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Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism (2024)
Journal Article
Hermosilla-Albala, N., Silva, F. E., Cuadros-Espinoza, S., Fontsere, C., Valenzuela-Seba, A., Pawar, H., …Boubli, J. P. (in press). Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism. Communications Biology, 7(1), Article 1283. https://doi.org/10.1038/s42003-024-06901-3

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first pop... Read More about Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism.

Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline (2024)
Journal Article
de Vries, D., Janiak, M. C., Batista, R., Boubli, J. P., Goodhead, I. B., Ridgway, E., …Beck, R. M. (2024). Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline. Journal of Mammalian Evolution, https://doi.org/10.1101/2023.08.31.555703

Dental topographic metrics (DTMs), which quantify different aspects of the shape of teeth, are powerful tools for studying dietary adaptation and evolution in mammals. However, comparative samples of scanned mammal teeth suitable for analysis with D... Read More about Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline.

Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline (2024)
Journal Article
de Vries, D., Janiak, M. C., Batista, R., Boubli, J. P., Goodhead, I. B., Ridgway, E., …Beck, R. M. D. (2024). Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline. Journal of Mammalian Evolution, 31(1), 12. https://doi.org/10.1007/s10914-024-09704-9

Dental topographic metrics (DTMs), which quantify different aspects of the shape of teeth, are powerful tools for studying dietary adaptation and evolution in mammals. Current DTM protocols usually rely on proprietary software, which may be unavailab... Read More about Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline.

Climate determines transmission hotspots of Polycystic Echinococcosis, a life-threatening zoonotic disease, across Pan-Amazonia (2023)
Journal Article
San-José, A., Mayor, P., Carvalho, B., El Bizri, H. R., Antunes, A. P., Antunez Correa, M., …Munari, D. P. (2023). Climate determines transmission hotspots of Polycystic Echinococcosis, a life-threatening zoonotic disease, across Pan-Amazonia. Proceedings of the National Academy of Sciences of the United States of America, 120(33), e2302661120. https://doi.org/10.1073/pnas.2302661120

Polycystic Echinococcosis (PE), a neglected life-threatening zoonotic disease caused by the cestode is endemic in the Amazon. Despite being treatable, PE reaches a case fatality rate of around 29% due to late or missed diagnosis. PE is sustained in... Read More about Climate determines transmission hotspots of Polycystic Echinococcosis, a life-threatening zoonotic disease, across Pan-Amazonia.

Molecular systematics of tamarins with emphasis on genus Tamarinus (Primates, Callitrichidae) (2023)
Journal Article
Lopes, G. P., Rohe, F., Bertuol, F., Polo, É., Valsecchi, J., Santos, T. C. M., …Hrbek, T. (in press). Molecular systematics of tamarins with emphasis on genus Tamarinus (Primates, Callitrichidae). Zoologica Scripta, https://doi.org/10.1111/zsc.12617

The genus Saguinus comprises three principal clades that diverged in the Middle to Late Miocene. Their taxa are ecologically differentiated and allopatrically distributed. These clades were recently recognized as different genera, Saguinus, Tamarinus... Read More about Molecular systematics of tamarins with emphasis on genus Tamarinus (Primates, Callitrichidae).

Molecular Evidence Supports Five Lineages within Chiropotes (Pitheciidae, Platyrrhini) (2023)
Journal Article
Carneiro, J., Sampaio, I., Silva-Júnior, J. D. S. E., Martins-Junior, A., Farias, I., Hrbek, T., …Schneider, H. (in press). Molecular Evidence Supports Five Lineages within Chiropotes (Pitheciidae, Platyrrhini). Genes, 14(7), 1309. https://doi.org/10.3390/genes14071309

Pitheciines have unique dental specializations among New World monkeys that allow them to feed on fruits with hard pericarps, thus playing a major role as seed predators. The three extant pitheciine genera, Pithecia, Cacajao and Chiropotes, are all e... Read More about Molecular Evidence Supports Five Lineages within Chiropotes (Pitheciidae, Platyrrhini).

