Combining genetic and demographic data for prioritizing conservation actions: insights from a threatened fish species
Article first published online: 9 JUL 2013
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Ecology and Evolution
Volume 3, Issue 8, pages 2696–2710, August 2013
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How to Cite
Ecology and Evolution 2013; 3(8): 2696–2710
- Issue published online: 12 AUG 2013
- Article first published online: 9 JUL 2013
- Manuscript Accepted: 19 MAY 2013
- Manuscript Revised: 16 MAY 2013
- Manuscript Received: 17 JAN 2013
- Commission of the European Communities, specific RTD programme "IWRMNET"
- 1997. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 25:4692–4693. , and .
- 2007. Species distribution models and ecological theory: a critical assessment and some possible new approaches. Ecol. Model. 200:1–19.
- 1999. Detecting population expansion and decline using microsatellites. Genetics 153:2013–2029.
- 2012. Concurrent habitat and life history influences on effective/census population size ratios in stream-dwelling trout. Ecol. Evol. 2:562–573. , , , , , and .
- 1995. Controlling the false discovery rate – a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 57:289–300. , and .
- 2012. “Back to the future”: how archaeological remains can describe salmon adaptation to climate change. Mol. Ecol. 21:2311–2314. , and .
- 2010. Species-specific responses to landscape fragmentation: implications for management strategies. Evol. Appl. 3:291–304. , , , , and .
- 2009. Molecular estimation of dispersal for ecology and population genetics. Annu. Rev. Ecol. Evol. Syst. 40:193–216. , and .
- 2010. Genetic bottlenecks driven by population disconnection. Conserv. Biol. 24:1596–1605. , , , , , , et al.
- 2008. Climate change hastens the turnover of stream fish assemblages. Glob. Change Biol. 14:2232–2248. , , , , and .
- 2011. CorrSieve: software for summarizing and evaluating structure output. Mol. Ecol. Resour. 11:349–352. , , , and .
- 2007. Evolution on ecological time-scales. Funct. Ecol. 21:387–393. , , , and .
- 2010. The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics 186:983–995. , , , , and .
- 2009. Reversal of evolutionary downsizing caused by selective harvest of large fish. Proc. Biol. Sci. 276:2015–2020. , , and .
- 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014. , and .
- 2005. Evolution of mosaic hybrid zone between invasive and endemic species of Cyprinidae through space and time. Biol. J. Linn. Soc. 85:135–155. , , , , and .
- 2007. Novelties in hybrid zones: crossroads between population genomic and ecological approaches. PLoS One 2:e357. , , , and .
- 2010. smogd: software for the measurement of genetic diversity. Mol. Ecol. Resour. 10:556–557.
- 2006. Parachondrostoma toxostoma. IUCN Red List of Threatened Species. Version 2012.2. Available at www.iucnredlist.org. (accessed 16 November 2012).
- 2007. Climate change impacts on structure and diversity of fish communities in rivers. Glob. Change Biol. 13:2467–2478. , and .
- 2004. Long-term changes within the invertebrate and fish communities of the Upper Rhone River: effects of climatic factors. Glob. Change Biol. 10:124–140. , , , and .
- 2010. Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world. Ecol. Lett. 13:1030–1040. , , , , , and .
- 2008. Understanding and predicting ecological dynamics: are major surprises inevitable? Ecology 89:952–961. , , , , , , et al.
- 2010. Cross-species amplification of 41 microsatellites in European cyprinids: a tool for evolutionary, population genetics and hybridization studies. BMC Res. Notes 3:135. , , , , , , et al.
- 2012. From late miocene to holocene: processes of differentiation within the Telestes genus (Actinopterygii: Cyprinidae). PLoS One 7:e34423. , , , , , and .
- 2008. Evaluating effects of deforestation, hunting, and El Niño events on a threatened lemur. Biol. Conserv. 141:287–297. , , , and .
- 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611–2620. , , and .
- 2006. Computer programs for population genetics data analysis: a survival guide. Nat. Rev. Genet. 7:745–758. , 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 .
- 2002. Connectivity, fragmentation, and extinction risk in dendritic metapopulations. Ecology 83:3243.
- 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587. , , and .
- 2007. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol. Ecol. Notes 7:574–578. , , and .
- 2010. Challenges and opportunities of genetic approaches to biological conservation. Biol. Conserv. 143:1919–1927.
- 2011. Integrative freshwater ecology and biodiversity conservation. Ecol. Ind. 11:1507–1516.
- 1992. Inference from iterative simulation using multiple sequences. Stat. Sci. 7:457–472. , and .
- 2011. Inferring population decline and expansion from microsatellite data: a simulation-based evaluation of the Msvar method. Genetics 188:165–179. , , , and .
- 2006. Genetic signature of anthropogenic population collapse in orang-utans. PLoS Biol. 4:e25. , , , , , and .
- 1995. FSTAT (Version 1.2): a computer program to calculate F-statistics. J. Hered. 86:485–486.
- 2005. Complexity in ecology and conservation: mathematical, statistical, and computational challenges. Bioscience 55:501. , , , , , , et al.
- 2011. Ensemble modelling of species distribution: the effects of geographical and environmental ranges. Ecography 34:9–17. , , , and .
- 2000. Predictive habitat distribution models in ecology. Ecol. Model. 135:147–186. , and .
