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4. Identification of constrained sequence elements across 239 primate genomes

Author

Kuderna, Lukas F.K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rouselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marques Bonet, Tomas, Farh, Kyle Kai How, Kuderna, Lukas F.K., Ulirsch, Jacob C., Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J., Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J., Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rouselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Karakikes, Ioannis, Wang, Kevin C., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marques Bonet, Tomas, and Farh, Kyle Kai How

Abstract

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3,4,5,6,7,8,9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals., Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3–9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.

Published
2024

5. Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

Author

Krueger, Johanna, primary, Fong Zazueta, Ricardo, additional, Alba, David M., additional, Aymerich, Xenia, additional, Beck, Robin M.D., additional, Cappellini, Enrico, additional, Carrillo Martin, Guillermo, additional, Cirilli, Omar, additional, Clark, Nathan, additional, Cornejo, Omar E., additional, Farh, Kyle, additional, Ferrandez-Peral, Luis, additional, Juan, David, additional, Kelley, Joanna L., additional, Kuderna, Lukas F. K., additional, Little, Jordan, additional, Orkin, Joseph D., additional, Paterson, Ryan S., additional, Pawar, Harvinder, additional, Marques-Bonet, Tomas, additional, and Lizano, Esther, additional

Published
2024
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7. Leaving Gondwana: the changing position of the Indian subcontinent in the global faunal network

Author

Halliday, Thomas J.D., Holroyd, Patricia A., Gheerbrant, Emmanuel, Prasad, Guntupalli V.R., Scanferla, Agustin, Beck, Robin M.D., Krause, David W., and Goswami, Anjali

Abstract

The paleogeographic history of the Indian subcontinent is unique among Earth’s landmasses. From being part of the southern supercontinent Gondwana for most of the Mesozoic, through a period of isolation as a drifting entity in the Late Cretaceous, to colliding with Asia near the Paleocene-Eocene boundary, the Indian subcontinent has been associated with, and dissociated from, a variety of landmasses. This paleogeographic history has been invoked to explain aspects of the subcontinent’s modern-day fauna, with a combination of endemic radiations, remnants from Gondwana, and more recent immigrants from Laurasia. Here, 2 network approaches document how vertebrate faunas of the Indian subcontinent, and specifically their relationships to those of other landmasses, changed during the subcontinent’s isolation from close faunal relationships with Madagascar and South America in the Late Cretaceous to a more Laurasian fauna most similar to those of Europe by the Eocene.

Published
2020

9. The landscape of tolerated genetic variation in humans and primates

Author

Gao, Hong, Hamp, Tobias, Ede, Jeffrey, Schraiber, Joshua G., McRae, Jeremy, Singer-Berk, Moriel, Yang, Yanshen, Dietrich, Anastasia S.D., Fiziev, Petko P., Kuderna, Lukas F.K., Sundaram, Laksshman, Wu, Yibing, Adhikari, Aashish, Field, Yair, Chen, Chen, Batzoglou, Serafim, Aguet, Francois, Lemire, Gabrielle, Reimers, Rebecca, Balick, Daniel, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, do Amaral, João Valsecchi, Messias, Mariluce, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Bataillon, Thomas, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda, Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Lek, Monkol, Sunyaev, Shamil, O'Donnell-Luria, Anne, Rehm, Heidi L., Xu, Jinbo, Rogers, Jeffrey, Marques-Bonet, Tomas, Farh, Kyle Kai How, Gao, Hong, Hamp, Tobias, Ede, Jeffrey, Schraiber, Joshua G., McRae, Jeremy, Singer-Berk, Moriel, Yang, Yanshen, Dietrich, Anastasia S.D., Fiziev, Petko P., Kuderna, Lukas F.K., Sundaram, Laksshman, Wu, Yibing, Adhikari, Aashish, Field, Yair, Chen, Chen, Batzoglou, Serafim, Aguet, Francois, Lemire, Gabrielle, Reimers, Rebecca, Balick, Daniel, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, do Amaral, João Valsecchi, Messias, Mariluce, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Bataillon, Thomas, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda, Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Lek, Monkol, Sunyaev, Shamil, O'Donnell-Luria, Anne, Rehm, Heidi L., Xu, Jinbo, Rogers, Jeffrey, Marques-Bonet, Tomas, and Farh, Kyle Kai How

Abstract

INTRODUCTION 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 i, Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

