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The Y chromosomes of the great apes

Journal: Human Genetics | Year: 2017


The great apes (orangutans, gorillas, chimpanzees, bonobos and humans) descended from a common ancestor around 13 million years ago, and since then their sex chromosomes have followed very different evolutionary paths. While great-ape X chromosomes are highly conserved, their Y chromosomes, reflecting the general lability and degeneration of this male-specific part of the genome since its early mammalian origin, have evolved rapidly both between and within species. Understanding great-ape Y chromosome structure, gene content and diversity would provide a valuable evolutionary context for the human Y, and would also illuminate sex-biased behaviours, and the effects of the evolutionary pressures exerted by different mating strategies on this male-specific part of the genome. High-quality Y-chromosome sequences are available for human and chimpanzee (and low-quality for gorilla). The chromosomes differ in size, sequence organisation and content, and while retaining a relatively stable set of ancestral single-copy genes, show considerable variation in content and copy number of ampliconic multi-copy genes. Studies of Y-chromosome diversity in other great apes are relatively undeveloped compared to those in humans, but have nevertheless provided insights into speciation, dispersal, and mating patterns. Future studies, including data from larger sample sizes of wild-born and geographically well-defined individuals, and full Y-chromosome sequences from bonobos, gorillas and orangutans, promise to further our understanding of population histories, male-biased behaviours, mutation processes, and the functions of Y-chromosomal genes.

Peoples: | Places: - | Topics: Great Apes, Speciation, and Y-chromosome | DNA Type: Y-DNA

The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

Journal: Molecular Biology and Evolution | Year: 2015


Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.

Peoples: - | Places: - | Topics: Mutation rate and Purifying selection | DNA Type: Y-SNP and Y-STR

Timing and deciphering mitochondrial DNA macro-haplogroup R0 variability in Central Europe and Middle East

Journal: BMC Evolutionary Biology | Year: 2008


Nearly half of the West Eurasian assemblage of human mitochondrial DNA (mtDNA) is fractioned into numerous sub-lineages of the predominant haplogroup (hg) R0. Several hypotheses have been proposed on the origin and the expansion times of some R0 sub-lineages, which were partially inconsistent with each other. Here we describe the phylogenetic structure and genetic variety of hg R0 in five European populations and one population from the Middle East.RESULTS:Our analysis of 1,350 mtDNA haplotypes belonging to R0, including entire control region sequences and 45 single nucleotide polymorphisms from the coding region, revealed significant differences in the distribution of different sub-hgs even between geographically closely located regions. Estimates of coalescence times that were derived using diverse algorithmic approaches consistently affirmed that the major expansions of the different R0 hgs occurred in the terminal Pleistocene and early Holocene.CONCLUSION:Given an estimated coalescence time of the distinct lineages of 10 – 18 kya, the differences in the distributions could hint to either limited maternal gene flow after the Last Glacial Maximum due to the alpine nature of the regions involved or to a stochastic loss of diversity due to environmental events and/or disease episodes occurred at different times and in distinctive regions. Our comparison of two different ways of obtaining the timing of the most recent common ancestor confirms that the time of a sudden expansion can be adequately recovered from control region data with valid confidence intervals. For reliable estimates, both procedures should be applied in order to cross-check the results for validity and soundness.

Peoples: - | Places: Europe | Topics: - | DNA Type: mtDNA

Timing of Replication Is a Determinant of Neutral Substitution Rates but Does Not Explain Slow Y Chromosome Evolution in Rodents

