Preface to the special issue: Advances in the analysis of spatial genetic data

Laboratoire d'Ecologie Alpine, UMR CNRS 5553, BP 53, Université Joseph Fourier, Grenoble, France.
Molecular Ecology Resources (Impact Factor: 3.71). 09/2010; 10(5):757-9. DOI: 10.1111/j.1755-0998.2010.02899.x
Source: PubMed
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    • "Analytical developments have also resulted in valuable new tools that make genetic analyses more applicable to freshwater restoration. For example, methods in landscape genetics have greatly improved the capacity for understanding how landscape elements affect the spatial genetic diversity of populations (Gaggiotti, 2010; Manel & Holderegger, 2013). However, they are mostly used in terrestrial systems and are waiting to be adopted by more freshwater ecologists. "
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    ABSTRACT: Molecular genetic techniques have been used in freshwater biology for more than 30 years. Early work focussed on studies of population structure, systematics and taxonomy. More recently, the range of studies has broadened to include ecology and adaptation. Advances in analytical methods and in technology (e.g. next-generation sequencing) and decreasing costs of data production ensure that the field will continue to develop and broaden in scope.At least three factors make the application of molecular techniques to freshwater biology exciting. First, the highly variable nature of many aquatic habitats makes them excellent models for the study of environmental change on ecological and evolutionary time scales. Second, the mature state of the field of freshwater biology provides an extensive foundation of ecological knowledge of freshwater organisms and their distinct adaptations. Third, the methodological advances allow researchers to focus more on merging molecular and ecological research and less on designing studies around technical limitations.We identified eight research areas in freshwater biology in which the integration of molecular and ecological approaches provides exceptional opportunities. The list is not exhaustive, but considers a broad range of topics and spans the continuum from basic to applied research. The areas identified use a combination of natural, experimental and in silico approaches.With advancing molecular techniques, freshwater biology is in an unusually strong position to link the genetic basis and ecological importance of adaptations across a wide range of taxa, ecosystems and spatiotemporal scales. Our aim was to identify opportunities for the integration of molecular and ecological approaches, to motivate greater collaboration and crossover, and to promote exploitation of the synergies of bridging ecological and evolutionary freshwater research.
    Freshwater Biology 04/2014; 59(8):1559-1576. DOI:10.1111/fwb.12381 · 2.74 Impact Factor
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    • "We attempted to sample the most important montane ecotones, as well as previously identified clade boundaries (Glor et al. 2003), and boundaries between major macrohabitats (e.g., coastal mangrove, xeric), and we attempted to generate high sampling coverage of the Dominican Republic overall. Because of the continuous distribution of the A. cybotes species complex over the studied landscape and the associated arbitrariness in defining populations, an individualbased sampling scheme was chosen (Lemmon and Lemmon 2008; Bloomquist et al. 2010; Gaggiotti 2010). Structural habitat used data were collected for 551 adult males, and 224 of these were taken as whole animal specimens for morphological analysis. "
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    ABSTRACT: The evolutionary processes that produce adaptive radiations are enigmatic. They can only be studied after the fact, once a radiation has occurred and been recognized, rather than while the processes are ongoing. One way to connect pattern to process is to study the processes driving divergence today among populations of species that belong to an adaptive radiation, and compare the results to patterns observed at a deeper, macroevolutionary level. We tested whether evolution is a deterministic process with similar outcomes during different stages of the adaptive radiation of Anolis lizards. Using a clade of terrestrial-scansorial lizards in the genus Anolis, we inferred the adaptive basis of spatial variation among contemporary populations and tested whether axes of phenotypic differentiation among them mirror known axes of diversification at deeper levels of the anole radiation. Nonparallel change associated with genetic divergence explains the vast majority of geographic variation. However, we found phenotypic variation to be adaptive as confirmed by convergence in populations occurring in similar habitats in different mountain ranges. Morphological diversification among populations recurs deterministically along two axes of diversification previously identified in the anole radiation, but the characters involved differ from those involved in adaptation at higher levels of anole phylogeny.
    Evolution 11/2013; 67(11):3175-90. DOI:10.1111/evo.12184 · 4.61 Impact Factor
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    ABSTRACT: Ever since the introduction of allozymes in the 1960s, evolutionary biologists and ecologists have continued to search for more powerful molecular markers to estimate important parameters such as effective population size and migration rates and to make inferences about the demographic history of populations, the relationships between individuals and the genetic architecture of phenotypic variation (Bensch & Akesson 2005; Bonin et al. 2007). Choosing a marker requires a thorough consideration of the trade-offs associated with the different techniques and the type of data obtained from them. Some markers can be very informative but require substantial amounts of start-up time (e.g. microsatellites), while others require very little time but are much less polymorphic. Amplified fragment length polymorphism (AFLP) is a firmly established molecular marker technique that falls in this latter category. AFLPs are widely distributed throughout the genome and can be used on organisms for which there is no a priori sequence information (Meudt & Clarke 2007). These properties together with their moderate cost and short start-up time have made them the method of choice for many molecular ecology studies of wild species (Bensch & Akesson 2005). However, they have a major disadvantage, they are dominant. This represents a very important limitation because many statistical genetics methods appropriate for molecular ecology studies require the use of codominant markers. In this issue, Foll et al. (2010) present an innovative hierarchical Bayesian method that overcomes this limitation. The proposed approach represents a comprehensive statistical treatment of the fluorescence of AFLP bands and leads to accurate inferences about the genetic structure of natural populations. Besides allowing a quasi-codominant treatment of AFLPs, this new method also solves the difficult problems posed by subjectivity in the scoring of AFLP bands.
    Molecular Ecology 11/2010; 19(21):4586-8. DOI:10.1111/j.1365-294X.2010.04821.x · 6.49 Impact Factor
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