Historic and contemporary levels of genetic variation in two New Zealand passerines with different histories of decline

Taylor, Sabrina S.; Jamieson, Ian G.; Wallis, Graham P.

doi:10.1111/j.1420-9101.2007.01362.x

Cited by 51 publications

(55 citation statements)

References 85 publications

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“…Viable DNA obtained from historical material such as museum specimens, scales, feathers, hair and/or bones [2] has been used to examine past population structure [3,4] and its persistence over time [5,6], population collapses [7] and bottlenecks [8], founder events [9] and the consequences of stocking of populations with non-native individuals [10]. However, a crucial limitation of historical samples is that they generally yield DNA of a lower amount/quality than is recommended for molecular genetic studies.…”

Section: Introductionmentioning

confidence: 99%

Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar)

Johnston

Lindqvist

Niemelä³

et al. 2013

BMC Genomics

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Background: DNA extracted from historical samples is an important resource for understanding genetic consequences of anthropogenic influences and long-term environmental change. However, such samples generally yield DNA of a lower amount and quality, and the extent to which DNA degradation affects SNP genotyping success and allele frequency estimation is not well understood. We conducted high density SNP genotyping and allele frequency estimation in both individual DNA samples and pooled DNA samples extracted from dried Atlantic salmon (Salmo salar) scales stored at room temperature for up to 35 years, and assessed genotyping success, repeatability and accuracy of allele frequency estimation using a high density SNP genotyping array. Results: In individual DNA samples, genotyping success and repeatability was very high (> 0.973 and > 0.998, respectively) in samples stored for up to 35 years; both increased with the proportion of DNA of fragment size > 1000 bp. In pooled DNA samples, allele frequency estimation was highly repeatable (Repeatability = 0.986) and highly correlated with empirical allele frequency measures (Mean Adjusted R 2 = 0.991); allele frequency could be accurately estimated in > 95% of pooled DNA samples with a reference group of at least 30 individuals. SNPs located in polyploid regions of the genome were more sensitive to DNA degradation: older samples had lower genotyping success at these loci, and a larger reference panel of individuals was required to accurately estimate allele frequencies.

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Section: Introductionmentioning

confidence: 99%

Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar)

Johnston

Lindqvist

Niemelä³

et al. 2013

BMC Genomics

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“…Hansson et al 2000;Ortego et al 2007c), or decreases after population bottlenecks (e.g. Groombridge et al 2000;Taylor et al 2007). The association between genetic diversity and the degree of connection/size of local subpopulations has also been extensively studied in a metapopulation context (e.g.…”

Section: Introductionmentioning

confidence: 99%

Individual genetic diversity correlates with the size and spatial isolation of natal colonies in a bird metapopulation

et al. 2008

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The genetic consequences of small population size and isolation are of central concern in both population and conservation biology. Organisms with a metapopulation structure generally show effective population sizes that are much smaller than the number of mature individuals and this can reduce genetic diversity especially in small sized and isolated subpopulations. Here, we examine the association between heterozygosity and the size and spatial isolation of natal colonies in a metapopulation of lesser kestrels (Falco naumanni ). For this purpose, we used capture-mark-recapture data to determine the patterns of immigration into the studied colonies, and 11 highly polymorphic microsatellite markers that allowed us to estimate genetic diversity of locally born individuals. We found that individuals born in smaller and more isolated colonies were genetically less diverse. These colonies received a lower number of immigrants, supporting the idea that both reduced gene flow and small population size are responsible for the genetic pattern observed. Our results are particularly intriguing because the lesser kestrel is a vagile and migratory species with great movement capacity and dispersal potential. Overall, this study provides evidence of the association between individual heterozygosity and the size and spatial isolation of natal colonies in a highly mobile vertebrate showing relatively frequent dispersal and low genetic differentiation among local subpopulations.

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“…However, relatively few studies have incorporated older museum specimens to assess changes in genetic diversity over time, despite their potential utility for informing conservation and management of threatened and endangered species (but see Godoy et al, 2004, Muñoz-Fuentes et al 2005, Brown et al 2007, Taylor et al 2007, Haig et al 2011. Our results highlight the importance and utility of incorporating museum specimens in conservation-genetic studies.…”

Section: Discussionmentioning

confidence: 98%

Temporal Analysis of mtDNA Variation Reveals Decreased Genetic Diversity in Least Terns

2012

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The Least Tern (Sternula antillarum) has undergone large population declines over the last century as a result of direct and indirect anthropogenic factors. The genetic implications of these declines are unknown. We used historical museum specimens {pre-1960) and contemporary (2001)(2002)(2003)(2004)(2005) samples to examine range-wide phylogeographic patterns and investigate potential loss in the species' genetic variation. We obtained sequences (522 bp) ofthe mitochondria! gene for NADH dehydrogenase subunit 6 (ND6) from 268 individuals from across the species' range. Phylogeographic analysis revealed no association with geography or traditional subspecies designations. However, we detected potential reductions in genetic diversity in contemporary samples frotn California and the Atlantic coast Least Tern from that in historical samples, suggesting that current genetic diversity in Least Tern populations is lower than in their pre-1960 counterparts. Our results offer unique insights into changes in the Least Tern's genetic diversity over the past century and highlight the importance and utility of museum specimens in studies of conservation genetics. El Análisis Temporal de la Variación de ADNmt Revela una Menor Diversidad Genética enSternula antillarumResumen. Sternula antillarum ha sufrido grandes disminuciones poblacionales a lo largo del tíltimo siglo como resultado de factores antrópicos directos e indirectos. Las implicancias genéticas de estas disminuciones son desconocidas. Usamos muestras de especímenes de museo históricas (antes de 1960) y contetnporáneas (2001)(2002)(2003)(2004)(2005) para examinar los patrones filogenéticos en todo el rango e investigar pérdidas potenciales en la variación genética de la especie. Obtuvimos secuencias (522 pares de bases) del gen mitocondrial para la subunidad 6 de la deshidrogenasa NADH (ND6) de 268 individuos provenientes de todo el rango de la especie. Los análisis filogené-ticos revelaron que no existen asociaciones con las designaciones de subespecies geográficas o tradicionales. Sin embargo, detectamos reducciones potenciales en la diversidad genética en muestras contemporáneas de S. antillarum de California y la costa atlántica en comparación con muestras históricas, sugiriendo que la diversidad genética actual en las poblaciones de S. antillarum es menor que la de sus congéneres de antes de 1960. Nuestros resultados brindan evidencias únicas de los cambios en la diversidad genética de S. antillarum a lo largo del último siglo y destacan la importancia y la utilidad de los especímenes de museo en los estudios de genética de la conservación.

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Historic and contemporary levels of genetic variation in two New Zealand passerines with different histories of decline

Cited by 51 publications

References 85 publications

Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar)

Fish scales and SNP chips: SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon (Salmo salar)

Individual genetic diversity correlates with the size and spatial isolation of natal colonies in a bird metapopulation

Temporal Analysis of mtDNA Variation Reveals Decreased Genetic Diversity in Least Terns

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