The Experts below are selected from a list of 801 Experts worldwide ranked by ideXlab platform
David Thybert - One of the best experts on this subject based on the ideXlab platform.
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repeat associated mechanisms of genome evolution and function revealed by the mus caroli and mus pahari genomes
Genome Research, 2018Co-Authors: David Thybert, Masa Roller, Fabio C P Navarro, Christine Feig, David Martingalvez, Mikhail Kolmogorov, Ian T Fiddes, Ian Streeter, Vaclav JanousekAbstract:Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.
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repeat associated mechanisms of genome evolution and function revealed by the mus caroli and mus pahari genomes
bioRxiv, 2017Co-Authors: David Thybert, Masa Roller, Fabio C P Navarro, Christine Feig, David Martingalvez, Mikhail Kolmogorov, Ian T Fiddes, Ian Streeter, Vaclav Janousek, Wasiu AkanniAbstract:Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 to 6 MYA, but that are absent in the Hominidae. In fact, Hominidae show between four- and seven-fold lower rates of nucleotide change and feature turnover in both neutral and functional sequences suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. For example, recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli. This process resulted in thousands of novel, species-specific CTCF binding sites. Our results demonstrate that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.
Woo Young Bang - One of the best experts on this subject based on the ideXlab platform.
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comparison of carnivore omnivore and herbivore mammalian genomes with a new leopard assembly
Genome Biology, 2016Co-Authors: S C Kim, Oksung Chung, Sungwoong Jho, Yun Sung Cho, Hak Min Kim, Hong Seomun, Hyunho Kim, Jeongho Kim, Woo Young BangAbstract:There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.
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Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly
Genome Biology, 2016Co-Authors: Soonok Kim, Oksung Chung, Sungwoong Jho, Yun Sung Cho, Hak Min Kim, Woo Young Bang, Hong Seomun, Hyunho Kim, Jeongho Kim, Changmu KimAbstract:Background: There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. Results: We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. Conclusions: Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.
Yun Sung Cho - One of the best experts on this subject based on the ideXlab platform.
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comparison of carnivore omnivore and herbivore mammalian genomes with a new leopard assembly
Genome Biology, 2016Co-Authors: S C Kim, Oksung Chung, Sungwoong Jho, Yun Sung Cho, Hak Min Kim, Hong Seomun, Hyunho Kim, Jeongho Kim, Woo Young BangAbstract:There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.
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Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly
Genome Biology, 2016Co-Authors: Soonok Kim, Oksung Chung, Sungwoong Jho, Yun Sung Cho, Hak Min Kim, Woo Young Bang, Hong Seomun, Hyunho Kim, Jeongho Kim, Changmu KimAbstract:Background: There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. Results: We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. Conclusions: Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.
Vaclav Janousek - One of the best experts on this subject based on the ideXlab platform.
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repeat associated mechanisms of genome evolution and function revealed by the mus caroli and mus pahari genomes
Genome Research, 2018Co-Authors: David Thybert, Masa Roller, Fabio C P Navarro, Christine Feig, David Martingalvez, Mikhail Kolmogorov, Ian T Fiddes, Ian Streeter, Vaclav JanousekAbstract:Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.
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repeat associated mechanisms of genome evolution and function revealed by the mus caroli and mus pahari genomes
bioRxiv, 2017Co-Authors: David Thybert, Masa Roller, Fabio C P Navarro, Christine Feig, David Martingalvez, Mikhail Kolmogorov, Ian T Fiddes, Ian Streeter, Vaclav Janousek, Wasiu AkanniAbstract:Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 to 6 MYA, but that are absent in the Hominidae. In fact, Hominidae show between four- and seven-fold lower rates of nucleotide change and feature turnover in both neutral and functional sequences suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. For example, recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli. This process resulted in thousands of novel, species-specific CTCF binding sites. Our results demonstrate that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.
Holly B Smith - One of the best experts on this subject based on the ideXlab platform.
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toward a life history of the Hominidae
Annual Review of Anthropology, 1995Co-Authors: Holly B Smith, Robert L TompkinsAbstract:Two new developments promise to greatly improve our ability to reconstruct the evolution of the human life cycle: 1. the introduction of the comparative methodology of life history into anthropology and 2. research on bone and dental development that reveals a world of life history preserved in the fossil record. Comparative study suggests that the human strategy depends on rich energy sources and low mortality and that our general rate of growth and aging evolved in parallel with brain size. It now appears that the australopithecines were a substantially primitive grade of hominid with life histories more like apes than humans. The life cycle of early Homo erectus was probably unlike any living hominoid: Evidence suggests that it grew up somewhat faster than living humans, it lacked an adolescent growth spurt, and H. erectus infants were more helpless than those of chimpanzees (but conceivably of more mature body proportion and motor advancement than our own). The appearance of fully modern life historie...
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dental development and the evolution of life history in Hominidae
American Journal of Physical Anthropology, 1991Co-Authors: Holly B SmithAbstract:Development of the dentition is critically integrated into the life cycle in living mammals. Recent work on dental development has given rise to three separate lines of evidence on the evolution of human growth and aging; these three, based on several independent studies, are reviewed and inte- grated here. First, comparative study of living primate species demonstrates that measures of development (e.g., age of emergence of the first permanent molar) are highly correlated with the morphological attributes brain and body weight (as highly as r = 0.98, N = 21 species). These data predict that small-bodied, small-brained Australopithecus erupted M, at 3-3.5 years and possessed a life span comparable to that of a chimpanzee. Second, chronologi- cal age at death for three australopithecines who died at or near emergence of MI is now estimated as -3.25 years based on incremental lines in teeth; this differs substantially from expectations based on human growth schedules (5.5-6 years). Third, developmental sequences (assessed by the coefficient of variation of human dental age) observed in gracile Australopithecus and great apes diverge from those of humans to a comparable degree; sequences become more like modern humans after the appearance of the genus Homo. These three lines of evidence agree that the unique rate and pattern of human life history did not exist at the australopithecine stage of human evolution. It is proposed that the life history of early Homo matched no living model precisely and that growth and aging evolved substantially in the Hominidae during the last 2 million years.