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12 - Genetics and conservation on islands: the Galaápagos giant tortoise as a case study
- from From genetic data to practical management: issues and case studies
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- By Claudio Ciofi, University of Florence, Adalgisa Caccone, Yale University, Luciano B. Beheregaray, Macquarie University, Michel C. Milinkovitch, University of Geneva, Michael Russello, University of British Columbia Okanagan, Jeffrey R. Powell, Yale University
- Giorgio Bertorelle, Università degli Studi di Ferrara, Italy, Michael W. Bruford, Cardiff University, Heidi C. Hauffe, Annapaolo Rizzoli, Cristiano Vernesi
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- Book:
- Population Genetics for Animal Conservation
- Published online:
- 05 July 2015
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- 28 May 2009, pp 269-293
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Summary
INTRODUCTION
The study of intraspecific genetic variation has demonstrated a vast potential to reconstruct phylogeographic patterns, infer historical demographic processes and define levels of gene flow of conservation relevance (Avise 2004). Evolutionary and demographic studies, along with evidence of current genetic and ecological diversity can, in fact, describe levels of population distinctiveness and direct management initiatives of importance to the retention of intraspecific genetic variability and the long-term fitness of endangered species (Fraser and Bernatchez 2001).
Population divergence and taxonomy
Molecular genetics is a particularly valuable tool for the study of island systems where different selective pressures and dispersal ability of endemic species can hamper clear patterns of morphological and ecological diversification for populations of taxonomic importance. In the Galápagos giant tortoise Geochelone nigra (or G. elephantopus: see Zug 1997), the taxonomy first proposed by Van Denburgh (1914) has been somewhat controversial. Taxon designation was originally based on two main tortoise morphologies and their variants: a large, dome morphotype with rounded carapace and short limbs, and a smaller saddlebacked form with a highly elevated anterior part of the carapace, longer neck and limbs, and thinner shell. Five saddlebacked subspecies were described, on the islands of Española (hoodensis), San Cristóbal (chatamensis), Pinzón (ephippium), Fernandina (phantastica) and Pinta (abingdoni). Domed tortoises were instead reported from Santa Cruz (porteri), Rábida (wallacei) and in Isabela on Volcan Darwin (microphyes), Volcan Alcedo (vandenburghi), Sierra Negra (guntheri) and Cerro Azul (vicina).
Tortoises from Santiago (darwini) are of intermediate morphology. Similarly, heterogeneous morphotypes, assigned to the becki subspecies, were described on Volcan Wolf, in northern Isabela. For the majority of island populations recent genetic analysis validated the proposed taxonomy, while for others new patterns were recovered which were inconsistent with previous morphologically based nomenclature (Caccone et al. 2002; Beheregaray et al. 2003a; Russello et al. 2005; Ciofi et al. 2006).
5 - A comparison of methods for constructing evolutionary networks from intraspecific DNA sequences
- from Statistical approaches, data analysis and inference
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- By Patrick Mardulyn, Universiteé Libre de Bruxelles, Insa Cassens, Max-Planck-Institut für demografische Forschung, Michel C. Milinkovitch, University of Geneva
- Giorgio Bertorelle, Università degli Studi di Ferrara, Italy, Michael W. Bruford, Cardiff University, Heidi C. Hauffe, Annapaolo Rizzoli, Cristiano Vernesi
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- Book:
- Population Genetics for Animal Conservation
- Published online:
- 05 July 2015
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- 28 May 2009, pp 104-120
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Summary
In phylogeography or population genetic studies, evolutionary relationships among DNA haplotypes can be depicted either as a graph, called a ‘network’, with cycles (or ‘loops’), or as a set of phylogenetic trees (i.e. connected graphs with no circuits), possibly with multifurcation(s) and/or ancestral haplotype(s) (both represented by collapsing zero-length branches). For example, several equally optimal trees inferred under the maximum parsimony (MP) criterion display alternative relationships among haplotypes (Fig. 5.1a, b). A strict consensus tree can be used to summarize this set of trees (Fig. 5.1c), but this approach discards much of the historical information. Indeed, a strict consensus tree is typically compatible with many more alternative trees than those used to build it: e.g. the consensus in Fig. 5.1c is compatible with 105 different strictly bifurcating topologies although only two haplotypic trees have been used to build it. Furthermore, the consensus tree cannot easily summarize branch length information (e.g. in Fig. 5.1, taxon 4 is at the tip of a 0 step-long or a 1 steplong branch in trees (a) and (b), respectively). On the contrary, a network graph allows display much of the information contained in the data in a single figure (Fig. 5.1d). Therefore, the major advantage of such graphs over traditional phylogenetic trees is the possibility of using cycles (loops) to represent either ambiguities in the data or genuine reticulate evolution (due to e.g. recombination or horizontal gene transfer). In parsimony networks, sampled and unsampled haplotypes (white circles and black dots, respectively, in Fig. 5.1d) are symbolized by nodes (vertices) that are connected by edges, where each edge represents a single nucleotide substitution. Unsampled haplotypes are inferred to connect sampled haplotypes when the latter are separated by more than a single substitution. The so-called ‘degree’ of a node corresponds to the number of edges to which it is connected (e.g. in Fig. 5.1d, haplotype 2 is a node of degree 4).
