Population Adaptive Index: a New Method to Help Measure Intraspecific Genetic Diversity and Prioritize Populations for Conservation

Abstract

In conservation biology genetic diversity is recognized as an important criterion to consider when prioritizing populations for protection. Today, population genomics offers the opportunity to evaluate both neutral and adaptive components of genetic diversity directly at the genome level with molecular tools. By screening the genome with many genetic markers, it is possible to detect loci supposedly under natural selection and thus of adaptive significance. We devised a new diversity index, the population adaptive index (PAI), which accounts for the adaptive value of the population it refers to. To estimate this index, we performed a genome scan with amplified fragment length polymorphism markers to identify neutral and selected loci in several populations of a widespread amphibian (common frog, Rana temporaria) and a threatened plant (Austrian dragonhead, Dracocephalum austriacum L.). We then investigated four different conservation strategies aimed at protecting the maximum amount of genetic diversity (neutral or selected). In particular we explored the relevance of the principle of complementarity, usually applied to the protection of species, in the management of intraspecific diversity. This principle advocates the conservation of sets of units that together maximize the species' or genetic diversity, which is in opposition to the traditional approach of targeting populations that are the most diverse individually. Four major conclusions emerged from these results. First, the PAI seemed to be a valuable index to evaluate the adaptive diversities within populations. Second, in the two species, the neutral and adaptive diversities within and among populations were not correlated, so conservation strategies based on the neutral and adaptive indexes would not select the same populations for protection. Third, because of its efficiency in conserving genetic diversity, the principle of complementarity deserves to be used more often for this purpose. Fourth, when neutral and adaptive results conflict, additional arguments (e.g., demography, ecology, and geographic proximity) should be considered together with levels of genetic diversity to determine a conservation strategy.

Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci

“…With recent advances in molecular technologies, it is anticipated that such information will become increasingly available. Moreover, loci under selection may allow for an estimation of the adaptive value of subpopulations, useful for conservation priorities (Bonin et al, 2007;Gebremedhin et al, 2009). …”

Historical isolation and hydrodynamically constrained gene flow in declining populations of the South-African abalone, Haliotis midae

“…SNPs for example are often combined with microsatellites in population studies of marine organisms (Smith et al 2007;Narum et al 2008) because of their wider coverage of the genome, frequent association with genes and potential for large scale and cost effective genotyping (Seddon et al 2005;Nielsen et al 2009 and references therein). Also, SNPs associated with genes are more likely to be under the influence of selection and such loci are particularly useful in stock identification in fisheries and estimating the adaptive potential of metapopulations (Nielsen et al 2009;Bonin et al 2007). It is therefore important to apply appropriate tests of neutrality above and beyond measuring population structure (Rand 1996).…”

Adaptive responses of independent traits to the same environmental gradient in the intertidal snail Bembicium vittatum

“…As expected from this perspective, levels of genetic subdivision for phenotypic traits are often higher than those for molecular markers (Spitze, 1993;Gockel et al, 2001;Storz, 2002;Steinger et al, 2002;Luttikhuizen et al, 2003;Volis et al, 2005;Schiffer et al, 2007). This approach has also been the basis for detecting subsets of potentially important loci, when using AFLP markers as genomic scans (Beaumont, 2005;Storz, 2005), with important implications for using genetics to set priorities in conservation (Bonin et al, 2007).…”

“…The results from both B. vittatum and L. saxatilis highlight the potential usefulness of identifying not just individual traits that are adaptively important, but also significant environmental gradients. In their proposal to use genomic scans to identify markers associated with local adaptation, as a basis for assessing conservation priorities, Bonin et al (2007) also found greatest divergence associated with apparently important environmental gradients. Thus, although the emphasis has been on the identification of adaptively important traits, an important question for further work is how widely are independent traits adapted to the same environmental gradients.…”