Category: Science

Global demographic history inferred from mitogenomes

Open access Global demographic history of human populations inferred from whole mitochondrial genomes, by Miller, Manica, and Amos, Royal Society Open Science (2018).

Relevant excerpts (emphasis mine):

Material

The Phase 3 sequence data from 20 populations, comprising five populations for each of the four main geographical regions of Europe, East Asia, South Asia and Africa, were downloaded from the 1000 Genomes Project website (www.1000genomes.org/data, [8]), including whole mitochondrial genome data for 1999 individuals. We decided not to analyse populations from the Americas due to the region’s complex history of admixture [13,14].

The European populations were as follows: Finnish sampled

… Read the rest “Global demographic history inferred from mitogenomes”

A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP

indo-european-indo-iranian-migrations

New open access paper (in Chinese) A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP, by liu et al. Acta Anthropologica Sinitica (2018)

Abstract:

The Keriyan, Lopnur and Dolan peoples are isolated populations with sparse numbers living in the western border desert of our country. By sequencing and typing the complete Y-chromosome of 179 individuals in these three isolated populations, all mutations and SNPs in the Y-chromosome and their corresponding haplotypes were obtained. Types and frequencies of each haplotype were analyzed to investigate genetic diversity and genetic structure in the three isolated populations. The results

… Read the rest “A study of genetic diversity of three isolated populations in Xinjiang using Y-SNP”

Long-term matrilineal continuity in a nonisolated region of Tuscany

iron_age_europe_mediterranean

New paper (behind paywall) The female ancestor’s tale: Long‐term matrilineal continuity in a nonisolated region of Tuscany, by Leonardi et al. Am J Phys Anthr (2018).

EDIT (10 SEP 2018): The main author has shared an open access link to read the PDF.

Interesting excerpts:

Here we analyze North-western Tuscany, a region that was a corridor of exchanges between Central Italy and the Western Mediterranean coast.

We newly obtained mitochondrial HVRI sequences from 28 individuals, and after gathering published data, we collected genetic information for 119 individuals from the region. Those span five periods during the last 5,000

… Read the rest “Long-term matrilineal continuity in a nonisolated region of Tuscany”

Early Medieval Alemannic graveyard shows diverse cultural and genetic makeup

alemannic-niederstotzingen

Open access Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard, by O’Sullivan et al., Science (2018) 4(9):eaao1262

Interesting excerpts:

Introduction

The Alemanni were a confederation of Germanic tribes that inhabited the eastern Upper Rhine basin and surrounding region (Fig. 1) (1). Roman ethnographers mentioned the Alemanni, but historical records from the 3rd to the 6th century CE contain no regular description of these tribes (2). The upheaval that occurred during the European Migration Period (Völkerwanderung) partly explains the interchangeability of nomenclature with the contemporaneous Suebi people of the same region and periods of geographic discontinuity

… Read the rest “Early Medieval Alemannic graveyard shows diverse cultural and genetic makeup”

Viking Age town shows higher genetic diversity than Neolithic and Bronze Age

sigtuna-vikings

Open access Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town, by Krzewińska et al., Current Biology (2018).

Interesting excerpts (emphasis mine, some references deleted for clarity):

The town of Sigtuna in eastern central Sweden was one of the pioneer urban hubs in the vast and complex communicative network of the Viking world. The town that is thought to have been royally founded was planned and organized as a formal administrative center and was an important focal point for the establishment of Christianity [19]. The material culture in Sigtuna indicates that the town had intense

… Read the rest “Viking Age town shows higher genetic diversity than Neolithic and Bronze Age”

The father tongue and mother tongue hypotheses in Indo-European populations

New paper (behind paywall) Reconciling the father tongue and mother tongue hypotheses in Indo-European populations, by Zhang et al. National Science Review (2018) nwy083.

Interesting excerpts:

Here, we reassessed the correlation between genetic and linguistic characteristics in 34 modern IE populations (Fig. 1a), for which all four types of datasets (lexicon, phonemes, Y-chromosomal composition, and mitochondrial DNA (mtDNA) composition) are available. We assembled compositions of the Y-chromosomal and mtDNA haplogroups or paragroups from the corresponding IE populations, which reflect paternal and maternal lines, respectively (…)

Neighbour-Nets were constructed to delineate the differences between 34 IE population groups clustering at

… Read the rest “The father tongue and mother tongue hypotheses in Indo-European populations”

Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component

invasion-from-the-steppe-yamnaya

Good timing for the publication of two interesting papers, that a lot of people should read very carefully:

ADMIXTURE

Open access A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots, by Daniel J. Lawson, Lucy van Dorp & Daniel Falush, Nature Communications (2018).

Interesting excerpts (emphasis mine):

Experienced researchers, particularly those interested in population structure and historical inference, typically present STRUCTURE results alongside other methods that make different modelling assumptions. These include TreeMix, ADMIXTUREGRAPH, fineSTRUCTURE, GLOBETROTTER, f3 and D statistics, amongst many others. These models can be used both to probe whether assumptions of the model

… Read the rest “Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component”

On the origin and spread of haplogroup R1a-Z645 from eastern Europe

indo-european-uralic-migrations-corded-ware

In my recent post about the origin and expansion of haplogroup R1b-L51, Chetan made an interesting comment on the origin and expansion of R1a-Z645. Since this haplogroup is also relevant for European history and dialectal North-West Indo-European and Indo-Iranian expansion, I feel compelled to do a similar post, although the picture right now is more blurry than that of R1b-L51.

I find it interesting that many geneticists would question the simplistic approach to the Out of Africa model as it is often enunciated, but they would at the same time consider the current simplistic model of Yamna expansion… Read the rest “On the origin and spread of haplogroup R1a-Z645 from eastern Europe”

Y-DNA haplogroups of Tuvinian tribes show little effect of the Mongol expansion

uralic-turkic

Open access Estimating the impact of the Mongol expansion upon the gene pool of Tuvans, by Balanovskaya et al., Vavilov Journal of genetics and breeding (2018), 22(5):611-619.

Abstract (emphasis mine):

With a view to trace the Mongol expansion in Tuvinian gene pool we studied two largest Tuvinian clans – those in which, according to data of humanities, one could expect the highest Central Asian ancestry, connected with the Mongol expansion. Thus, the results of Central Asian ancestry in these two clans component may be used as upper limit of the Mongol influence upon the Tuvinian gene pool in a

… Read the rest “Y-DNA haplogroups of Tuvinian tribes show little effect of the Mongol expansion”