Journal: Molecular Biology and Evolution | Year: 2010


Mutation rates, assayed as substitution rates of putatively neutral sites, are highly variable around mammalian genomes: There is heterogeneity between genes, between autosomes, and between X, Y, and autosomes. The differences between X, Y, and autosomes are typically assumed to reflect the greater number of cell divisions in the male germ-line. Such an effect can neither account for within-autosome differences nor does it predict the differences between X, Y, and autosome observed in rodents. It has recently been proposed that in primates, the time during S-phase when a gene is replicated is an important determinant of neutral rates of evolution. Here we ask 1) whether we can replicate this result in rodents, 2) whether different autosomes replicate on average at different times, and 3) whether this might explain differences in their substitution rates. Finally we ask 4) whether X, Y, and autosome replicate at different times and 5) whether any difference might explain why the number of replication events alone cannot explain their substitution rates. We find that, as in primates, autosomal intronic rates of evolution increase significantly during S-phase. Different autosomes do have different average replication times, and together with rearrangement, this is a significant predictor of between-autosome differences in substitution rate. Although we find that autosomal, X-, and Y-linked genes replicate at different times, it is paradoxical that the Y-linked genes replicate latest, and replicate more often, but are not especially fast evolving. These results support the hypothesis that replication timing is an important source of substitution rate heterogeneity.

Peoples: - | Places: - | Topics: Mutation rate | DNA Type: Y-DNA

Tissue dependent co-segregation of the novel pathogenic G12276A mitochondrial tRNALeu(CUN) mutation with the A185G D-loop polymorphism

Journal: Journal of Medical Genetics | Year: 2004


Peoples: | Places: | Topics: | DNA Type: mtDNA

Toward resolution of the debate regarding purported crypto-Jews in a Spanish-American population: Evidence from the Y chromosome

Journal: Annals of Human Biology | Year: 2010


The ethnic heritage of northernmost New Spain, including present-day northern New Mexico and southernmost Colorado, USA, is intensely debated. Local Spanish-American folkways and anecdotal narratives led to claims that the region was colonized primarily by secret- or crypto-Jews. Despite ethnographic criticisms, the notion of substantial crypto-Jewish ancestry among Spanish-Americans persists. Aim: We tested the null hypothesis that Spanish-Americans of northern New Mexico carry essentially the same profile of paternally inherited DNA variation as the peoples of Iberia, and the relevant alternative hypothesis that the sampled Spanish-Americans possess inherited DNA variation that reflects Jewish ancestry significantly greater than that in present-day Iberia. Subjects and Methods: We report frequencies of 19 Y-chromosome unique event polymorphism (UEP) biallelic markers for 139 men from across northern New Mexico and southern Colorado, USA, who self-identify as ?Spanish-American?. We used three different statistical tests of differentiation to compare frequencies of major UEP-defined clades or haplogroups with published data for Iberians, Jews, and other Mediterranean populations. We also report frequencies of derived UEP markers within each major haplogroup, compared with published data for relevant populations. Results: All tests of differentiation showed that, for frequencies of the major UEP-defined clades, Spanish-Americans and Iberians are statistically indistinguishable. All other pairwise comparisons, including between Spanish-Americans and Jews, and Iberians and Jews, revealed highly significant differences in UEP frequencies. Conclusion: Our results indicate that paternal genetic inheritance of Spanish-Americans is indistinguishable from that of Iberians and refute the popular and widely publicized scenario of significant crypto-Jewish ancestry of the Spanish-American population. R'esum'e. Arriere plan:?L?h'eritage ethnique de la partie la plus septentrionale de la Nouvelle Espagne, incluant aux USA l?actuel nord du Nouveau-Mexique et le sud du Colorado, est intens'ement discut'e. Des traditions hispano-am'ericaines locales et des anecdotes tendent a proclamer que cette r'egion a ‘et'e colonis'ee primitivement par des crypto-juifs. En d'epit de critiques ethnographiques, la notion d?ancestralit'e substantielle crypto-juive persiste chez les hispano-am'ericains. But:?Tester l?hypothese nulle que les hispano-am'ericains du Nouveau-Mexique septentrional pr'esentent essentiellement le m^eme profil de variation d?ADN paternel que les populations de la p'eninsule ib'erique et l?hypothese alternative que les hispano-am'ericains ‘echantillonn'es possedent une variation d?ADN qui reflete significativement plus l?ancestralit'e juive que l?ib'erique. Sujets et m'ethodes:?On reporte les fr'equences de 19 polymorphismes uniques du chromosome Y (PU-Y) de marqueurs bi-all'eliques chez 139 hommes du nord du Nouveau-Mexique et du sud du Colorado qui s?auto-identifient comme hispano-am'ericains. On utilise trois tests statistiques de diff'erenciation afin de comparer les fr'equences des clades ou haplogroupes de PU-Y majeurs, ainsi que les fr'equences des marqueurs PU-Y singularis'es a l?int'erieur de chaque haplogroupe majeur, avec les donn'ees publi'ees pour les espagnols, les juifs et d?autres populations m'editerran'eennes. R'esultats:?Tous les tests de diff'erenciation montrent que les hispano-am'ericains et les iberes sont statistiquement indistincts pour les fr'equences des clades majeurs a d'efinition PU-Y. Toutes les autres comparaisons deux a deux incluant hispano-am'ericains et juifs et iberes et juifs, montrent des diff'erences hautement significatives des fr'equences PU-Y. Conclusion: Nos r'esultats indiquent que l?h'er'edit'e paternel des hispano-am'ericains ne peut ^etre distingu'ee de celle des iberes et r'efute le sc'enario populaire et largement diffus'e, de l?existence d?une origine significative crypto-juive de la population hispano-am'ericaine. Zusammenfassung. Hintergrund:?Das ethnische Erbe des nordlichsten Teils von Neuspanien

