, Volume 143, Issue 4, pp 403–411 | Cite as

Population structure and effective/census population size ratio in threatened three-spined stickleback populations from an isolated river basin in northwest Spain

  • A. Pérez-Figueroa
  • C. Fernández
  • R. Amaro
  • M. Hermida
  • E. San MiguelEmail author


Variability at 20 microsatellite loci was examined to assess the population genetic structure, gene flow, and effective population size (N e) in three populations of three-spined stickleback (Gasterosteus aculeatus) from the upper basin of the Miño River in Galicia, NW Spain, where this species is threatened. The three populations showed similar levels of genetic diversity. There is a significant genetic differentiation between the three populations, but also significant gene flow. N e estimates based on linkage disequilibrium yielded values of 355 for the Miño River population and 241 and 311 for the Rato and Guisande Rivers, respectively, although we expect that these are overestimates. N e estimates based on temporal methods, considering gene flow or not, for the tributaries yielded values of 30–56 and 47–56 for the Rato and Guisande Rivers, respectively. Estimated census size (N c ) for the Rato River was 880 individuals. This yielded a N e/N c estimate of 3–6 % for temporal estimation of Ne, which is within the empirical range observed in freshwater fishes. We suggest that the three populations analyzed have a sufficient level of genetic diversity with some genetic structure. Additionally, the absence of physical barriers suggests that conservation efforts and monitoring should focus in the whole basin as a unit.


Gasterosteus aculeatus Microsatellites Population structure Effective population size Ne/Nc 



We thank J. Galindo and four anonymous reviewers for helpful discussions on a previous version of the manuscript. We also thank to all the forest guards, especially to Mr. Latas, that accompanied us in the sampling trips. This work was funded by Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA; RZ2012-00011-C02-01), Xunta de Galicia (GPC2013-011 and INCITE08ENA261066ES) and Fondos Feder: “Unha maneira de facer Europa.”


