Characterization and Isolation of Five Microsatellite Loci in Northern Flying Squirrels,<i>Glaucomys sabrinus</i>(Sciuridae, Rodentia)

Kiesow, Alyssa M.; Wallace, Lisa E.; Britten, Hugh B.

doi:10.3398/064.071.0413

Cited by 6 publications

(7 citation statements)

References 11 publications

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“…We tested three sample types: tissue, 'high', and 'low' concentration museum samples to evaluate amplification across microsatellites of varying lengths. Previously published microsatellites from Glaucomys sabrinus (northern flying squirrel)-a species which historically included G. oregonensis-were used in this study (GS-2, GS-4; Zittlau et al 2000, and GLSA-12, GLSA-22, GLSA-52; Kiesow et al 2011, Table 2). Two 'short' microsatellites were selected (GS-2 and GS-4), which included any marker under 150 bp in length according to published allele sizes, two 'medium' , and one 'long' microsatellite > 200 bp).…”

Section: Microsatellite Selectionmentioning

confidence: 99%

Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

Yuan

Malekos

Hawkins

2021

Conservation Genet Resour

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The use of museum specimens held in natural history repositories for population and conservation genetic research is increasing in tandem with the use of massively parallel sequencing technologies. Short Tandem Repeats (STRs), or microsatellite loci, are commonly used genetic markers in wildlife and population genetic studies. However, they traditionally suffered from a host of issues including length homoplasy, high costs, low throughput, and difficulties in reproducibility across laboratories. Massively parallel sequencing technologies can address these problems, but the incorporation of museum specimen derived DNA suffers from significant fragmentation and exogenous DNA contamination. Combatting these issues requires extra measures of stringency in the lab and during data analysis, yet there have not been any high-throughput sequencing studies evaluating microsatellite allelic dropout from museum specimen extracted DNA. In this study, we evaluate genotyping errors derived from mammalian museum skin DNA extracts for previously characterized microsatellites across PCR replicates utilizing high-throughput sequencing. We found it useful to classify samples based on DNA concentration, which determined the rate by which genotypes were accurately recovered. Longer microsatellites performed worse in all museum specimens. Allelic dropout rates across loci were dependent on sample quantity, with high concentration museum specimens performing as well and recovering quality metrics nearly as high as the frozen tissue sample. Based on our results, we provide a set of best practices for quality assurance and incorporation of reliable genotypes from museum specimens.

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Section: Microsatellite Selectionmentioning

confidence: 99%

Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

Yuan

Malekos

Hawkins

2021

Conservation Genet Resour

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“…1) for microsatellite analysis (CON = 23, PC = 38; Appendix I). Individuals were genotyped at 8 polymorphic microsatellite loci using primers developed for G. sabrinus: GS-04, GS-08, GS-10, GS-13, GS-16 (Zittlau et al 2000), GLSA-12, GLSA-48, GLSA-52 (Kiesow et al 2011). PCR conditions and fragment analysis for these loci were conducted as described by Schumacher (2012).…”

Section: Methodsmentioning

confidence: 99%

Genetic data reveal a cryptic species of New World flying squirrel: Glaucomys oregonensis

Arbogast

Schumacher

Kerhoulas

et al. 2017

Journal of Mammalogy

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The genus Glaucomys (New World flying squirrels) is currently considered to be comprised of 2 species, the northern flying squirrel (G. sabrinus) and the southern flying squirrel (G. volans). We synthesize new information from mitochondrial DNA (mtDNA) control region sequences and microsatellite data to demonstrate that the genus consists of 3, rather than 2 species, and that Glaucomys sabrinus, as currently recognized, is actually composed of 2 separate, apparently non-hybridizing species. Control region mtDNA data from 185 individuals across North America revealed 2 distinct clades embedded within G. sabrinus: a widespread "Continental" lineage and a more geographically restricted "Pacific Coastal" lineage. The geographic distributions of these 2 lineages are largely mutually exclusive, with sympatry observed at only 3 sites in the Pacific Northwest. Analysis of 8 microsatellite loci showed no evidence of hybridization between the 2 lineages of G. sabrinus in the region of sympatry. This lack of gene flow is noteworthy given that populations of the Continental lineage of G. sabrinus have been shown to hybridize with G. volans in southeastern Canada. Finally, phylogenetic analyses and estimates of divergence times show that G. volans and Continental G. sabrinus are actually sister taxa that diverged from one another more recently than either did from Pacific Coastal G. sabrinus. We propose that these observations provide strong evidence for a third, previously unrecognized species of North American flying squirrel, whose geographic range extends along the Pacific Coast from southern British Columbia to southern California. Glaucomys oregonensis (Bachman, 1839), whose type locality is in Oregon, is the senior available name for this taxon. We propose that this newly recognized species be given the common name "Humboldt's flying squirrel."

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“…These simple tandem-repeats are abundantly and randomly distributed throughout genomes, and due to their high polymorphism and rapid evolutionary rate, microsatellite loci are useful for analyses of genetic diversity, population structure, gene flow, and hybridization (Pritchard et al, 2000;Wang et al, 2014). SSR genotyping, which is based on the numbers of repeats, may improve our understanding of genetic relationships within populations or among close relatives (Roy et al, 1994). SSR allele inheritance proceeds in accordance with Mendelian laws of segregation and independent assortment.…”

Section: Genetic Bias In Egmentioning

confidence: 99%

Genetic Variation in an Experimental Goldfish Derived From Hybridization

Wang

Zeng

et al. 2020

Front. Genet.

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Owning to the extreme difficulty in identifying the primary generation (G0), the common ancestor of various twin-tail goldfish strains remains unclear. However, several authors have hypothesized that this ancestor may have been the crucian carp (Carassius auratus). Previously, we generated an experimental hybrid goldfish (EG) from the interspecific hybridization of red crucian carp (Carassius auratus ♀, RCC) × common carp (Cyprinus carpio ♂, CC). Unlike either parent, EG possessed twin caudal fins similar to those of natural goldfish (Carassius auratus, NG). The genetic characteristics of EG, as well as the mechanisms underlying its formation, are largely unknown. Here, we identified the genetic variation in the chordin gene that was associated with the formation of the twin-tail phenotype in EG: a stop codon mutation at the 127th amino acid. Furthermore, simple sequence repeat (SSR) genotyping indicated that, among the six alleles, all of the EG alleles were also present in female parent (RCC), but alleles specific to the male parent (CC) were completely lost. At some loci, EG and NG alleles differed, showing that these morphologically similar goldfish were genetically dissimilar. Collectively, our results demonstrated that genetic variations and differentiation contributed to the changes of morphological characteristics in hybrid offspring. This analysis of genetic variation in EG sheds new light on the common ancestor of NG, as well as on the role of hybridization and artificial breeding in NG speciation.

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Characterization and Isolation of Five Microsatellite Loci in Northern Flying Squirrels,Glaucomys sabrinus(Sciuridae, Rodentia)

Cited by 6 publications

References 11 publications

Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

Genetic data reveal a cryptic species of New World flying squirrel: Glaucomys oregonensis

Genetic Variation in an Experimental Goldfish Derived From Hybridization

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