Please use this identifier to cite or link to this item: http://hdl.handle.net/2381/37258
Title: Great-ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal
Authors: Hallast, Pille
Maisano Delser, P.
Batini, Chiara
Zadik, Daniel
Rocchi, M.
Schempp, W.
Tyler-Smith, C.
Jobling, Mark Alexander
First Published: 16-Feb-2016
Publisher: Cold Spring Harbor Laboratory Press
Citation: Genome Research, 2016 (Published in Advance)
Abstract: The distribution of genetic diversity in great-ape species is likely to have been affected by patterns of dispersal and mating. This has previously been investigated by sequencing autosomal and mitochondrial DNA (mtDNA), but large-scale sequence analysis of the male-specific region of the Y Chromosome (MSY) has not yet been undertaken. Here, we use the human MSY reference sequence as a basis for sequence capture and read mapping in 19 great-ape males, combining the data with sequences extracted from the published whole genomes of 24 additional males to yield a total sample of 19 chimpanzees, four bonobos, 14 gorillas, and six orangutans, in which interpretable MSY sequence ranges from 2.61 to 3.80 Mb. This analysis reveals thousands of novel MSY variants and defines unbiased phylogenies. We compare these with mtDNA-based trees in the same individuals, estimating time-to-most-recent common ancestor (TMRCA) for key nodes in both cases. The two loci show high topological concordance and are consistent with accepted (sub)species definitions, but time depths differ enormously between loci and (sub)species, likely reflecting different dispersal and mating patterns. Gorillas and chimpanzees/bonobos present generally low and high MSY diversity, respectively, reflecting polygyny versus multimale-multifemale mating. However, particularly marked differences exist among chimpanzee subspecies: The western chimpanzee MSY phylogeny has a TMRCA of only 13.2 (10.8-15.8) thousand years, but that for central chimpanzees exceeds 1 million years. Cross-species comparison within a single MSY phylogeny emphasizes the low human diversity, and reveals species-specific branch length variation that may reflect differences in long-term generation times.
DOI Link: 10.1101/gr.198754.115
ISSN: 1088-9051
eISSN: 1549-5469
Links: http://genome.cshlp.org/content/26/4/427
http://hdl.handle.net/2381/37258
TBA
Version: Publisher Version
Status: Peer-reviewed
Type: Journal Article
Rights: Copyright © 2016 Hallast et al.; Published by Cold Spring Harbor Laboratory Press. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
Appears in Collections:Published Articles, Dept. of Genetics

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