The puzzling demographic history and genetic differentiation of the twaite shad (Alosa fallax) in the Ebro River
详细信息 查看全文
- 作者：Graciela Sotelo ; Karl B. Andree ; Miguel A. López…
- 关键词：European shads ; Mitochondrial DNA ; Microsatellites ; Effective population size ; Introgressive hybridization
- 刊名：Conservation Genetics
- 出版年：2014
- 出版时间：October 2014
- 年：2014
- 卷：15
- 期：5
- 页码：1037-1052
- 全文大小：1,547 KB
- 参考文献：1. Alexandrino P, Faria R, Linhares D, Castro F, Le Corre M, Sabatié R, Baglinière JL, Weiss S (2006) Interspecific differentiation and intraspecific substructure in two closely related clupeids with extensive hybridisation, / Alosa alosa and / Alosa fallax. J Fish Biol 69:242-59 CrossRef
2. Andree KB, López MA, Alexandrino P, Faria R, Gisbert E (2011) A preliminary genetic analysis of a recently rediscovered population of twaite shad ( / Alosa fallax) in the Ebro river, Spain (Western Mediterranean). J Appl Ichthyol 27(Suppl. 3):21-3 CrossRef
3. Aparicio E, Pintor C, Durán C, Carmona-Catot G (2012) Fish passage assessment at the most downstream barrier of the Ebro River (NE Iberian Peninsula). Limnetica 31:37-6
4. Aparicio E, Vargas MJ, Olmo JM, de Sostoa A (2000) Decline of native freshwater fishes in a Mediterranean watershed on the Iberian Peninsula: a quantitative assessment. Environ Biol Fish 59:11-9 CrossRef
5. Aprahamian MW, Aprahamian CD, Baglinière JL, Sabatié MR, Alexandrino P (2003) / Alosa alosa and / Alosa fallax spp.: literature review and bibliography. R&D Technical Report W1-014/TR. Environment Agency, Bristol
6. Aprahamian MW, Aprahamian CD, Knights AM (2010) Climate change and the green energy paradox: the consequences for twaite shad / Alosa fallax from the River Severn, UK. J Fish Biol 77:1912-930 CrossRef
7. Baglinière JL (2000) Le genre / Alosa sp. In: Baglinière JL, Elie P (eds) Les aloses / Alosa alosa et / Alosa fallax spp. INRA-Cemagref, Paris, pp 1-2
8. Bálint M, Málnás K, Nowak C, Geismar J, Váncsa é, Polyák L, Lengyel S, Haase P (2012) Species history masks the effects of human-induced range loss?- unexpected genetic diversity in the endangered giant mayfly / Palingenia longicauda. PLoS One 7:e31872
9. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-8 CrossRef
10. Belliard J, Marchal J, Ditche JM, Tales E, Sabatié R, Baglinière JL (2009) Return of anadromous allis shad ( / Alosa alosa L.) in the River Seine, France: a sign of river recovery? River Res Appl 25:788-94 CrossRef
11. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II
12. Benjamini Y, Yekutieli D (2001) The control of false discovery rate under dependency. Ann Stat 29:1165-188 CrossRef
13. Boisneau P, Mennesson-Boisneau C, Guyomard R (1992) Electrophoretic identity between allis shad, / Alosa alosa (L.), and twaite shad, / A. fallax (Lacepede). J Fish Biol 40:731-38 CrossRef
14. Boisneau C, Moatar F, Bodin M, Boisneau Ph (2008) Does global warming impact on migration patterns and recruitment of Allis shad ( / Alosa alosa L.) young of the year in the Loire River, France? Hydrobiologia 602:179-86 CrossRef
15. Castelnaud G, Rochard E, Le Gat Y (2001) Abundance trend analysis of the allis shad / Alosa alosa in the Gironde basin during the 1977-998 period on the basis of estimated fishing indicators. B Fr Peche Piscic 362/363:989-015
16. Chapman RW, Patton JC, Eleby B (1994) Comparisons of mitochondrial DNA variation in four alosid species as revealed by the total genome, the NADH dehydrogenase I and cytochrome b regions. In: Beaumont A (ed) Genetics and evolution of aquatic organisms. Chapman and Hall, London, pp 249-63
17. Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001-014
18. Coscia I, Rountree V, King JJ, Roche WK, Mariani S (2010) A highly permeable species boundary between two anadromous fishes. J Fish Biol 77:1137-149 CrossRef
19. Cushman E, Tarpey C, Post B, Ware K, Darden T (2012) Genetic characterization of American shad in the Edisto River, South Carolina, and initial evaluation of an experimental stocking program. T Am Fish Soc 141:1338-348 CrossRef
