References

Allendorf, F. W. (2017). Genetics and the conservation of natural populations: allozymes to genomes. Molecular Ecology ,26 (2), 420–430. doi: 10.1111/mec.13948
Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G., & Hohenlohe, P. A. (2016). Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics , 17 (2), 81–92. doi: 10.1038/nrg.2015.28
Araújo, M. B., Guilhaumon, F., Neto, D. R., Ortego, I. P., & Calmaestra, R. (2011). Impactos, Vulnerabilidad y Adaptación al Cambio Climático de la Biodiversidad Española. 2 Fauna de Vertebrados . doi: 10.13140/RG.2.1.3766.3200
Avise, J. C. (2004). Molecular Markers, Natural History and Evolution (2nd Editio). Sunderland, Massachusetts: Sinauer Associates, Inc.
Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., … Johnson, E. A. (2008). Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. PLoS ONE ,3 (10), e3376. doi: 10.1371/journal.pone.0003376
Bohling, J., Small, M., Von Bargen, J., Louden, A., & DeHaan, P. (2019). Comparing inferences derived from microsatellite and RADseq datasets: a case study involving threatened bull trout.Conservation Genetics , 20 (2), 329–342. doi: 10.1007/s10592-018-1134-z
Bradbury, I. R., Hamilton, L. C., Dempson, B., Robertson, M. J., Bourret, V., Bernatchez, L., & Verspoor, E. (2015). Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure.Molecular Ecology , 24 (20), 5130–5144. doi: 10.1111/mec.13395
Clark, A. G., Hubisz, M. J., Bustamante, C. D., Williamson, S. H., & Nielsen, R. (2005). Ascertainment bias in studies of human genome-wide polymorphism. Genome Research , 15 (11), 1496–1502. doi: 10.1101/gr.4107905
Coltman, D. W., Pilkington, J. G., Smith, J. A., & Pemberton, J. M. (1999). Parasite-mediated selection against inbred soay sheep in a free-living, island population. Evolution , 53 (4), 1259–1267. doi: 10.1111/j.1558-5646.1999.tb04538.x
Cuvier, G. (1829). Le règne animal distribué d’après son organisation pour servir de base à l’histoire naturelle des animaux, et d’introduction à l’anatomie comparée (2ème éditi). Paris: Déterville & Crochard.
Dallas, J. F. (1992). Estimation of microsatellite mutation rates in recombinant inbred strains of mouse. Mammalian Genome ,3 (8), 452–456. doi: 10.1007/BF00356155
Davey, J. W., Hohenlohe, P. A., Etter, P. D., Boone, J. Q., Catchen, J. M., & Blaxter, M. L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics , 12 (7), 499–510. doi: 10.1038/nrg3012
DeFaveri, J., Viitaniemi, H., Leder, E., & Merilä, J. (2013). Characterizing genic and nongenic molecular markers: comparison of microsatellites and SNPs. Molecular Ecology Resources ,13 (3), 377–392. doi: 10.1111/1755-0998.12071
Di Rienzo, A., Peterson, A. C., Garzat, J. C., Valdes, A. M., Slatkint, M., & Freimer, N. B. (1994). Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the United States of America , 91 (8), 3166–3170. Retrieved from https://www.pnas.org/content/pnas/91/8/3166.full.pdf
Dufresnes, C., Brelsford, A., Béziers, P., & Perrin, N. (2014). Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: Evidence from Hylid frogs. Molecular Ecology Resources , 14 (4), 716–725. doi: 10.1111/1755-0998.12215
Elbers, J. P., Clostio, R. W., & Taylor, S. S. (2017). Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites. Molecular Ecology Resources , 17 (3), 481–491. doi: 10.1111/1755-0998.12591
Ellegren, H. (2004). Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics , 5 (6), 435–445. doi: 10.1038/nrg1348
Estoup, A., Jarne, P., & Cornuet, J.-M. (2002). Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Molecular Ecology , 11 (9), 1591–1604. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/12207711
Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology , 14 (8), 2611–2620. doi: 10.1111/j.1365-294X.2005.02553.x
Falush, D., Stephens, M., & Pritchard, J. K. (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics , 164 (4), 1567–1587. doi: 10.1001/jama.1987.03400040069013
Fischer, M. C., Rellstab, C., Leuzinger, M., Roumet, M., Gugerli, F., Shimizu, K. K., … Widmer, A. (2017). Estimating genomic diversity and population differentiation - an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri .BMC Genomics , 18 (1), 1–15. doi: 10.1186/s12864-016-3459-7
Garza, J. C., & Freimer, N. B. (1996). Homoplasy for size at microsatellite loci in humans and chimpanzees. Genome Research ,6 (3), 211–217. doi: 10.1101/gr.6.3.211
Gelman, A., & Rubin, D. B. (1992). Inference from Iterative Simulation Using Multiple Sequences. Statistical Science , 7 (4), 457–472.