  1. Allendorf FW, Luikart G (2007) Conservation and the genetics of populations. Blackwell Publishing, MaldenGoogle Scholar
  2. Allendorf FW, Ryman N (2002) The role of genetics in population viability analysis. In: Beissinger SR, McCullough DR (eds) Population viability analysis. University of Chicago Press, Chicago, pp 50–85Google Scholar
  3. Antao T, Pérez-Figueroa A, Luikart G (2011) Early detection of population declines: high power of genetic monitoring using effective population size estimators. Evol Appl 4:144–154PubMedCentralPubMedCrossRefGoogle Scholar
  4. Araguas RM, Vidal O, Pla C, Sanz N (2012) High genetic diversity of the endangered Iberian three-spined stickleback (Gasterosteus aculeatus) at the Mediterranean edge of its range. Freshw Biol 57:143–154CrossRefGoogle Scholar
  5. Bell MA, Foster SA (1994) The evolutionary biology of the threespine stickleback. Oxford University Press, OxfordGoogle Scholar
  6. Caballero A (1994) Developments in the prediction of effective population size. Heredity 73:657–879PubMedCrossRefGoogle Scholar
  7. Cano JM, Matsuba C, Mäkinen H, Merilä J (2006) The utility of QTL-linked markers to detect selective sweeps in natural populations—a case study of the EDA gene and a linked marker in threespine stickleback. Mol Ecol 15:4613–4621PubMedCrossRefGoogle Scholar
  8. Cano JM, Mäkinen HS, Leinonen T et al (2008) Extreme neutral genetic and morphological divergence supports classification of Adriatic three-spined stickleback (Gasterosteus aculeatus) populations as distinct conservation units. Biol Conserv 141:1055–1066CrossRefGoogle Scholar
  9. Charlesworth B (2009) Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat Rev Genet 10:195–205PubMedCrossRefGoogle Scholar
  10. Clavero M, Pou-Rovira Q, Zamora L (2009) Biology and habitat use of three-spined stickleback (Gasterosteus aculeatus) in intermittent Mediterranean streams. Ecol Freshw Fish 18:550–559CrossRefGoogle Scholar
  11. Colosimo PF, Hosemann KE, Balabhadra S et al (2005) Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science 307:1928–1933PubMedCrossRefGoogle Scholar
  12. Crivelli AJ, Britton RH (1987) Life history adaptations of Gasterosteus aculeatus in a Mediterranean wetland. Env Biol Fish 18:109–125CrossRefGoogle Scholar
  13. Defaveri J, Merilä J (2013) Evidence for adaptive phenotypic differentiation in Baltic Sea sticklebacks. J Evol Biol 26:1700–1715PubMedCrossRefGoogle Scholar
  14. Do C, Waples RS, Peel D et al (2014) NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol Ecol Resour 14:209–214PubMedCrossRefGoogle Scholar
  15. Doadrio I (2002) Atlas y libro rojo de los peces continentales de España. Dirección General de Conservación de la Naturaleza: Museo Nacional de Ciencias Naturales, MadridGoogle Scholar
  16. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14(8):2611–2620PubMedCrossRefGoogle Scholar
  17. Fernández C, Hermida M, Amaro R, San Miguel E (2000) Lateral plate variation in Galician stickleback populations in the rivers Miño and Limia, NW Spain. Behaviour 137:965–979CrossRefGoogle Scholar
  18. FishBase (2013) Reviewed native distribution map for Gasterosteus aculeatus aculeatus (Three-spined stickleback)., version of Aug. 2013. Accessed 4 Dec 2013
  19. Foster SA, Baker JA, Bell MA (2003) The case for conserving threespine stickleback populations. Fisheries 28:10–18CrossRefGoogle Scholar
  20. Frankham R (2005) Genetics and extinction. Biol Conserv 126:131–140CrossRefGoogle Scholar
  21. Frankham R, Ballou JD, Briscoe DA (2010) Introduction to conservation genetics, 2nd edn. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  22. Frankham R, Bradshaw CJA, Brook BW (2014) Genetics in conservation management: revised recommendations for the 50/500 rules, red list criteria and population viability analyses. Biol Conserv 170:56–63Google Scholar
  23. Giller PS (2005) River restoration: seeking ecological standards. Editor’s introduction. J Appl Ecol 42:201–207CrossRefGoogle Scholar
  24. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620CrossRefGoogle Scholar
  25. Heckel G, Zbinden M, Mazzi D, Kohler A, Reckeweg G, Bakker TCM, Largiadèr CR (2002) Microsatellite markers for the three-spined stickleback (Gasterosteus aculeatus L.) and their applicability in a freshwater and an anadromous population. Conserv Genet 3:77–79CrossRefGoogle Scholar
  26. Hendry AP, Taylor EB, McPhail JD (2002) Adaptive divergence and the balance between selection and gene flow: lake and stream stickleback in the Misty system. Evolution 56:1199–1216PubMedCrossRefGoogle Scholar
  27. IUCN (2013) IUCN Red List of Threatened Species. Version 2013.1. Accessed 04 Dec 2013
  28. Jones OR, Wang J (2010) COLONY: a program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour 10:551–555PubMedCrossRefGoogle Scholar
  29. Jorde P, Ryman N (2007) Unbiased estimator for genetic drift and effective population size. Genetics 177:927–935PubMedCentralPubMedCrossRefGoogle Scholar
  30. Kalinowski ST (2011) The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure. Heredity 106:625–632PubMedCentralPubMedCrossRefGoogle Scholar
  31. Kalinowski ST, Waples RS (2002) Relationship of effective to census size in fluctuating populations. Conserv Biol 16:129–136CrossRefGoogle Scholar
  32. Largiader CR, Fries V, Kobler B, Bakker TCM (1999) Isolation and characterization of microsatellite loci from the three-spined stickleback (Gasterosteus aculeatus L.). Mol Ecol 8:342–344Google Scholar
