Populations at risk: conservation genetics of kangaroo mice (Microdipodops) of the Great Basin Desert
Article first published online: 26 JUN 2013
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Ecology and Evolution
Volume 3, Issue 8, pages 2497–2513, August 2013
How to Cite
Ecology and Evolution 2013; 3(8): 2497–2513
- Issue published online: 12 AUG 2013
- Article first published online: 26 JUN 2013
- Manuscript Accepted: 14 MAY 2013
- Manuscript Revised: 10 MAY 2013
- Manuscript Received: 8 FEB 2013
- Texas A&M University
- State Wildlife Grants Program. Grant Number: T-3-19
- 2012. Primate DNA suggests long-term stability of an African rainforest. Ecol. Evol. 2:2829–2842. , , , , , , et al.
- 1952. Cenezoic climates of the Great Basin. Geol. Rundsch. 40:94–108.
- 1994. Molecular markers, natural history, and evolution. Sinauer, Sunderland, MA.
- 1999. Detecting population expansion and decline using microsatellites. Genetics 153:2013–2029.
- 2006. Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 22:341–345.
- 1999. Maximum-likelihood estimation of a migration matrix and effective population size in n subpopulations by using coalescent approach. Genetics 152:763–773. , and .
- 1981. Paleoclimatic significance of lake-level fluctuations in the Lahontan Basin. Quatern. Res. 16:390–403.
- 2001. M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods. Biotechniques 31:26–28. , , and .
- 1998. Regional trends of biological resources – Great Basin. Pp. 505–542 in M. Mac, C. Opler, P. Haecker and P. Doran, eds. Status and trends of the nation's biological resources. U.S. Department of the Interior, U.S. Geological Survey, Reston, VA. , , and .
- 2000. The geography of imperilment: targeting conservation toward critical biodiversity areas. Pp. 159–199 in B. A. Stein, L. S. Kutner and J. S. Adams, eds. Precious heritage: the nature conservancy and association for biodiversity information. Oxford Univ. Press, Inc., New York, NY. , , , , and .
- 2005. Mammalian beta diversity in the Great Basin, western USA: palaeontological data suggest deep origin of modern macroecological structure. Glob. Ecol. Biogeogr. 14:479–490.
- 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4:359–361. , and .
- 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611–2620. , , and .
- 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10:564–567. , and .
- 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinform. 1:47–50. , , and .
- 2008. A new Bayesian method to identify the environmental factors that influence recent migration. Genetics 178:1491–1504. , and .
- 1986. Pp. 1–212 in Geology of the Great Basin. University of Nevada Press, Reno, Nevada.
- 2011. Minimum viable populations: is there a ‘magic number’ for conservation practitioners? Trends Ecol. Evol. 26:307–316. , , , and .
- 1995. Effective population size/adult population size ratios in wildlife: a review. Genet. Res. 66:95–107.
- 1980. Evolutionary change in small populations. Pp. 135–140 in M. Soule and B. Wilcox, eds. Conservation biology: an evolutionary-ecological perspective. Sinauer Associates, Sunderland, MA.
- 1995. FSTAT (version 1.2): a computer program to calculate F-statistics. J. Hered. 86:485–486.
- 2005. A brief history of Great Basin pikas. J. Biogeogr. 32:2103–2111.
- 1981. Evolution, systematic, and historical biogeography of kangaroo mice, genus Microdipodops. Ph.D. Dissertation. University of California, Berkeley.
- 1998. Microdipodops megacephalus Merriam 1891 dark kangaroo mouse. Pp. 79–80 in D. J. Hafner, E. Yensen and G. L. Jr. Kirkland, eds. North American rodents: status survey and conservation action plan. Gland, Switzerland and Cambridge, U.K. , and .
- 2011. Phylogeography of the dark kangaroo mouse, Microdipodops megacephalus: cryptic lineages and dispersal routes in North America's Great Basin. J. Biogeogr. 38:1077–1097. , and .
- 2006. Kangaroo mice (Microdipodops megacephalus) of the Mono Basin: phylo-geography of a peripheral isolate. J. Mammal. 87:1204–1217. , , and .
- 2008. Phylogeography of the pallid kangaroo mouse, Microdipodops pallidus: a sand-obligate endemic of the Great Basin, western North America. J. Biogeogr. 35:2102–2118. , , , and .
- 2012. Sampling for microsatellite-based population genetic studies: 25 to 30 individuals per population is enough to accurately estimate allele frequencies. PLoS One 7:e45170. , , and .
- 1941. Revision of the rodent genus Microdipodops. Field museum of natural history. Zool. Ser. 27:233–277.
- 2002. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes 2:618–620. , and .
- 2008. Bayesian inference of population size history from multiple loci. BMC Evol. Biol. 8:289. , and .
- 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA 104:2785–2790. , and .
- 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747–760. , and .
- 1981. Estimation of effective population size from data on linkage disequilibrium. Genet. Res. 38:209–216.
