The history of the Y chromosome in man

Studies of the Y chromosome over the past few decades have opened a window into the history of our species, through the reconstruction and exploitation of a patrilineal (Y-genealogical) tree based on several hundred single-nucleotide variants (SNVs). A new study validates, refines and extends this tree by incorporating >65,000 Y-linked variants identified in 1,244 men representing worldwide diversity

Founders, Drift, and Infidelity: The Relationship between Y Chromosome Diversity and Patrilineal Surnames

Most heritable surnames, like Y chromosomes, are passed from father to son. These unique cultural markers of coancestry might therefore have a genetic correlate in shared Y chromosome types among men sharing surnames, although the link could be affected by mutation, multiple foundation for names, nonpaternity, and genetic drift. Here, we demonstrate through an analysis of 1,678 Y-chromosomal haplotypes within 40 British surnames a remarkably high degree of coancestry that generally increases as surnames become rarer. On average, the proportion of haplotypes lying within descent clusters is 62% but ranges from 0% to 87%. The shallow time depth of many descent clusters within names, the lack of a detectable effect of surname derivation on diversity, and simulations of surname descent suggest that genetic drift through variation in reproductive success is important in structuring haplotype diversity. Modern patterns therefore provide little reliable information about the original founders of surnames some 700 years ago. A comparative analysis of published data on Y diversity within Irish surnames demonstrates a relative lack of surname frequency dependence of coancestry, a difference probably mediated through distinct Irish and British demographic histories including even more marked genetic drift in Ireland

Uniparental Genetic Heritage of Belarusians: Encounter of Rare Middle Eastern Matrilineages with a Central European Mitochondrial DNA Pool

Ethnic Belarusians make up more than 80% of the nine and half million people inhabiting the Republic of Belarus. Belarusians together with Ukrainians and Russians represent the East Slavic linguistic group, largest both in numbers and territory, inhabiting East Europe alongside Baltic-, Finno-Permic- and Turkic-speaking people. Till date, only a limited number of low resolution genetic studies have been performed on this population. Therefore, with the phylogeographic analysis of 565 Y-chromosomes and 267 mitochondrial DNAs from six well covered geographic sub-regions of Belarus we strove to complement the existing genetic profile of eastern Europeans. Our results reveal that around 80% of the paternal Belarusian gene pool is composed of R1a, I2a and N1c Y-chromosome haplogroups – a profile which is very similar to the two other eastern European populations – Ukrainians and Russians. The maternal Belarusian gene pool encompasses a full range of West Eurasian haplogroups and agrees well with the genetic structure of central-east European populations. Our data attest that latitudinal gradients characterize the variation of the uniparentally transmitted gene pools of modern Belarusians. In particular, the Y-chromosome reflects movements of people in central-east Europe, starting probably as early as the beginning of the Holocene. Furthermore, the matrilineal legacy of Belarusians retains two rare mitochondrial DNA haplogroups, N1a3 and N3, whose phylogeographies were explored in detail after de novo sequencing of 20 and 13 complete mitogenomes, respectively, from all over Eurasia. Our phylogeographic analyses reveal that two mitochondrial DNA lineages, N3 and N1a3, both of Middle Eastern origin, might mark distinct events of matrilineal gene flow to Europe: during the mid-Holocene period and around the Pleistocene-Holocene transition, respectively

