Genetic diversity Goals and Targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators

Samples from subdivided populations yield biased estimates of effectivee size that overestimate the rate of loss of genetic variation

Abstract Many empirical studies estimating effective population size apply the temporal method that provides an estimate of the variance effective size through the amount of temporal allele frequency change under the assumption that the study population is completely isolated. This assumption is frequently violated, and the magnitude of the resulting bias is generally unknown. We studied how gene flow affects estimates of effective size obtained by the temporal method when sampling from a population system and provide analytical expressions for the expected estimate under an island model of migration. We show that the temporal method tends to systematically underestimate both local and global effective size when populations are connected by gene flow, and the bias is sometimes dramatic. The problem is particularly likely to occur when sampling from a subdivided population where high levels of gene flow obscure identification of subpopulation boundaries. In such situations, sampling in a manner that prevents biased estimates can be difficult. This phenomenon might partially explain the frequently reported unexpectedly low effective population sizes of marine populations that have raised concern regarding the genetic vulnerability of even exceptionally large populations

Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

The sympatric existence of genetically distinguishable populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves certain parts of the genome. We returned to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verified the existence of the two coexisting demes using a 96-SNP fluidigm array. We then applied whole- genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity was higher in deme I than in deme II. Strong genetic divergence is observed with genome-wide FST ≈ 0.2. Compared with data from populations of similar small lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in deme II versus deme I, indicating different degree of isolation. We located two gene-copies for LDH-A and found divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.coexisting populations, conservation genetics, conservation genomics, hidden biodiversity, population genetic structure, salmonidpublishedVersio

Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

The sympatric existence of genetically distinguishable populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves certain parts of the genome. We returned to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verified the existence of the two coexisting demes using a 96-SNP fluidigm array. We then applied whole- genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity was higher in deme I than in deme II. Strong genetic divergence is observed with genome-wide FST ≈ 0.2. Compared with data from populations of similar small lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in deme II versus deme I, indicating different degree of isolation. We located two gene-copies for LDH-A and found divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.coexisting populations, conservation genetics, conservation genomics, hidden biodiversity, population genetic structure, salmoni

Neglect of Genetic Diversity in Implementation of the Convention on Biological Diversity

Genetic diversity is the foundation for all biological diversity; the persistence and evolutionary potential of species depend on it. World leaders have agreed on the conservation of genetic diversity as an explicit goal of the Convention on Biological Diversity (CBD). Nevertheless, actions to protect genetic diversity are largely lacking. With only months left to the 2010-biodiversity target, when the 191 parties to the CBD have agreed on achieving a significant reduction of the rate of biodiversity loss, gene-level diversity is still not being monitored, and indicators and thresholds that can be used to devise strategies to conserve this important component of biodiversity are missing. Immediate action is needed to ensure that genetic diversity is not neglected in conservation targets beyond 2010. The risks associated with depletion of genetic diversity were recognized in classic publications 4 decades ago (Frankel 1970, 1974), and this message has been repeatedly stressed ever since (e.g., Schonewald-Cox 1983; Ryman & Utter 1987; Frankham 1995; Allendorf & Ryman 2002; Hughes et al. 2008). In that time, a body of theory (Lynch & Lande 1993; Lande 1995; Lynch et al. 1995) and empirical work has emerged that demonstrates how populations and even species can collapse due to loss of genetic diversity (e.g., Newman & Pilson 1997; Briskie & Mackintosh 2004; Frankham 2005). Evidence supporting the importance of maintaining genetic variation to sustain species and ecosystems continues to accumulate (Wimp et al. 2004; Crutsinger et al. 2006; Whitham et al. 2006). Gene-level biodiversity is recognized in the CBD (www.cbd.int) as one of three levels of diversity— ecosystems, species, and genes—that are to be conserved and sustainably used. Since its adoption in 1992, this convention has become the most important international political instrument for halting biodiversity loss. At present, 192 nations are parties to the CBD, representing every nation in the world except for Andorra, the Holy See (the Vatican), Somalia (party from mid December 2009), and the United States. Integral to the CBD is the task of “monitor[ing], through sampling and other techniques, the components of biological diversity” to “identify processes and categories of activities which have or are likely to have significant adverse impacts on the conservation and sustainable use of biological diversity, and monitor their effects.” In 2002 parties to the CBD committed themselves to reduce significantly by 2010 the current rates of biodiversity loss at global, regional, and national levels as a “contribution to poverty alleviation and to the benefit of all life on Earth.” This 2010 biodiversity target was subsequently endorsed by the World Summit on Sustainable Development and the United Nations General Assembly and incorporated as a new target under the UN Millennium Development Goals (http://www.un.org/millenniumgoals/). To evaluate progress toward the 2010 biodiversity target for genetic variation it is necessary to assess and monitor this critical level of diversity. The CBD is not a mandatory instrument; it is the responsibility of each country to develop and implement a National Biodiversity Strategy and Action Plan (NBSAP). To assess the extent to which genetic diversity is currently recognized in national biodiversity policy programs, we used information available at the convention’s website to review NBSAPs of a subset of countries party to the CBD (http://www.cbd.int; subheading: Countries; assessed January–March 2009). Our aim was to investigate whether individual parties state in their strategies and action plans that genetic variation of wild animals and plants is to be conserved in their country and whether they explicitly recognize the need for developing monitoring programs for this diversity. For our analysis we selected every 10th country ranked according to its gross national product (GNP; http:// www.studentsoftheworld.info/infopays/rank/PN B2.html). If a country was not part of the CBD or not a sovereign nation, or if a document was missing, not searchable, or not in English, we chose the next country on the list. We reviewed 24 NBSAPs. Of these, 67% (16 countries) state that genetic variation should be conserved. Nevertheless, 38% (six) of these plans focus only on the genetic diversity of domesticated populations compared with 62% (10) that also recognize the genetic diversity of wild animals and plants as a conservation concern. Although most (90%; 21 countries) of the reviewed NBSAPs state that monitoring of biodiversity should be carried out, only 21% (five) explicitly acknowledge the need for developing means for monitoring diversity at the genetic level. These five countries all grouped in the upper 20% of the GNP ranking (i.e., larger countries with strong economic performance). In contrast, countries sharing the general goal of conserving genetic diversity represent the full spectrum of GNP ranks

Complex genetic diversity patterns of cryptic, sympatric brown trout (Salmo trutta) populations in tiny mountain lakes

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Moose genomes reveal past glacial demography and the origin of modern lineages

Abstract Background: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America. Results: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines. Conclusions: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies