Population differentiation from environmental DNA: Investigating the potential of haplotype presence/absence‐based analysis of molecular variance

Azarian, Clara; Foster, Scott D.; Devloo‐Delva, Floriaan; Feutry, Pierre

doi:10.1002/edn3.143

Cited by 14 publications

(15 citation statements)

References 68 publications

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“…If we had studied eDNA‐concentration per se in order to estimate the number of eel individuals, these factors could easily have led to misleading results. This supports the suggestion that population structure estimates based on eDNA from water samples should origin from the presence/absence of haplotypes (Azarian et al, 2021 ). In addition, a high copy number of one haplotype would also be observed if two individuals share the same haplotype.…”

Section: Discussionsupporting

confidence: 88%

Estimating number of European eel (Anguilla anguilla) individuals using environmental DNA and haplotype count in small rivers

Halvorsen

Korslund

Mattingsdal

et al. 2023

Ecology and Evolution

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Knowledge about population genetic data is important for effective conservation management. Genetic research traditionally requires sampling directly from the organism, for example tissue, which can be challenging, time‐consuming, and harmful to the animal. Environmental DNA (eDNA) approaches offer a way to sample genetic material noninvasively. In attempts to estimate population size of aquatic species using eDNA, researchers have found positive correlations between biomass and eDNA concentrations, but the approach is debated because of variations in the production and degrading of DNA in water. Recently, a more accurate eDNA‐approach has emerged, focusing on the genomic differences between individuals. In this study, we used eDNA from water samples to estimate the number of European eel (Anguilla anguilla) individuals by examining haplotypes in the mitochondrial D‐loop region, both in a closed aquatic environment with 10 eels of known haplotypes and in three rivers. The results revealed that it was possible to find every eel haplotype in the eDNA sample collected from the closed environment. We also found 13 unique haplotypes in the eDNA samples from the three rivers, which probably represent 13 eel individuals. This means that it is possible to obtain genomic information from European eel eDNA in water; however, more research is needed to develop the approach into a possible future tool for population quantification.

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Section: Discussionsupporting

confidence: 88%

Estimating number of European eel (Anguilla anguilla) individuals using environmental DNA and haplotype count in small rivers

Halvorsen

Korslund

Mattingsdal

et al. 2023

Ecology and Evolution

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“…Relative read frequency data are not an appropriate abundance measure for analyses based on haplotype frequencies (Turon et al, 2020). Following the method tested in Azarian et al (2021), we used the frequency of occurrence in the three replicates per locality as a proxy for haplotype abundances. Thus, an ESV can have an abundance value between 0 and 3 at a given locality.…”

Section: Methodsmentioning

confidence: 99%

“…Following the method tested in Azarian et al (2021), we used the frequency of occurrence in the three replicates per locality as a proxy for haplotype abundances. Thus, an ESV can have an abundance value between 0 and 3 at a given locality.…”

Section: Metaphylogeography Datasetmentioning

confidence: 99%

Metabarcoding reveals high‐resolution biogeographical and metaphylogeographical patterns through marine barriers

Antich

Palacín

Zarcero

et al. 2022

Journal of Biogeography

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Aim: It has been predicted that there should be concordance between biogeographical and phylogeographical processes structuring multi-species regional assemblages.We hypothesise that oceanographic barriers in the marine environment affect concomitantly the distribution and the connectivity of the marine biota, thus producing congruent biogeographical and phylogeographical structures. We also predict that macro-and meio-eukaryotes will be differentially affected by hydrological features. Location:The Atlanto-Mediterranean transition along the E Iberian coast marked by the Almeria-Oran Front (AOF) and the Ibiza Channel hydrological discontinuities. Taxon: Eukaryotes.Methods: A new analytical framework based in the metabarcoding of community DNA and a hypervariable marker is presented. This framework allows the simultaneous detection of multispecies biogeographical and phylogeographical structures.Shallow hard-bottom communities were sampled at 12 sites over the littoral zone and community-DNA metabarcoding was performed using the cytochrome c oxidase I marker. The resulting dataset was analysed at several levels: beta diversity of Molecular Operational Taxonomic Units (MOTUs) as surrogate for species, and Exact Sequence Variants as surrogate for haplotypes. We also assessed genetic differentiation within MOTUs (metaphylogeography). Analyses were performed for the combined dataset and separately for macro-and meio-eukaryotes.Results: Both hydrological discontinuities had a detectable effect, more marked at all levels for the AOF than for the Ibiza Channel. The MOTU dataset provided more clear-cut patterns than the ESVs. The metaphylogeographical approach provided the highest resolution in terms of differentiating localities and identifying geographical barriers. The separate analyses of macro-and meio-eukaryotes showed a higher differentiation of the latter, both in terms of beta diversity and genetic differentiation.Main Conclusions: Metabarcoding coupled with metaphylogeography allowed the characterisation of the heterogeneity in community composition and population genetic structure along the Atlanto-Mediterranean transition, coherent with known

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“…There is mounting interest to consider the potential of metabarcoding data sets that could unlock population‐specific patterns included in intraspecific biodiversity (Azarian et al, 2020; Sigsgaard et al, 2020). This allows the simultaneous study of intraspecific diversity and phylogeographical patterns for hundreds of species, referred to as the study of “meta‐phylogeography” (Turon et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Testing small‐scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding

Shum

Palumbi

2021

Molecular Ecology

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In marine ecosystems, regime shifts triggered by ocean warming and acidification are putting increasing pressure on habitat-forming species, such as corals and large seaweeds, resulting in less complex and less productive habitats (Arafeh-Dalmau et al., 2020). Monitoring biodiversity has been crucial in clarifying the ways ecological disturbances, such as abrupt heat waves or shifts in grazing or predation pressure, affect the geographical distribution of habitat-forming species (Melis et al., 2019). The ability to monitor changes in community

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Population differentiation from environmental DNA: Investigating the potential of haplotype presence/absence‐based analysis of molecular variance

Cited by 14 publications

References 68 publications

Estimating number of European eel (Anguilla anguilla) individuals using environmental DNA and haplotype count in small rivers

Estimating number of European eel (Anguilla anguilla) individuals using environmental DNA and haplotype count in small rivers

Metabarcoding reveals high‐resolution biogeographical and metaphylogeographical patterns through marine barriers

Testing small‐scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding

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