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Towards an understanding of the genetics of human male infertility: lessons from flies

Journal: Trends in Genetics | Year: 2000


It has been argued that about 4–5% of male adults suffer from infertility due to a genetic causation. From studies in the fruitfly Drosophila , there is evidence that up to 1500 recessive genes contribute to male fertility in that species. Here we suggest that the control of human male fertility is of at least comparable genetic complexity. However, because of small family size, conventional positional cloning methods for identifying human genes will have little impact on the dissection of male infertility. A critical selection of well-defined infertility phenotypes in model organisms, combined with identification of the genes involved and their orthologues in man, might reveal the genes that contribute to human male infertility.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Traces of Archaic Mitochondrial Lineages Persist in Austronesian-Speaking Formosan Populations

Journal: PLoS Biology | Year: 2005


Peoples: | Places: | Topics: | DNA Type: mtDNA

Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations

Journal: European Journal of Human Genetics | Year: 2009


Islam is the second most practiced religion in India, next to Hinduism. It is still unclear whether the spread of Islam in India has been only a cultural transformation or is associated with detectable levels of gene flow. To estimate the contribution of West Asian and Arabian admixture to Indian Muslims, we assessed genetic variation in mtDNA, Y-chromosomal and LCT/MCM6 markers in 472, 431 and 476 samples, respectively, representing six Muslim communities from different geographical regions of India. We found that most of the Indian Muslim populations received their major genetic input from geographically close non-Muslim populations. However, low levels of likely sub-Saharan African, Arabian and West Asian admixture were also observed among Indian Muslims in the form of L0a2a2 mtDNA and E1b1b1a and J*(xJ2) Y-chromosomal lineages. The distinction between Iranian and Arabian sources was difficult to make with mtDNA and the Y chromosome, as the estimates were highly correlated because of similar gene pool compositions in the sources. In contrast, the LCT/MCM6 locus, which shows a clear distinction between the two sources, enabled us to rule out significant gene flow from Arabia. Overall, our results support a model according to which the spread of Islam in India was predominantly cultural conversion associated with minor but still detectable levels of gene flow from outside, primarily from Iran and Central Asia, rather than directly from the Arabian Peninsula.

Peoples: | Places: | Topics: | DNA Type:

Tracing Arab-Islamic Inheritance in Madagascar: Study of the Y-chromosome and Mitochondrial DNA in the Antemoro

Journal: PLoS ONE | Year: 2013


Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.

Peoples: - | Places: - | Topics: - | DNA Type: mtDNA

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