90 Japanese and 100 Korean individuals, together with the data of 630 individuals representing 8 populations wordwide. Our analyses revealed

… Read the rest

Basal Eurasians split off ca. 80kya and contributed ca. 10% to EEF

Efficiently inferring the demographic history of many populations with allele count data, by Kamm, Terhorst, Durbin, & Song (2018).

Abstract

The sample frequency spectrum (SFS), or histogram of allele counts, is an important summary statistic in evolutionary biology, and is often used to infer the history of population size changes, migrations, and other demographic events affecting a set of populations. The expected multipopulation SFS under a given demographic model can be efficiently computed when the populations in the model are related by a tree, scaling to hundreds of populations. Admixture, back-migration, and introgression are common natural processes that violate

… Read the rest

The time and place of European admixture in Ashkenazi Jewish history

Open access The time and place of European admixture in Ashkenazi Jewish history, by Xue, Lencz, Darvasi, Pe’er, & Carmi, PLOS Genetics (2018).

Abstract (emphasis mine):

The Ashkenazi Jewish (AJ) population is important in genetics due to its high rate of Mendelian disorders. AJ appeared in Europe in the 10th century, and their ancestry is thought to comprise European (EU) and Middle-Eastern (ME) components. However, both the time and place of admixture are subject to debate. Here, we attempt to characterize the AJ admixture history using a careful application of new and existing methods on a large AJ sample.

… Read the rest