The Experts below are selected from a list of 531 Experts worldwide ranked by ideXlab platform
Warren E. Johnson - One of the best experts on this subject based on the ideXlab platform.
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puma genomes from north and south america provide insights into the genomic consequences of inbreeding
Nature Communications, 2019Co-Authors: Nedda F Saremi, Warren E. Johnson, Megan A Supple, Ashley Byrne, James A Cahill, Luiz Lehmann Coutinho, Love Dalen, Henrique V FigueiroAbstract:Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida Panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.
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puma genomes from north and south america provide insights into the genomic consequences of inbreeding
Nature Communications, 2019Co-Authors: Nedda F Saremi, Warren E. Johnson, Megan A Supple, Ashley Byrne, James A Cahill, Luiz Lehmann Coutinho, Love Dalen, Henrique V FigueiroAbstract:Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300–100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida Panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations. Pumas are experiencing increased isolation as human persecution and habitat loss fragment the populations of this once widespread species. Here, the authors estimate the genomic consequences of this isolation by analyzing the genomes of ten pumas from across North and South America.
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mountain lion genomes provide insights into genetic rescue of inbred populations
bioRxiv, 2018Co-Authors: Nedda F Saremi, Warren E. Johnson, Megan A Supple, Ashley Byrne, James A Cahill, Luiz Lehmann Coutinho, Love Dalen, Henrique V Figueiro, Heather J Milne, Stephen J ObrienAbstract:Introduction paragraph/Abstract Across the geographic range of mountain lions, which includes much of North and South America, populations have become increasingly isolated due to human persecution and habitat loss. To explore the genomic consequences of these processes, we assembled a high-quality mountain lion genome and analyzed a panel of resequenced individuals from across their geographic range. We found strong geographical structure and signatures of severe inbreeding in all North American populations. Tracts of homozygosity were rarely shared among populations, suggesting that assisted gene flow would restore local genetic diversity. However, the genome of an admixed Florida Panther that descended from a translocated individual from Central America had surprisingly long tracts of homozygosity, indicating that genomic gains from translocation were quickly lost by local inbreeding. Thus, to sustain diversity, genetic rescue will need to occur at regular intervals, through repeated translocations or restoring landscape connectivity. Mountain lions provide a rare opportunity to examine the potential to restore diversity through genetic rescue, and to observe the long-term effects of translocation. Our methods and results provide a framework for genome-wide analyses that can be applied to the management of small and isolated populations.
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Genetic introgression and the survival of Florida Panther kittens
Biological Conservation, 2010Co-Authors: Jeffrey A. Hostetler, David P. Onorato, James D. Nichols, Warren E. Johnson, Melody E. Roelke, Stephen J. O'brien, Deborah Jansen, Madan K. OliAbstract:Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982–2008 and a live-recapture dead-recovery modeling framework to estimate and model survival of Florida Panther (Puma concolor coryi) kittens (age 0–1 year). Overall, annual survival of Florida Panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied Panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F1 admixed and backcrossed to Texas kittens survived better than canonical Florida Panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older Panther survival, whereas index of Panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida Panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida Panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data.
Elliott S Chiu - One of the best experts on this subject based on the ideXlab platform.
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presence of endogenous viral elements negatively correlates with feline leukemia virus susceptibility in puma and domestic cat cells
Journal of Virology, 2020Co-Authors: Elliott S ChiuAbstract:While feline leukemia virus (FeLV) has been shown to infect felid species other than the endemic domestic cat host, differences in FeLV susceptibility among species has not been evaluated. Previous reports have noted a negative correlation between endogenous FeLV (enFeLV) copy number and exogenous FeLV (exFeLV) infection outcomes in domestic cats. Since felids outside the genus Felis do not harbor enFeLV genomes, we hypothesized absence of enFeLV results in more severe disease consequences in felid species lacking these genomic elements. We infected primary fibroblasts isolated from domestic cats (Felis catus) and pumas (Puma concolor) with FeLV and quantitated proviral and viral antigen loads. Domestic cat enFeLV env and long terminal repeat (LTR) copy numbers were determined for each individual and compared to FeLV viral outcomes. FeLV proviral and antigen levels were also measured in 6 naturally infected domestic cats and 11 naturally infected Florida Panthers (P. concolor coryi). We demonstrated that puma fibroblasts are more permissive to FeLV than domestic cat cells, and domestic cat FeLV restriction was highly related to enFeLV-LTR copy number. Terminal tissues from FeLV-infected Florida Panthers and domestic cats had similar exFeLV proviral copy numbers, but Florida Panther tissues have higher FeLV antigen loads. Our work indicates that enFeLV-LTR elements negatively correlate with exogenous FeLV replication. Further, Puma concolor samples lacking enFeLV are more permissive to FeLV infection than domestic cat samples, suggesting that endogenization can play a beneficial role in mitigating exogenous retroviral infections. Conversely, presence of endogenous retroelements may relate to new host susceptibility during viral spillover events.IMPORTANCE Feline leukemia virus (FeLV) can infect a variety of felid species. Only the primary domestic cat host and related small cat species harbor a related endogenous virus in their genomes. Previous studies noted a negative association between the endogenous virus copy number and exogenous virus infection in domestic cats. This report shows that puma cells, which lack endogenous FeLV, produce more virus more rapidly than domestic cat fibroblasts following cell culture challenge. We document a strong association between domestic cat cell susceptibility and FeLV long terminal repeat (LTR) copy number, similar to observations in natural FeLV infections. Viral replication does not, however, correlate with FeLV env copy number, suggesting that this effect is specific to FeLV-LTR elements. This discovery indicates a protective capacity of the endogenous virus against the exogenous form, either via direct interference or indirectly via gene regulation, and may suggest evolutionary outcomes of retroviral endogenization.
