Microsatellite markers for the deer mouse <i>Peromyscus maniculatus</i>

Chirhart, Scott E.; Honeycutt, Rodney L.; Greenbaum, Ira F.

doi:10.1046/j.1365-294x.2000.01044-6.x

Cited by 33 publications

(18 citation statements)

References 4 publications

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“…Appendices sizes, and numbers of alleles for the 12 populations analyzed in this study Schmidt (1999) and were GT repeats and the remaining primers were from Chirhart et al (2000) and were CA repeats. T A is the optimal annealing temperature.…”

Section: Discussionmentioning

confidence: 99%

“…We used eight Peromyscus-specific dinucleotide microsatellite primers designed by Schmidt (1999; PLGT15, PLGT62, and PLGT67) and Chirhart et al (2000; Pml01, Pml04, Pml06, Pml10, and Pml12; Appendix 2). Polymerase chain reaction (PCR) amplification was performed in 25 ll-volumes containing approximately 5 ll DNA at 5 ng/ll, 2.5 ll 109 PCR buffer (Promega) or Ancient buffer, 4 ll of 5 mM dNTPs (Sigma), 0.25 ll of fluorescent labeled (forward) and unlabeled (reverse; Qiagen) primers at 100 lM each, 0.15 ll Taq DNA Polymerase (5 U/ll; Promega), and appropriate volumes of MgCl 2 (25 mM; Promega) and ddH 2 O (Appendix 2).…”

Section: Study Area and Trapping Designmentioning

confidence: 99%

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Genetic estimates of immigration and emigration rates in relation to population density and forest patch area in Peromyscus leucopus

Anderson

Meikle

2010

Conserv Genet

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An emerging pattern is that population densities of generalist rodents are higher in small compared to large forest patches in fragmented landscapes. We used genetically based measures of migration between patches to test two dispersal-based hypotheses for this negative densityarea relationship: (1) emigration rates from small patches should be relatively lower compared to large patches (''inhibited dispersal hypothesis''), or (2) immigration rates should be higher into small than large patches (''immigration hypothesis''). Neither hypothesis was supported using data on dispersal inferred from eight microsatellite loci for 12 populations of Peromyscus leucopus in six small (1.3-2.7 ha) and six large (8-150 ha) forest patches. Emigration rates were not lower from and immigration rates were not higher into small than large patches. In fact, contrary to both hypotheses, emigration rates were higher from populations of P. leucopus in small compared to large patches. Based on a combination of genetic and field data, we speculate that higher reproduction in smaller patches resulted in higher densities which led to higher emigration rates from those patches. Rates of reproduction (presumably driven by better habitat conditions in smaller patches), rather than dispersal, seems to drive density differences in forest patches. We conclude that smaller forest patches within an agricultural matrix act as a source of individuals, and that migration rates are fairly high among forest patches regardless of size.

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Section: Discussionmentioning

confidence: 99%

Section: Study Area and Trapping Designmentioning

confidence: 99%

Genetic estimates of immigration and emigration rates in relation to population density and forest patch area in Peromyscus leucopus

Anderson

Meikle

2010

Conserv Genet

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“…Therefore, heterozygous individuals with null alleles may be falsely identified as homozygotes, resulting in erroneous estimations of equilibrium parameters (Reese et al, 2001). However, the inequality between H o and H e we observed may not be unexpected considering the distinction between the large number of alleles per locus and the relatively small sample sizes surveyed per population (Chirhart et al, 2000).…”

Section: Discussionmentioning

confidence: 76%

“…(Reese et al, 2001), and Peromyscus sp. (Schmidt, 1999;Wooten et al, 1999;Chirhart et al, 2000). Within the genus Peromyscus, P. maniculatus has received the most attention in terms of systematic biology and evolutionary genetics (Chirhart et al, 2000); however, surprisingly few microsatellite studies have addressed P. maniculatus.…”

Section: Introductionmentioning

confidence: 99%

Analyses of Gene Flow Among Populations of Deer Mice (Peromyscus Maniculatus) at Sites Near Hantavirus Pulmonary Syndrome Case-Patient Residences

