Genetic Variation among Ambystoma Breeding Populations on the Savannah River Site

Kinkead, Karen E.; Abbott, Albert G.; Otis, David L.

doi:10.1007/s10592-006-9168-z

Cited by 16 publications

(18 citation statements)

References 46 publications

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“…We found all estimates of N e to be near or above census size for A. talpoideum at RB. Metapopulation structure with genetically relevant migration between breeding ponds has been found in Ambystoma species at this site (Kinkead et al 2006). We also found signatures of admixture between the two wetlands in the current study.…”

Section: Discussionsupporting

confidence: 81%

Temporal genetic and demographic monitoring of pond-breeding amphibians in three contrasting population systems

2015

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Quantifying the relationship between demographic patterns and genetic diversity are important in predicting temporal population genetic changes. To make predictions there must be an understanding of the relationship between census size, the effective number of breeders (N b ) and effective population size (N e ). We evaluate the temporal genetic variation between three populations of Ambystoma salamanders, and compare genetic and demographic estimates of N b and N e . We sampled two wetlands, RB and GB for A. opacum and sampled A. talpoideum at RB, over a 20-year period. Ambystoma opacum colonized the RB wetland in 1980 and the population has steadily expanded as A. talpoideum has declined towards local extinction; the GB population of A. opacum has remained relatively large and stable over this same time period. Genetic variation at 10 microsatellites remained stable at each population over the sampled time frame, and did not reflect changes in population size. Genetic estimates of N b also did not reflect demographic trends, and were lower than demographic estimates of N b . Genetic methods of determining N e gave similar estimates to demographic methods. Our findings indicate that sample sizes and number of markers typically used in genetic studies do not provide enough precision to monitor population size changes in amphibians, which likely violate many of the assumptions of N b and N e estimation models. These findings should be considered when using N e in conservation and management assessments of amphibian populations.

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Section: Discussionsupporting

confidence: 81%

Temporal genetic and demographic monitoring of pond-breeding amphibians in three contrasting population systems

2015

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“…Amplified fragment length polymorphism has been used as genetic markers for paternity studies in newts (Lissotriton; Whitlock et al 2006;Jehle et al 2007); to study the genetic variation in alpine salamanders (Salamandra; Riberon et al 2004), coastal giant salamanders (Dicamptodon; Curtis and Taylor 2003), and mole salamanders (Ambystoma; Kinkead et al 2007); and to investigate lineage mapping in mole salamanders (Ambystoma; Voss and Schaffer 1997). a Lineages were derived from the maximum-likelihood procedure (Fig.…”

Section: Phylogenetic Structure-aflp Fragmentsmentioning

confidence: 99%

“…Fine-scaled genetic markers are often necessary to investigate genetic diversity, and one technique now gaining popularity is amplified fragment length polymorphism (AFLP; Voss et al 1995). This technique is a PCR-based, anonymous dominant-marker technique that has been used to delimit species boundaries, uncover new species, and investigate intraspecific phylogeographic patterns (Shaw 2002;Seman et al 2003;Wang et al 2003;Creer et al 2004;Finn et al 2006;Mendelson and Simons 2006;Garoia et al 2007;Kinkead et al 2007;Nicolè et al 2007). Amplified fragment length polymorphism has been extensively used in analyses of genetic variation in plants (Hoarau et al 2001;Van Cutsem et al 2003;Garcia et al 2004;Albach et al 2006;Agrimonti et al 2007;Andrade et al 2007;Assefa et al 2007;Nicolè et al 2007), microbes and fungi (Blears et al 1998;Bensch and Å kesson 2005), and invertebrates (Wilding et al 2001;Shaw 2002;Carisio et al 2004;Mock et al 2004;Pizzo et al 2006).…”

Section: Introductionmentioning

confidence: 99%

“…Amplified fragment length polymorphism has been extensively used in analyses of genetic variation in plants (Hoarau et al 2001;Van Cutsem et al 2003;Garcia et al 2004;Albach et al 2006;Agrimonti et al 2007;Andrade et al 2007;Assefa et al 2007;Nicolè et al 2007), microbes and fungi (Blears et al 1998;Bensch and Å kesson 2005), and invertebrates (Wilding et al 2001;Shaw 2002;Carisio et al 2004;Mock et al 2004;Pizzo et al 2006). Although AFLP studies on vertebrate taxa are limited (Bensch and Å kesson 2005), the number has increased over the past few years (Voss and Schaffer 1997;Ogden and Thorpe 2002;Curtis and Taylor 2003;Wang et al 2003;Riberon et al 2004;Lowe et al 2006;Whitlock et al 2006;Jehle et al 2007;Kinkead et al 2007;Makowsky et al 2009). At present, only seven known studies report the use of AFLP in salamander taxa (Voss and Schaffer 1997;Curtis and Taylor 2003;Riberon et al 2004;Lowe et al 2006;Whitlock et al 2006;Jehle et al 2007;Kinkead et al 2007), even though AFLP is a useful marker that can be used to investigate population structure and genetic variability at the species level (Mueller and Wolfenbarger 1999).…”

