Biology subjects

Paz-Vinas, I.

Publications and source records attributed to Paz-Vinas, I..

5 recordsLinked to original sources

bioRxiv2024

Genetic-based inference of densities, effective and census sizes of expanding riverine meta-populations of an invasive large-bodied freshwater fish (Silurus glanis L.).

Effective (Ne) and census (Nc) population sizes are key eco-evolutionary parameters. Jointly estimating them have an important practical value for efficient conservation and wildlife monitoring and management. Assessing Ne and Nc remains however challenging for elusive, rare species or species inhabiting in complex habitats like large rivers. Genetic-based Ne estimations could help resolve complex situations, as only a handful of genotyped individuals are needed to estimate Ne, and then NC can be subsequently using an Ne/NC ratio. However, most Ne estimation methods are based on restrictive assumptions (e.g. Wright-Fisher model) making them inappropriate for inferring Ne and Nc for populations and species exhibiting complex dynamics. Here, we aimed at estimating Ne, NC and densities for meta-populations of a large invasive freshwater fish (the European catfish Silurus glanis) that has been introduced in the Garonne-Dordogne river basin (Southwestern France), using a framework that combines multiple data sources and approaches. First, we characterized spatial patterns of genetic variation using microsatellite genotype data, revealing a significant isolation by distance pattern informing about the species dispersal capacities. We then detected four genetically-distinct clusters of individuals coexisting in the river basin that might be the result of multiple introductions from different genetic sources. Further, we characterized the demographic expansion of the species at the river basin scale by analyzing data from a multidecadal demographic monitoring survey, and estimated a specific Ne/Nc ratio for this species. We finally combined all the gathered information to design four competing demo-genetic models accounting for all the complexity of S. glanis meta-populations inhabiting the river basin. We simulated data under these models and then inferred Ne, Nc and densities through approximate Bayesian computation and random forest procedures. We show how multiple genetic and non-genetic approaches can be combined to estimate Ne and Nc in hard-to-monitor meta-populations exhibiting complex demo-evolutionary dynamics.

ecology↗

bioRxiv2023

Estimation of contemporary effective population size in plant populations: limitations of genomic datasets

Effective population size (Ne) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate Ne 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 software programme based on the linkage disequilibrium method, GONE, looks particularly promising to estimate contemporary and recent-historical Ne (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 SNP 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 Ne using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect Ne estimation using the linkage disequilibrium method, such as the occurrence of population structure. We show how accuracy and precision of Ne 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. We finally compare the Ne estimates obtained in GONE for the last generations with the contemporary Ne estimates obtained in the programmes currentNe and NeEstimator.

evolutionary biology↗

bioRxiv2023

Conserving genetic diversity during climate change:Niche marginality and discrepant monitoring capacity in Europe

Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. Genetic diversity has been largely neglected in biodiversity monitoring, and when addressed is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. Genetic monitoring supports the conservation and management of fisheries, game, and threatened populations. It also can contribute to the assessment of predicted and realized impacts of climate change, and their management. We report the first accounting of genetic monitoring efforts among countries in Europe (their genetic monitoring capacity, GMC) to determine where GMC suggests the combination of national infrastructure, political support and resources for continued and expanded monitoring. Overlaying GMC with areas where species ranges approach current and future climate niche limits (i.e., niche marginality) helps identify whether GMC coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area extent, financial resources, and conservation policy influence GMC, high values of which inconsistently match joint species patterns of climate niche marginality. Populations at niche margins likely hold genetic diversity that is important to adaptation to changing climate, and our results illuminate the need in Europe for expanded genetic monitoring across the climate gradients occupied by species, a need arguably greatest in southeastern European countries.

ecology↗

bioRxiv2020

Reporting to the Convention on Biology Diversity: How are countries assessing and protecting their genetic diversity?

Genetic diversity is critically important for all species-domesticated and wild- to adapt to environmental change, and for ecosystem resilience to extreme events. International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve and sustainably and equitably use all levels of biodiversity-genes, species and ecosystems-globally. However, assessment and monitoring of genetic diversity are often overlooked, and there are large knowledge and policy gaps regarding genetic diversity conservation. In this study, we present the first quantitative analysis of genetic diversity assessments conducted by Parties to the CBD. We conducted a detailed, systematic analysis of 114 CBD 5th (submitted 2014) and 6th (submitted 2018) National Reports to quantitatively assess actions, progress on targets, values and indicators related to genetic diversity. First, we found that the importance of genetic diversity is recognised by most Parties to the CBD, and that recognition increased over time. However, genetic targets mainly addressed genetic diversity within cultivated plants, farm animals, and crop wild relatives, with little focus on other wild species. Also, actions for conserving genetic diversity primarily concerned ex-situ facilities and policy, rather than monitoring and intervention for maintaining genetic diversity in situ. The most commonly used indicators of genetic diversity status were the number of genetic resources in conservation facilities, number of threatened breeds, and Red List Index, which are not well correlated to genetic erosion in most species -- highlighting that genetic change is poorly monitored by current indicators. Lastly, analyses of genetic data observations, indigenous use and knowledge of genetic diversity, and strategies being developed and implemented to conserve genetic diversity are highly under-reported. We make several recommendations for the post-2020 CBD Biodiversity Framework to improve awareness, assessment, and monitoring, and facilitate consistent and complete reporting of progress of genetic diversity in future National Reports. Article Impact StatementAn analysis of genetic diversity in CBD National Reports neglects non-domesticated species and demonstrates need for sufficient indicators.

scientific communication and education↗

bioRxiv2017

The systematic conservation planning for intraspecific genetic diversity.

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 cold-spots 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, 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.

evolutionary biology↗