Palaeogenomic and biostatistical analysis of ancient DNA data from Mesolithic and Neolithic skeletal remains

lepenski-vir-mesolithic-anatolia-neolithic

PhD Thesis Palaeogenomic and biostatistical analysis of ancient DNA data from Mesolithic and Neolithic skeletal remains, by Zuzana Hofmanova (2017) at the University of Mainz.
Abstract:

Palaeogenomic data have illuminated several important periods of human past with surprising im- plications for our understanding of human evolution. One of the major changes in human prehistory was Neolithisation, the introduction of the farming lifestyle to human societies. Farming originated in the Fertile Crescent approximately 10,000 years BC and in Europe it was associated with a major population turnover. Ancient DNA from Anatolia, the presumed source area of the demic spread to

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New pre-print papers on ancient and modern population genetics

Two pre-print papers reposted or published recently, interesting for the genetic analysis of ancient and modern populations (emphasis mine):

Assessing the relationship of ancient and modern populations, by Joshua G Schraiber (2017) Abstract:

Genetic material sequenced from ancient samples is revolutionizing our understanding of the recent evolutionary past. However, ancient DNA is often degraded, resulting in low coverage, error-prone sequencing. Several solutions exist to this problem, ranging from simple approach such as selecting a read at random for each site to more complicated approaches involving genotype likelihoods. In this work, we present a novel method for assessing the relationship

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Another hint at the role of Corded Ware peoples in spreading Uralic languages into north-eastern Europe, found in mtDNA analysis of the Finnish population

Open article at Scientific Reports (Nature): Identification and analysis of mtDNA genomes attributed to Finns reveal long-stagnant demographic trends obscured in the total diversity, by Översti et al. (2017).

Of special interest is its depiction of Finland’s past as including the expansion of Corded Ware population of mtDNA U5b1b2 (and probably Y-DNA R1a-M417 subclades), most likely Uralic speakers of the Forest Zone, to the north of the Yamna culture (where Late Proto-Indo-European was spoken).

A later expansion of other subclades – particularly Y-DNA N1c -, was probably associated with the later western expansion of the Eurasian Seima-Turbino phenomenon… Read the rest “Another hint at the role of Corded Ware peoples in spreading Uralic languages into north-eastern Europe, found in mtDNA analysis of the Finnish population”

Germanic–Balto-Slavic and Satem (‘Indo-Slavonic’) dialect revisionism by amateur geneticists, or why R1a lineages must have spoken Proto-Indo-European

I feel there has recently been an increase in references to quite old – and generally outdated – terms, such as Germano-Balto-Slavic and “Indo-Slavonic” (i.e. Satem), described as Late Indo-European dialects. This is happening in forums and blogs that deal with “Indo-European genetics”, and only marginally (if at all) with the main anthropological subjects that form Indo-European studies, that is Linguistics and Archaeology.

Firstly, let me go apparently against the very aim of this post, by supporting the common traits that these dialects actually share.

Satem Indo-European or Indo-Slavonic

Balto-Slavic is a complex dialect, whose known proto-history and … Read the rest “Germanic–Balto-Slavic and Satem (‘Indo-Slavonic’) dialect revisionism by amateur geneticists, or why R1a lineages *must* have spoken Proto-Indo-European”

Indo-European and Central Asian admixture in Indian population, dependent on ethnolinguistic and geodemographic divisions

Preprint paper at BioRxiv, Dissecting Population Substructure in India via Correlation Optimization of Genetics and Geodemographics, by Bose et al. (2017), a mixed group from Purdue University and IBM TJ Watson Research Center. A rather simple paper, which is nevertheless interesting in its approach to the known multiple Indian demographic divisions, and in its short reported methods and results.

Abstract:

India represents an intricate tapestry of population substructure shaped by geography, language, culture and social stratification operating in concert. To date, no study has attempted to model and evaluate how these evolutionary forces have interacted to shape the patterns

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Ancient DNA samples from Mesolithic Scandinavia show east-west genetic gradient

New pre-print article at BioRxiv, Genomics of Mesolithic Scandinavia reveal colonization routes and high-latitude adaptation, by Günther et al. (2017), from the Uppsala University (group led by Mattias Jakobsson).

Abstract (emphasis mine):

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the last glaciation. However, the origin(s) of the first colonizers and their migration routes remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient

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Islands across the Indonesian archipelago show complex patterns of admixture

An open access article Complex patterns of admixture across the Indonesian archipelago, by Hudjashov et al. (2017), has appeared in Molecular Biology and Evolution, and clarifies further the Austronesian (AN) expansion.

Abstract:

Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly under-characterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine

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When linguistics does not seem to be a science

An interesting essay by Arika Okrent has appeared in Aeon – Is linguistics a science? It concerns the central position of Chomsky’s Universal Grammar to modern Linguistics, and revolves around a story in Tom Wolfe’s book The Kingdom of Speech (2016), Everett’s discovery of the Pirahã culture’s (and language’s) emphasis on the here and now: not embedding one phrase inside another, the simple kinship system, lack of numbers, and absence of fiction or creation myths. Some excerpts of the essay:

This looks suspiciously like defiance of a central feature of the scientific archetype, one first put forward by

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Two more studies on the genetic history of East Asia: Han Chinese and Thailand

A comprehensive map of genetic variation in the world’s largest ethnic group – Han Chinese, by Charleston et al. (2017).

It is believed – based on uniparental markers from modern and ancient DNA samples and array-based genome-wide data – that Han Chinese originated in the Central Plain region of China during prehistoric times, expanding with agriculture and technology northward and southward, to become the largest Chinese ethnic group.

Abstract:

As are most non-European populations around the globe, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we

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