7 - A pragmatic approach for selecting evo-devo model species in amniotes
- Edited by Alessandro Minelli, Università degli Studi di Padova, Italy
- Giuseppe Fusco, Università degli Studi di Padova, Italy
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- Book:
- Evolving Pathways
- Published online:
- 08 August 2009
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- 10 January 2008, pp 123-143
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Summary
One major classical justification of using a model metazoan species for experimentation has been that discoveries of biological phenomena in that species could be extrapolated to other multicellular species. Because the chances that this extrapolation is valid in humans depend on the phylogenetic distance between humans and the model species, many researchers have somewhat sacrificed the major benefits of small size, short generation time and ease of manipulation that characterise some invertebrates in order to use species that humans can more readily relate to, such as the laboratory mouse (Mus musculus). However, the community of biologists has continued to use additional model species because each of the selected taxa have specific features that make experimental manipulation easier (e.g. easy-to-score morphological variation and giant polytene chromosomes in Drosophila melanogaster, or accurate description of the largely invariant complete cell lineage and full neural connectivity in the roundworm Caenorhabditis elegans).
Ever since the molecular genetic revolution, a constant concern has been the possibility of manipulating the genome of model species. For example, generations of Drosophila scientists have developed and applied ingenious approaches that allow, in principle, screening for any phenotype at any stage of development (reviewed in St Johnston 2002). Even for the mouse model, multiple techniques, such as homologous recombination, tissue-specific activation/inactivation techniques, cloning and RNA interference (RNAi), have been developed for performing genotype- or phenotype-driven experiments. Furthermore, recent access to full genome sequences makes genome engineering of some model species easier.
The origin of captive Galápagos tortoises based on DNA analysis: implications for the management of natural populations
- Catherine E. Burns, Claudio Ciofi, Luciano B. Beheregaray, Thomas H. Fritts, James P. Gibbs, Cruz Márquez, Michel C. Milinkovitch, Jeffrey R. Powell, Adalgisa Caccone
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- Journal:
- Animal Conservation forum / Volume 6 / Issue 4 / November 2003
- Published online by Cambridge University Press:
- 29 October 2003, pp. 329-337
- Print publication:
- November 2003
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Giant tortoises once thrived throughout the Galápagos archipelago, but today three island populations are extinct, only one individual survives from the island of Pinta, and several populations are critically endangered. We established the geographic origin of 59 captive tortoises housed at the Charles Darwin Research Station in the Galápagos Islands in an effort to find a mate for the sole survivor from Pinta (‘Lonesome George’) and to augment the number of breeders in other imperilled populations. By comparison with an extensive database of mtDNA control region (CR) haplotypes and nine microsatellites, we determined the geographic and evolutionary origin of the captive individuals. All individuals had CR haplotypes and multilocus microsatellite genotypes identical to or closely related to known haplotypes from natural populations. No obvious mate was found for Lonesome George, although we found several captive individuals carrying an evolutionarily close but geographically distinct mtDNA haplotype. Tortoises with mtDNA haplotypes closely related to another at-risk population (San Cristóbal) were also identified. These individuals could be considered as candidates for augmentation of natural populations or captive-breeding programmes and exemplify how molecular techniques can provide insights for the development of endangered species management plans.