Root

Black

Calisher

et al. 2003

Journal of Wildlife Diseases

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Gene flow and potential for Sin Nombre virus (SNV) trafficking of the deer mouse (Peromyscus maniculatus) was studied in Delta and Mesa counties of western Colorado (USA). The study areas included Grand Mesa and surrounding grazing and agricultural areas. This area has several natural potential barriers to rodent gene flow, including rivers, cliffs, and mountains. Ten study sites were utilized in a spatially nested design ranging from 0.65-81 km apart; four of these sites were at or near human hantavirus pulmonary syndrome (HPS) case-patient residences. One HPS case occurred on the north side of Grand Mesa in 1993; the other three (two confirmed, one presumptive) occurred on the south side of Grand Mesa between 1999-2000. Blood and tissue samples were collected from each of 221 deer mice captured from 1999-2000. Blood samples were tested for IgG antibody to SNV. At least one deer mouse had antibody to SNV at nine of 10 sites. Genomic DNA was isolated from tissue samples and alleles at six microsatellite loci were amplified by polymerase chain reaction (PCR). Polymorphisms were resolved on denaturing polyacrylamide gels and visualized by silver staining. Traditional population genetic analyses of this study indicated moderate population subdivision among the populations surveyed, slight evidence of isolation by distance, and that the Gunnison River system may hinder gene flow in this area. Application of assignment tests indicated that approximately 73-85% of mice were assigned to their population of capture. Many of the misclassifications occurred among sites less than 1 km apart; however, some long-distance misclassifications were noted. Additionally, some misclassifications were noted among study sites on different sides of the Gunnison River system, indicating that the riparian corridor of this system may facilitate some gene flow. Overall, these data indicate that SNV trafficking is more likely at the local level, but some long-distance trafficking may be possible, especially where select habitat variables favor long-distance movements.

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“…To enable a comparison between AFLP markers and the more widely used microsatellite markers, all 179 samples were also genotyped at 12 microsatellite loci: Pml1, Pml2, Pml4, Pml6, Pml7, Pml10, Pml11 (Chirhart et al, 2000), Plgt58, Plgt62, Plgt66 (Schmidt, 1999), Po3-68 and Po97 (Prince et al, 2002). Amplification was carried out in 10 ml volumes containing 0.5 ml of diluted template DNA, 1 Â buffer (100 mM Tris-HCl pH 8.0, 50 mM KCl, 1.5 mM MgCl 2 , 0.01% Tween 20, 0.01% gelatine, 0.01% IGepal), 0.5 mM additional MgCl 2 , 0.2 mM each of dATP, dTTP and dGTP, 0.05 mM dCTP, 400 nM of each primer, 0.25 U Taq polymerase, and 0.1 mCi [a 32 P]-dCTP.…”

Section: Empirical Datamentioning

confidence: 99%

Estimating levels of inbreeding using AFLP markers

2007

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In the absence of detailed pedigree records, researchers have attempted to estimate individuals' levels of inbreeding using molecular markers, generally making use of heterozygosity measures based on microsatellite markers. Here we report and validate a method for estimating an individual's inbreeding coefficient, f, using amplified fragment length polymorphism (AFLP) markers. We use simulations to confirm that our measure scales appropriately with f when allele frequencies can be estimated from a subset of outbred individuals. We also present an approach for obtaining satisfactory estimates even in the absence of an independent set of known outbred individuals from which to estimate allele frequencies. We then test our method against empirical data from 179 wild and captive-bred old-field mice, Peromyscus polionotus subgriseus, comprising pedigree-based estimates of f, along with genetic data from 94 AFLP markers and 12 microsatellites. Inbreeding estimates based on both AFLP and microsatellite markers were found to correlate strongly with pedigree-based inbreeding coefficients. Owing to their ease of amplification in any species, AFLP markers may prove to be a valuable new tool for estimating f in natural populations and for examining correlations between heterozygosity and fitness.

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Microsatellite markers for the deer mouse Peromyscus maniculatus

Cited by 33 publications

References 4 publications

Genetic estimates of immigration and emigration rates in relation to population density and forest patch area in Peromyscus leucopus

Genetic estimates of immigration and emigration rates in relation to population density and forest patch area in Peromyscus leucopus

Analyses of Gene Flow Among Populations of Deer Mice (Peromyscus Maniculatus) at Sites Near Hantavirus Pulmonary Syndrome Case-Patient Residences

Estimating levels of inbreeding using AFLP markers

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