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multiple introductions of domestic cat feline leukemia virus in endangered Florida Panthers1
Emerging Infectious Diseases, 2019Co-Authors: Elliott S Chiu, Mark W Cunningham, Simona Kraberger, Lara Cusack, Melody E. RoelkeAbstract:The endangered Florida Panther (Puma concolor coryi) had an outbreak of infection with feline leukemia virus (FeLV) in the early 2000s that resulted in the deaths of 3 animals. A vaccination campaign was instituted during 2003-2007 and no additional cases were recorded until 2010. During 2010-2016, six additional FeLV cases were documented. We characterized FeLV genomes isolated from Florida Panthers from both outbreaks and compared them with full-length genomes of FeLVs isolated from contemporary Florida domestic cats. Phylogenetic analyses identified at least 2 circulating FeLV strains in Panthers, which represent separate introductions from domestic cats. The original FeLV virus outbreak strain is either still circulating or another domestic cat transmission event has occurred with a closely related variant. We also report a case of a cross-species transmission event of an oncogenic FeLV recombinant (FeLV-B). Evidence of multiple FeLV strains and detection of FeLV-B indicate Florida Panthers are at high risk for FeLV infection.
James A Cahill - One of the best experts on this subject based on the ideXlab platform.
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puma genomes from north and south america provide insights into the genomic consequences of inbreeding
Nature Communications, 2019Co-Authors: Nedda F Saremi, Warren E. Johnson, Megan A Supple, Ashley Byrne, James A Cahill, Luiz Lehmann Coutinho, Love Dalen, Henrique V FigueiroAbstract:Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300–100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida Panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations. Pumas are experiencing increased isolation as human persecution and habitat loss fragment the populations of this once widespread species. Here, the authors estimate the genomic consequences of this isolation by analyzing the genomes of ten pumas from across North and South America.
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puma genomes from north and south america provide insights into the genomic consequences of inbreeding
Nature Communications, 2019Co-Authors: Nedda F Saremi, Warren E. Johnson, Megan A Supple, Ashley Byrne, James A Cahill, Luiz Lehmann Coutinho, Love Dalen, Henrique V FigueiroAbstract:Pumas are the most widely distributed felid in the Western Hemisphere. Increasingly, however, human persecution and habitat loss are isolating puma populations. To explore the genomic consequences of this isolation, we assemble a draft puma genome and a geographically broad panel of resequenced individuals. We estimate that the lineage leading to present-day North American pumas diverged from South American lineages 300-100 thousand years ago. We find signatures of close inbreeding in geographically isolated North American populations, but also that tracts of homozygosity are rarely shared among these populations, suggesting that assisted gene flow would restore local genetic diversity. The genome of a Florida Panther descended from translocated Central American individuals has long tracts of homozygosity despite recent outbreeding. This suggests that while translocations may introduce diversity, sustaining diversity in small and isolated populations will require either repeated translocations or restoration of landscape connectivity. Our approach provides a framework for genome-wide analyses that can be applied to the management of similarly small and isolated populations.
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mountain lion genomes provide insights into genetic rescue of inbred populations
bioRxiv, 2018Co-Authors: Nedda F Saremi, Warren E. Johnson, Megan A Supple, Ashley Byrne, James A Cahill, Luiz Lehmann Coutinho, Love Dalen, Henrique V Figueiro, Heather J Milne, Stephen J ObrienAbstract:Introduction paragraph/Abstract Across the geographic range of mountain lions, which includes much of North and South America, populations have become increasingly isolated due to human persecution and habitat loss. To explore the genomic consequences of these processes, we assembled a high-quality mountain lion genome and analyzed a panel of resequenced individuals from across their geographic range. We found strong geographical structure and signatures of severe inbreeding in all North American populations. Tracts of homozygosity were rarely shared among populations, suggesting that assisted gene flow would restore local genetic diversity. However, the genome of an admixed Florida Panther that descended from a translocated individual from Central America had surprisingly long tracts of homozygosity, indicating that genomic gains from translocation were quickly lost by local inbreeding. Thus, to sustain diversity, genetic rescue will need to occur at regular intervals, through repeated translocations or restoring landscape connectivity. Mountain lions provide a rare opportunity to examine the potential to restore diversity through genetic rescue, and to observe the long-term effects of translocation. Our methods and results provide a framework for genome-wide analyses that can be applied to the management of small and isolated populations.
