Beyond Biodiversity: Can Environmental DNA (eDNA) Cut it as a Population Genetics Tool?

Adams, Clare I. M.; Knapp, Michael; Gemmell, Neil J.; Jeunen, Gert‐Jan; Bunce, Michael; Lamare, Miles D.; Taylor, Helen R.

doi:10.20944/preprints201902.0048.v1

Cited by 66 publications

(81 citation statements)

References 153 publications

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“…We have shown that it can be also an important source for species-level genetic diversity information for a wide assemblage of taxonomic groups. The mining of metabarcoding data for intraspecies information opens up a vast field with both basic and applied implications (Adams et al 2019). Among the latter, the possibility of effectively basing conservation efforts on multispecies genetic metrics to preserve community-level evolutionary patterns (Nielsen et al 2017).…”

Section: Discussionmentioning

confidence: 99%

From metabarcoding to metaphylogeography: separating the wheat from the chaff

Turon

Antich

Palacín

et al. 2019

Ecological Applications

160

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Metabarcoding is by now a well‐established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α‐ and β‐diversity estimates, that is, interspecies (or inter‐MOTU [molecular operational taxonomic unit]) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra‐MOTU) information—mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding data sets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field that we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra‐MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co‐occurrence patterns of sequences. Using a data set of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two‐step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole data set. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between seas component as well. There were intergroup differences in the amount of variability between and within communities in each sea. For two species, the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra‐ and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.

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Section: Discussionmentioning

confidence: 99%

From metabarcoding to metaphylogeography: separating the wheat from the chaff

Turon

Antich

Palacín

et al. 2019

Ecological Applications

160

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“…To maximize the potential to leverage population-level information from any killer whale DNA isolated from the seawater samples (see Adams et al, 2019;Jones & Good, 2016), the eDNA extracts were enriched for killer whale DNA using targeted whole-genome capture with killer whale RNA baits (Enk et al, 2014). Our goal here was to map the sequencing reads generated from eDNA libraries enriched for killer whale DNA to the killer whale reference genome (Foote et al, 2015) and then compare to a global dataset of killer whale genomes (Foote et al, 2019) setting the minor allele frequency, so that only SNPs (single nucleotide polymorphisms) also present in the global dataset would be called in the eDNA datasets.…”

Section: Whole-genome Enrichment Capturementioning

confidence: 99%

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

et al. 2019

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While environmental DNA (eDNA) is becoming increasingly established in biodiversity monitoring of freshwater ecosystems, the use of eDNA surveys in the marine environment is still in its infancy. Here, we use two approaches: targeted quantitative PCR (qPCR) and whole-genome enrichment capture followed by shotgun sequencing in an effort to amplify killer whale DNA from seawater samples. Samples were collected in close proximity to killer whales in inshore and offshore waters, in varying sea conditions and from the surface and subsurface but none returned strongly positive detections of killer whale eDNA. We validated our laboratory methodologies by successfully amplifying a dilution series of a positive control of killer whale DNA. Furthermore, DNA of Atlantic mackerel, which was present at all sites during sampling, was successfully amplified from the same seawater samples, with positive detections found in ten of the eighteen eDNA extracts. We discuss the various eDNA collection and amplification methodologies used and the abiotic and biotic factors that influence eDNA detection. We discuss possible explanations for the lack of positive killer whale detections, potential pitfalls, and the apparent limitations of eDNA for genetic research on cetaceans, particularly in offshore regions. K E Y W O R D S eDNA, environmental DNA, metagenomics, Orcinus orca, PCR, Scomber scombrus, wholegenome enrichment | 317 PINFIELD Et aL. S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section at the end of the article. How to cite this article: Pinfield R, Dillane E, Runge AKW, et al. False-negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca).

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“…Especially for taxonomically diverse and complex groups such as insects or marine organisms, mtDNA is a marker of choice to identify deeply diverged lineages, including cryptic species, that is, reproductively isolated entities that do not differ morphologically. Furthermore, mtDNA is increasingly used in community ecology as a barcode to quantify animal diversity distributions and to assess biodiversity patterns from environmental samples (eDNA), based on MOTU (molecular operational taxonomic units) defined according to their mitochondrial nucleotide divergence, skipping the tedious step of individual morphological identification of each component of the community (see Adams et al, for a recent review). But does mtDNA divergence indeed reflect the number of local species?…”

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confidence: 99%

One, two or more species? Mitonuclear discordance and species delimitation

Després

2019

Molecular Ecology

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Delimiting species boundaries is central to understand ecological and evolutionary processes, and to monitor biodiversity patterns over time and space. Yet, most of our current knowledge on animal diversity and phylogeny relies on morphological and mitochondrial (mt) DNA variation, a popular molecular marker also used as a barcode to assign samples to species. For morphologically undistinguishable sympatric species (cryptic species), the congruence of several independent markers is necessary to define separate species. Nuclear markers are becoming more accessible, and have confirmed that cryptic species are widespread in all animal phyla (Fišer, Robinson, & Malard, 2018). However, striking differences between the mitochondrial and nuclear variation patterns are also commonly found within single species. Mitonuclear discordance can result from incomplete lineage sorting, sex‐biased dispersal, asymmetrical introgression, natural selection or Wolbachia‐mediated genetic sweeps. But more generally, the distinct mode of transmission of these two types of markers (maternal vs. biparental) is sufficient to explain their distinct sensitivity to purely demographic events such as spatial range and population size fluctuations over time. In a From the Cover manuscript in this issue of Molecular Ecology, Hijonosa et al. (2019) show that highly divergent mtDNA lineages coexist in a widespread European butterfly (Figure 1). None of the hundreds of nuclear markers analyzed was associated with mt lineages, nor was Wolbachia variation. These findings rule out the presence of cryptic species but shed light on complex demographic history of lineage divergence/fusion during the Pleistocene climatic fluctuations, and pave the way to a better integration of both mt and nuclear information in demographic models.

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Beyond Biodiversity: Can Environmental DNA (eDNA) Cut it as a Population Genetics Tool?

Cited by 66 publications

References 153 publications

From metabarcoding to metaphylogeography: separating the wheat from the chaff

From metabarcoding to metaphylogeography: separating the wheat from the chaff

False‐negative detections from environmental DNA collected in the presence of large numbers of killer whales (Orcinus orca)

One, two or more species? Mitonuclear discordance and species delimitation

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