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Microsatellite and mt-DNA phylogenies of the chamois (genus Rupicapra) and taxonomic implications
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Microsatellite and mt-DNA phylogenies of the chamois (genus Rupicapra) and taxonomic implications

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To elucidate the evolutionary history of chamois, we had analysed DNA sequences of four mitochondrial regions and 20 loci microsatellites including all subspecies along its entire distribution range

To elucidate the evolutionary history of chamois, we had analysed DNA sequences of four mitochondrial regions and 20 loci microsatellites including all subspecies along its entire distribution range

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  • @archeozoologiasassari Thanks a lot for your offer. It is very interesting for us. We tried sometime ago with some cantabrian samples but we have to put that on hold because we had problems with contamination and lack of time. However Do you mind if we contact you if we manage to take up the matter again?
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  • Do you study also archaeological samples? I can furnish mesolithic/neolithic samples of R.ornata. B.Wilkens Sassari
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  • 1. MICROSATELLITE AND mt-DNA PHYLOGENIES OF THE CHAMOIS (GENUS RUPICAPRA ) AND TAXONOMIC IMPLICATIONS OVIEDO UNIVERSITY DEPARTMENT OF FUNCTIONAL BIOLOGY Mª Trinidad Pérez Méndez
  • 2. PRESENT DISTRIBUTION OF RUPICAPRA GENUS R. pyrenaica R. rupicapra
  • 3. EVOLUTION OF Rupicapra GENUS CLASIFICATION OVER TIME Lydekker 1913 Rupicapra rupicapra Taxonomy of the genus has been object of continuos revisions. parva pyrenaica ornata cartusiana rupicapra tatrica carpatica balcanica asiatica caucasica
  • 4. EVOLUTION OF Rupicapra GENUS CLASIFICATION OVER TIME Taxonomy of the genus has been object of continuos revisions. Rupicapra rupicapra Rupicapra ornata Rupicapra pyrenaica Lydekker 1913 1914 Camerano parva pyrenaica ornata cartusiana rupicapra tatrica carpatica balcanica asiatica caucasica
  • 5. EVOLUTION OF Rupicapra GENUS CLASIFICATION OVER TIME Rupicapra rupicapra Taxonomy of the genus has been object of continuos revisions. Lydekker 1913 1914 Camerano Couturier 1938 Dolan 1963 parva pyrenaica ornata cartusiana rupicapra tatrica carpatica balcanica asiatica caucasica
  • 6. EVOLUTION OF Rupicapra GENUS CLASIFICATION OVER TIME Taxonomy of the genus has been object of continuos revisions. Rupicapra rupicapra Rupicapra pyrenaica Lydekker 1913 Couturier 1938 Dolan 1963 Nascetti 1985 1987 Lovari 1914 Camerano parva pyrenaica ornata cartusiana rupicapra tatrica carpatica balcanica asiatica caucasica
  • 7. GEOLOGIC TIME LINE AND GLACIAL PERIODS IN EUROPE
  • 8. CHAMOIS PALEONTOLOGICAL DATA Caune de l´Arago - Mindel Riss’ fossils Riss-Würm’ fossils Distribution limit during Würm Chamois fossils (Masini y Lovari, 1988)
  • 9. PHYLOGEOGRAPHY & COLONIZATION ROUTES IN EUROPE Phylogeographic analyses can evaluate the relative role of different historical forces in shaping the present genetic structure of populations. I.e.- Glaciation cycles of the Quaternary, have periodically restricted some species into disjoint refugia. Once a reversal in climate change allows for rapid migration out of refugial areas, these species spread rapidly into newly available habitat. A number of empirical studies find genetic signatures that support this scenario of refugia and postglacial expansion. Taberlet et al., 1998
  • 10. MAIN GOALS
    • Study of the evolutionary history of the genus
    • Revision of chamois taxonomy
    • Evolutionary Significant Units (ESU).
    • Equivalent to species under the Phylogenetic Species Concept (Vogler y DeSalle, 1994).
    • Conspecific populations which are reciprocally monophyletic for mtDNA alleles and differ significantly for the frequency of alleles at nuclear loci (Moritz, 1994).
  • 11. 20 loci microsatellite and 5 mitochondrial regions are analyzed 486 bp 400 bp 484 bp 471 bp 525-584 bp Control Region mtDNA regions analyzed
  • 12.
    • Microsatellite markers are inherited in a Mendelian way meanwhile mtDNA is transmitted predominantly through maternal lineages in most species.
