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Niles Lehman - One of the best experts on this subject based on the ideXlab platform.

  • genetic consequences of a severe Population Bottleneck in the guadalupe fur seal arctocephalus townsendi
    Journal of Heredity, 2004
    Co-Authors: D S Weber, Brent S. Stewart, Niles Lehman
    Abstract:

    Population Bottlenecks may lead to diminished genetic variability and correlative effects on fitness. The Guadalupe fur seal was nearly exterminated by commercial sealers during the late 18th and early 19th centuries. To determine the genetic consequences of this Population Bottleneck, we compared the variation at a 181 bp section of the mitochondrial DNA (mtDNA) control region from the bones of 26 preBottleneck fur seals versus variation in the extant Population. We found 25 different mtDNA genotypes in the preBottleneck fur seals and only 7 genotypes among 32 extant fur seals, including only one of the ancient genotypes. These data demonstrate a substantial loss of genetic variability correlating with the recent Population Bottleneck. We also found from several genetic measures that the prehistoric Population of Guadalupe fur seals was robust and that it had been increasing at some time during the late prehistoric period. Continued recovery of this species may, however, owe more to more immediate nongenetic factors, such as poaching and local availability of food resources during the breeding season and consequent effects on pup survival, than on the reduced genetic variability.

  • major histocompatibility complex variation at three class ii loci in the northern elephant seal
    Molecular Ecology, 2004
    Co-Authors: Dianas Weber, Niles Lehman, John Schienman, Brent S. Stewart
    Abstract:

    Northern elephant seals were hunted to near extinction in the 19th century, yet have recovered remarkably and now number around 175 000. We surveyed 110 seals for single-strand conformation polymorphism (SSCP) and sequence variation at three major histocompatibility (MHC) class II loci (DQA, DQB and DRB) to evaluate the genetic consequences of the Population Bottleneck at these loci vs. other well-studied genes. We found very few alleles at each MHC locus, significant variation among breeding sites for the DQA locus, and linkage disequilibrium between the DQB and DRB loci. Northern elephant seals are evidently inbred, although there is as yet no evidence of correlative reductions in fitness.

  • an empirical genetic assessment of the severity of the northern elephant seal Population Bottleneck
    Current Biology, 2000
    Co-Authors: Dianas Weber, Carlos J Garza, Brent S. Stewart, Niles Lehman
    Abstract:

    Abstract A Bottleneck in Population size of a species is often correlated with a sharp reduction in genetic variation. The northern elephant seal ( Mirounga angustirostris ) has undergone at least one extreme Bottleneck, having rebounded from 20–100 individuals a century ago to over 175,000 individuals today. The relative lack of molecular-genetic variation in contemporary Populations has been documented, but the extent of variation before the late 19th century remains unknown. We have determined the nucleotide sequence of a 179base-pair segment of the mitochondrial DNA (mtDNA) control region from seals that lived before, during and after a Bottleneck low in 1892. A ‘primerless' PCR was used to improve the recovery of information from older samples. Only two mtDNA genotypes were present in all 150+ seals from the 1892 Bottleneck on, but we discovered four genotypes in five pre-Bottleneck seals. This suggests a much greater amount of mtDNA genotypic variation before this Bottleneck, and that the persistence of two genotypes today is a consequence of random lineage sampling. We cannot correlate the loss of mtDNA genotypes with a lowered mean fitness of individuals in the species today. However, we show that the species historically possessed additional genotypes to those present now, and that sampling of ancient DNA could elucidate the genetic consequences of severe reductions in Population size.

Robert H Robichaux - One of the best experts on this subject based on the ideXlab platform.

  • microsatellite analysis of a Population crash and Bottleneck in the mauna kea silversword argyroxiphium sandwicense ssp sandwicense asteraceae and its implications for reintroduction
    Molecular Ecology, 2000
    Co-Authors: Elizabeth Friar, T Ladoux, Eric H Roalson, Robert H Robichaux
    Abstract:

    The Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense, has experienced both a severe Population crash associated with an increase in alien ungulate Populations on Mauna Kea, and a Population Bottleneck associated with reintroduction. In this paper, we address the genetic consequences of both demographic events using eight microsatellite loci. The Population crash was not accompanied by a significant reduction in number of alleles or heterozygosity. However, the Population Bottleneck was accompanied by significant reductions in observed number of alleles, effective number of alleles, and expected heterozygosity, though not in observed heterozygosity. The effective size of the Population Bottleneck was calculated using both observed heterozygosities and allele frequency variances. Both methods corroborated the historical census size of the Population Bottleneck of at most three individuals. The results suggest that: (i) small Populations, even those that result from severe reductions in historical Population size and extent, are not necessarily genetically depauperate; and (ii) species reintroduction plans need to be conceived and implemented carefully, with due consideration to the genetic impact of sampling for reintroduction.

