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Publications (48)
Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other spec...
In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently ei...
Archaic admixture has had a significant impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. Within the great apes archaic admixture has been identified in chimpanzees and bonobos, but the possibility of such events has not been explored in ot...
Low genetic variation and high levels of inbreeding are usually a consequence of recent population declines in endangered species. From a conservation point of view, it is essential to genetically screen endangered populations to help assess their vulnerability to extinction and to properly create informed management actions towards their conservat...
Background: The evolutionary relationships of Felidae during their Early–Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths.
Methods: Here, we sequenced...
Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros...
Background: The evolutionary relationships of Felidae during their Early–Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths.
Methods: Here, we sequenced...
Significance
Surviving challenging environments, living long lives, and engaging in complex cognitive processes are hallmark human characteristics. 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 explor...
Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1, 2, 3, 4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predati...
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Sled dog arctic adaptations go far back
Dogs have been used for sledding in the Arctic as far back as ∼9500 years ago. However, the relationships among the earliest sled dogs, other dog populations, and wolves are unknown. Sinding et al. sequenced an ancient sled dog, 10 modern sled dogs, and an ancient wolf and analyzed their genetic relationships...
Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface "self-associated molecular patterns" (SAMPs) that modulate innate immunity via engagement of CD33-related-Siglec receptors. The Alu-fusion-mediated loss-of-function...
Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore suffered a remarkable population reduction in the last 150 years due to human activities. The two white rhinoceros subspecies, the northern (NWR)...
Lions are one of the world’s most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions ( Panthera leo spelaea ), 12 historic lions ( Panthera leo leo/Panthera leo melanochaita ) that lived between the...
The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1–5. For the oldest remains, the molecular study of these relationships is hindered by the degradation of...
As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati Zoo in 1918 [1]. The cause of its extinction remains contentious: besides excessive mortality associated to habitat destructio...
Gigantopithecus blacki was a giant hominid that inhabited densely forested environments of Southeast Asia during the Pleistocene epoch¹. Its evolutionary relationships to other great ape species, and the divergence of these species during the Middle and Late Miocene epoch (16–5.3 million years ago), remain unclear2,3. Hypotheses regarding the relat...
Chimpanzees, humans’ closest relatives, are in danger of extinction. Aside from direct human impacts such as hunting and habitat destruction, a key threat is transmissible disease. As humans continue to encroach upon their habitats, which shrink in size and grow in density, the risk of inter-population and cross-species viral transmission increases...
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack...
Admixture, the genetic exchange between differentiated populations appears to be common in the history of species, but has not yet been comparatively studied across mammals. This limits the understanding of its mechanisms and potential role in mammalian evolution. The authors want to summarize the current knowledge on admixture in non‐human primate...
Denisovans are an extinct group of humans whose morphology remains unknown. Here, we present a method for reconstructing skeletal morphology using DNA methylation patterns. Our method is based on linking unidirectional methylation changes to loss-of-function phenotypes. We tested performance by reconstructing Neanderthal and chimpanzee skeletal mor...
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack...
Declining populations are expected to experience negative genetic consequences of inbreeding, which over time can drive them to extinction. Yet, many species have survived in small populations for thousands of generations without apparent fitness effects, possibly due to genetic purging of partially deleterious recessive alleles in inbred populatio...
All four subspecies of chimpanzees are endangered. Differing in their demographic histories and geographical ranges within sub-Saharan Africa, they have likely adapted to different environmental factors. We show that highly differentiated SNPs in eastern chimpanzees are uniquely enriched in genic sites in a way that is expected under recent adaptat...
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 unde...
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 indiv...
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.
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 fro...
(Current Biology 27, 3487–3498; November 20, 2017) It has been brought to the authors’ attention that two small typographical errors occurred in Figures 2 and 3. In Figure 2, the correct sample size for the number of sequenced individuals from Central Kalimantan is n = 8. In Figure 3C, the correct assumed mutation rate in the RCCR analysis is 1.50...
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 unc...
Six extant species of non-human great apes are currently recognized: Sumatran and Bornean orangutans, eastern and western gorillas, and chimpanzees and bonobos [1]. However, large gaps remain in our knowledge of fine-scale variation in hominoid morphology, behavior, and genetics, and aspects of great ape taxonomy remain in flux. This is particularl...
The Eurasian sympatry of Neandertals and anatomically modern humans – beginning at least 45,000 years ago and possibly lasting for more than 5000 years – has sparked immense anthropological interest into the factors that potentially contributed to Neandertal extinction. Among many different hypotheses, the “differential pathogen resistance” extinct...
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 today's chimpanzees and bonobos (see the Perspective by Hoelzel). The study also prov...
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. The...
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
b...
The Eurasian sympatry of Neandertals and anatomically modern humans – beginning at least 45,000 years ago and lasting for more than 5,000 years – has long sparked anthropological interest into the factors that potentially contributed to Neandertal extinction. Among many different hypotheses, the “differential pathogen resistance” extinction model p...
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 DN...
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....