DNA from lake sediments reveals long-term ecosystem changes after a biological invasion

Ficetola, Gentile Francesco; Poulenard, Jérôme; Sabatier, Pierre; Messager, Erwan; Gielly, Ludovic; Leloup, Anouk; Étienne, David; Bakke, Jostein; Malet, Emmanuel; Fanget, Bernard; Støren, Eivind; Reyss, Jean-Louis; Taberlet, Pierre; Arnaud, Fabien

doi:10.1126/sciadv.aar4292

Cited by 93 publications

(84 citation statements)

References 53 publications

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“…flatworms, gastrotrichs, acoels, gnathostomulids, rotifers, for which sampling and preservation for morphological analyses is more problematic 18 . Metabarcoding from meiofauna is now a common approach in biodiversity studies 21,25 and our results demonstrate that we can strengthen the support for the use of metabarcoding of meiofauna in routine environmental monitoring, potentially not only for sandy beaches 26,27 . We found an indication of the effect of human presence notwithstanding the use of one single marker and with a certain proportion of samples that did not work, potentially because of non-optimal processing and storage before DNA extraction.…”

Section: Discussionsupporting

confidence: 74%

Human access impacts biodiversity of microscopic animals in sandy beaches

et al. 2020

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Whereas most work to understand impacts of humans on biodiversity on coastal areas has focused on large, conspicuous organisms, we highlight effects of tourist access on the diversity of microscopic marine animals (meiofauna). We used a DNA metabarcoding approach with an iterative and phylogeny-based approach for the taxonomic assignment of meiofauna and relate diversity patterns to the numbers of tourists accessing sandy beaches on an otherwise un-impacted island National Park. Tourist frequentation, independently of differences in sediment granulometry, beach length, and other potential confounding factors, affected meiofaunal diversity in the shallow "swash" zone right at the mean water mark; the impacts declined with water depth (up to 2 m). The indicated negative effect on meiofauna may have a consequence on all the biota including the higher trophic levels. Thus, we claim that it is important to consider restricting access to beaches in touristic areas, in order to preserve biodiversity.

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Section: Discussionsupporting

confidence: 74%

Human access impacts biodiversity of microscopic animals in sandy beaches

et al. 2020

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“…, Ficetola et al. ). All of them are highly relevant for basic biodiversity research and for establishing management policies.…”

Section: Introductionmentioning

confidence: 97%

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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“…As shown here, freshwater habitats can show a higher degradation than terrestrial landscapes, even within areas that are considered traditionally managed. In particular, introduced species were shown in the present case to have a stronger effect on amphibian decline and on the almost extinct emblematic paedomorphic phenotype than be those of climate change (see also Ficetola et al 2018). Therefore, it is urgent that ponds and small lakes receive as much attention as large lakes and rivers in conservation policy (Davies et al 2008).…”

Section: Discussionmentioning

confidence: 63%

Traditionally managed landscapes do not prevent amphibian decline and the extinction of paedomorphosis

Denoël

Ficetola

Sillero

et al. 2019

Ecological Monographs

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Eco‐cultural landscapes are assumed to be favorable environments for the persistence of biodiversity, but global change may affect differently their terrestrial and aquatic components. Few long‐term studies have examined how multiple, global change stressors may affect wetland biodiversity in such environments. Facultative paedomorphosis is a spectacular example of intra‐specific variation, in which biphasic (metamorphosing) amphibians coexist with fully aquatic conspecifics that do not metamorphose (paedomorphs). Paedomorphosis is seriously threatened by global change stressors, but it is unknown to what extent traditional management will allow its long‐term persistence. Here, we tested the effects of alien species introductions while taking into account land use and climate changes on the distribution of two polymorphic newt species (Ichthyosaura alpestris and Lissotriton graecus) in Montenegro by using a 68‐yr data set and Bayesian mixed models integrating complex spatial and temporal structures. We found that, despite the persistence of natural landscapes, metamorphs dramatically declined and paedomorphs were nearly extirpated, losing 99.9% of their aquatic area of occupancy and all the major populations. Fish introduction was the main determinant of decline for both phenotypes. Climate and the presence of crayfish further contributed to the decline of metamorphs, which started later and was less dramatic than that of paedomorphs. The near extinction of paedomorphosis on a country‐wide scale shows how invasive species determine broad‐scale impacts, which can be even stronger than other global change stressors, and underlines the need for immediate management actions to avoid the extinction of a unique developmental process, paedomorphosis.

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DNA from lake sediments reveals long-term ecosystem changes after a biological invasion

Abstract: Rabbits have had a stronger impact on the landscape and plant communities of a remote island than one century of climate change.

Cited by 93 publications

References 53 publications

Human access impacts biodiversity of microscopic animals in sandy beaches

Human access impacts biodiversity of microscopic animals in sandy beaches

From metabarcoding to metaphylogeography: separating the wheat from the chaff

Traditionally managed landscapes do not prevent amphibian decline and the extinction of paedomorphosis

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