20. Douchement C (1981) Les aloses des fleuves fran?ais / Alosa fallax (Lacépède, 1803) et / Alosa alosa (Linné, 1758). Biométrie, ecobiologie, autonomie des populations. PhD thesis, U.S.T.L. Montpellier
21. Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359-61 CrossRef
22. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611-620 CrossRef
23. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47-0
24. Faria R, Weiss S, Alexandrino P (2006) A molecular phylogenetic perspective on the evolutionary history of / Alosa spp. (Clupeidae). Mol Phylogenet Evol 40:298-04 CrossRef
25. Faria R, Weiss S, Alexandrino P (2012) Comparative phylogeography and demographic history of European shads ( / Alosa spp.) inferred from mitochondrial DNA. BMC Evol Biol 12:194 CrossRef
26. Faria R, Wellgner B, Weiss S, Alexandrino P (2004) Isolation and characterization of eight di-nucleotide microsatellite loci from two closely related clupeid species ( / Alosa alosa and / A. fallax). Mol Ecol Notes 4:586-88 CrossRef
27. Freyhof J, Brooks E (2011) European red list of freshwater fishes. Publications Office of the European Union, Luxembourg
28. Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915-25
29. Funk DJ, Omland KE (2003) Species level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst 34:397-23 CrossRef
30. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-04 CrossRef
31. Hall TA (1999) BioEdit: a user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-8
32. Hasselman DJ, Bradford RG, Bentzen P (2010) Taking stock: defining populations of American shad ( / Alosa sapidissima) in Canada using neutral genetic markers. Can J Fish Aquat Sci 67:1021-039 CrossRef
33. Hasselman DJ, Ricard D, Bentzen P (2013) Genetic diversity and differentiation in a wide ranging anadromous fish, American shad ( / Alosa sapidissima), is correlated with latitude. Mol Ecol 22:1558-573 CrossRef
34. Hauser L, Adcock GJ, Smith PJ, Bernal Ramírez JH, Carvalho GR (2002) Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper ( / Pagrus auratus). Proc Natl Acad Sci USA 99:11742-1747 CrossRef
35. Hauser L, Carvalho GR (2008) Paradigm shifts in marine fisheries genetics: ugly hypotheses slain by beautiful facts. Fish Fish 9:333-62 CrossRef
36. Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9:1322-332 CrossRef
37. Jakobsson M, Rosenberg N (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801-806 CrossRef
38. Jolly MT, Maitland PS, Genner MJ (2011) Genetic monitoring of two decades of hybridization between allis shad ( / Alosa alosa) and twaite shad ( / Alosa fallax). Conserv Genet 12:1087-100 CrossRef
39. Jolly MT, Aprahamian MW, Hawkins SJ, Henderson PA, Hillman R, O’Maoiléidigh N, Maitland PS, Piper R, Genner MJ (2012) Population genetic structure of protected allis shad ( / Alosa alosa) and twaite shad ( / Alosa fallax). Mar Biol 159:581-83 CrossRef
40. Julian SE, Bartron ML (2007) Microsatellite DNA markers for American shad ( / Alosa sapidissima) and cross-species amplification within the family Clupeidae. Mol Ecol Notes 7:805-07 CrossRef
41. Kalinowski ST (2005) HP-RARE 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5:187-89 CrossRef
42. King JJ, Roche WK (2008) Aspects of anadromous Allis shad ( / Alosa alosa Linnaeus) and twaite shad ( / Alosa fallax Lacépède) biology in four Irish Special Areas of Conservation (SACs): status spawning indications and implications for conservation designation. Hydrobiologia 602:145-54 CrossRef
43. Lanfear R, Calcott B, Ho SYW, Guindon S (2012) PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol 29:1695-701 CrossRef
44. Lebel I, Menella JY, Le Corre M (2001) Balance sheet of the migratory fish program actions for the twaite shad population ( / Alosa fallax rhodanensis) on the Rhone-Mediterranean–Corsica basin. B Fr Peche Piscic 362/363:1077-100
45. Le Corre M, Alexandrino P, Sabatié MR, Aprahamian MW, Baglinière JL (2005) Genetic characterisation of the Rhodanian twaite shad, / Alosa fallax rhodanensis. Fish Manag Ecol 12:275-82 CrossRef