Section: Introductionmentioning

confidence: 99%

“…Although AFLP studies on vertebrate taxa are limited (Bensch and Å kesson 2005), the number has increased over the past few years (Voss and Schaffer 1997;Ogden and Thorpe 2002;Curtis and Taylor 2003;Wang et al 2003;Riberon et al 2004;Lowe et al 2006;Whitlock et al 2006;Jehle et al 2007;Kinkead et al 2007;Makowsky et al 2009). At present, only seven known studies report the use of AFLP in salamander taxa (Voss and Schaffer 1997;Curtis and Taylor 2003;Riberon et al 2004;Lowe et al 2006;Whitlock et al 2006;Jehle et al 2007;Kinkead et al 2007), even though AFLP is a useful marker that can be used to investigate population structure and genetic variability at the species level (Mueller and Wolfenbarger 1999).…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity in a narrowly endemic, recently described dusky salamander, Desmognathus folkertsi, from the southern Appalachian Mountains

2009

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To understand patterns of biodiversity and whether populations and species are in decline, the detection and description of cryptic biodiversity are essential. Salamanders are of particular conservation interest because they potentially harbor many undescribed species due to morphological conservatism. The dusky salamanders, genus Desmognathus, are a species-rich group in which morphologically cryptic species are especially common. Using a portion of the mitochondrial genome and amplified fragment length polymorphism (AFLP), we investigated the genetic diversity of the highly endemic, stream-dwelling salamander, Desmognathus folkertsi, across its known range in the Appalachian Mountains. Mitochondrial data revealed three well-supported lineages, one of which consisted of only one specimen; however, AFLP data were not congruent with the mitochondrial data. There was 1.11% uncorrected sequence divergence between the two wellsampled lineages. Desmognathus folkertsi exhibited 4.29% sequence divergence from the closely related D. quadramaculatus. Isolation by distance was found for both the AFLP and mitochondrial data when stream distance, rather than when straight-line (i.e., geographic) distance was used. Although genetic diversity is often partitioned by river drainages in freshwater taxa, we did not observe such a pattern in D. folkertsi. We propose that human-mediated dispersal by bait-bucket release may augment natural gene flow via aquatic dispersal across streams. Because this species was only recently discovered, the full extent of the geographic range is unknown. Therefore, an ecological niche model, using climate variables and the Maxent algorithm, was used to determine whether additional regions may be suitable for the species. The model predicted a small range limited to extreme southwestern North Carolina and extreme northeastern Georgia. We suggest future surveys be focused in these regions.

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Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian

O’Connell

Mulder

Maldonado

et al. 2019

Ecology and Evolution

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Effective conservation and management of pond‐breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding‐site connectivity. Population‐level studies of pond‐breeding amphibians typically sample larval life stages because they are easily captured and can be sampled nondestructively. These studies often identify high levels of relatedness between individuals from the same pond, which can be exacerbated by sampling the larval stage. Yet, the effect of these related individuals on population genetic studies using genomic data is not yet fully understood. Here, we assess the effect of within‐pond relatedness on population and landscape genetic analyses by focusing on the barred tiger salamanders (Ambystoma mavortium) from the Nebraska Sandhills. Utilizing genome‐wide SNPs generated using a double‐digest RADseq approach, we conducted standard population and landscape genetic analyses using datasets with and without siblings. We found that reduced sample sizes influenced parameter estimates more than the inclusion of siblings, but that within‐pond relatedness led to the inference of spurious population structure when analyses depended on allele frequencies. Our landscape genetic analyses also supported different models across datasets depending on the spatial resolution analyzed. We recommend that future studies not only test for relatedness among larval samples but also remove siblings before conducting population or landscape genetic analyses. We also recommend alternative sampling strategies to reduce sampling siblings before sequencing takes place. Biases introduced by unknowingly including siblings can have significant implications for population and landscape genetic analyses, and in turn, for species conservation strategies and outcomes.

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Genetic Variation among Ambystoma Breeding Populations on the Savannah River Site

Cited by 16 publications

References 46 publications

Temporal genetic and demographic monitoring of pond-breeding amphibians in three contrasting population systems

Temporal genetic and demographic monitoring of pond-breeding amphibians in three contrasting population systems

Genetic diversity in a narrowly endemic, recently described dusky salamander, Desmognathus folkertsi, from the southern Appalachian Mountains

Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian

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