Development and characterization of 18 microsatellite loci for the Southern Leopard Frog, Rana sphenocephala

McKee, Anna M.; Lance, Stacey L.; Jones, Kenneth L.; Hagen, Cris; Glenn, Travis C.

doi:10.1007/s12686-010-9338-7

Cited by 5 publications

(6 citation statements)

References 10 publications

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“…Total genomic DNA was extracted and purified using DNeasy Blood and Tissue Kits (Qiagen, Hilden, Germany). Eleven microsatellite loci were amplified using primers developed by Hoffman, Arden, and Blouin () for R. pipiens (Rpi 100, Rpi 101, Rpi 103, Rpi 104, Rpi 106, Rpi 107, Rpi 108), by Hoffman and Blouin () for the Oregon spotted frog ( Rana pretiosa ; RP197 and RP415), and by McKee, Lance, Jones, Hagen, and Glenn () for the southern leopard frog ( Rana sphenocephala ; Rasp09 and Rasp20). Amplifications were conducted following the procedures published for each locus (Hoffman & Blouin, ; Hoffman et al, ; McKee et al, ).…”

Section: Methodsmentioning

confidence: 99%

Landscape genetics reveal broad and fine‐scale population structure due to landscape features and climate history in the northern leopard frog (Rana pipiens) in North Dakota

Waraniak

Fisher

Purcell

et al. 2019

Ecology and Evolution

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Prehistoric climate and landscape features play large roles structuring wildlife populations. The amphibians of the northern Great Plains of North America present an opportunity to investigate how these factors affect colonization, migration, and current population genetic structure. This study used 11 microsatellite loci to genotype 1,230 northern leopard frogs (Rana pipiens) from 41 wetlands (30 samples/wetland) across North Dakota. Genetic structure of the sampled frogs was evaluated using Bayesian and multivariate clustering methods. All analyses produced concordant results, identifying a major east–west split between two R. pipiens population clusters separated by the Missouri River. Substructuring within the two major identified population clusters was also found. Spatial principal component analysis (sPCA) and variance partitioning analysis identified distance, river basins, and the Missouri River as the most important landscape factors differentiating R. pipiens populations across the state. Bayesian reconstruction of coalescence times suggested the major east–west split occurred ~13–18 kya during a period of glacial retreat in the northern Great Plains and substructuring largely occurred ~5–11 kya during a period of extreme drought cycles. A range‐wide species distribution model (SDM) for R. pipiens was developed and applied to prehistoric climate conditions during the Last Glacial Maximum (21 kya) and the mid‐Holocene (6 kya) from the CCSM4 climate model to identify potential refugia. The SDM indicated potential refugia existed in South Dakota or further south in Nebraska. The ancestral populations of R. pipiens in North Dakota may have inhabited these refugia, but more sampling outside the state is needed to reconstruct the route of colonization. Using microsatellite genotype data, this study determined that colonization from glacial refugia, drought dynamics in the northern Great Plains, and major rivers acting as barriers to gene flow were the defining forces shaping the regional population structure of R. pipiens in North Dakota.

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Section: Methodsmentioning

confidence: 99%

Landscape genetics reveal broad and fine‐scale population structure due to landscape features and climate history in the northern leopard frog (Rana pipiens) in North Dakota

Waraniak

Fisher

Purcell

et al. 2019

Ecology and Evolution

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“…DNA was extracted from Southern Leopard frog tissue using silica‐binding techniques (Lance et al., ) and from Dwarf salamander tissue using phenol chloroform extractions (Sambrook, Fritsch, & Maniatis, ). Southern Leopard frog DNA samples were screened at 11 microsatellite loci (Rasp03, Rasp07, Rasp09, Rasp10, Rasp13, Rasp17, Rasp37, Rasp45, Rasp50, Rasp53, and Rasp55) (McKee, Lance, Jones, Hagen, & Glenn, ) and Dwarf salamander DNA samples at 12 microsatellite loci (Mckee, Lance, Jones, Hagen, & Glenn, ) using a 3730xl Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). No template controls and DNA extraction negative controls were analyzed with samples to ensure systematic contamination was not an issue.…”

Section: Methodsmentioning

confidence: 99%

Habitat predictors of genetic diversity for two sympatric wetland‐breeding amphibian species

