A Short Tandem Repeat–Based Phylogeny for the Human Y Chromosome

Human Y-chromosomal short tandem repeat (STR) data provide a potential model system for the understanding of autosomal STR mutations in humans and other species. Yet, the reconstruction of STR evolution is rarely attempted, because of the absence of an appropriate methodology. We here develop and validate a phylogenetic-network approach. We have typed 256 Y chromosomes of indigenous descent from Africa, Asia, Europe, Australia, and highland Papua New Guinea, for the STR loci DYS19, DXYS156Y, DYS389, DYS390, DYS392, and DYS393, as well as for five ancient biallelic mutation events: two poly (A) length variants associated with the YAP insertion, two independent SRY-1532 mutations, and the 92R7 mutation. We have used our previously published pedigree data from 11,000 paternity-tested autosomal STR-allele transfers to produce a two-class weighting system for the Y-STR loci that is based on locus lengths and motif lengths. Reduced-median-network analysis yields a phylogeny that is independently supported by the five biallelic mutations, with an error of 6%. We find the earliest branch in our African San (Bushmen) sample. Assuming an age of 20,000 years for the Native American DYS199 T mutation, we estimate a mutation rate of 2.6×10−4 mutations/20 years for slowly mutating Y STRs, ∼10-fold slower than the published average pedigree rate

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

Geographical Affinities of the HapMap Samples

The HapMap samples were collected for medical-genetic studies, but are also widely used in population-genetic and evolutionary investigations. Yet the ascertainment of the samples differs from most population-genetic studies which collect individuals who live in the same local region as their ancestors. What effects could this non-standard ascertainment have on the interpretation of HapMap results?We compared the HapMap samples with more conventionally-ascertained samples used in population- and forensic-genetic studies, including the HGDP-CEPH panel, making use of published genome-wide autosomal SNP data and Y-STR haplotypes, as well as producing new Y-STR data. We found that the HapMap samples were representative of their broad geographical regions of ancestry according to all tests applied. The YRI and JPT were indistinguishable from independent samples of Yoruba and Japanese in all ways investigated. However, both the CHB and the CEU were distinguishable from all other HGDP-CEPH populations with autosomal markers, and both showed Y-STR similarities to unusually large numbers of populations, perhaps reflecting their admixed origins.The CHB and JPT are readily distinguished from one another with both autosomal and Y-chromosomal markers, and results obtained after combining them into a single sample should be interpreted with caution. The CEU are better described as being of Western European ancestry than of Northern European ancestry as often reported. Both the CHB and CEU show subtle but detectable signs of admixture. Thus the YRI and JPT samples are well-suited to standard population-genetic studies, but the CHB and CEU less so

Sex-Specific Genetic Structure and Social Organization in Central Asia: Insights from a Multi-Locus Study

In the last two decades, mitochondrial DNA (mtDNA) and the non-recombining portion of the Y chromosome (NRY) have been extensively used in order to measure the maternally and paternally inherited genetic structure of human populations, and to infer sex-specific demography and history. Most studies converge towards the notion that among populations, women are genetically less structured than men. This has been mainly explained by a higher migration rate of women, due to patrilocality, a tendency for men to stay in their birthplace while women move to their husband's house. Yet, since population differentiation depends upon the product of the effective number of individuals within each deme and the migration rate among demes, differences in male and female effective numbers and sex-biased dispersal have confounding effects on the comparison of genetic structure as measured by uniparentally inherited markers. In this study, we develop a new multi-locus approach to analyze jointly autosomal and X-linked markers in order to aid the understanding of sex-specific contributions to population differentiation. We show that in patrilineal herder groups of Central Asia, in contrast to bilineal agriculturalists, the effective number of women is higher than that of men. We interpret this result, which could not be obtained by the analysis of mtDNA and NRY alone, as the consequence of the social organization of patrilineal populations, in which genetically related men (but not women) tend to cluster together. This study suggests that differences in sex-specific migration rates may not be the only cause of contrasting male and female differentiation in humans, and that differences in effective numbers do matter

Human genetic variation from a Y-chromosomal perspective

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Cancer- and behavior-related genes are targeted by selection in the Tasmanian devil (Sarcophilus harrisii)

Devil Facial Tumor Disease (DFTD) is an aggressive cancer notorious for its rare etiology and its impact on Tasmanian devil populations. Two regions underlying an evolutionary response to this cancer were recently identified using genomic time-series pre- and post-DTFD arrival. Here, we support that DFTD shaped the genome of the Tasmanian devil in an even more extensive way than previously reported. We detected 97 signatures of selection, including 148 protein coding genes having a human orthologue, linked to DFTD. Most candidate genes are associated with cancer progression, and an important subset of candidate genes has additional influence on social behavior. This confirms the influence of cancer on the ecology and evolution of the Tasmanian devil. Our work also demonstrates the possibility to detect highly polygenic footprints of short-term selection in very small populations

Cancer- and behavior-related genes are targeted by selection in the Tasmanian devil (Sarcophilus harrisii).

Devil Facial Tumor Disease (DFTD) is an aggressive cancer notorious for its rare etiology and its impact on Tasmanian devil populations. Two regions underlying an evolutionary response to this cancer were recently identified using genomic time-series pre- and post-DTFD arrival. Here, we support that DFTD shaped the genome of the Tasmanian devil in an even more extensive way than previously reported. We detected 97 signatures of selection, including 148 protein coding genes having a human orthologue, linked to DFTD. Most candidate genes are associated with cancer progression, and an important subset of candidate genes has additional influence on social behavior. This confirms the influence of cancer on the ecology and evolution of the Tasmanian devil. Our work also demonstrates the possibility to detect highly polygenic footprints of short-term selection in very small populations

Performance comparison of laying hens segregating for the frizzle gene under thermoneutral and high ambient temperatures

Chantier qualité GAThe effect on thermotolerance of the incompletely dominant frizzle (F) gene, which causes feather curling and feather mass reduction, was investigated in 281 laying hens that were homozygous for the frizzle mutation (FF), heterozygous (FN), or normally feathered (NN). One-half of the birds were kept under standard conditions (22°C) and half were exposed to high ambient temperatures (32°C) between 24 and 46 wk of age. Egg production, egg quality, feed efficiency, and dissection traits were recorded and compared. At standard conditions, egg production and quality traits did not differ among the 3 genotypes, whereas feed efficiency was lower for the homozygous birds. Under heat stress conditions, the superiority of the FF hens was evident for all egg quantity and quality traits. No significant difference was measured between heterozygous carriers and normally feathered hens, indicating that the incomplete dominant frizzle mutation behaved as a recessive mutation regarding heat tolerance. From this study, we deduced that the F mutation in its homozygous state has a beneficial effect in decreasing heat stress in poultry production, and it could be particularly advantageous in tropical countries where average temperatures are never too low to negatively affect feed efficiency