- 1993. Meta-analysis: combining the results of independent experiments Pp. 378–398. in M. Scheiner, J. Gurevitch, eds. Design and analysis of ecological experiments. Chapman and Hall, New York, NY. , and .
- 1998. A modified Mann–Kendall trend test for autocorrelated data. J. Hydrol. 204:182–196. , and .
- 2005. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25:1965–1978. , , , , and .
- 2009. Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Resour. 9:1322–1332. , , , and .
- 2008. G(ST) and its relatives do not measure differentiation. Mol. Ecol. 17:4015–4026.
- 2004. Evidence for the impact of global warming on the long-term population dynamics of common birds. Proc. Biol. Sci. 271:S490–S492. , , and .
- 2011. P. 552 in Les poissons d'eau douce de France. Biotope, Mèze; Muséum national d'Histoire naturelle, Paris (collection Inventaires et biodiversité). , , , and .
- 1962. Rank correlation methods, 3rd ed. Hafner Publishing Company, New York, NY.
- 2010. Quantifying the lag time to detect barriers in landscape genetics. Mol. Ecol. 19:4179–4191. , , , , , and .
- 2010. Improved probability of detection of ecological “surprises”. Proc. Natl. Acad. Sci. 107:21957–21962. , , , and .
- 2005. Selecting thresholds of occurrence in the prediction of species distributions. Ecography 28:385–393. , , , and .
- 2011. Assisted colonization: integrating conservation strategies in the face of climate change. Biol. Conserv. 144:92–100. , , and .
- 1998. Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv. Biol. 12:228–237. , and .
- 2010. Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conserv. Genet. 11:355–373. , , , , and .
- 2003. Landscape genetics: combining landscape ecology and population genetics. Trends Ecol. Evol. 18:189–197. , , , and .
- 2000. Systematic conservation planning. Nature 405:243–253. , and .
- 2009. Evaluation of consensus methods in predictive species distribution modelling. Divers. Distrib. 15:59–69. , , , , and .
- 2011. Improving assessment and modelling of climate change impacts on global terrestrial biodiversity. Trends Ecol. Evol. 26:249–259. , , , , , , et al.
- 2011. Choice of threshold alters projections of species range shifts under climate change. Ecol. Model. 222:3346–3354. , and .
- 2006. Monitoring for conservation. Trends Ecol. Evol. 21:668–673. , and .
- 2008. From genetic diversity and structure to conservation: genetic signature of recent population declines in three mouse lemur species (Microcebus spp.). Biol. Conserv. 141:1257–1271. , , , and .
- 2010. Genetic effective size tracks abundance in a small-bodied cyprinid, Pecos bluntnose shiner. Mol. Ecol. 14:2832–2844. , , , and .
- 2012. Genetic monitoring and complex population dynamics: insights from a 12-year study of the Rio Grande silvery minnow. Evol. Appl. 5:553–574. , , and .
- 2012. Effective/census population size ratio estimation: a compendium and appraisal. Ecol. Evol. 2:2357–2365. , and .
- 2006. Ecological and evolutionary responses to recent climate change. Annu. Rev. Ecol. Evol. Syst. 37:637–669.
- 2013. The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data. Mol. Ecol. doi:10.1111/mec.12321. , , , , and .
- 1998. Identifying populations for conservation on the basis of genetic markers. Conserv. Biol. 12:844–855. , , and .
- 1999. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data. J. Hered. 90:502–503.
- 2006. CODA: convergence diagnosis and output analysis for MCMC. R News 6:7–11. , , , and .
- 2011. Time trends in fish populations in metropolitan France: insights from national monitoring data. J. Fish Biol. 79:1436–1452. , , and .
- 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–959. , , and .
- 2000. Getting the measure of biodiversity. Nature 405:212–219. , and .
- 2009. Distribution models for the amphibian chytrid Batrachochytrium dendrobatidis in Costa Rica: proposing climatic refuges as a conservation tool. Divers. Distrib. 15:401–408. , , , , , , et al.
- R Development Core Team. 2011. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
- 2008. genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Mol. Ecol. Resour. 8:103–106.
- 2006. Hierarchical models of animal abundance and occurrence. J. Agric. Biol. Environ. Stat. 11:249–263. , and .
- 1998. Inbreeding and extinction in a butterfly metapopulation. Nature 392:491–494. , , , , , and .
- 2007. Genetic monitoring as a promising tool for conservation and management. Trends Ecol. Evol. 22:25–33. , , and .
- 1998. The role of natural history collections in documenting species declines. Trends Ecol. Evol. 13:27–30. , , and .
- 2006. Detecting climate change induced range shifts: where and how should we be looking? Austral Ecol. 31:22–29. , , and .
- 2008. Evolutionary change in human-altered environments. Mol. Ecol. 17:1–8. , and .
- 2004. Most species are not driven to extinction before genetic factors impact them. Proc. Natl. Acad. Sci. 101:15261–15264.
- 2002. Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical bayesian model. Evolution 56:154. , and .
- 2008. ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24:2498–2504. , , and .
- 2004. Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4:535–538. , , , and .
- 2008. LDNe: a program for estimating effective population size from data on linkage disequilibrium. Mol. Ecol. Resour. 8:753–756. , and .
- 2002. Estimating F-statistics. Annu. Rev. Genet. 36:721–750. , and .
- 2005. Comparison of methods for detecting bottlenecks from microsatellite loci. Conserv. Genet. 6:551–562.