McKee

Maerz

Smith

et al. 2017

Ecology and Evolution

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Population genetic diversity is widely accepted as important to the conservation and management of wildlife. However, habitat features may differentially affect evolutionary processes that facilitate population genetic diversity among sympatric species. We measured genetic diversity for two pond‐breeding amphibian species (Dwarf salamanders, Eurycea quadridigitata; and Southern Leopard frogs, Lithobates sphenocephalus) to understand how habitat characteristics and spatial scale affect genetic diversity across a landscape. Samples were collected from wetlands on a longleaf pine reserve in Georgia. We genotyped microsatellite loci for both species to assess population structures and determine which habitat features were most closely associated with observed heterozygosity and rarefied allelic richness. Both species exhibited significant population genetic structure; however, structure in Southern Leopard frogs was driven primarily by one outlier site. Dwarf salamander allelic richness was greater at sites with less surrounding road area within 0.5 km and more wetland area within 1.0 and 2.5 km, and heterozygosity was greater at sites with more wetland area within 0.5 km. In contrast, neither measure of Southern Leopard frog genetic diversity was associated with any habitat features at any scale we evaluated. Genetic diversity in the Dwarf salamander was strongly associated with land cover variables up to 2.5 km away from breeding wetlands, and/or results suggest that minimizing roads in wetland buffers may be beneficial to the maintenance of population genetic diversity. This study suggests that patterns of genetic differentiation and genetic diversity have associations with different habitat features across different spatial scales for two syntopic pond‐breeding amphibian species.

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“…A total of 166 specimens (Table 1) were genotyped for six microsatellite loci that were developed for R. sphenocephala (McKee et al. 2011): Rasp03, Rasp07, Rasp09, Rasp10, Rasp42 and Rasp67.…”

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“…2011): Rasp03, Rasp07, Rasp09, Rasp10, Rasp42 and Rasp67. Based on the PCR protocol used by McKee et al. (2011), a 12.5‐μL reaction was used, containing 1.0 μL PCR Buffer II (10X, Applied Biosystems), 1.3 μL MgCl 2 (25 m m ), 0.76 μL labelled primer (10 μ m ), 0.76 μL unlabelled primer (10 μ m ), 1.7 μL dNTP solution (5 m m ), 1 U AmpliTaq (Applied Biosystems) and 2–5 ng of genomic DNA.…”

mentioning

confidence: 99%

“…(2011), a 12.5‐μL reaction was used, containing 1.0 μL PCR Buffer II (10X, Applied Biosystems), 1.3 μL MgCl 2 (25 m m ), 0.76 μL labelled primer (10 μ m ), 0.76 μL unlabelled primer (10 μ m ), 1.7 μL dNTP solution (5 m m ), 1 U AmpliTaq (Applied Biosystems) and 2–5 ng of genomic DNA. Amplification was carried out according to the specifications in McKee et al. (2011), using either touchdown protocols or constant annealing temperatures.…”

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Phylogeographic analyses of the southern leopard frog: the impact of geography and climate on the distribution of genetic lineages vs. subspecies

Newman

Rissler

2011

Molecular Ecology

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The southeastern United States is a major phylogeographic break hotspot for amphibians, but the processes underlying this hotspot remain to be explicitly tested. We test the correlation of genetic lineages with subspecies breaks in the southeastern United States and the association of such breaks with climate, using Rana sphenocephala as a case study, and place our results in the broader context of the Alabama-Appalachian suture zone (AL-Appalachian SZ). We use genetic and ecological methods to (i) determine whether genetic lineages are coincident with the AL-Appalachian SZ or the subspecies and (ii) test the correlation of major climatic breaks with genetic structure and morphological variation in R. sphenocephala. Bayesian phylogenetic analyses of the ND1 mtDNA gene and microsatellite cluster analyses revealed two distinct lineages with over 4% sequence divergence. The geographic distributions of the two lineages are concordant with the AL-Appalachian SZ but do not correspond to the ranges of the subspecies based on morphology. Mantel tests revealed that isolation by distance and historical barriers to gene flow, rather than climate, are the major drivers of genetic divergence at neutral loci. Examination of climate breaks across the Southeast revealed a pattern incongruent with suture zone hotspots, suggesting that phylogenetic structure has been driven primarily by historical factors, such as isolation, the Appalachian Mountains and the Apalachicola/Chattahoochee/Flint River Basin. However, climate breaks are consistent with the geographic distribution of the subspecies of R. sphenocephala, suggesting that environmental pressures may be driving divergence in morphological traits that outpaces molecular evolution.

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Development and characterization of 18 microsatellite loci for the Southern Leopard Frog, Rana sphenocephala

Cited by 5 publications

References 10 publications

Landscape genetics reveal broad and fine‐scale population structure due to landscape features and climate history in the northern leopard frog (Rana pipiens) in North Dakota

Landscape genetics reveal broad and fine‐scale population structure due to landscape features and climate history in the northern leopard frog (Rana pipiens) in North Dakota

Habitat predictors of genetic diversity for two sympatric wetland‐breeding amphibian species

Phylogeographic analyses of the southern leopard frog: the impact of geography and climate on the distribution of genetic lineages vs. subspecies

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