Barriers to chimpanzee gene flow at the south‐east edge of their distribution (2023)
Journal Article
Bonnin, N., Piel, A. K., Brown, R. P., Li, Y., Connell, A. J., Avitto, A. N., …Stewart, F. A. (2023). Barriers to chimpanzee gene flow at the south‐east edge of their distribution. Molecular Ecology, https://doi.org/10.1111/mec.16986

Populations on the edge of a species' distribution may represent an important source of adaptive diversity, yet these populations tend to be more fragmented and are more likely to be geographically isolated. Lack of genetic exchanges between such pop... Read More about Barriers to chimpanzee gene flow at the south‐east edge of their distribution.

A New Assessment of Robust Capuchin Monkey (Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation (2023)
Journal Article
Martins, A. B., Valença-Montenegro, M. M., Lima, M. G. M., Lynch, J. W., Svoboda, W. K., Silva-Júnior, J. D. S. E., …Fiore, A. D. (2023). A New Assessment of Robust Capuchin Monkey (Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation. Genes, 14(5), 970. https://doi.org/10.3390/genes14050970

Robust capuchin monkeys, Sapajus genus, are among the most phenotypically diverse and widespread groups of primates in South America, with one of the most confusing and often shifting taxonomies. We used a ddRADseq approach to generate genome-wide SN... Read More about A New Assessment of Robust Capuchin Monkey (Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation.

Taxonomic review of Saguinus mystax (Spix, 1823) (Primates, Callitrichidae), and description of a new species (2023)
Journal Article
Lopes, G., Rohe, F., Bertuol, F., Polo, E., Lima, I., Valsecchi, J., …Hrbek, T. (2023). Taxonomic review of Saguinus mystax (Spix, 1823) (Primates, Callitrichidae), and description of a new species. PeerJ, 11, e14526. https://doi.org/10.7717/peerj.14526

Although the Amazon has the greatest diversity of primates, there are still taxonomic uncertainties for many taxa, such as the species of the Saguinus mystax group. The most geographically broadly distributed and phenotypically diverse species in thi... Read More about Taxonomic review of Saguinus mystax (Spix, 1823) (Primates, Callitrichidae), and description of a new species.

Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches (2022)
Journal Article
Beck, R., de Vries, D., Janiak, M., Goodhead, I., & Boubli, J. (2022). Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches. Journal of Human Evolution, 174, https://doi.org/10.1016/j.jhevol.2022.103293

There have been multiple published phylogenetic analyses of platyrrhine primates (New World
monkeys) using both morphological and molecular data, but relatively few that have integrated
both types of data into a total evidence approach. Here, we pr... Read More about Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches.

Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates (2022)
Journal Article
Janiak, M. C., Silva, F. E., Beck, R. M. D., de Vries, D., Kuderna, L. F. K., Torosin, N. S., …Boubli, J. P. (2022). Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates. Molecular Ecology, 31(14), 3888-3902. https://doi.org/10.1111/mec.16554

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 ar... Read More about Two hundred and five newly assembled mitogenomes provide mixed evidence for rivers as drivers of speciation for Amazonian primates.

Phylogenetics and an updated taxonomic status of the Tamarins (Callitrichinae, Cebidae) (2022)
Journal Article
Brcko, I., Carneiro, J., Ruiz-García, M., Boubli, J., Silva-Júnior, J., Farias, I., …Sampaio, I. (2022). Phylogenetics and an updated taxonomic status of the Tamarins (Callitrichinae, Cebidae). Molecular Phylogenetics and Evolution, 173, 107504. https://doi.org/10.1016/j.ympev.2022.107504

Traditionally, Saguinus has been organized into six taxonomic groups: bicolor, inustus, midas, mystax, nigricollis, and oedipus. After recent revisions, taxonomic reclassifications were proposed, including (1) the recognition of Leontocebus as a new... Read More about Phylogenetics and an updated taxonomic status of the Tamarins (Callitrichinae, Cebidae).