  33. Leinonen T, Cano JM, Mäkinen H, Merilä J (2006) Contrasting patterns of body shape and neutral genetic divergence in marine and lake populations of threespine sticklebacks. J Evol Biol 19:1803–1812PubMedCrossRefGoogle Scholar
  34. Luikart G, Ryman N, Tallmon D, Schwartz M, Allendorf FW (2010) Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conserv Genet 11:355–373CrossRefGoogle Scholar
  35. Mäkinen HS, Merilä J (2008) Mitochondrial DNA phylogeography of the three-spined stickleback (Gasterosteus aculeatus) in Europe-evidence for multiple glacial refugia. Mol Phylogenet Evol 46:167–182PubMedCrossRefGoogle Scholar
  36. Mäkinen HS, Cano JM, Merilä J (2006) Genetic relationships among marine and freshwater populations of the European three-spined stickleback (Gasterosteus aculeatus) revealed by microsatellites. Mol Ecol 15:1519–1534PubMedCrossRefGoogle Scholar
  37. Michalakis Y, Excoffier L (1996) A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics 142:1061–1064PubMedCentralPubMedGoogle Scholar
  38. Moran PAP (1951) A mathematical theory of animal trapping. Biometrika 38:307–311CrossRefGoogle Scholar
  39. Nunney L, Elam DR (1994) Estimating the effective population size of conserved populations. Conserv Biol 8:175–184CrossRefGoogle Scholar
  40. Oksanen J, Guillaume Blanchet F, Kindt R, et al (2013) vegan: community ecology package. R package version 2.0–9.
  41. Palstra FP, Fraser DJ (2012) Effective/census population size ratio estimation: a compendium and appraisal. Ecol Evol 2:2357–2365PubMedCentralPubMedCrossRefGoogle Scholar
  42. Palstra FP, Ruzzante DE (2008) Genetic estimates of contemporary effective population size: what can they tell us about the importance of genetic stochasticity for wild population persistence? Mol Ecol 17:3428–3447PubMedCrossRefGoogle Scholar
  43. Peichel CL, Nereng KS, Ohgi KA, Cole BL, Colosimo PF, Buerkle CA et al (2001) The genetic architecture of divergence between threespine stickleback species. Nature 414:901–905PubMedCrossRefGoogle Scholar
  44. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedCentralPubMedGoogle Scholar
  45. R Development Core Team (2011) R: a language and environment for statistical computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
  46. Raeymaekers JAM, Maes GE, Geldof S, Hontis I, Nackaerts K, Volckaert FAM (2008) Modeling genetic connectivity in sticklebacks as a guideline for river restoration. Evol Appl 1:475–488PubMedCentralPubMedCrossRefGoogle Scholar
  47. Rioux Paquette S (2012) PopGenKit: useful functions for (batch) file conversion and data resampling in microsatellite datasets. R package version 1.0.
  48. Rundle HD, Nagel L, Boughman JW, Schluter D (2000) Natural selection and parallel speciation in sympatric sticklebacks. Science 287:306–308PubMedCrossRefGoogle Scholar
  49. Salgueiro P, Carvalho G, Collares-Pereira MJ, Coelho MM (2003) Microsatellite analysis of genetic population structure of the endangered cyprinid Anaecypris hispanica in Portugal: implications for conservation. Biol Conserv 109:47–56CrossRefGoogle Scholar
  50. Tallmon DA, Koyuk A, Luikart G, Beaumont MA (2008) ONeSAMP: a program to estimate effective population size using approximate Bayesian computation. Mol Ecol 8:299–301CrossRefGoogle Scholar
  51. Von Hippel F (2008) Conservation of threespine and ninespine stickleback radiations in the Cook Inlet Basin, Alaska. Behaviour 145:693–724CrossRefGoogle Scholar
  52. Wang J (2001) A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genet Res 78:243–257PubMedCrossRefGoogle Scholar
  53. Wang J, Santure A (2009) Parentage and sibship inference from multilocus genotype data under polygamy. Genetics 181:1579–1594PubMedCentralPubMedCrossRefGoogle Scholar
  54. Wang J, Whitlock MC (2003) Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163:429–446PubMedCentralPubMedGoogle Scholar
  55. Waples RS (2002) Effective size of fluctuating salmon populations. Genetics 161:783–791PubMedCentralPubMedGoogle Scholar
  56. Waples RS, Do C (2008) LDNE: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Resour 8:753–756PubMedCrossRefGoogle Scholar
  57. Waples RS, Do C (2010) Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evol Appl 3:244–262PubMedCentralPubMedCrossRefGoogle Scholar
  58. Waples RS, England PR (2011) Estimating contemporary effective population size based on linkage disequilibrium in the face of migration. Genetics 189:633–644PubMedCentralPubMedCrossRefGoogle Scholar
  59. Wootton RJ, Adams CE, Attrill MJ (2005) Empirical modeling of the population dynamics of a small population of the threespine stickleback, Gasterosteus aculeatus. Env Biol Fish 74:151–161CrossRefGoogle Scholar
  60. Xunta de Galicia (2007) DECRETO 88/2007, do 19 de abril, polo que se regula o Catálogo galego de especies ameazadas. Diario Oficial de Galicia 89:7409Google Scholar
  61. Zippin C (1956) An evaluation of the removal method of estimating animal populations. Biometrics 12:163–189CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • A. Pérez-Figueroa
    • 1
  • C. Fernández
    • 2
  • R. Amaro
    • 2
  • M. Hermida
    • 2
  • E. San Miguel
    • 2
    Email author
  1. 1.Departamento de Bioquímica, Genética e Inmunología, Facultad de BiologíaUniversidad de VigoVigoSpain
  2. 2.Departamento de Genética, Facultad de VeterinariaUniversidad de Santiago de CompostelaLugoSpain

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