Published
2023

10. A global catalog of whole-genome diversity from 233 primate species

Author

Kuderna, Lukas F.K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai How, Marques Bonet, Tomas, Kuderna, Lukas F.K., Gao, Hong, Janiak, Mareike C., Kuhlwilm, Martin, Orkin, Joseph D., Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rousselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R. Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idrissa S., Horvath, Julie E., Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G., de Melo, Fabiano R., Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria N.F., Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J., Zaramody, Alphonse, Jolly, Clifford J., Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H., Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D., Knauf, Sascha, Le, Minh D., Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C., Zinner, Dietmar, Gut, Ivo, Melin, Amanda D., Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin M.D., Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P., Rogers, Jeffrey, Farh, Kyle Kai How, and Marques Bonet, Tomas

Abstract

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., 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.

Published
2023

13. First known extinct feathertail possums (Acrobatidae, Marsupialia): palaeobiodiversity, phylogenetics, palaeoecology and palaeogeography

Author

Fabian, Prudence R., Archer, Michael, Hand, Suzanne J., and Beck, Robin M.D.

Abstract

AbstractFour new fossil feathertail possum species (Marsupialia, Diprotodontia, Phalangerida, Petauroidea, Acrobatidae) are described from late Oligocene to middle Miocene fossil deposits in the Riversleigh World Heritage Area, northwestern Queensland. They are the first pre-Pleistocene fossil representatives of this family to be described. Two species are referred to the modern genus Acrobatesand two to the modern genus Distoechurus. These species are distinguished from each other and from the living Distoechurus pennatusand Acrobates pygmaeuson the basis of qualitative and quantitative characters of the first lower molar (m1), which is the only tooth known for all four fossil species. Fortunately, m1 is morphologically the most variable tooth in the cheektooth row of acrobatids, and it exhibits numerous genus- and species-specific features. Phylogenetic analyses based on dental characters strongly support monophyly of Acrobatidae relative to other petauroids, as well as providing relatively strong support for reciprocal monophyly of Acrobatesand Distoechurus, including the newly described fossil members of these genera. Recognition of species of Acrobatesand Distoechurusin these fossil deposits is broadly congruent with recent estimates for the time of divergence of the two modern genera based on molecular data, and also provides an additional fossil calibration point for future studies of marsupial divergence times. These fossil species provide new insights into the biogeographical and ecological history of this enigmatic family of small possums, specifically that the oldest known species of Acrobatesoccurred in closed forest environments (in contrast to the living species, A. pygmaeusand Acrobates frontalis, which today inhabit open sclerophyll forests and woodlands) and that Distoechurusappears to have originated in Australia, only subsequently dispersing to New Guinea before becoming extinct in its Australian homeland.Prudence R. Fabian [pruefabian@gmail.com], Michael Archer [m.archer@unsw.edu.au], Suzanne J. Hand [s.hand@unsw.edu.au], Earth and Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, NSW 2052, Australia; Robin M.D. Beck [r.m.d.beck@salford.ac.uk], School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK.

Published
2023
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15. Earliest evidence of mammalian social behaviour in the basal Tertiary of Bolivia

Author

Ladeveze, Sandrine, de Muizon, Christian, Beck, Robin M.D., Germain, Damien, and Cespedes-Paz, Ricardo

Subjects
Promiscuity -- Research, Evolutionary biology -- Research, Mammals -- Physiological aspects -- Research, Fossils -- Physiological aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The vast majority of Mesozoic and early Cenozoic metatherian mammals (extinct relatives of modern marsupials) are known only from partial jaws or isolated teeth, which give insight into their probable diets and phylogenetic relationships but little else. The few skulls known are generally crushed, incomplete or both (1-4), and associated postcranial material is extremely rare. Here we report the discovery of an exceptionally large number of almost undistorted, nearly complete skulls and skeletons of a stem-metatherian, Pucadelphys andinus, in the early Palaeocene epoch (5) of Tiupampa in Bolivia (6-8). These give an unprecedented glimpse into early metatherian morphology, evolutionary relationships and, especially, ecology. The remains of 35 individuals have been collected, with 22 of these represented by nearly complete skulls and associated postcrania. These individuals were probably buried in a single catastrophic event, and so almost certainly belong to the same population9. The preservation of multiple adult, sub-adult and juvenile individuals in close proximity (, The locality of Tiupampa, Bolivia (10,11), has yielded an abundant and remarkably preserved mammal fauna from the earliest Palaeocene (5). Some of the most spectacular fossils are numerous partial skulls [...]

