The Y chromosomes of the great apes

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

High divergence in primate-specific duplicated regions: Human and chimpanzee genes-0

Quences from []. Phylogenetic analysis of intergenic regions was conducted with segments without (B-D) and with (E-G) covering pseudogenes. The homologous segments used for each respective phylogenetic analysis are indicated with a circle on a consensus structure of the intergenic regions in cluster (boxed; from Figure 1B). The nomenclature of the intergenic regions is as on Figure 1B. Bootstrap support values are shown at the nodes (1000 bootstrap replications). Abbreviations: hu – human, ch – chimpanzee, gor – gorilla, orang – orangutan.<p><b>Copyright information:</b></p><p>Taken from "High divergence in primate-specific duplicated regions: Human and chimpanzee genes"</p><p>http://www.biomedcentral.com/1471-2148/8/195</p><p>BMC Evolutionary Biology 2008;8():195-195.</p><p>Published online 7 Jul 2008</p><p>PMCID:PMC2478647.</p><p></p

High divergence in primate-specific duplicated regions: Human and chimpanzee genes-1

(Ch)/7,973 bp (Hu) from gene to the end of and 29,136 bp (Ch)/28,568 bp (Hu) from to gene. The species-specific large duplications (human 12,700 bp, chimp 6,725 bp) have been excluded from the comparison. The percents of nucleotide substitutions and indels are calculated per 500 bp non-overlapping windows. Grey arrows indicate the locations of coding genes drawn to an approximate scale. – denote intergenic regions from Figure 1B. Intergenic repeat fraction includes , satellites, simple repeats and low complexity DNA sequences within each intergenic region.<p><b>Copyright information:</b></p><p>Taken from "High divergence in primate-specific duplicated regions: Human and chimpanzee genes"</p><p>http://www.biomedcentral.com/1471-2148/8/195</p><p>BMC Evolutionary Biology 2008;8():195-195.</p><p>Published online 7 Jul 2008</p><p>PMCID:PMC2478647.</p><p></p

Divergence was estimated by using the human (GenBank: ) and chimpanzee (this study, Genbank: ) reference sequences alone or by incorporating the diversity data obtained from re-sequencing for one or both species into the calculations

The re-sequencing data for human (n = 95) originated from the published study[] and for chimpanzee (n = 11) from the unpublished dataset of the authors.<p><b>Copyright information:</b></p><p>Taken from "High divergence in primate-specific duplicated regions: Human and chimpanzee genes"</p><p>http://www.biomedcentral.com/1471-2148/8/195</p><p>BMC Evolutionary Biology 2008;8():195-195.</p><p>Published online 7 Jul 2008</p><p>PMCID:PMC2478647.</p><p></p

High divergence in primate-specific duplicated regions: Human and chimpanzee genes-2

and genes (in total 6,878 bp; GC-nucleotide content 64%; 161 substitutions). (B) Nucleotide substitutions in the whole orthologous region of the genome cluster (in total 36,211 bp, GC-nucleotide content 57%, 835 substitutions). Percents for all substitution types are shown with summarized information for transversions and transitions.<p><b>Copyright information:</b></p><p>Taken from "High divergence in primate-specific duplicated regions: Human and chimpanzee genes"</p><p>http://www.biomedcentral.com/1471-2148/8/195</p><p>BMC Evolutionary Biology 2008;8():195-195.</p><p>Published online 7 Jul 2008</p><p>PMCID:PMC2478647.</p><p></p

Massively parallel sequencing of autosomal STRs and identity-informative SNPs highlights consanguinity in Saudi Arabia

While many studies have been undertaken of Middle Eastern populations using autosomal STR profiling by capillary electrophoresis, little has so far been published from this region on the forensic use of massively parallel sequencing (MPS). Here, we carried out MPS of 27 autosomal STRs and 91 identity-informative SNPs (iiSNPs) with the Verogen ForenSeq™ DNA Signature Prep Kit on a representative sample of 89 Saudi Arabian males, and analysed the resulting sequence data using Verogen's ForenSeq Universal Analysis Software (UAS) v1.3 and STRait Razor v3.0. This revealed sequence variation in the composition of complex STR arrays, and SNPs in their flanking regions, which raised the number of STR alleles from 238 distinct length variants to 357 sequence sub-variants. Similarly, between one and three additional polymorphic sites were observed within the amplicons of 37 of the 91 iiSNPs, forming up to six microhaplotypes per locus. These further enhance discrimination compared to the biallelic target SNP data presented by the primary UAS interface. In total, we observed twenty-two STR alleles previously unrecognised in the STRait Razor v3.0 default allele list, along with nine SNPs flanking target iiSNPs that were not highlighted by the UAS. Sequencing reduced the STR-based random match probability (RMP) from 2.62E-30 to 3.49E-34, and analysis of the iiSNP microhaplotypes reduced RMP from 9.97E-37 to 6.83E-40. The lack of significant linkage disequilibrium between STRs and target iiSNPs allowed the two marker types to be combined using the product rule, yielding a RMP of 2.39E-73. Evidence of consanguinity was apparent from both marker types. While TPOX was the only locus displaying a significant deviation from Hardy-Weinberg equilibrium, 23 out of 27 STRs and 63 out of 91 iiSNPs showed fewer than expected heterozygotes, demonstrating an overall homozygote excess probably reflecting the high frequency of first-cousin marriages in Saudi Arabia. We placed our data in a global context by considering the same markers in the Human Genome Diversity Panel (HGDP), revealing that the Saudi sample was typical of Middle Eastern populations, with a higher level of inbreeding than is seen in most European, African and Central/South Asian populations, correlating with known patterns of endogamy. Given reduced levels of diversity within endogamous groups, the ability to combine the discrimination power of both STRs and SNPs offers significant benefits in the analysis of forensic evidence in Saudi Arabia and the Middle East region more generally

Location and structure of palindrome P6, showing positions of PSVs analysed.

<p>a) Idiogram of Y chromosome, showing positions of the 8 palindromes, with structure and coordinates (in GRCh37) of P6 below. b) Position and nature of the differences between the arms of P6, indicating the 10 SN-PSVs analysed, and the positions of PCR primers used in arm-specific amplifications. STSs marking the arm boundaries are also shown (with ‘sY’ prefixes). Asterisks indicate the two SN-PSVs identified from a haplogroup O3a chromosome.</p

Recognition of gene conversion, co-conversion and inversion events.

<p>a) Existence of three genotypes at a hypothetical PSV indicates that gene conversion has taken place, if recurrent mutation is neglected. Genotyping the PSV in a phylogenetic context, and applying the principle of maximum parsimony, allows the recognition of: b) Haplogroup descending from an ancestor in which the PSV mutation has not yet arisen (G/G), and is therefore uninformative; c) Haplogroup descending from an ancestor in which the PSV mutation has arisen (G/A), but shows no variation, and therefore no evidence for gene conversion; d) Haplogroup descending from an ancestor in which the PSV mutation has arisen, and shows evidence of at least two bidirectional conversion events (G/G and A/A); e) Recognition of co-conversion of more than one PSV requires ‘phase’ information, as does (f) recognition of inversions.</p

Inter-specific sequence divergence in arms and spacers of palindrome P6.

a<p>2×2 contingency table, Chi-square test with Yates correction.</p

Patterns of P6 nucleotide replacements in the human and chimpanzee lineages.

a<p>2×2 contingency table, Chi-square test with Yates correction.</p>*<p>p-value<0.05.</p>**<p>p-value<0.01.</p