Gaia Data Release 2: Properties and validation of the radial velocities

Context. For Gaia DR2, 280 million spectra collected by the Radial Velocity Spectrometer instrument on board Gaia were processed, and median radial velocities were derived for 9.8 million sources brighter than GRVS = 12 mag. Aims. This paper describes the validation and properties of the median radial velocities published in Gaia DR2. Methods. Quality tests and filters were applied to select those of the 9.8 million radial velocities that have the quality to be published in Gaia DR2. The accuracy of the selected sample was assessed with respect to ground-based catalogues. Its precision was estimated using both ground-based catalogues and the distribution of the Gaia radial velocity uncertainties. Results. Gaia DR2 contains median radial velocities for 7 224 631 stars, with Teff in the range [3550, 6900] K, which successfully passed the quality tests. The published median radial velocities provide a full-sky coverage and are complete with respect to the astrometric data to within 77.2% (for G larger than or equal to 12.5 mag). The median radial velocity residuals with respect to the ground-based surveys vary from one catalogue to another, but do not exceed a few 100 m s-1. In addition, the Gaia radial velocities show a positive trend as a function of magnitude, which starts around GRVS - 9 mag and reaches about +500 m s-1 at GRVS = 11.75 mag. The origin of the trend is under investigation, with the aim to correct for it in Gaia DR3. The overall precision, estimated from the median of the Gaia radial velocity uncertainties, is 1.05 km s-1. The radial velocity precision is a function of many parameters, in particular, the magnitude and effective temperature. For bright stars, GRVS E [4, 8] mag, the precision, estimated using the full dataset, is in the range 220-350 m s-1, which is about three to five times more precise than the pre-launch specification of 1 km s-1. At the faint end, GRVS = 11.75 mag, the precisions for Teff = 5000 and 6500 K are 1.4 and 3.7 km s-1, respectively.Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. Most of the authors are current or past members of the ESA Gaia mission team and of the Gaia DPAC and their work has been supported by the French Centre National de la Recherche Scientifique (CNRS), the Centre National d’Etudes Spatiales (CNES), the Agence Nationale de la Recherche, the Région Aquitaine, the Université de Bordeaux, the Utinam Institute of the Université de Franche-Comté, and the Institut des Sciences de l’ Univers (INSU); the Science and Technology Facilities Council and the United Kingdom Space Agency; the Belgian Federal Science Policy Office (BELSPO) through various Programme de Développement d’Expériences Scientifiques (PRODEX) grants; the German Aerospace Agency (Deutsches Zentrum fur Luft- und Raumfahrt e.V., DLR); the Algerian Centre de Recherche en Astronomie, Astrophysique et Géophysique of Bouzareah Observatory; the Swiss State Secretariat for Education, Research, and Innovation through the ESA PRODEX programme, the Mesures d’Accompagnement, the Swiss Activités Nationales Complémentaires, and the Swiss National Science Foundation; the Slovenian Research Agency (research core funding No. P1-0188

Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations

International audienceHigh-frequency microsatellite haplotypes of the male-specific Y-chromosome can signal past episodes of high reproductive success of particular men and their patrilineal descendants. Previously, two examples of such successful Y-lineages have been described in Asia, both associated with Altaic-speaking pastoral nomadic societies, and putatively linked to dynasties descending, respectively, from Genghis Khan and Giocangga. Here we surveyed a total of 5321 Y-chromosomes from 127 Asian populations, including novel Y-SNP and microsatellite data on 461 Central Asian males, to ask whether additional lineage expansions could be identified. Based on the most frequent eight-microsatellite haplotypes, we objectively defined 11 descent clusters (DCs), each within a specific haplogroup, that represent likely past instances of high male reproductive success, including the two previously identified cases. Analysis of the geographical patterns and ages of these DCs and their associated cultural characteristics showed that the most successful lineages are found both among sedentary agriculturalists and pastoral nomads, and expanded between 2100 BCE and 1100 CE. However, those with recent origins in the historical period are almost exclusively found in Altaic-speaking pastoral nomadic populations, which may reflect a shift in political organisation in pastoralist economies and a greater ease of transmission of Y-chromosomes through time and space facilitated by the use of horses

A Worldwide Survey of Human Male Demographic History Based on Y-SNP and Y-STR Data from the HGDP–CEPH Populations