- 2005. Genetic structure in the coral-reef-associated Banggai cardinalfish, Pterapogon kauderni. Mol. Ecol. 14:1367–1375. , , , , and .
- 2012. Conservation genetics of the critically endangered Saint Croix ground lizard (Ameiva polops Cope 1863). Conserv. Genet. 13:665–679. , , and .
- 2012. How does the 50/500 rule apply to MVPs? Trends Ecol. Evol. 27:578–584. , and .
- 1995. Temporal allele frequency change and estimation of effective size in populations with overlapping generations. Genetics 139:1369–1381. , and .
- 2010. Isolation and characterization of 17 polymorphic microsatellite loci in the kangaroo mouse, genus Microdipodops (Rodentia: Heteromyidae). Conserv. Genet. Resour. 2:139–141. , , , , and .
- 1995. Mutation and conservation. Conserv. Biol. 9:782–791.
- 2013. Conservation genetics of kangaroo mice, genus Microdipodops. J. Mamm. Evol. 20:129–146. , , , and .
- 2008. Microdipodops megacephalus in IUCN 2011. IUCN Red List of Threatened Species. Version 2011.2. Available at http://www.iucnredlist.org (acccessed September 22, 2011). , and .
- 2008. Microdipodops pallidus in IUCN 2011. IUCN Red List of Threatened Species. Version 2011.2. Available at http://www.iucnredlist.org (accessed September 22, 2011). , , and .
- 2010. Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conserv. Genet. 11:355–373. , , , , and .
- 2011. Cryptic diversity in widespread North American songbird: phylogeography of the Brown Creeper (Certhia americana). Mol. Phylogenet. Evol. 58:502–512. , , and .
- 1993. The influence of mating system and overlapping generations on effective population size. Evolution 47:1329–1341.
- 1993. Assessing minimum viable population size: demography meets population genetics. Trends Ecol. Evol. 8:234–239. , and .
- 2011. Comparative analyses of effective population size within and among species: ranid frogs as a case study. Evolution 65:2927–2945. , , , , and .
- 2009. Effective size closely approximates the census size in the heavily exploited western Atlantic population of the sandbar shark, Carcharhinus plumbeus. Conserv. Genet. 10:1697–1705. , , , , and .
- 2010. World phylogeography and male-mediated gene flow in the sandbar shark, Carcharhinus plumbeus. Mol. Ecol. 19:1994–2010. , , , , and .
- 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–959. , , and .
- R Development Core Team. 2011. R: a language and environment for statistical computing. The R Foundation for Statistical Computing, Vienna, Australia. Available at http://www.R-project.org.
- 2007. Tracer v 1.5. Available at http://beast.bio.ed.ac.uk/Tracer (accessed September 1, 2009). , and .
- 1995. GENEPOP Version 1.2: population genetics software for exact tests and ecumenicism. J. Hered. 86:248–249. , and .
- 1979. Biogeography of the intermountain region: a speculative appraisal. Mentzelia 4:1–92.
- 1989. Analyzing table of statistical tests. Evolution 43:223–225.
- 1995. Molecular biogeography in the pocket mice (Perognathus and Chaetodipus) and grasshopper mice (Onychomys) – the late Cenozoic development of a North American aridlands rodent guild. J. Mammal. 76:283–301.
- 2008. Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resour. 8:103–106.
- 1999. Using genetics to estimate the size of wild populations: many methods, much potential, uncertain utility. Anim. Conserv. 2:321–323. , , and .
- The Animal Care and Use Committee of the American Society of Mammalogists. 2011. Guidelines of the American Society of Mammalogists for the use of wild mammals in research. J. Mammal. 92:235–253. , and
- 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462.
- 2005. Bayesian output analysis program (BOA), version 1.1.5. The University of Iowa. Available from http://cph.uiowa.edu/boa (accessed 23 January 2012).
- 2007. Phylogeography of the mountain chickadee (Poecile gambeli): diversification, introgression, and expansion in response to Quaternary climate change. Mol. Ecol. 16:1055–1068. , , and .
- 2010. Pragmatic population viability targets in a rapidly changing world. Biol. Conserv. 143:28–34. , , , and .
- 2005. Estimation of effective population sizes from data on genetic markers. Philos. Trans. R. Soc. Lon. Boil. Sci. 260:1395–1409.
- 2005. Genetic estimates of contemporary effective population size: to what time periods do the estimates apply? Mol. Ecol. 14:3335–3352.
- 2006. A bias correction for estimates of effective population size based on linkage disequilibrium. Biometrics 35:235–254.
- 2008. LDNE: a program for estimating effective population size from data on linkage disequilibrium. Mol. Ecol. Resour. 8:753–756. , and .
- 2010. Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evol. Appl. 3:244–262. , and .
- 2009. Nuclear and mitochondrial DNA reveal contrasting evolutionary processes in population of deer mice (Peromyscus maniculatus). Mol. Ecol. 18:5115–5125. , and .