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  • de Melo, Fabiano R.  (5)
  • Biodiversitätsforschung  (5)
  • 1
    Online-Ressource
    Online-Ressource
    ATLANTIC ‐ PRIMATES : a dataset of communities and occurrences of primates in the Atlantic Forests of South America
    Wiley ; 2019
    In:  Ecology Vol. 100, No. 1 ( 2019-01)
    Details
    In: Ecology, Wiley, Vol. 100, No. 1 ( 2019-01)
    Kurzfassung: Primates play an important role in ecosystem functioning and offer critical insights into human evolution, biology, behavior, and emerging infectious diseases. There are 26 primate species in the Atlantic Forests of South America, 19 of them endemic. We compiled a dataset of 5,472 georeferenced locations of 26 native and 1 introduced primate species, as hybrids in the genera Callithrix and Alouatta . The dataset includes 700 primate communities, 8,121 single species occurrences and 714 estimates of primate population sizes, covering most natural forest types of the tropical and subtropical Atlantic Forest of Brazil, Paraguay and Argentina and some other biomes. On average, primate communities of the Atlantic Forest harbor 2 ± 1 species (range = 1–6). However, about 40% of primate communities contain only one species. Alouatta guariba (N = 2,188 records) and Sapajus nigritus (N = 1,127) were the species with the most records. Callicebus barbarabrownae (N = 35), Leontopithecus caissara (N = 38), and Sapajus libidinosus (N = 41) were the species with the least records. Recorded primate densities varied from 0.004 individuals/km 2 ( Alouatta guariba at Fragmento do Bugre, Paraná, Brazil) to 400 individuals/km 2 ( Alouatta caraya in Santiago, Rio Grande do Sul, Brazil). Our dataset reflects disparity between the numerous primate census conducted in the Atlantic Forest, in contrast to the scarcity of estimates of population sizes and densities. With these data, researchers can develop different macroecological and regional level studies, focusing on communities, populations, species co‐occurrence and distribution patterns. Moreover, the data can also be used to assess the consequences of fragmentation, defaunation, and disease outbreaks on different ecological processes, such as trophic cascades, species invasion or extinction, and community dynamics. There are no copyright restrictions. Please cite this Data Paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.
    Materialart: Online-Ressource
    ISSN: 0012-9658 , 1939-9170
    URL: Issue
    URL: Article
    DOI: 10.1002/ecy.2019.100.issue-1
    DOI: 10.1002/ecy.2525
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2019
    ZDB Id: 1797-8
    ZDB Id: 2010140-5
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 2
    Online-Ressource
    Online-Ressource
    The landscape of tolerated genetic variation in humans and primates
    American Association for the Advancement of Science (AAAS) ; 2023
    In:  Science Vol. 380, No. 6648 ( 2023-06-02)
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 380, No. 6648 ( 2023-06-02)
    Kurzfassung: Millions of people have received genome and exome sequencing to date, a collective effort that has illuminated for the first time the vast catalog of small genetic differences that distinguish us as individuals within our species. However, the effects of most of these genetic variants remain unknown, limiting their clinical utility and actionability. New approaches that can accurately discern disease-causing from benign mutations and interpret genetic variants on a genome-wide scale would constitute a meaningful initial step towards realizing the potential of personalized genomic medicine. RATIONALE As a result of the short evolutionary distance between humans and nonhuman primates, our proteins share near-perfect amino acid sequence identity. Hence, the effects of a protein-altering mutation found in one species are likely to be concordant in the other species. By systematically cataloging common variants of nonhuman primates, we aimed to annotate these variants as being unlikely to cause human disease as they are tolerated by natural selection in a closely related species. Once collected, the resulting resource may be applied to infer the effects of unobserved variants across the genome using machine learning. RESULTS Following the strategy outlined above we obtained whole-genome sequencing data for 809 individuals from 233 primate species and cataloged 4.3 million common missense variants. We confirmed that human missense variants seen in at least one nonhuman primate species were annotated as benign in the ClinVar clinical variant database in 99% of cases. By contrast, common variants from mammals and vertebrates outside the primate lineage were substantially less likely to be benign in the ClinVar database (71 to 87% benign), restricting this strategy to nonhuman primates. Overall, we reclassified more than 4 million human missense variants of previously unknown consequence as likely benign, resulting in a greater than 50-fold increase in the number of annotated missense variants compared to existing clinical databases. To infer the pathogenicity of the remaining missense variants in the human genome, we constructed PrimateAI-3D, a semisupervised 3D-convolutional neural network that operates on voxelized protein structures. We trained PrimateAI-3D to separate common primate variants from matched control variants in 3D space as a semisupervised learning task. We evaluated the trained PrimateAI-3D model alongside 15 other published machine learning methods on their ability to distinguish between benign and pathogenic variants in six different clinical benchmarks and demonstrated that PrimateAI-3D outperformed all other classifiers in each of the tasks. CONCLUSION Our study addresses one of the key challenges in the variant interpretation field, namely, the lack of sufficient labeled data to effectively train large machine learning models. By generating the most comprehensive primate sequencing dataset to date and pairing this resource with a deep learning architecture that leverages 3D protein structures, we were able to achieve meaningful improvements in variant effect prediction across multiple clinical benchmarks. PrimateAI-3D, a deep learning model trained on millions of benign primate variants. Common primate variants generated from 233 primate species (left) were validated as benign (98.7%) in the human ClinVar database. Voxelized protein structures (middle) with benign primate variants (spheres) were used to train a 3D convolution neural network to predict variant pathogenicity based on regional enrichment or depletion of primate variants. The resulting model was validated in independent clinical cohorts, as illustrated by the correlation of PrimateAI-3D scores and blood cholesterol levels for UK Biobank individuals (right).
    Materialart: Online-Ressource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.abn8197
    RVK:
    TA 1000
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2023
    ZDB Id: 128410-1
    ZDB Id: 2066996-3
    ZDB Id: 2060783-0
    SSG: 11
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 3
    Online-Ressource
    Online-Ressource
    A global catalog of whole-genome diversity from 233 primate species
    American Association for the Advancement of Science (AAAS) ; 2023
    In:  Science Vol. 380, No. 6648 ( 2023-06-02), p. 906-913
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 380, No. 6648 ( 2023-06-02), p. 906-913
    Kurzfassung: The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.
    Materialart: Online-Ressource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.abn7829
    RVK:
    TA 1000
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2023
    ZDB Id: 128410-1
    ZDB Id: 2066996-3
    ZDB Id: 2060783-0
    SSG: 11
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 4
    Online-Ressource
    Online-Ressource
    On a new species of titi monkey (Primates: Plecturocebus Byrne et al., 2016), from Alta Floresta, southern Amazon, Brazil
    Elsevier BV ; 2019
    In:  Molecular Phylogenetics and Evolution Vol. 132 ( 2019-03), p. 117-137
    Details
    In: Molecular Phylogenetics and Evolution, Elsevier BV, Vol. 132 ( 2019-03), p. 117-137
    Materialart: Online-Ressource
    ISSN: 1055-7903
    URL: Article
    DOI: 10.1016/j.ympev.2018.11.012
    Sprache: Englisch
    Verlag: Elsevier BV
    Publikationsdatum: 2019
    ZDB Id: 1471402-4
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
  • 5
    Online-Ressource
    Online-Ressource
    Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates
    Wiley ; 2022
    In:  Molecular Ecology Vol. 31, No. 14 ( 2022-07), p. 3888-3902
    Details
    In: Molecular Ecology, Wiley, Vol. 31, No. 14 ( 2022-07), p. 3888-3902
    Kurzfassung: Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high‐quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic phylogeny based on these samples along with additional published platyrrhine mitogenomes, and use this to assess support for the long‐standing riverine barrier hypothesis (RBH), which proposes that river formation was a major driver of speciation in Amazonian primates. Along the Amazon, Negro, and Madeira rivers, we found mixed support for the RBH. While we identified divergences that coincide with a river barrier, only some occur synchronously and also overlap with the proposed dates of river formation. The most compelling evidence is for the Amazon river potentially driving speciation within bearded saki monkeys ( Chiropotes spp.) and within the smallest extant platyrrhines, the marmosets and tamarins. However, we also found that even large rivers do not appear to be barriers for some primates, including howler monkeys ( Alouatta spp.), uakaris ( Cacajao spp.), sakis ( Pithecia spp.), and robust capuchins ( Sapajus spp.). Our results support a more nuanced, clade‐specific effect of riverine barriers and suggest that other evolutionary mechanisms, besides the RBH and allopatric speciation, may have played an important role in the diversification of platyrrhines.
    Materialart: Online-Ressource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.v31.14
    DOI: 10.1111/mec.16554
    RVK:
    WA 15000
    Sprache: Englisch
    Verlag: Wiley
    Publikationsdatum: 2022
    ZDB Id: 2020749-9
    ZDB Id: 1126687-9
    SSG: 12
    Standort Signatur Einschränkungen Verfügbarkeit
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    Online-Ressource
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