Marc de Manuel

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

Genomes in the mist The mountain gorilla is an iconic species that is at high risk of extinction. Xue et al. have sequenced 13 gorillas from two different populations to probe their genetic diversity. The genomes show large tracts of homozygosity and the loss of highly deleterious genetic variants, indicating population bottlenecks and inbreeding. This loss of genetic diversity appears to have started over 20,000 years ago and may have been caused by changes in climate and human-associated effects. Science, this issue p. 242 Inbreeding in mountain gorillas increases the threat from disease and environmental change but has purged deleterious mutations. Mountain gorillas are an endangered great ape subspecies and a prominent focus for conservation, yet we know little about their genomic diversity and evolutionary past. We sequenced whole genomes from multiple wild individuals and compared the genomes of all four Gorilla subspecies. We found that the two eastern subspecies have experienced a prolonged population decline over the past 100,000 years, resulting in very low genetic diversity and an increased overall burden of deleterious variation. A further recent decline in the mountain gorilla population has led to extensive inbreeding, such that individuals are typically homozygous at 34% of their sequence, leading to the purging of severely deleterious recessive mutations from the population. We discuss the causes of their decline and the consequences for their future survival.

Chimpanzee genomic diversity reveals ancient admixture with bonobos

Of chimpanzees and bonobos Modern non-African human genomes contain genomic remnants that suggest that there was interbreeding between ancient humans and archaic hominoid lineages. Now, de Manuel et al. show similar ancestral interbreeding between the ancestors of todays chimpanzees and bonobos (see the Perspective by Hoelzel). The study also provides population-specific genetic markers that may be valuable for conservation efforts. Science, this issue p. 477; see also p. 414 Genome sequences reveal ancient interbreeding between chimpanzees and bonobos. 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.

Genomic Legacy of the African Cheetah, Acinonyx jubatus

BackgroundPatterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations.ResultsHere the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years ago coincident with cheetah migrations out of the Americas and into Eurasia and Africa, and a second 11,084–12,589 years ago in Africa coincident with late Pleistocene large mammal extinctions. MHC class I gene loss and dramatic reduction in functional diversity of MHC genes would explain why cheetahs ablate skin graft rejection among unrelated individuals. Significant excess of non-synonymous mutations in AKAP4 (p<0.02), a gene mediating spermatozoon development, indicates cheetah fixation of five function-damaging amino acid variants distinct from AKAP4 homologues of other Felidae or mammals; AKAP4 dysfunction may cause the cheetah’s extremely high (>80 %) pleiomorphic sperm.ConclusionsThe study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species’ natural history, physiological adaptations and unique reproductive disposition.

Demographic History of the Genus Pan Inferred from Whole Mitochondrial Genome Reconstructions

The genus Pan is the closest genus to our own and it includes two species, Pan paniscus (bonobos) and Pan troglodytes (chimpanzees). The later is constituted by four subspecies, all highly endangered. The study of the Pan genera has been incessantly complicated by the intricate relationship among subspecies and the statistical limitations imposed by the reduced number of samples or genomic markers analyzed. Here, we present a new method to reconstruct complete mitochondrial genomes (mitogenomes) from whole genome shotgun (WGS) datasets, mtArchitect, showing that its reconstructions are highly accurate and consistent with long-range PCR mitogenomes. We used this approach to build the mitochondrial genomes of 20 newly sequenced samples which, together with available genomes, allowed us to analyze the hitherto most complete Pan mitochondrial genome dataset including 156 chimpanzee and 44 bonobo individuals, with a proportional contribution from all chimpanzee subspecies. We estimated the separation time between chimpanzees and bonobos around 1.15 million years ago (Mya) [0.81–1.49]. Further, we found that under the most probable genealogical model the two clades of chimpanzees, Western + Nigeria-Cameroon and Central + Eastern, separated at 0.59 Mya [0.41–0.78] with further internal separations at 0.32 Mya [0.22–0.43] and 0.16 Mya [0.17–0.34], respectively. Finally, for a subset of our samples, we compared nuclear versus mitochondrial genomes and we found that chimpanzee subspecies have different patterns of nuclear and mitochondrial diversity, which could be a result of either processes affecting the mitochondrial genome, such as hitchhiking or background selection, or a result of population dynamics.

