Development of 24 microsatellite markers for the white nosed coati (Nasua narica) using 454 sequencing

Garibay, Eduardo Sánchez; Silva-Caballero, Adrián; Real-Monroy, Melina Del; Lance, Stacey L.; Valenzuela‐Galván, David; Ortega, Jorge

doi:10.1007/s12686-012-9617-6

Cited by 4 publications

(2 citation statements)

References 6 publications

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“…The set of 12 microsatellite primers used in this study was designed specifically for N. narica (Nasua 71, Nasua 193, Nasua 504, Nasua 833, Nasua 895, Nasua 931, Nasua 1050, Nasua 1251, Nasua 1757, Nasua 1785, Nasua 1990, and Nasua 2841- [53]). For these primers, the polymerase chain reactions (PCRs) were performed in a volume of 25 µL with 0.2 µL Platinum Taq DNA polymerase (Invitrogen TM ), 2.5 µL 10x RXN buffer, 2.5 µL of dNTP's, 2 µL of each primer 10 mM, 2.5 µL of BSA 100x, 1.5 µL of 50 mM MgCl 2 , 4 µL of DNA, and 9.8 µL of bidistilled water.…”

Section: Microsatellite Amplification and Genotypingmentioning

confidence: 99%

Patterns of Genetic Diversity of the White-Nosed Coati Reveals Phylogeographically Structured Subpopulations in Mexico

Silva-Caballero¹,

León-Ávila²,

Valenzuela‐Galván³

et al. 2017

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Coatis (Procyonidae; Nasua) are considered the only truly social mesocarnivore mammals in Neotropical forests. In Mexico, white-nosed coatis (Nasua narica) are suspected to have undergone population reduction due to habitat loss and fragmentation and led to a lack of genetic adaptability and genetic isolation throughout its range. We examined patterns of genetic diversity and connectivity of five populations of Nasua narica distributed throughout Mexico (n = 60) by sequencing an ≈ 800 bp fragment of the mitochondrial cytochrome-b gene and also by screening 12 microsatellite loci. We found moderate to high levels of genetic variability for both genetic markers. We recorded twenty-two different cytochrome-b haplotypes throughout the 5 sampled areas and found that each of the sampled population of white-nosed coatis in Mexico harbors unique haplotypes and only three haplotypes were shared among two different populations that were closer geographically. All populations had high haplotype diversity (h) (0.968 ± 0.008 (SD)) but lower levels of nucleotide diversity (π) of 0.007 ± 0.001 (SD). All microsatellite loci were polymorphic in all of the populations and the mean number of alleles per locus was 5.033 ± 1.545 (SD) with expected (H E ) and observed (H O 32F IT = 0.310). Significant differences between the five populations confirmed isolation by distance, which suggests genetic structure among five subpopulations.

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Section: Microsatellite Amplification and Genotypingmentioning

confidence: 99%

Patterns of Genetic Diversity of the White-Nosed Coati Reveals Phylogeographically Structured Subpopulations in Mexico

Silva-Caballero¹,

León-Ávila²,

Valenzuela‐Galván³

et al. 2017

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“…For example, Whitney & Karl () developed 38 loci in hawkfish, and Garibay et al . () developed 24 loci in the white‐nosed coati. To determine what number of microsatellites will probably be available for conservation genetics studies in the near future, we examined abstracts for three recent issues of Conservation Genetics Resources (March, June and September 2012), for number of novel microsatellite loci (161 articles).…”

Section: Point B: Marker Sets In the Genomic Agementioning

confidence: 99%

The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation‐based study

2013

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Detecting bottlenecks is a common task in molecular ecology. While several bottleneck detection methods exist, evaluations of their power have focused only on severe bottlenecks (e.g. to Ne~10). As a component of a recent review, Peery et al. (2012) analysed the power of two approaches, the M-ratio and heterozygote excess tests, to detect moderate bottlenecks (e.g. to Ne~100), which is realistic for many conservation situations. In this Comment, we address three important points relevant to but not considered in Peery et al. Under moderate bottleneck scenarios, we test the (i) relative advantage of sampling more markers vs. more individuals, (ii) potential power to detect the bottleneck when utilizing dozens of microsatellites (a realistic possibility for contemporary studies) and (iii) reduction in power when postbottleneck recovery has occurred. For the realistic situations examined, we show that (i) doubling the number of loci shows equal or better power than tripling the number of individuals, (ii) increasing the number of markers (up to 100) results in continued additive gains in power, and (iii) recovery after a moderate amount of time or gradual change in size reduces power, by up to one-half. Our results provide a practical supplement to Peery et al. and encourage the continued use of bottleneck detection methods in the genomic age, but also emphasize that the power under different sampling schemes should be estimated, using simulation modelling, as a routine component of molecular ecology studies.

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Conservation genetics of two critically endangered island dwarf carnivores

et al. 2021

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Development of 24 microsatellite markers for the white nosed coati (Nasua narica) using 454 sequencing

Cited by 4 publications

References 6 publications

Patterns of Genetic Diversity of the White-Nosed Coati Reveals Phylogeographically Structured Subpopulations in Mexico

Patterns of Genetic Diversity of the White-Nosed Coati Reveals Phylogeographically Structured Subpopulations in Mexico

The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation‐based study

Conservation genetics of two critically endangered island dwarf carnivores

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