46. Limburg KE, Waldman JR (2009) Dramatic declines in North Atlantic diadromous fishes. Bio Sci 59:955-65
47. Lobón-Cerviá J (2009) Why, when and how do fish populations decline, collapse and recover? The example of brown trout ( / Salmo trutta) in Rio Chaballos (northwestern Spain). Freshw Biol 54:1149-162
48. López MA, Andree KB, Sánchez R, Queral JM, Franch N, Schneider P, Gisbert E (2011) First characterization of the spawning habitat and mating behaviour of twaite shad in the Ebro River (Western Mediterranean). J Appl Ichthyol 27(Suppl. 3):53-5 CrossRef
49. López MA, Gázquez N, Olmo-Vidal JM, Aprahamian M, Gisbert E (2007) The presence of the anadromous twaite shad ( / Alosa fallax) in the Ebro River (Western Mediterranean, Spain): an indicator of population’s recovery? J Appl Ichthyol 23:163-66 CrossRef
50. Lotze HK, Lenihan HS, Bourque BJ, Bradbury RH, Cooke RG, Kay MC, Kidwell SM, Kirby MX, Peterson CH, Jackson JB (2006) Depletion, degradation, and recovery potential of estuaries and coastal seas. Science 312:1806-809 CrossRef
51. Lozano-Rey L (1929) Los clupeidos de la península Ibérica y del Rif. Mem R Soc Esp Hist Nat 15:647-66
52. Lozano-Rey L (1935) Los peces fluviátiles de Espa?a. Mem Acad Cienc Exact Fisic Nat 5:1-90
53. Maceda-Veiga A, Monleon-Getino A, Caiola N, Casals F, de Sostoa A (2010) Changes in fish assemblages in catchments in north-eastern Spain: biodiversity, conservation status and introduced species. Freshw Biol 55:1734-746
54. Maes J, Stevens M, Breine J (2008) Poor water quality constrains the distribution and movements of twaite shad / Alosa fallax fallax (Lacépède, 1803) in the watershed of river Scheldt. Hydrobiologia 602:129-43 CrossRef
55. Maitland PS, Lyle AA (2005) Ecology of allis shad / Alosa alosa and twaite shad / Alosa fallax in the Solway Firth, Scotland. Hydrobiologia 534:205-21 CrossRef
56. Narum S (2006) Beyond Bonferroni: less conservative analyses for conservation genetics. Conserv Genet 7:783-87 CrossRef
57. Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL (2008) AWTY (are we there yet): a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Bioinformatics 24:581-83 CrossRef
58. 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 17:3428-447 CrossRef
59. Peery MZ, Kirby R, Reid BN, Stoelting R, Doucet-B?er E, Robinson SJ, Vasquez-Carrillo C, Pauli JN, Palsb?ll PJ (2012) Reliability of genetic bottleneck tests for detecting recent population declines. Mol Ecol 21:3403-418 CrossRef
60. Piry S, Luikart G, Cornuet JM (1999) Bottleneck: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90:502-03 CrossRef
61. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure from multilocus genotype data. Genetics 155:945-59
62. Reyjol Y, Hugueny B, Pont D, Bianco PG, Beier U, Caiola N, Casals F, Cowx I, Economou A, Ferreira T, Haidvogl G, Noble R, Sostoa A, Vigneron T, Virbickas T (2007) Patterns in species richness and endemism of European freshwater fish. Glob Ecol Biogeogr 16:65-5 CrossRef
63. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-574 CrossRef
64. Rosenberg N (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137-38 CrossRef
65. Rougier T, Lambert P, Drouineau H, Girardin M, Castelnaud G, Carry L, Aprahamianm M, Rivot E, Rochard E (2012) Collapse of allis shad, / Alosa alosa, in the Gironde system (southwest France): environmental change, fishing mortality, or Allee effect? ICES J Mar Sci 69:1802-811 CrossRef
66. Rousset F (2008) Genepop-07: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103-06 CrossRef
67. Sabatié MR, Baglinière JL (2001) Some ecobiological traits in Morrocan shads: a cultural and socio-economic value interest which has disappeared. B Fr Peche Piscic 362/363:903-17
68. Sabatié MR, Baglinière JL, Boisneau P (2004) Shad of the Northeastern Atlantic and the Western Mediterranean ( / Alosa alosa L. 1758 and / A. fallax Lac., 1803): biology, ecology and harvesting - fisheries and aquaculture. In: UNESCO, United Nations Educational Scientific and Cultural Organization - (FRA), Encyclopedia of Life Support Systems (EOLSS on line). Food and Agricultural Sciences, Engineering and Technology Resources. Eolss Publishers, Oxford, pp 1-9
69. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Press, New York
70. Sostoa A, Sostoa FJ (1979) Notas sobre la ictiofauna continental del Delta del Ebro (NE de la Peninsula Iberica). Miscellan Zool 5:178-79
71. Strayer DL, Dudgeon D (2010) Freshwater biodiversity conservation: recent progress and future challenges. J N Am Benthol Soc 29:344-58 CrossRef
72. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-95
73. Thiel R, Riel P, Neumann R, Winkler HM, B?ttcher U, Gr?hsler T (2008) Return of twaite shad / Alosa fallax (Lacépède, 1803) to the Southern Baltic Sea and the transitional area between the Baltic and North Seas. Hydrobiologia 602:161-77 CrossRef
74. Toews DPL, Brelsford A (2012) The biogeography of mitochondrial and nuclear discordance in animals. Mol Ecol 21:3907-930 CrossRef
75. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535-38 CrossRef
76. Villesen P (2007) FaBox: an online toolbox for fasta sequences. Mol Ecol Notes 7:965-68 CrossRef
77. Vonlanthen P, Bittner D, Hudson AG, Young KA, Müller R, Lundsgaard-Hansen B, Roy D, Di Piazza S, Largiader CR, Seehausen O (2012) Eutrophication causes speciation reversal in whitefish adaptive radiations. Nature 482:357-62 CrossRef
78. Waters JM, Epifanio JM, Gunter T, Brown BL (2000) Homing behaviour facilitates subtle genetic differentiation among river populations of / Alosa sapidissima: microsatellites and mtDNA. J Fish Biol 52:622-36 CrossRef
79. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358-370 CrossRef - 作者单位：Graciela Sotelo (1)
Karl B. Andree (2)
Miguel A. López (3)
Paulo Alexandrino (4) (5)
Enric Gisbert (2)
Rui Faria (1) (4)
1. IBE, Institut de Biologia Evolutiva (CSIC-UPF), Facultat de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra-PRBB, Barcelona, Spain
2. IRTA-SCR, Institut de Recerca i Tecnologia Agroalimentàries, Sant Carles de la Ràpita, Tarragona, Spain
3. Forestal Catalana S.A., Barcelona, Spain
4. CIBIO, Centro de Investiga??o em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vair?o, Portugal
5. Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal - ISSN：1572-9737
文摘
The Ebro, the largest Iberian river draining into the Mediterranean, historically supported one of the most important twaite shad (Alosa fallax) populations in the region. However, during the twentieth century multiple anthropogenic changes caused a severe decline and the presumed extinction of this species from the river by the 1970s. Its unexpected reappearance in 2004 thus provoked sound interest and raised important questions on the origin of those individuals and their genetic variability, which we address in this study. Adult shads captured in the Ebro from 2005 to 2008, together with samples from three other Mediterranean populations (Rhone, Corsica and Adriatic), were analyzed for two mitochondrial genes and six microsatellite loci. Results confirm the Mediterranean origin of A. fallax caught in the Ebro and reveal that it carries some genetic variation typical of Allis shad (A. alosa), suggesting historical introgression between these two closely related species. In addition, the A. fallax population from the Ebro presents a unique genetic composition and unexpectedly high levels of genetic diversity, when compared with the other Mediterranean populations analyzed. These findings raise important doubts on the demographic history of this population and underline the need for further studies to disentangle natural population dynamics from the role of anthropogenic factors on abrupt population fluctuations such as those reported here. The puzzling demographic history of A. fallax from the Ebro not only brings some hope for the recovery of similarly endangered populations but also provides a unique opportunity to study the factors underlying species-persistence capacity when facing changing environmental conditions.