FOXP2 variation in great ape populations offers insight into the evolution of communication skills

The gene coding for the forkhead box protein P2 (FOXP2) is associated with human language disorders. Evolutionary changes in this gene are hypothesized to have contributed to the emergence of speech and language in the human lineage. Although FOXP2 is highly conserved across most mammals, humans differ at two functional amino acid substitutions from chimpanzees, bonobos and gorillas, with an additional fixed substitution found in orangutans. However, FOXP2 has been characterized in only a small number of apes and no publication to date has examined the degree of natural variation in large samples of unrelated great apes. Here, we analyzed the genetic variation in the FOXP2 coding sequence in 63 chimpanzees, 11 bonobos, 48 gorillas, 37 orangutans and 2 gibbons and observed undescribed variation in great apes. We identified two variable polyglutamine microsatellites in chimpanzees and orangutans and found three nonsynonymous single nucleotide polymorphisms, one in chimpanzees, one in gorillas and one in orangutans with derived allele frequencies of 0.01, 0.26 and 0.29, respectively. Structural and functional protein modeling indicate a biochemical effect of the substitution in orangutans, and because of its presence solely in the Sumatran orangutan species, the mutation may be associated with reported population differences in vocalizations.

Evolution and demography of the great apes

The great apes are the closest living relatives of humans. Chimpanzees and bonobos group together with humans, while gorillas and orangutans are more divergent from humans. Here, we review insights into their evolution pertaining to the topology of species and subspecies and the reconstruction of their demography based on genome-wide variation. These advances have only become possible recently through next-generation sequencing technologies. Given the close relationship to humans, they provide an important evolutionary context for human genetics.

Unbiased whole genomes from mammalian feces using fluorescence-activated cell sorting

Ecological flexibility, extended lifespans, and large brains, have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have the largest relative brain size of any monkey and a lifespan that exceeds 50 years, despite their small (3-5 kg) body size. We assemble a de novo reference genome for Cebus imitator and provide the first genome annotation of a capuchin monkey. Through high-depth sequencing of DNA derived from blood, various tissues and feces via fluorescence activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of non-invasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides new insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity. SIGNIFICANCE Surviving challenging environments, living long lives, and engaging in complex cognitive processes are hallmark characteristics of human evolution. Similar traits have evolved in parallel in capuchin monkeys, but their genetic underpinnings remain unexplored. We developed and annotated a reference assembly for white-faced capuchin monkeys to explore the evolution of these phenotypes. By comparing populations of capuchins inhabiting rainforest versus dry forests with seasonal droughts, we detected selection in genes associated with kidney function, muscular wasting, and metabolism, suggesting adaptation to periodic resource scarcity. When comparing capuchins to other mammals, we identified evidence of selection in multiple genes implicated in longevity and brain development. Our research was facilitated by our new method to generate high- and low-coverage genomes from non-invasive biomaterials.Non-invasive genomic research on free-ranging mammals typically relies on the use of fecal DNA. This requires the isolation and enrichment of endogenous DNA, given its small proportion compared to bacterial DNA. Current approaches for acquiring large-scale genomic data from feces rely on bait-and-capture techniques. While this technique has greatly improved our understanding of mammalian population genomics, it is limited by biases inherent to the capture process, including allele dropout, low mapping rates, PCR duplication artifacts, and structural biases. We report here a new method for generating whole mammalian genomes from feces using fluorescence-activated cell sorting (FACS). Instead of enriching endogenous DNA from extracted fecal DNA, we isolated mammalian cells directly from feces. We then built fragment libraries with low input material from commercially available kits, which we sequenced at high and low coverage. We validated this method on feces collected from primates stored in RNAlater for up to three years. We sequenced one fecal genome at high coverage (12X) and 15 additional fecal genomes at low coverage (0.1X - 4X). For comparative purposes, we also sequenced DNA from nine blood or tissue samples opportunistically collected from capuchin monkeys that died of natural causes or were treated in a local rehabilitation center. Across all fecal samples, we achieved median mapping and duplication rates of 82% and 6%, respectively. Our high-depth fecal genome did not differ in the distribution of coverage, heterozygosity, or GC content from those derived from blood or tissue origin. As a practical application of our new approach with low coverage fecal genomes, we were able to resolve the population genetic structure of capuchin monkeys from four sites in Costa Rica.Background: Capuchins have the largest relative brain size of any monkey and a remarkable lifespan of 55 years, despite their small body size. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence, dietary diversity, and ecological flexibility. Despite decades of research into their ecology and life history, little is known about the genomics of this radiation. Results: We assemble a de novo reference genome for Cebus imitator, and provide the first genome annotation of a capuchin monkey. We identified 20,740 and 9,556 for protein-coding and non-coding genes, and recovered 23,402 orthologous groups. Through a comparative genomics approach across a diversity of mammals, we identified genes under positive selection associated with longevity and brain development, which are of particular relevance to capuchin and primate comparative biology. Additionally, we compared populations in distinct habitats, facilitated by our novel method for minimally-biased, whole-genome sequencing from fecal DNA using fluorescence activated cell sorting (FACS). By analyzing 23 capuchin genomes from tropical dry forest and rainforest, we identified population divergence in genes involved in water balance, kidney function, and metabolism, consistent with local adaptation to resource seasonality. Conclusions: Our comparative study of capuchin genomics provides new insights into the molecular basis of brain evolution and longevity. These data also improve our understanding of processes of local adaptation to diverse and physiologically challenging environments. Additionally, we provide a technological advancement in use of non-invasive genomics to study free-ranging mammals through FACS.

Whole genome sequencing in the search for genes associated with the control of SIV infection in the Mauritian macaque model

In the Mauritian macaque experimentally inoculated with SIV, gene polymorphisms potentially associated with the plasma virus load at a set point, approximately 100 days post inoculation, were investigated. Among the 42 animals inoculated with 50 AID50 of the same strain of SIV, none of which received any preventive or curative treatment, nine individuals were selected: three with a plasma virus load (PVL) among the lowest, three with intermediate PVL values and three among the highest PVL values. The complete genomes of these nine animals were then analyzed. Initially, attention was focused on variants with a potential functional impact on protein encoding genes (non-synonymous SNPs (NS-SNPs) and splicing variants). Thus, 424 NS-SNPs possibly associated with PVL were detected. The 424 candidates SNPs were genotyped in these 42 SIV experimentally infected animals (including the nine animals subjected to whole genome sequencing). The genes containing variants most probably associated with PVL at a set time point are analyzed herein.

Author Correction: Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation

The genus Pan is the closest related to humans (Homo sapiens) and it includes two species: Pan troglodytes (chimpanzees) and Pan paniscus (bonobos). Different characteristics, some of biomedical aspect, separate them from us. For instance, some common human medical conditions are rare in chimpanzees (menopause, Alzheimer disease) although it is unclear to which extent longevity plays an active role in these differences. However, both humans and chimpanzees present similar pathologies, thus, understanding traits in chimpanzees can help unravel the molecular basis of human conditions. Here, we sequenced the genome of Nico, a central chimpanzee diagnosed with a particular biomedical condition, the Chiari malformation. We performed a variant calling analysis comparing his genome to 25 whole genomes from healthy individuals (bonobos and chimpanzees), and after predicting the effects of the genetic variants, we looked for genes within the OMIM database. We found a novel, private, predicted as damaging mutation in Nico in LRP5, a gene related to bone density alteration pathologies, and we suggest a link between this mutation and his Chiari malformation as previously shown in humans. Our results reinforce the idea that a comparison between humans and chimpanzees can be established in this genetic frame of common diseases.