    • Microsatellite markers have a higher evolution rate than mtDNA.
    • Microsatellite markers narrate the recent phylogenetic history of tens or thousands of years while mitochondrial ones shed light on the deeper phylogenetic history.
    MICROSATELLITE DNA vs. mtDNA
  • 13. SCORED INDIVIDUALS Total 215 samples Microsatellites 179 samples mtDNA 152 samples Both markers 116 samples Subspecies 29 11 4 Only microsatellites Both markers Only mtDNA Parva 29 11 4 Pyrenaica 15 26 0 Cartusiana 0 8 0 ornata 0 12 0 rupicapra 2 29 20 tatrica 0 10 0 carpatica 7 10 6 caucasica 4 6 0 asiatica 0 1 0 balcanica 6 3 6
  • 14. Haplotypic diversity % Nucleotidic diversity % Microsatellite dataset 184 alleles 9.20 alleles/locus ***P<0.001 Mitochondrial combined dataset 1646 nt 79 haplotypes 239 variable sites 196 parsimony-informative He vs Ho % POPULATION DIVERSITY *** *** - - 100 80 60 40 20 0
  • 15. INDIVIDUAL MICROSATELLITE N-J TREE pyrenaica parva caucasica rupicapra balcanica carpatica tatrica cartusiana ornata asiatica
  • 16. MICROSATELLITE GENETIC DISTANCES (  ) 2 VS GEOGRAPHIC DISTANCES Distancia geográfica en Km.   Geographical distance in Km. (  ) 2 Between subpopulations Between R. pyrenaica populations ( AN-Others) Between R. rupicapra populations Between species
  • 17. INDIVIDUAL mtDNA N-J TREE East Central West
  • 18. MITOCHONDRIAL DNA PHYLOGENY OF CHAMOIS Clade West Clade Central Clade East 1/1/0.71/1 1/1/0.97/1 1/1/0.72/1 0.51/0.50/-/0.55
  • 19. NETWORK OF mtDNA HAPLOTYPES Clade East Clade Central Clade West
  • 20. DISCORDANT PHYLOGENIES: MICROSATELLITE & mtDNA Clade East Clade Central Clade West R. pyrenaica R. rupicapra R. pyr. ornata
  • 21. BEAST & BEAUti (MY: million years ) Bovidae-Caprinae: 25,8 MY± 0,6 Caprinae: 14,1 MY ± 1,1 Capra-Ovis : 11,5 MY ± 0,9 Hernández y Vrba, 2005. Clade West Clade Central Clade East DIVERGENCY TIMES BETWEEN CLADES PLEISTOCENE
  • 22. time Holocene: present PHYLOGEOGRAPHY AND EVOLUTIONARY HISTORY Pleistocene glacial-interglacial periods
  • 23. RELATED BIBLIOGRAPHY Perez Trinidad; Hammer Sabine E.; Albornoz Jesus; et al. (2011) Y-chromosome phylogeny in the evolutionary net of chamois (genus Rupicapra ) .BMC EVOLUTIONARY BIOLOGY  11: 272 Rodriguez Fernando; Perez Trinidad; Hammer Sabine E.; et al. (2010) Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra ). BMC EVOLUTIONARY BIOLOGY 10: 222 Rodriguez Fernando; Hammer Sabine; Perez Trinidad; et al. (2009) Cytochrome b Phylogeography of Chamois ( Rupicapra spp.). Population Contractions, Expansions and Hybridizations Governed the Diversification of the Genus. JOURNAL OF HEREDITY  100:47-55 Rodriguez Fernando; Albornoz Jesus; Dominguez Ana (2007) Cytochrome b pseudogene originated from a highly divergent mitochondrial lineage in genus Rupicapra . JOURNAL OF HEREDITY  98: 243-249 Perez T; Albornoz J; Dominguez A (2002) Phylogeography of chamois ( Rupicapra spp.) inferred from microsatellites MOLECULAR PHYLOGENETICS AND EVOLUTION  25: 524-534    Perez T; Albornoz J; Dominguez A (2000) A panel of bovine and caprine microsatellites suitable as markers in chamois ANIMAL GENETICS  31: 344-345 Perez T; Albornoz J; GarciaVazquez E; et al. (1996) Application of DNA fingerprinting to population study of chamois ( Rupicapra rupicapra ). BIOCHEMICAL GENETICS 34: 313-320
  • 24. RESEARCH TEAM Fernando Rodriguez Jesús Albornoz Ana Domínguez Sabine Hammer ( University of Veterinary Medicine Vienna, Austria) To all the people and institutions that had contributed to the recollection of the samples over more than ten years… Jose Francisco Quiros, Javier Pérez-Barbería, Carlos Nores, L. Rossi, Juan Carlos del Campo, Juan Bejar, Paloma Barracina, H. Papaioannou, M. Brown, W. Gasienica-Byrcyn, T. Skalski, J. Meana, S. Erceg, P. Veinberg, J. Badridge, Alvaro Mazón, Michal Adamec, Richard Kraft , Juan Herrero, Athanassios I. Sfougaris, Friederike Spitzenberger, Rita Lorenzini, Jacques Michallet, Natalia Martinkova, Franz Suchentrunk. Institutions: the Regional Governments of Principado de Asturias (Consejeria de Agricultura) and Aragón (Diputación General de Aragón), the hunting wardens from Asturias and Aragón, Camino Real Hunting.