  • molecular genetic consequences of a Population Bottleneck associated with reintroduction of the mauna kea silversword arg yroxiphium sandwicense ssp sandwicense asteraceae
    Conservation Biology, 1997
    Co-Authors: Robert H Robichaux, Elizabeth Friar, David W Mount
    Abstract:

    The endangered Mauna Kea silversword (Argyroxiphium sandwicense ssp. sandwicense) has experienced a severe decline in distribution and abundance because of predation by alien ungulates. By the late 1970s only a small remnant natural Population persisted on the Mauna Kea volcano on the Island of Hawaii. The Hawaii Department of Land and Natural Resources, Division of Forestry and Wildlife, initiated an outplanting program in the 1970s to promote recovery of A. sandwicense ssp. sandwicense. Intermittent outplanting since 1973 has generated an outplanted Population of over 450 plants on Mauna Kea, but the program has unintentionally resulted in a major Population Bottleneck. All plants in the outplanted Population appear to be first- or subsequent-generation offspring of only two maternal founders from the natural Population. Genetic variation in the natural and outplanted Populations was assessed for 90 random amplified polymorphic DNA loci. Eleven loci were detectably polymorphic in the natural Population, whereas only three loci were detectably polymorphic in the outplanted Population. Thus, the Population Bottleneck has been accompanied by a 73% reduction in the level of detectable polymorphism. In addition, for eight loci, the Population Bottleneck has resulted in the loss of the marker allele in the outplanted Population. A management strategy involving manual pollen transfer has recently been implemented to incorporate additional founders from the natural Population into the outplanting program. As a supplement to the outplanting program, the strategy also includes a program promoting direct seedling establishment following manual pollen transfer. Incorporating additional founders may serve to overcome the legacy of the Population Bottleneck, especially if founder representation can be equalized. La Espada Plateada de Mauna Kea (Argyroxiphium sandwicense ssp. sandwicense) esta en peligro de extincion debido a una severa declinacion de su distribucion y abundancia en tiempos historicos causada por la depredacion de ungulados introducidos. A fines de la decada de 1970 solo persistia una pequena poblacion natural en el volcan Mauna Kea en la Isla de Hawaii. Tambien en esa decada el Departamento de Tierras y Recursos Naturales de Hawaii, por medio de la Division de Bosques y Vida Silvestre, inicio un programa de siembra para promover la recuperacion de Argyroxiphium sandwicense ssp. sandwicense. La siembra intermitente desde 1973 ha generado una poblacion de mas de 450 plantas en Mauna Kea. Sin embargo el programa de siembra, aunque sin intencion, ha resultado en un gran cuello de botella poblacional. Todas las plantas en la poblacion sembrada parecen ser la primera o subsecuentes generaciones de descendientes de solo dos fundadores maternos de la poblacion natural. Se determino la variacion genetica para 90 loci de ADN polimorficos amplificados en la poblacion natural y la sembrada. Once loci fueron marcadamente polimorficos en la poblacion natural, mientras que solo tres lo fueron en la poblacion sembrada. Por tanto, el cuello de botella poblacional esta acompanado por una reduccion del 73% en el nivel de polimorfismo detectable. Adicionalmente, el cuello de botella poblacional ha resultado en la perdida del alelo marcador para ocho loci en la poblacion sembrada. Recientemente se ha instrumentado una estrategia de manejo que involucra la transferencia manual de polen para incorporar fundadores adicionales de la poblacion natural al programa de siembra. Como un suplemento del programa de siembra, la estrategia tambien incluye un programa que promueve el establecimiento directo de plantulas despues de la transferencia manual de polen. La incorporacion de fundadores adicionales puede servir para superar el legado del cuello de botella, especialmente si la representacion de fundadores se equilibra.

Bruce C Robertson - One of the best experts on this subject based on the ideXlab platform.

  • genetic evidence of a Population Bottleneck and inbreeding in the endangered new zealand sea lion phocarctos hookeri
    Journal of Heredity, 2016
    Co-Authors: Amy J Osborne, Sandra S Negro, Louise B Chilvers, Bruce C Robertson, Martin A Kennedy, Neil J Gemmell
    Abstract:

    The New Zealand sea lion (NZSL) is of high conservation concern due to its limited distribution and its declining Population size. Historically, it occupied most of coastal New Zealand, but is now restricted to a few coastal sites in southern mainland New Zealand and the sub-Antarctic Islands. NZSLs have experienced a recent reduction in Population size due to sealing in the 1900s, which is expected to have resulted in increased inbreeding and a loss of genetic variation, potentially reducing the evolutionary capacity of the species and negatively impacting on its long-term prospects for survival. We used 17 microsatellite loci, previously shown to have cross-species applications in pinnipeds, to determine locus- and Population-specific statistics for 1205 NZSLs from 7 consecutive breeding seasons. We show that the NZSL Population has a moderate level of genetic diversity in comparison to other pinnipeds. We provide genetic evidence for a Population reduction, likely caused by historical sealing, and a measure of allele sharing/parental relatedness (internal relatedness) that is suggestive of increased inbreeding in pups that died during recent epizootic episodes. We hypothesize that Population Bottlenecks and nonrandom mating have impacted on the Population genetic architecture of NZSLs, affecting its Population recovery.