Gómez, A., & Lunt, D. H. (2007). Refugia within Refugia: Patterns of Phylogeographic Concordance in the Iberian Peninsula. In S. Weiss & N. Ferrand (Eds.), Phylogeography of Southern European Refugia: Evolutionary Perspectives on the Origins and Conservation of European Biodiversity (pp. 155–188). doi: 10.1007/1-4020-4904-8_5
Gruber, B., Unmack, P. J., Berry, O. F., & Georges, A. (2018). DARTR : An R package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Molecular Ecology Resources ,18 (3), 691–699. doi: 10.1111/1755-0998.12745
Guillot, G., & Foll, M. (2009). Correcting for ascertainment bias in the inference of population structure. Bioinformatics ,25 (4), 552–554. doi: 10.1093/bioinformatics/btn665
Gutiérrez-Rodríguez, J., Barbosa, A. M., & Martínez-Solano, Í. (2017). Present and past climatic effects on the current distribution and genetic diversity of the Iberian spadefoot toad (Pelobates cultripes ): an integrative approach. Journal of Biogeography ,44 (2), 245–258. doi: 10.1111/jbi.12791
Haasl, R. J., & Payseur, B. A. (2011). Multi-locus inference of population structure: A comparison between single nucleotide polymorphisms and microsatellites. Heredity , 106 (1), 158–171. doi: 10.1038/hdy.2010.21
Hedrick, P. W. (1999). Perspective: Highly Variable Loci and Their Interpretation in Evolution and Conservation. Evolution ,53 (2), 313. doi: 10.2307/2640768
Hodel, R. G. J., Chen, S., Payton, A. C., McDaniel, S. F., Soltis, P., & Soltis, D. E. (2017). Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: Comparing microsatellites and RAD-Seq and investigating loci filtering.Scientific Reports , 7 (1), 1–14. doi: 10.1038/s41598-017-16810-7
Hodel, R. G. J., Segovia-Salcedo, M. C., Landis, J. B., Crowl, A. A., Sun, M., Liu, X., … Soltis, P. S. (2016). The Report of My Death was an Exaggeration: A Review for Researchers Using Microsatellites in the 21st Century. Applications in Plant Sciences , 4 (6), 1600025. doi: 10.3732/apps.1600025
Jakobsson, M., & Rosenberg, N. A. (2007). CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure.Bioinformatics , 23 (14), 1801–1806. doi: 10.1093/bioinformatics/btm233
Janes, J. K., Miller, J. M., Dupuis, J. R., Malenfant, R. M., Gorrell, J. C., Cullingham, C. I., & Andrew, R. L. (2017). The K = 2 conundrum.Molecular Ecology , 26 (14), 3594–3602. doi: 10.1111/mec.14187
Jeffries, D. L., Copp, G. H., Handley, L. L., Håkan Olsén, K., Sayer, C. D., & Hänfling, B. (2016). Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius , L. Molecular Ecology ,25 (13), 2997–3018. doi: 10.1111/mec.13613
Kalinowski, S. T. (2002). How many alleles per locus should be used to estimate genetic distances? Heredity , 88 , 62–65. doi: 10.1038/sj/hdy/6800009
Kopelman, N. M., Mayzel, J., Jakobsson, M., Rosenberg, N. A., & Mayrose, I. (2015). CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K .Molecular Ecology Resources , 15 (5), 1179–1191. doi: 10.1111/1755-0998.12387
Lachance, J., & Tishkoff, S. A. (2013). SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it.BioEssays , 35 (9), 780–786. doi: 10.1002/bies.201300014
Lambert, M. R., Skelly, D. K., & Ezaz, T. (2016). Sex-linked markers in the North American green frog (Rana clamitans ) developed using DArTseq provide early insight into sex chromosome evolution. BMC Genomics , 17 (1), 844. doi: 10.1186/s12864-016-3209-x
Lawson, D. J., van Dorp, L., & Falush, D. (2018). A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. Nature Communications , 9 (1), 1–11. doi: 10.1038/s41467-018-05257-7
Lemopoulos, A., Prokkola, J. M., Uusi-Heikkilä, S., Vasemägi, A., Huusko, A., Hyvärinen, P., … Vainikka, A. (2019). Comparing RADseq and microsatellites for estimating genetic diversity and relatedness — Implications for brown trout conservation. Ecology and Evolution , 9 (4), 2106–2120. doi: 10.1002/ece3.4905
Linck, E., & Battey, C. J. (2019). Minor allele frequency thresholds strongly affect population structure inference with genomic data sets.Molecular Ecology Resources , 19 (3), 639–647. doi: 10.1111/1755-0998.12995
Liu, N., Chen, L., Wang, S., Oh, C., & Zhao, H. (2005). Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure. BMC Genetics , 6 (1), S26. doi: 10.1186/1471-2156-6-S1-S26
Luikart, G., & Cornuet, J.-M. (1998). Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conservation Biology , 12 (1), 228–237.
Lynch, M. (2010). Evolution of the mutation rate. Trends in Genetics , 26 (8), 345–352. doi: 10.1016/j.tig.2010.05.003
Malenfant, R. M., Coltman, D. W., & Davis, C. S. (2015). Design of a 9K illumina BeadChip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing. Molecular Ecology Resources ,15 (3), 587–600. doi: 10.1111/1755-0998.12327
McCartney-Melstad, E., Vu, J. K., & Shaffer, H. B. (2018). Genomic data recover previously undetectable fragmentation effects in an endangered amphibian. Molecular Ecology , 27 (22), 4430–4443. doi: 10.1111/mec.14892
Miller, M. R., Dunham, J. P., Amores, A., Cresko, W. A., & Johnson, E. A. (2007). Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers.Genome Research , 17 (2), 240–248. doi: 10.1101/gr.5681207
Morin, P. A., Luikart, G., & Wayne, R. K. (2004). SNPs in ecology, evolution and conservation. Trends in Ecology and Evolution ,19 (4), 208–216. doi: 10.1016/j.tree.2004.01.009
O’Leary, S. J., Puritz, J. B., Willis, S. C., Hollenbeck, C. M., & Portnoy, D. S. (2018). These aren’t the loci you’e looking for: Principles of effective SNP filtering for molecular ecologists.Molecular Ecology , (June), 3193–3206. doi: 10.1111/mec.14792
Pereira, P., Teixeira, J., & Velo-Antón, G. (2018). Allele surfing shaped the genetic structure of the European pond turtle via colonization and population expansion across the Iberian Peninsula from Africa. Journal of Biogeography , 45 (9), 2202–2215. doi: 10.1111/jbi.13412
Petersen, J. L., Mickelson, J. R., Cothran, E. G., Andersson, L. S., Axelsson, J., Bailey, E., … McCue, M. E. (2013). Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data.PLoS ONE , 8 (1). doi: 10.1371/journal.pone.0054997
Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS One , 7 (5), e37135. doi: 10.1371/journal.pone.0037135
Pina-Martins, F., Silva, D. N., Fino, J., & Paulo, O. S. (2017). Structure_threader: An improved method for automation and parallelization of programs structure, fastStructure and MavericK on multicore CPU systems. Molecular Ecology Resources , 17 (6), e268–e274. doi: 10.1111/1755-0998.12702
Plummer, M., Best, N., Cowles, K., & Vines, K. (2006). {CODA}: Convergence Diagnosis and Output Analysis for {MCMC}. R News . Retrieved from https://www.r-project.org/doc/Rnews/Rnews_2006-1.pdf
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics ,155 (2), 945–959. doi: 10.1111/j.1471-8286.2007.01758.x
Puckett, E. E. (2017). Variability in total project and per sample genotyping costs under varying study designs including with microsatellites or SNPs to answer conservation genetic questions.Conservation Genetics Resources , 9 (2), 289–304. doi: 10.1007/s12686-016-0643-7
Puckett, E. E., & Eggert, L. S. (2016). Comparison of SNP and microsatellite genotyping panels for spatial assignment of individuals to natal range: A case study using the American black bear (Ursus americanus ). Biological Conservation , 193 , 86–93. doi: 10.1016/j.biocon.2015.11.020
Puechmaille, S. J. (2016). The program structure does not reliably recover the correct population structure when sampling is uneven: Subsampling and new estimators alleviate the problem. Molecular Ecology Resources , 16 (3), 608–627. doi: 10.1111/1755-0998.12512
Putman, A. I., & Carbone, I. (2014). Challenges in analysis and interpretation of microsatellite data for population genetic studies.Ecology and Evolution , 4 (22), 4399–4428. doi: 10.1002/ece3.1305
Queney, G., Ferrand, N., Weiss, S., Mougel, F., & Monnerot, M. (2001). Stationary distributions of microsatellite loci between divergent population groups of the European rabbit (Oryctolagus cuniculus).Molecular Biology and Evolution , 18 (12), 2169–2178. doi: 10.1093/oxfordjournals.molbev.a003763
Rašić, G., Filipović, I., Weeks, A. R., & Hoffmann, A. A. (2014). Genome-wide SNPs lead to strong signals of geographic structure and relatedness patterns in the major arbovirus vector, Aedes aegypti . BMC Genomics , 15 (1), 1–12. doi: 10.1186/1471-2164-15-275
Sánchez‐Montes, G., Recuero, E., Barbosa, A. M., & Martínez‐Solano, Í. (2019). Complementing the Pleistocene biogeography of European amphibians: Testimony from a southern Atlantic species. Journal of Biogeography , 46 (3), 568–583. doi: 10.1111/jbi.13515
Stoffel, M. A., Esser, M., Kardos, M., Humble, E., Nichols, H., David, P., & Hoffman, J. I. (2016). inbreedR: an R package for the analysis of inbreeding based on genetic markers. Methods in Ecology and Evolution , 7 (11), 1331–1339. doi: 10.1111/2041-210X.12588
Tonkin-Hill, G., & Lee, S. (2016). starmie: Population Structure Model Inference and Visualisation . Retrieved from https://cran.r-project.org/package=starmie
Valdes, A. M., Slatkin, M., & Freimer, N. B. (1993). Allele frequencies at microsatellite loci: The stepwise mutation model revisited.Genetics , 133 (3), 737–749.
Väli, Ü., Einarsson, A., Waits, L., & Ellegren, H. (2008). To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations? Molecular Ecology , 17 (17), 3808–3817. doi: 10.1111/j.1365-294X.2008.03876.x
Vats, D., & Knudson, C. (2018). Revisiting the Gelman-Rubin Diagnostic . 1–22. Retrieved from http://arxiv.org/abs/1812.09384
Wang, J. (2019). A parsimony estimator of the number of populations from a STRUCTURE‐like analysis. Molecular Ecology Resources ,19 (4), 970–981. doi: 10.1111/1755-0998.13000
Wang, S., Lewis, C. M., Jakobsson, M., Ramachandran, S., Ray, N., Bedoya, G., … Ruiz-Linares, A. (2007). Genetic variation and population structure in Native Americans. PLoS Genetics ,3 (11), 2049–2067. doi: 10.1371/journal.pgen.0030185
Weber, J. L., & Wong, C. (1993). Mutation of human short tandem repeats. Human Molecular Genetics , 2 (8), 1123–1128. doi: 10.1093/hmg/2.8.1123
Webster, M. T., Smith, N. G. C., & Ellegren, H. (2002). Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments.Proceedings of the National Academy of Sciences of the United States of America , 99 (13), 8748–8753. doi: 10.1073/pnas.122067599
Zhang, D. X., & Hewitt, G. M. (2003). Nuclear DNA analyses in genetic studies of populations: Practice, problems and prospects.Molecular Ecology . doi: 10.1046/j.1365-294X.2003.01773.x