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We analyzed 83 fully sequenced great ape genomes for mobile element insertions, predicting a total of 49,452 fixed and polymorphic Alu and long interspersed element 1 (L1) insertions not present in the human reference assembly and assigning each retrotransposition event to a different time point during great ape evolution. We used these homoplasy-free markers to construct a mobile element insertions-based phylogeny of humans and great apes and demonstrate their differential power to discern ape subspecies and populations. Within this context, we find a good correlation between L1 diversity and single-nucleotide polymorphism heterozygosity (r(2) = 0.65) in contrast to Alu repeats, which show little correlation (r(2) = 0.07). We estimate that the "rate" of Alu retrotransposition has differed by a factor of 15-fold in these lineages. Humans, chimpanzees, and bonobos show the highest rates of Alu accumulation--the latter two since divergence 1.5 Mya. The L1 insertion rate, in contrast, has remained relatively constant, with rates differing by less than a factor of three. We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human-great ape evolution, with increases and decreases occurring over very short periods of evolutionary time.

Trabajo presentado en la XIII Jornada de Biologia Evolutiva, celebrada en Barcelona el 2 de julio de 2013., Despite being the native homeland of modern humans, the source of the geographic expansion of ancestral populations into other regions of the world, and as a result, the most genetically diverse place in the world, African genetic diversity has been poorly studied to date. This study provides insights into African genetic diversity and demographic history by identifying and typifying genetic variants in Y chromosome high-coverage complete sequences. We analysed twenty-one Y chromosomes from African individuals belonging to characteristic populations representing four of the major African Y haplogroups (A, B, E and T). We based our analyses on single-nucleotide polymorphisms (SNPs). A total of 10221 high-confidence SNPs were detected, of which 7544 were in the male-specific Y sequence. We constructed phylogenetic trees using these variants and subsets of them, which recapitulated the known structure of the Y chromosome phylogeny. Finally, we provide a highly significant increase in the number of Y markers with phylogenetic information, which might be used in future studies and be considered candidates to update the Y chromosome phylogeny.

Trabajo presentado en la XIII Jornada de Biologia Evolutiva, celebrada en Barcelona el 2 de julio de 2013., Humans have been recently shown to harbor an unexpectedly high number of polymorphic stop gain or loss codon mutations, frameshift indels and large deletions. Loss of function (LoF) variants are predicted to disrupt gene function, and these results suggest an important level of pathway robustness and gene redundancy in the human genome. We have analyzed the mutational load and performed a systematic research based on human gene annotations of the LoF variants in the Great Ape Genome Diversity Project dataset, including 73 whole-genome sequences from chimpanzee, bonobo, gorilla and orangutan populations. The site frequency spectrum (SFS) shows differences across the primate species, since it is shaped by the particular demographic history of each population. One common pattern of SFS, also seen in humans, is that missense variants are enriched relative to synonymous variants at the lower frequencies, because of the action of purifying selection. However the relative amount of nonsynonymous compared to synonymous variants shows differences across the different populations, related to the different efficiency of natural selection to remove detrimental mutations in each population as a consequence of more efficient purifying selection at larger population sizes. After applying stringent filters on mapping, sequence quality and gene annotation, we observed that the total number of polymorphic LoF variants per individual varies from similar estimates to the one hundred reported in humans up to two or three fold across primate species. Homozygous variants potentially producing a complete lack of function also follow this tendency. Because of their functional impact LoF variants accumulate at low frequencies, and the proportion of LoF to synonymous variants per individual correlates negatively with the Ne, concordant with the same findings on the overall mutational load. This high and seemingly excessive individual mutational load is found to proportionally increase with diversity and effective population size, suggesting that a fraction of LoF variants may not have an important functional effect. Enrichment analysis of genes with polymorphic LoF variants did not detect an accumulation of mutations in particular pathways and functional categories, and we found little sharing both at the gene, pathway or functional levels across ape species.

Trabajo presentado en la 4th Meeting of the Spanish Society of the Evolutionary Biology (SESBE 2013) celebrada en Barcelona del 27 al 29 de noviembre de 2013., Despite African great apes and orangutans are human’s closest evolutionary relatives, the assessment of their genetic diversity has been systematically delayed in comparison to similar studies in our species. To overcome this limitation, we sequenced to high coverage a total of 79 great ape individuals representing all species and seven subspe- cies across the African continent and South East Asia. We discover ~86.5 million single nucleotide polymorphisms and report a three-fold range in nucleotide diversity among different ape populations. We find extensive inbreeding in almost all wild populations with Eastern gorillas being the most extreme population. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/Western and Central/Eastern populations. Using these data, we develop a framework to understand the recent evolutionary history of hominidae. This resource provides the first catalog of great-ape genome diversity to assist in better understanding our species and more effectively managing wild and captive great ape populations.

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa.We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.