Identifying landscape features that affect functional connectivity among populations is a major challenge in fundamental and applied sciences. Landscape genetics combines landscape and genetic data ...to address this issue, with the main objective of disentangling direct and indirect relationships among an intricate set of variables. Causal modeling has strong potential to address the complex nature of landscape genetic data sets. However, this statistical approach was not initially developed to address the pairwise distance matrices commonly used in landscape genetics. Here, we aimed to extend the applicability of two causal modeling methods—that is, maximum-likelihood path analysis and the directional separation test—by developing statistical approaches aimed at handling distance matrices and improving functional connectivity inference. Using simulations, we showed that these approaches greatly improved the robustness of the absolute (using a frequentist approach) and relative (using an information-theoretic approach) fits of the tested models. We used an empirical data set combining genetic information on a freshwater fish species (Gobio occitaniae) and detailed landscape descriptors to demonstrate the usefulness of causal modeling to identify functional connectivity in wild populations. Specifically, we demonstrated how direct and indirect relationships involving altitude, temperature, and oxygen concentration influenced within- and between-population genetic diversity of G. occitaniae.
Intraspecific diversity informs the demographic and evolutionary histories of populations, and should be a main conservation target. Although approaches exist for identifying relevant biological ...conservation units, attempts to identify priority conservation areas for intraspecific diversity are scarce, especially within a multi-specific framework. We used neutral molecular data on six European freshwater fish species (Squalius cephalus, Phoxinus phoxinus, Barbatula barbatula, Gobio occitaniae, Leuciscus burdigalensis and Parachondrostoma toxostoma) sampled at the riverscape scale (i.e. the Garonne-Dordogne river basin, France) to determine hot- and coldspots of genetic diversity, and to identify priority conservation areas using a systematic conservation planning approach. We demonstrate that systematic conservation planning is efficient for identifying priority areas representing a predefined part of the total genetic diversity of a whole landscape. With the exception of private allelic richness (PA), classical genetic diversity indices (allelic richness, genetic uniqueness) were poor predictors for identifying priority areas. Moreover, we identified weak surrogacies among conservation solutions found for each species, implying that conservation solutions are highly species-specific. Nonetheless, we showed that priority areas identified using intraspecific genetic data from multiple species provide more effective conservation solutions than areas identified for single species or on the basis of traditional taxonomic criteria.
Abstract Measuring genetic diversity of wild species using DNA-based data remains resource intensive and time consuming for nearly all species. However, genetic assessments are needed for global ...conservation commitments, including the Convention on Biological Diversity, and for governments and managers to evaluate conservation progress, as well as prioritizing species and populations to preserve and recover genetic diversity (e.g., via genetic rescue). Recently, indicators were developed for tracking and reporting genetic diversity status and trends for hundreds of species. The indicators quantify two simple proxies of within-population and among-population genetic diversity and adaptive potential: small effective population size (Ne < 500) and the loss of genetically distinct populations. The indicators must balance scientific credibility, practicality, and simplicity. In the present article, we summarize the advantages of these pragmatic indicators, address critiques by scientists for simplifying assumptions and by policymakers for complexity, and propose potential solutions and next steps. We aim to support practitioners putting indicators into policy, action, legislation, and reporting.
Effective population size ( N e ) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate N e have been preferred over ...demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium, in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A recently developed software based on linkage disequilibrium, GONE, looks particularly promising to estimate contemporary and recent-historical N e (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNPs genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating N e using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect N e estimation using the linkage disequilibrium method, such as the occurrence of population structure. We show how accuracy and precision of N e estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data.
Biological invasions are a major component of global change worldwide. But paradoxically, an invasive species might also have threatened populations within its native range. Designing efficient ...management policies is needed to prevent and mitigate range expansions of invasive alien species (IAS) in non-native areas, while protecting them within their native range. Characterizing genetic variation patterns for IAS populations and deciphering the links between their native and introduced populations is helpful to (i) assess the genetic state of both native and non-native populations, (ii) reveal potential invasion pathways, (iii) define IAS management strategies in invaded areas, and (iv) identify native populations requiring conservation measures. The European catfish (
Silurus glanis
) is the largest European predatory fish. Introduced since the seventies from Eastern to Western Europe, it has colonized many waterbodies. Yet, little is known about the genetic status of non-native populations and the invasion pathways used by the species. Besides, some native populations are threatened, requiring conservation actions. Here, we describe current patterns of genetic variability of native and non-native
S. glanis
populations across Europe. Using microsatellite markers, we first assessed genetic variation within and between native and non-native populations. Second, we performed genetic clustering analyses to determine the genetic structure of multiple catfish populations across Europe and highlight their potential links. We revealed that native populations are more genetically diverse than non-native populations, and highlight complex introduction pathways involving several independent sources of introduction, which likely explain the invasion success of this large predatory fish across western Europe.
International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve, and sustainably and equitably use, biodiversity. The CBD is a vital instrument for global ...conservation because it guides 195 countries and the European Union in setting priorities and allocating resources, and requires regular reporting on progress. However, the CBD and similar policy agreements have often neglected genetic diversity. This is a critical gap because genetic diversity underlies adaptation to environmental change and ecosystem resilience. Here we aim to inform future policy, monitoring, and reporting efforts focused on limiting biodiversity loss by conducting the largest yet evaluation of how Parties to the CBD report on genetic diversity. A large, globally representative sample of 114 CBD National Reports was examined to assess reported actions, progress, values and indicators related to genetic diversity. Although the importance of genetic diversity is recognized by most Parties to the CBD, genetic diversity targets mainly addressed variation within crops and livestock (a small fraction of all species). Reported actions to conserve genetic diversity primarily concerned ex situ facilities and legislation, rather than monitoring and in situ intervention. The most commonly reported status indicators are not well correlated to maintaining genetic diversity. Lastly, few reports mentioned genetic monitoring using DNA data, indigenous use and knowledge of genetic diversity, or development of strategies to conserve genetic diversity. We make several recommendations for the post-2020 CBD Biodiversity Framework, and similar efforts such as IPBES, to improve awareness, assessment, and monitoring of genetic diversity, and facilitate consistent and complete reporting in the future.
•We assessed genetic diversity in reports to the Convention on Biological Diversity•Countries recognize diverse values of, and threats to, genetic diversity•Most countries neglect to monitor or develop strategies for genetic diversity•Many countries focus on ex situ genetic conservation, neglecting in situ actions•Many countries use insufficient indicators and focus strongly on domesticated species
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.
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