Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation

Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation

Study of the human African genome landscape through the analysis of complete genomes

Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2015), celebrada en Viena del 12 al 16 de julio de 2015.Understanding the genetic diversity in humans within the African continent is pivotal to have a full picture of the demographic history of the human species. Here, we study complete genome sequeces of a diverse panel of African individuals in terms of geographical location, linguistic context and lifestyle. Most African diversity studies have mainly focused on uniparental markers or selected autosomal markers, which introduce an ascertainment bias in the analysis. The analysis of complete genomes has been poorly developed in the study of African human genomics and internal population diversity. The main goals of this study are: 1. Characterisation of the internal human diversity in Africa overcoming ascertainment bias-related problems by using complete genomes. 2. Characterization of the deepest splits in the human lineage and the processes (such as migrations and admixtures) that have shaped the current genetic map.Funded by: MINECO CGL 2013-44351-P.N

Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum

The pygmy marmoset, the smallest of the anthropoid primates, has a broad distribution in Western Amazonia. Recent studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimões-Amazonas rivers. However, reconciling this new biological evidence with current taxonomy, i.e., two subspecies, Cebuella pygmaea pygmaea (Spix, 1823) and Cebuella pygmaea niveiventris (Lönnberg, 1940), was problematic given the uncertainty as to whether Spix's pygmy marmoset (Cebuella pygmaea pygmaea) was collected north or south of the Napo and Solimões-Amazonas rivers, making it unclear to which of the two newly revealed species the name pygmaea would apply. Here, we present the first molecular data from Spix's type specimen of Cebuella pygmaea, as well as novel mitochondrial genomes from modern pygmy marmosets sampled near the type locality (Tabatinga) on both sides of the river. With these data, we can confirm the correct names of the two species identified, i.e., C. pygmaea for animals north of the Napo and Solimões-Amazonas rivers and C. niveiventris for animals south of these two rivers. Phylogenetic analyses of the novel genetic data placed into the context of cytochrome b gene sequences from across the range of pygmy marmosets further led us to reevaluate the geographical distribution for the two Cebuella species. We dated the split of these two species to 2.54 million years ago. We discuss additional, more recent, subdivisions within each lineage, as well as potential contact zones between the two species in the headwaters of these rivers

Insights from the rescue and breeding management of Cuvier’s gazelle (Gazella cuvieri) through whole-genome sequencing

Captive breeding programmes represent the most intensive type of ex situ population management for threatened species. One example is the Cuvier’s gazelle programme that started in 1975 with only four founding individuals, and after more than four decades of management in captivity, a reintroduction effort was undertaken in Tunisia in 2016, to establish a population in an area historically included within its range. Here, we aim to determine the genetic consequences of this reintroduction event by assessing the genetic diversity of the founder stock as well as of their descendants. We present the first whole-genome sequencing dataset of 30 Cuvier’s gazelles including captive-bred animals, animals born in Tunisia after a reintroduction and individuals from a genetically unrelated Moroccan population. Our analyses revealed no difference between the founder and the offspring cohorts in genome-wide heterozygosity and inbreeding levels, and in the amount and length of runs of homozygosity. The captive but unmanaged Moroccan gazelles have the lowest genetic diversity of all genomes analysed. Our findings demonstrate that the Cuvier’s gazelle captive breeding programme can serve as source populations for future reintroductions of this species. We believe that this study can serve as a starting point for global applications of genomics to the conservation plan of this species.K-P. Koepfli and B. Pukazhenthi acknowledge the Sichel Endowment Fund for research support on dama gazelle genomics. M.A.E. is supported by an FPI (Formación de Personal Investigador) PRE2018-083966 from Ministerio de Ciencia, Universidades e Investigación. P.D. was supported as a postdoctoral fellow by the Smithsonian Institution Fellowship Program. K.-P.K. was supported by funding from the Smithsonian Institution's George E. Burch Fellowship in Theoretical Medicine and Affiliated Theoretical Science. T.M.-B. is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 864203), BFU2017-86471-P (MINECO/FEDER, UE), ‘Unidad de Excelencia María de Maeztu’, funded by the AEI (CEX2018-000792-M), Howard Hughes International Early Career and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). E.M. received financial support from the project PGC2018-097426-B-C22 (Spanish Ministry of Universities. Spanish State Research Agency. FEDER Program, European Union). E.L. is supported by CGL2017-82654-P (MINECO/FEDER, UE).Peer reviewe

Demographic inferences from a diverse panel of African human genomes

Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2015), celebrada en Viena del 12 al 16 de julio de 2015.Understanding genetic variation across ethnically and geographically diverse extant African populations is of great importance for reconstructing human complex demographic history. Here, we study the recent history and relationships among 15 different African populations, by analyzing the whole-genome sequence data of 21 individuals sequenced at deep coverage covering all major contine ntal linguistic groups, ecosystems and life-styles within Africa. We detected 12 million single nucleotide substitutions, providing a rich picture of the genome diversity and population history in Africa. We observe a remarkable correlation among genetic diversity and geographic origins and recent demographic history of the individuals studied. While different hunter-gatherer groups show more differentiation compared with the rest of samples, Bantu individuals are genetically more homogeneous and present evidence of admixture with neighboring hunter-gatherer groups, depending on the geographic area. Northern African individuals are closely related to non-African populations, in agreement with a recent split of both groups and continuous gene flow. To gain in sight into the deepest split of our species, we explore if recent admixture of Pygmies and Khoesan with other populations may cover up their real diversity, becoming the human most diverse groups.N

Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations

BackgroundPopulation demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level.ResultsHere, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbor populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (similar to 4.0% in Khoisan, similar to 4.3% in Mbuti Pygmies, and similar to 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.ConclusionThe present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level.Peer reviewe

Genomic Legacy of the African Cheetah, Acinonyx jubatus

Background Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. Results Here 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 \u3e100,000 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\u3c0.02), 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 (\u3e80 %) pleiomorphic sperm. Conclusions The study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species’ natural history, physiological adaptations and unique reproductive disposition

Giant tortoise genomes provide insights into longevity and age-related disease

© 2018, The Author(s), under exclusive licence to Springer Nature Limited. Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George—the iconic last member of Chelonoidis abingdonii—and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations

Eighty million years of rapid evolution of the primate Y chromosome

The Y chromosome usually plays a critical role in determining male sex and comprises sequence classes that have experienced unique evolutionary trajectories. Here we generated 19 new primate sex chromosome assemblies, analysed them with 10 existing assemblies and report rapid evolution of the Y chromosome across primates. The pseudoautosomal boundary has shifted at least six times during primate evolution, leading to the formation of a Simiiformes-specific evolutionary stratum and to the independent start of young strata in Catarrhini and Platyrrhini. Different primate lineages experienced different rates of gene loss and structural and chromatin change on their Y chromosomes. Selection on several Y-linked genes has contributed to the evolution of male developmental traits across the primates. Additionally, lineage-specific expansions of ampliconic regions have further increased the diversification of the structure and gene composition of the Y chromosome. Overall, our comprehensive analysis has broadened our knowledge of the evolution of the primate Y chromosome.This study was supported by grants from Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31020000 to G.Z.), International Partnership Program of Chinese Academy of Sciences (no. 152453KYSB20170002 to G.Z.), Villum Investigator Grant (no. 25900 to G.Z.), National Natural Science Foundation of China (31822048 to D.-D.W.), Yunnan Fundamental Research Project (2019FI010 to D.-D.W.) and The Animal Branch of the Germplasm Bank of Wild Species of Chinese Academy of Science (the Large Research Infrastructure Funding to D.-D.W.).N