  • ancient and contemporary dna reveal a pre human decline but no Population Bottleneck associated with recent human persecution in the kea nestor notabilis
    PLOS ONE, 2015
    Co-Authors: Nicolas Dussex, Nicolas J Rawlence, Bruce C Robertson
    Abstract:

    The impact of Population Bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent Population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000–5,000 individuals in the wild and it is likely that the recent Population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent Bottleneck for only one Population and a range-wide decline in Ne dating back some 300 – 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large Population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

  • ancient and contemporary dna reveal a pre human decline but no Population Bottleneck associated with recent human persecution in the kea nestor notabilis
    PLOS ONE, 2015
    Co-Authors: Nicolas Dussex, Nicolas J Rawlence, Bruce C Robertson
    Abstract:

    The impact of Population Bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent Population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000–5,000 individuals in the wild and it is likely that the recent Population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent Bottleneck for only one Population and a range-wide decline in Ne dating back some 300 – 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large Population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

Elizabeth Friar - One of the best experts on this subject based on the ideXlab platform.

  • microsatellite analysis of a Population crash and Bottleneck in the mauna kea silversword argyroxiphium sandwicense ssp sandwicense asteraceae and its implications for reintroduction
    Molecular Ecology, 2000
    Co-Authors: Elizabeth Friar, T Ladoux, Eric H Roalson, Robert H Robichaux
    Abstract:

    The Mauna Kea silversword, Argyroxiphium sandwicense ssp. sandwicense, has experienced both a severe Population crash associated with an increase in alien ungulate Populations on Mauna Kea, and a Population Bottleneck associated with reintroduction. In this paper, we address the genetic consequences of both demographic events using eight microsatellite loci. The Population crash was not accompanied by a significant reduction in number of alleles or heterozygosity. However, the Population Bottleneck was accompanied by significant reductions in observed number of alleles, effective number of alleles, and expected heterozygosity, though not in observed heterozygosity. The effective size of the Population Bottleneck was calculated using both observed heterozygosities and allele frequency variances. Both methods corroborated the historical census size of the Population Bottleneck of at most three individuals. The results suggest that: (i) small Populations, even those that result from severe reductions in historical Population size and extent, are not necessarily genetically depauperate; and (ii) species reintroduction plans need to be conceived and implemented carefully, with due consideration to the genetic impact of sampling for reintroduction.

  • molecular genetic consequences of a Population Bottleneck associated with reintroduction of the mauna kea silversword arg yroxiphium sandwicense ssp sandwicense asteraceae
    Conservation Biology, 1997
    Co-Authors: Robert H Robichaux, Elizabeth Friar, David W Mount
    Abstract:

    The endangered Mauna Kea silversword (Argyroxiphium sandwicense ssp. sandwicense) has experienced a severe decline in distribution and abundance because of predation by alien ungulates. By the late 1970s only a small remnant natural Population persisted on the Mauna Kea volcano on the Island of Hawaii. The Hawaii Department of Land and Natural Resources, Division of Forestry and Wildlife, initiated an outplanting program in the 1970s to promote recovery of A. sandwicense ssp. sandwicense. Intermittent outplanting since 1973 has generated an outplanted Population of over 450 plants on Mauna Kea, but the program has unintentionally resulted in a major Population Bottleneck. All plants in the outplanted Population appear to be first- or subsequent-generation offspring of only two maternal founders from the natural Population. Genetic variation in the natural and outplanted Populations was assessed for 90 random amplified polymorphic DNA loci. Eleven loci were detectably polymorphic in the natural Population, whereas only three loci were detectably polymorphic in the outplanted Population. Thus, the Population Bottleneck has been accompanied by a 73% reduction in the level of detectable polymorphism. In addition, for eight loci, the Population Bottleneck has resulted in the loss of the marker allele in the outplanted Population. A management strategy involving manual pollen transfer has recently been implemented to incorporate additional founders from the natural Population into the outplanting program. As a supplement to the outplanting program, the strategy also includes a program promoting direct seedling establishment following manual pollen transfer. Incorporating additional founders may serve to overcome the legacy of the Population Bottleneck, especially if founder representation can be equalized. La Espada Plateada de Mauna Kea (Argyroxiphium sandwicense ssp. sandwicense) esta en peligro de extincion debido a una severa declinacion de su distribucion y abundancia en tiempos historicos causada por la depredacion de ungulados introducidos. A fines de la decada de 1970 solo persistia una pequena poblacion natural en el volcan Mauna Kea en la Isla de Hawaii. Tambien en esa decada el Departamento de Tierras y Recursos Naturales de Hawaii, por medio de la Division de Bosques y Vida Silvestre, inicio un programa de siembra para promover la recuperacion de Argyroxiphium sandwicense ssp. sandwicense. La siembra intermitente desde 1973 ha generado una poblacion de mas de 450 plantas en Mauna Kea. Sin embargo el programa de siembra, aunque sin intencion, ha resultado en un gran cuello de botella poblacional. Todas las plantas en la poblacion sembrada parecen ser la primera o subsecuentes generaciones de descendientes de solo dos fundadores maternos de la poblacion natural. Se determino la variacion genetica para 90 loci de ADN polimorficos amplificados en la poblacion natural y la sembrada. Once loci fueron marcadamente polimorficos en la poblacion natural, mientras que solo tres lo fueron en la poblacion sembrada. Por tanto, el cuello de botella poblacional esta acompanado por una reduccion del 73% en el nivel de polimorfismo detectable. Adicionalmente, el cuello de botella poblacional ha resultado en la perdida del alelo marcador para ocho loci en la poblacion sembrada. Recientemente se ha instrumentado una estrategia de manejo que involucra la transferencia manual de polen para incorporar fundadores adicionales de la poblacion natural al programa de siembra. Como un suplemento del programa de siembra, la estrategia tambien incluye un programa que promueve el establecimiento directo de plantulas despues de la transferencia manual de polen. La incorporacion de fundadores adicionales puede servir para superar el legado del cuello de botella, especialmente si la representacion de fundadores se equilibra.

Mark J Daly - One of the best experts on this subject based on the ideXlab platform.

  • whole genome view of the consequences of a Population Bottleneck using 2926 genome sequences from finland and united kingdom
    European Journal of Human Genetics, 2017
    Co-Authors: Himanshu Chheda, Priit Palta, Matti Pirinen, Shane Mccarthy, Klaudia Walter, Seppo Koskinen, Veikko Salomaa, Mark J Daly
    Abstract:

    Isolated Populations with enrichment of variants due to recent Population Bottlenecks provide a powerful resource for identifying disease-associated genetic variants and genes. As a model of an isolate Population, we sequenced the genomes of 1463 Finnish individuals as part of the Sequencing Initiative Suomi (SISu) Project. We compared the genomic profiles of the 1463 Finns to a sample of 1463 British individuals that were sequenced in parallel as part of the UK10K Project. Whereas there were no major differences in the allele frequency of common variants, a significant depletion of variants in the rare frequency spectrum was observed in Finns when comparing the two Populations. On the other hand, we observed >2.1 million variants that were twice as frequent among Finns compared with Britons and 800 000 variants that were more than 10 times more frequent in Finns. Furthermore, in Finns we observed a relative proportional enrichment of variants in the minor allele frequency range between 2 and 5% (P<2.2 × 10-16). When stratified by their functional annotations, loss-of-function variants showed the highest proportional enrichment in Finns (P=0.0291). In the non-coding part of the genome, variants in conserved regions (P=0.002) and promoters (P=0.01) were also significantly enriched in the Finnish samples. These functional categories represent the highest a priori power for downstream association studies of rare variants using Population isolates.

  • whole genome view of the consequences of a Population Bottleneck using 2926 genome sequences from finland and united kingdom
    bioRxiv, 2016
    Co-Authors: Himanshu Chheda, Priit Palta, Matti Pirinen, Shane Mccarthy, Klaudia Walter, Seppo Koskinen, Veikko Salomaa, Mark J Daly, Richard Durbin, Aarno Palotie
    Abstract:

    Isolated Populations with enrichment of variants due to recent Population Bottlenecks provide a powerful resource for identifying disease-associated genetic variants and genes. As a model of an isolate Population, we sequenced the genomes of 1463 Finnish individuals as part of the Sequencing Initiative Suomi (SISu) Project. We compared the genomic profiles of the 1463 Finns to a sample of 1463 British individuals that were sequenced in parallel as part of the UK10K Project. Whereas there were no major differences in the allele frequency of common variants, a significant depletion of variants in the rare frequency spectrum was observed in Finns when comparing the two Populations. On the other hand, we observed >2.1 million variants that were twice as frequent among Finns compared to Britons and 800,000 variants that were more than 10 times more frequent in Finns. Furthermore, in Finns we observed a relative proportional enrichment of variants in the minor allele frequency range between 2 - 5% (p