Stephen J. O'brien - One of the best experts on this subject based on the ideXlab platform.
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Genetic introgression and the survival of Florida Panther kittens
Biological Conservation, 2010Co-Authors: Jeffrey A. Hostetler, David P. Onorato, James D. Nichols, Warren E. Johnson, Melody E. Roelke, Stephen J. O'brien, Deborah Jansen, Madan K. OliAbstract:Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982–2008 and a live-recapture dead-recovery modeling framework to estimate and model survival of Florida Panther (Puma concolor coryi) kittens (age 0–1 year). Overall, annual survival of Florida Panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied Panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F1 admixed and backcrossed to Texas kittens survived better than canonical Florida Panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older Panther survival, whereas index of Panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida Panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida Panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data.
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Conservation Genetics of the Far Eastern Leopard (Panthera pardus orientalis)
The Journal of heredity, 2002Co-Authors: Olga Uphyrkina, Dale G Miquelle, Howard B Quigley, Carlos A. Driscoll, Stephen J. O'brienAbstract:The Far Eastern or Amur leopard (Panthera pardus orientalis) survives today as a tiny relict population of 25-40 individuals in the Russian Far East. The population descends from a 19th-century northeastern Asian subspecies whose range extended over southeastern Russia, the Korean peninsula, and northeastern China. A molecular genetic survey of nuclear microsatellite and mitochondrial DNA (mtDNA) sequence variation validates subspecies distinctiveness but also reveals a markedly reduced level of genetic variation. The amount of genetic diversity measured is the lowest among leopard subspecies and is comparable to the genetically depleted Florida Panther and Asiatic lion populations. When considered in the context of nonphysiological perils that threaten small populations (e.g., chance mortality, poaching, climatic extremes, and infectious disease), the genetic and demographic data indicate a critically diminished wild population under severe threat of extinction. An established captive population of P. p. orientalis displays much higher diversity than the wild population sample, but nearly all captive individuals are derived from a history of genetic admixture with the adjacent Chinese subspecies, P. p. japonensis. The conservation management implications of potential restoration/augmentation of the wild population with immigrants from the captive population are discussed.
Melody E. Roelke - One of the best experts on this subject based on the ideXlab platform.
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multiple introductions of domestic cat feline leukemia virus in endangered Florida Panthers1
Emerging Infectious Diseases, 2019Co-Authors: Elliott S Chiu, Mark W Cunningham, Simona Kraberger, Lara Cusack, Melody E. RoelkeAbstract:The endangered Florida Panther (Puma concolor coryi) had an outbreak of infection with feline leukemia virus (FeLV) in the early 2000s that resulted in the deaths of 3 animals. A vaccination campaign was instituted during 2003-2007 and no additional cases were recorded until 2010. During 2010-2016, six additional FeLV cases were documented. We characterized FeLV genomes isolated from Florida Panthers from both outbreaks and compared them with full-length genomes of FeLVs isolated from contemporary Florida domestic cats. Phylogenetic analyses identified at least 2 circulating FeLV strains in Panthers, which represent separate introductions from domestic cats. The original FeLV virus outbreak strain is either still circulating or another domestic cat transmission event has occurred with a closely related variant. We also report a case of a cross-species transmission event of an oncogenic FeLV recombinant (FeLV-B). Evidence of multiple FeLV strains and detection of FeLV-B indicate Florida Panthers are at high risk for FeLV infection.
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Genetic introgression and the survival of Florida Panther kittens
Biological Conservation, 2010Co-Authors: Jeffrey A. Hostetler, David P. Onorato, James D. Nichols, Warren E. Johnson, Melody E. Roelke, Stephen J. O'brien, Deborah Jansen, Madan K. OliAbstract:Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982–2008 and a live-recapture dead-recovery modeling framework to estimate and model survival of Florida Panther (Puma concolor coryi) kittens (age 0–1 year). Overall, annual survival of Florida Panther kittens was 0.323 ± 0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied Panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F1 admixed and backcrossed to Texas kittens survived better than canonical Florida Panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older Panther survival, whereas index of Panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida Panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida Panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data.