We have investigated human male demographic history using 590 males from 51 populations in the Human Genome Diversity Project - Centre d’Étude du Polymorphisme Humain worldwide panel, typed with 37 Y-chromosomal Single Nucleotide Polymorphisms and 65 Y-chromosomal Short Tandem Repeats and analyzed with the program Bayesian Analysis of Trees With Internal Node Generation. The general patterns we observe show a gradient from the oldest population time to the most recent common ancestors (TMRCAs) and expansion times together with the largest effective population sizes in Africa, to the youngest times and smallest effective population sizes in the Americas. These parameters are significantly negatively correlated with distance from East Africa, and the patterns are consistent with most other studies of human variation and history. In contrast, growth rate showed a weaker correlation in the opposite direction. Y-lineage diversity and TMRCA also decrease with distance from East Africa, supporting a model of expansion with serial founder events starting from this source. A number of individual populations diverge from these general patterns, including previously documented examples such as recent expansions of the Yoruba in Africa, Basques in Europe, and Yakut in Northern Asia. However, some unexpected demographic histories were also found, including low growth rates in the Hazara and Kalash from Pakistan and recent expansion of the Mozabites in North Africa

Genetic diversity and the emergence of ethnic groups in Central Asia

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Layers response to a suboptimal diet through phenotype and transcriptome changes in four tissues

Poultry meat and eggs are major sources of nutrients in the human diet. The long production career of laying hens expose them to biotic or abiotic stressors, lowering their production. Understanding the mechanisms of adaptation to stress is crucial for selecting robust animals and meeting the needs of a growing human population. In this study, financed by the French ChickStress and the European Feed-a-Gene (grant agreement no. 633531) programs, we compared the effects of a 15%-energy-reduced diet (feed stress, FS) vs a commercial diet (control, CT) on phenotypic traits and adipose, blood, hypothalamus and liver transcriptomes in two feed-efficiency-diverging lines. Phenotypic traits showed differences between lines or diets, but no line × diet interaction. In the FS group, feed intake (FI) increased and hens had lower body- and abdominal adipose weight, compared to CT group. We found no differences in egg production or quality. At the transcriptomic level, 16,461 genes were expressed in one or more tissues, 41% of which were shared among tissues. We found differentially expressed genes between lines or diet in all tissues, and almost no line × diet interactions. Focusing on diet, adipose and liver transcriptomes were unaffected. In blood, pathways linked to amino acids, monosaccharides, and steroid metabolism were affected, while in the hypothalamus, changes were observed in fatty acid metabolism and endocannabinoid signalling. Given the similarities in egg production, the FS animals seem to have adapted to the stress by increasing FI and by mobilizing adipose reserves. Increase in FI did not appear to affect liver metabolism, and the mobilization of adipose reserves was apparently not driven at the transcriptomic level. In blood, the pathways linked to metabolic processes suggest a metabolic role for this tissue in chicken, whose erythrocytes are nucleated and contain mitochondria. FI increase might be linked to the hypothalamic pathway of endocannabinoid signalling, which are lipid-based neurotransmitters, notably involved in the regulation of appetite

Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit

Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used.In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies

The Galah survey: classification and diagnostics with t-SNE reduction of spectral information

Galah is an ongoing high-resolution spectroscopic survey with the goal of disentangling the formation history of the Milky Way, using the fossil remnants of disrupted star formation sites which are now dispersed around the Galaxy. it is targeting a randomly selected, magnitude limited (V ≤ 14) sample of stars, with the goal of observing one million objects. To date, 300,000 spectra have been obtained. Not all of them are correctly processed by parameter estimation pipelines and we need to know about them. We present a semi-automated classification scheme which identifies different types of peculiar spectral morphologies, in an effort to discover and flag potentially problematic spectra and thus help to preserve the integrity of the survey's results. To this end we employ a recently developed dimensionality reduction technique t-SNE (t-distributed Stochastic Neighbour Embedding), which enables us to represent the complex spectral morphology in a two-dimensional projection map while still preserving the properties of the local neighbourhoods of spectra. We find that the majority (178,483) of the 209,533 Galah spectra considered in this study represents normal single stars, whereas 31,050 peculiar and problematic spectra with very diverse spectral features pertaining to 28,579 stars are distributed into 10 classification categories: Hot stars, Cool metal-poor giants, Molecular absorption bands, Binary stars, Ha\Hβ emission, Ha/Hβ emission superimposed on absorption, Ha/Hβ P-Cygni, Ha/Hβ inverted P-Cygni, Lithium absorption, and Problematic. Classified spectra with supplementary information are presented in the catalogue, indicating candidates for follow-up observations and population studies of the short-lived phases of stellar evolution