Published
2011
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16. A bizarre new family of marsupialia (incertae sedis) from the early Pliocene of northeastern Australia: implications for the phylogeny of bunodont marsupials

Author

Beck, Robin M.D., Archer, Michael, Godthelp, Henk, Mackness, Brian S., Hand, Suzanne J., and Muirhead, Jeannette

Subjects
Northern Australia -- Natural history, Phylogeny -- Research, Marsupialia -- Identification and classification, Biological sciences, Science and technology
Abstract

We describe Numbigilga ernielundeliusi new genus and species, a highly unusual marsupial represented by a partial right mandible with p2-m4 and a left upper molar from early Pliocene deposits at Bluff Downs, Queensland, northeastern Australia. Numbigilga n. gen. is characterized by a bunodont dentition with a number of striking specializations, and we refer it to Numbigilgidae new family. This taxon shares a range of dental apomorphies with various bunodont marsupial groups from the Late Cretaceous of North America and Paleogene of Gondwana. However, many of these features are most likely highly homoplastic within marsupials, reflecting convergent adaptations to a frugivorous-omnivorous diet. Other dental characters suggest possible affinities to the Australian order Peramelemorphia (bandicoots). Alternatively, Numbigilga may be a representative of an entirely new order of Australian marsupials. In the absence of more nearly complete specimens that might clarify its relationships, we refer Numbigilga to Marsupialia incertae sedis. We consider the distributions of a number of dental characters in bunodont marsupials and argue that no North American Late Cretaceous taxa can be convincingly referred to the order Polydolopimorphia. Thus, polydolopimorphians continue to be known only from the Cenozoic of Gondwana, with no fossil evidence that their initial divergences occurred in North America.

Published
2008

17. A dated phylogeny of marsupials using a molecular supermatrix and multiple fossil constraints

Author

Beck, Robin M.D.

Subjects
Marsupialia -- Natural history, Marsupialia -- Genetic aspects, Marsupialia -- Varieties, Phylogeny -- Research, Bayesian statistical decision theory -- Methods, Molecular genetics -- Methods, Mammals, Fossil -- Varieties, Mammals, Fossil -- Genetic aspects, Zoology and wildlife conservation
Abstract

Phylogenetic relationships within marsupials were investigated based on a 20.1-kilobase molecular supermatrix comprising 7 nuclear and 15 mitochondrial genes analyzed using both maximum likelihood and Bayesian approaches and 3 different partitioning strategies. The study revealed that base composition bias in the 3rd codon positions of mitochondrial genes misled even the partitioned maximum-likelihood analyses, whereas Bayesian analyses were less affected. After correcting for base composition bias, monophyly of the currently recognized marsupial orders, of Australidelphia, and of a clade comprising Dasyuromorphia, Notoryctes, and Peramelemorphia, were supported strongly by both Bayesian posterior probabilities and maximum-likelihood bootstrap values. Monophyly of the Australasian marsupials, of Notoryctes + Dasyuromorphia, and of Caenolestes + Australidelphia were less well supported. Within Diprotodontia, Burramyidae + Phalangeridae received relatively strong support. Divergence dates calculated using a Bayesian relaxed molecular clock and multiple age constraints suggested at least 3 independent dispersals of marsupials from North to South America during the Late Cretaceous or early Paleocene. Within the Australasian clade, the macropodine radiation, the divergence of phascogaline and dasyurine dasyurids, and the divergence of peranaeline and peroryctine peramelemorphians all coincided with periods of significant environmental change during the Miocene. An analysis of 'unrepresented basal branch lengths' suggests that the fossil record is particularly poor for didelphids and most groups within the Australasian radiation. Key words: Ameridelphia, Australidelphia, Bayesian analysis, fossil record, marsupials, phylogenetic fuse, phylogeny, relaxed molecular clock, supermatrix

Published
2008

18. Miocene mammal reveals a mesozoic ghost lineage on insular New Zealand, southwest Pacific

Author

Worthy, Trevor H., Tennyson, Alan J.D., Archer, Michael, Musser, Anne M., Hand, Suzanne J., Jones, Craig, Douglas, Barry J., McNamara, James A., and Beck, Robin M.D.