Molecular phylogeny and systematics of bald uakaris, genus Cacajao (Primates: Pitheciidae), with the description of a new species. (2022)
Journal Article
Ennes Silva, F., Valsecchi do Amaral, J., Roos, C., Bowler, M., Röhe, F., Sampaio, R., …Boubli, J. (2022). Molecular phylogeny and systematics of bald uakaris, genus Cacajao (Primates: Pitheciidae), with the description of a new species. Molecular Phylogenetics and Evolution, 173, https://doi.org/10.1016/j.ympev.2022.107509

Bald uakaris, genus Cacajao, are Amazonian primates currently classified as one species and four subspecies based on the patterns of pelage coloration. In this study, we test if their current taxonomy is represented by the phylogenetic relationship o... Read More about Molecular phylogeny and systematics of bald uakaris, genus Cacajao (Primates: Pitheciidae), with the description of a new species..

Amazonia camtrap: A dataset of mammal, bird, and reptile species recorded with camera traps in the Amazon forest. (2022)
Journal Article
Antunes, A., Montanarin, A., Gräbin, D., Monteiro, E., de Pinho, F., Alvarenga, G., …Ribeiro, M. (2022). Amazonia camtrap: A dataset of mammal, bird, and reptile species recorded with camera traps in the Amazon forest. Ecology, 103(9), e3738. https://doi.org/10.1002/ecy.3738

The Amazon forest has the highest biodiversity on earth. However, information on Amazonian vertebrate diversity is still deficient and scattered across the published, peer-reviewed and grey literature and in unpublished raw data. Camera traps are an... Read More about Amazonia camtrap: A dataset of mammal, bird, and reptile species recorded with camera traps in the Amazon forest..

Out of the shadows : multilocus systematics and biogeography of night monkeys suggest a Central Amazonian origin and a very recent widespread southeastward expansion in South America (2022)
Journal Article
Martins-Junior, A., Sampaio, I., Silva, A., Boubli, J., Hrbek, T., Farias, I., …Schneider, H. (2022). Out of the shadows : multilocus systematics and biogeography of night monkeys suggest a Central Amazonian origin and a very recent widespread southeastward expansion in South America. Molecular Phylogenetics and Evolution, 107426. https://doi.org/10.1016/j.ympev.2022.107426

Neotropical primates with a poorly understood taxonomy and biogeography. The number of species in the genus varies from one to nine, depending on the author, and there are at least 18 known karyotypes, varying from 2n = 46 to 2n = 58. Historically, n... Read More about Out of the shadows : multilocus systematics and biogeography of night monkeys suggest a Central Amazonian origin and a very recent widespread southeastward expansion in South America.

Uncertainty regarding species delimitation, geographic distribution, and the evolutionary history of south-central Amazonian titi monkey species (Plecturocebus, Pitheciidae) (2021)
Journal Article
Byrne, H., Costa-Araujo, R., Farias, I., Silva, M., Messias, M., Hrbek, T., & Boubli, J. (2021). Uncertainty regarding species delimitation, geographic distribution, and the evolutionary history of south-central Amazonian titi monkey species (Plecturocebus, Pitheciidae). International Journal of Primatology,

Platyrrhine primate taxonomy is a rapidly evolving area of research. The recent description of the Parecis titi monkey, Plecturocebus parecis, has raised substantial questions regarding the taxonomy, distribution, and evolutionary history of titi tax... Read More about Uncertainty regarding species delimitation, geographic distribution, and the evolutionary history of south-central Amazonian titi monkey species (Plecturocebus, Pitheciidae).

Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum (2021)
Journal Article
Boubli, J., Janiak, M., Porter, L., de la Torre, S., Cortés-Ortiz, L., da Silva, M., …Roos, C. (2021). Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum. Zoological Research, 42(6), 761-771. https://doi.org/10.24272/j.issn.2095-8137.2021.143

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

Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome (2021)
Journal Article
Harrison, X., McDevitt, A., Dunn, J., Grifftihs, S., Benvenuto, C., Birtles, R., …Antwis, R. (2021). Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome. Proceedings of the Royal Society B: Biological Sciences, 288(1957), 20210552. https://doi.org/10.1098/rspb.2021.0552

Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, compara... Read More about Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome.