Opportunities and inherent limits of using environmental DNA for population genetics

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(5), P. 1048 - 1064

Published: Aug. 9, 2023

Abstract Molecular techniques using DNA retrieved from community or environmental samples, in particular (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template population genetics, several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types “community‐based” such possibility to target multiple species same time, generated great enthusiasm expectations genetics. However, not every aspect genetics can be addressed eDNA‐based data some inherent limitations may challenge its conclusions. Here, we firstly review state current knowledge samples Then, focusing on eDNA, summarize but detail four main use population‐level inferences, namely, (1) difficulty retrieve species‐specific dataset, (2) potential lack correlation between observed true allelic frequencies, (3) loss information multi‐locus genotyping linkage loci, (4) uncertainty about individuals contributing sampled pool (e.g., number, life‐stage, sex). Some might overcome development new technologies models that account specificities eDNA. Others, however, inherent, their effect inferences must thoroughly evaluated. The gaining insights into genetic diversity structure is appealing scientists, conservation managers, other practitioners. Yet, avoid false incorrect it imperative known considered alongside advantages.

Language: Английский

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Balancing Inbreeding and Outbreeding Risks to Inform Translocations Throughout the Range of an Imperiled Darter

Evolutionary Applications, Journal Year: 2025, Volume and Issue: 18(3)

Published: March 1, 2025

ABSTRACT Restoring connectivity via assisted migration is a useful but currently underused approach for maintaining genetic diversity and preventing extirpations of threatened species. The use as conservation strategy may be limited by the difficulty balancing benefits reconnecting populations (including reduced inbreeding depression increased adaptive capacity) with perceived risk outbreeding depression, which requires comprehensive knowledge landscape adaptive, neutral, deleterious, structural variation across species' range. Using combination reduced‐representation whole‐genome sequencing, we characterized genomic differentiation Arkansas Darter ( Etheostoma cragini ) its range in Midwestern US. We found strong population structure large differences effective sizes drainages. strength isolation river distance differed among drainages, type surrounding streams impoundments also contributing to isolation. Despite low some populations, there was surprisingly little evidence recent (based on absence long runs homozygosity) or elevated levels deleterious smaller populations. Considering allowed us identify several potential recipient that benefit from translocations donor sites throughout Planning translocation strategies intended restored possible rescue at earlier stages species decline will likely increase probability retaining persistence over term while minimizing risks associated translocation.

Language: Английский

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Reduced genetic diversity of freshwater amphipods in rivers with increased levels of anthropogenic organic micropollutants

Evolutionary Applications, Journal Year: 2022, Volume and Issue: 15(6), P. 976 - 991

Published: April 21, 2022

Anthropogenic chemicals in freshwater environments contribute majorly to ecosystem degradation and biodiversity decline. In particular anthropogenic organic micropollutants (AOM), a diverse group of compounds, including pesticides, pharmaceuticals, industrial chemicals, can significantly impact organisms. AOM were found genetic diversity species; however, which degree cause changes population structure allelic richness macroinvertebrates remains poorly understood. Here, the on common amphipod

Language: Английский

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Spatiotemporal dynamics in freshwater amphipod assemblages are associated with surrounding terrestrial land use type

Ecosphere, Journal Year: 2023, Volume and Issue: 14(3)

Published: March 1, 2023

Abstract Biological assemblages are the result of dynamic processes that have explicit temporal and spatial dimensions. Although biodiversity patterns can be directly inferred from structure these assemblages, an assessment changes through time space is needed to understand how organisms initially assembled they responding local environmental biotic factors. Small freshwater streams particularly affected by contemporary anthropogenic activities biological invasions, yet commonly less studied, as studies often focus on lakes large streams. Here, we conducted a spatially analysis keystone shredder across eight years in 12 replicated small tributary In each stream, monitored multiple sites per kilometer stream length. By assessing beta diversity dynamics, defined gain or loss species abundance at individual sites, show amphipod occur within context surrounding terrestrial matrix reflect recent colonization history. While composition was mostly constant located forested catchments, embedded catchments with more extensive agricultural land use displayed pronounced changes, either driven unoccupied upstream locations but undirected fluctuations gains losses species. Our study thus suggests landscapes might destabilize aquatic causing higher community structures highlighting vulnerability ecosystems drivers.