Subjects
Gondwana -- Environmental aspects, Gondwana -- Research, Mammals, Fossil -- Research, Science and technology
Abstract

New Zealand (NZ) has long been upheld as the archetypical example of a land where the biota evolved without nonvolant terrestrial mammals. Their absence before human arrival is mysterious, because NZ was still attached to East Antarctica in the Early Cretaceous when a variety of terrestrial mammals occupied the adjacent Australian portion of Gondwana. Here we report discovery of a nonvolant mammal from Miocene (19-16 Ma) sediments of the Manuherikia Group near St Bathans (SB) in Central Otago, South Island, NZ. A partial relatively plesiomorphic femur and two autapomorphically specialized partial mandibles represent at least one mouse-sized mammal of unknown relationships. The material implies the existence of one or more ghost lineages, at least one of which (based on the relatively plesiomorphic partial femur) spanned the Middle Miocene to at least the Early Cretaceous, probably before the time of divergence of marsupials and placentals >125 Ma. Its presence in NZ in the Middle Miocene and apparent absence from Australia and other adjacent landmasses at this time appear to reflect a Gondwanan vicariant event and imply persistence of emergent land during the Oligocene marine transgression of NZ. Nonvolant terrestrial mammals disappeared from NZ some time since the Middle Miocene, possibly because of late Neogene climatic cooling. Gondwana | Miocene | nontherian mammal | vicariant event

Published
2006

19. Global elongation and high shape flexibility as an evolutionary hypothesis of accommodating mammalian brains into skulls

Author

Weisbecker, Vera, primary, Rowe, Timothy, additional, Wroe, Stephen, additional, Macrini, Thomas E., additional, Garland, Kathleen L. S., additional, Travouillon, Kenny J., additional, Black, Karen, additional, Archer, Michael, additional, Hand, Suzanne J., additional, Berlin, Jeri, additional, Beck, Robin M.D., additional, Ladevèze, Sandrine, additional, Sharp, Alana C., additional, Mardon, Karine, additional, and Sherratt, Emma, additional

Published
2020
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23. Current status of species-level representation in faunas from selected fossil localities in the Riversleigh World Heritage Area, northwestern Queensland

Author

ARCHER, MICHAEL, primary, ARENA, DERRICK A., additional, BASSAROVA, MINA, additional, BECK, ROBIN M.D., additional, BLACK, KAREN, additional, BOLES, WALTER E., additional, BREWER, PHILLIPA, additional, COOKE, BERNARD N., additional, CROSBY, KIRSTEN, additional, GILLESPIE, ANNA, additional, GODTHELP, HENK, additional, HAND, SUZANNE J., additional, KEAR, BENJAMIN P., additional, LOUYS, JULIEN, additional, MORRELL, ADAM, additional, MUIRHEAD, JEANETTE, additional, ROBERTS, KAREN K., additional, SCANLON, JOHN D., additional, TRAVOUILLON, KENNY J., additional, and WROE, STEPHEN, additional

Published
2006
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24. A higher-level MRP supertree of placental mammals.

Author

Beck, Robin M.D., Bininda-Emonds, Olaf R.P., Cardillo, Marcel, Liu, Fu-Guo Robert, and Purvis, Andy

Subjects
*MAMMALS, *BIOLOGICAL evolution, *PHYLOGENY, *BIOLOGY, *CETACEA
Abstract

Background: The higher-level phylogeny of placental mammals has long been a phylogenetic Gordian knot, with disagreement about both the precise contents of, and relationships between, the extant orders. A recent MRP supertree that favoured 'outdated' hypotheses (notably, monophyly of both Artiodactyla and Lipotyphla) has been heavily criticised for including low-quality and redundant data. We apply a stringent data selection protocol designed to minimise these problems to a much-expanded data set of morphological, molecular and combined source trees, to produce a supertree that includes every family of extant placental mammals. Results: The supertree is well-resolved and supports both polyphyly of Lipotyphla and paraphyly of Artiodactyla with respect to Cetacea. The existence of four 'superorders' ― Afrotheria, Xenarthra, Laurasiatheria and Euarchontoglires ― is also supported. The topology is highly congruent with recent (molecular) phylogenetic analyses of placental mammals, but is considerably more comprehensive, being the first phylogeny to include all 113 extant families without making a priori assumptions of suprafamilial monophyly. Subsidiary analyses reveal that the data selection protocol played a key role in the major changes relative to a previously published higher-level supertree of placentals. Conclusion: The supertree should provide a useful framework for hypothesis testing in phylogenetic comparative biology, and supports the idea that biogeography has played a crucial role in the evolution of placental mammals. Our results demonstrate the importance of minimising poor and redundant data when constructing supertrees. [ABSTRACT FROM AUTHOR]

Published
2006
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