Language: Английский

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Population structure and insecticide response of Gammarus spp. in agricultural and upstream forested sites of small streams

Environmental Sciences Europe, Journal Year: 2023, Volume and Issue: 35(1)

Published: June 3, 2023

Abstract Exposure to pesticides may cause adaptation not only in agricultural pests and pathogens, but also non-target organisms. Previous studies mainly searched for adaptations organisms pesticide-polluted sites. However, propagate heritable pesticide effects, such as increased tolerance, non-exposed populations through gene flow. We examined the tolerance—as one of pre-assumptions local adaptation—of freshwater crustacean Gammarus spp. (at genus level reflecting gammarid community). The tolerance was quantified acute toxicity tests using insecticide imidacloprid. Gammarids were sampled at sites (termed agriculture), least impacted upstream refuge) transitional edge) six small streams south-west Germany. Furthermore, we population genetic structure fossarum energy reserves (here lipid content) G. well three site types (i.e. agriculture, edge refuge). found significantly lower imidacloprid from compared refuge sites, potentially due higher environmental stress indicated by a slightly content per mg tissue. no differences between populations, indicating propagation effects edges. among showed significant differentiation streams, within stream across types. suggest that high flow each hindered resulted similar (pre)adaptations levels types, although they exhibited different pollution. Further on target genes (e.g., conferring tolerance), fitness phenotypes particular are required adjacent pristine ecosystems detect potential propagations effects.

Language: Английский

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Dispersal behaviour and riverine network connectivity shape the genetic diversity of freshwater amphipod metapopulations

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(24), P. 6551 - 6565

Published: Oct. 1, 2021

Theory predicts that the distribution of genetic diversity in a landscape is strongly dependent on connectivity metapopulation and dispersal individuals between patches. However, influence explicit spatial configurations such as dendritic landscapes metapopulations still understudied, theoretical corroborations empirical patterns are largely lacking. Here, we used microsatellite data stochastic simulations two freshwater amphipods 28,000 km2 riverine network to study strategies their diversity. We found significant imprint effects local global both amphipod species. Data from 95 sites showed allelic richness significantly increased towards more central nodes network. This was also seen for observed heterozygosity, yet not expected heterozygosity. Genetic differentiation with instream distance. In simulation models, depending mutational model assumed, upstream movement probability rate, respectively, emerged key factors explaining empirically differentiation. Surprisingly, role site-specific carrying capacities, example by assuming direct dependency population size river size, less clear cut: while our best fitting scenario included this feature, over all simulations, scaling capacities did increase data-model fit. highlights importance behaviour along networks shaping

Language: Английский

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Optimizing laboratory cultures of Gammarus fossarum (Crustacea: Amphipoda) as a study organism in environmental sciences and ecotoxicology

The Science of The Total Environment, Journal Year: 2022, Volume and Issue: 855, P. 158730 - 158730

Published: Sept. 16, 2022

Amphipods are among the most abundant macroinvertebrates in freshwater ecosystems of Palaearctic and crucial for ecosystem functioning. Furthermore, their high sensitivity to environmental change pollutants makes them widely used model organisms sciences ecotoxicology. In field studies surveys across Eurasia, species genus Gammarus commonly used, yet laboratory-based ecotoxicological tests often restricted parts world non-native Hyalella azteca, as is much harder breed maintain under laboratory conditions. However, direct comparisons extrapolations results field- vs. studies, use same would be desirable. Here, we investigated different settings with respect feeding, shelter day length successfully increase survival, juvenile production respective growth ultimately multi-generation breeding amphipod fossarum. Amphipod populations persisted reproduced optimized husbandry conditions 12 months were partially maintained another year up a few hundred individuals. Specifically, supplementing diet protein-rich food sources well provisioning shelters improved survival rate G. fossarum significantly. found no significant effect treatments on overall relative reproductive activity or total abundance maintained. We conclude that can kept reared standardized Despite longer generation times higher effort required maintenance compared H. ecological relevance comparability natural systems may justify its future development study organism

Language: Английский

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

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 9, 2024

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

Language: Английский

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Contrasts in riverscape patterns of intraspecific genetic variation in a diverse Neotropical fish community of high conservation value

Heredity, Journal Year: 2023, Volume and Issue: 131(1), P. 1 - 14

Published: April 25, 2023

Language: Английский

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Long transients and dendritic network structure affect spatial predator–prey dynamics in experimental microcosms

Journal of Animal Ecology, Journal Year: 2023, Volume and Issue: 92(7), P. 1416 - 1430

Published: May 16, 2023

Abstract Spatial dynamics can promote persistence of strongly interacting predators and prey. Theory predicts that spatial predator–prey systems are prone to long transients, meaning the leading or extinction manifest over hundreds generations. Furthermore, form duration transients may be altered by network structure. Few empirical studies have examined importance in food webs, especially a context, due difficulty collecting large scale long‐term data required. We protist microcosms using three experimental structures: isolated, river‐like dendritic networks regular lattice networks. Densities patterns occupancy were followed for both prey time equates >100 predator >500 found persisted whereas they went extinct isolated treatment. The played out with distinct phases. transient phases showed differences between structures, as did underlying occupancy. differed among organisms different trophic positions. Predators higher local more connected bottles while this spatially ones. Predictions based on connectivity derived from metapopulation theory explained occupancy, was better Our results support hypothesized role promoting but ultimately occur which turn influenced structure interactions.

Language: Английский

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