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Macé B, Mouillot D, Dalongeville A, Bruno M, Deter J, Varenne A, Gudefin A, Boissery P, Manel S. The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves. Mol Ecol 2024:e17373. [PMID: 38703047 DOI: 10.1111/mec.17373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/08/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Coastal areas host a major part of marine biodiversity but are seriously threatened by ever-increasing human pressures. Transforming natural coastlines into urban seascapes through habitat artificialization may result in loss of biodiversity and key ecosystem functions. Yet, the extent to which seaports differ from nearby natural habitats and marine reserves across the whole Tree of Life is still unknown. This study aimed to assess the level of α and β-diversity between seaports and reserves, and whether these biodiversity patterns are conserved across taxa and evolutionary lineages. For that, we used environmental DNA (eDNA) metabarcoding to survey six seaports on the French Mediterranean coast and four strictly no-take marine reserves nearby. By targeting four different groups-prokaryotes, eukaryotes, metazoans and fish-with appropriate markers, we provide a holistic view of biodiversity on contrasted habitats. In the absence of comprehensive reference databases, we used bioinformatic pipelines to gather similar sequences into molecular operational taxonomic units (MOTUs). In contrast to our expectations, we obtained no difference in MOTU richness (α-diversity) between habitats except for prokaryotes and threatened fishes with higher diversity in reserves than in seaports. However, we observed a marked dissimilarity (β-diversity) between seaports and reserves for all taxa. Surprisingly, this biodiversity signature of seaports was preserved across the Tree of Life, up to the order. This result reveals that seaports and nearby marine reserves share few taxa and evolutionary lineages along urbanized coasts and suggests major differences in terms of ecosystem functioning between both habitats.
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Affiliation(s)
- Bastien Macé
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - David Mouillot
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
| | | | - Morgane Bruno
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
| | - Julie Deter
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
- Andromède Océanologie, Mauguio, France
| | - Alix Varenne
- Université Côte d'Azur, CNRS, ECOSEAS, Nice, France
- Ecocean, Montpellier, France
| | | | - Pierre Boissery
- Agence de l'eau Rhône-Méditerranée-Corse, Délégation de Marseille, Marseille, France
| | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE-PSL University, IRD, Montpellier, France
- Institut Universitaire de France, Paris, France
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Smale DA, Epstein G, Parry M, Attrill MJ. Spatiotemporal variability in the structure of seagrass meadows and associated macrofaunal assemblages in southwest England (UK): Using citizen science to benchmark ecological pattern. Ecol Evol 2019; 9:3958-3972. [PMID: 31015980 PMCID: PMC6467847 DOI: 10.1002/ece3.5025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 11/20/2022] Open
Abstract
Seagrass meadows underpin a variety of ecosystem services and are recognized as globally important habitats and a conservation priority. However, seagrass populations are currently impacted by a range of biotic and abiotic stressors, and many are in decline globally. As such, improved understanding of seagrass populations and their associated faunal assemblages is needed to better detect and predict changes in the structure and functioning of these key habitats. Here, we analyzed a large dataset-collected by recreational scuba divers volunteering on a citizen science project-to examine spatiotemporal patterns in ecological structure and to provide a robust and reliable baseline against which to detect future change. Seagrass (Zostera marina) shoot density and the abundance of associated faunal groups were quantified across 2 years at 19 sites nested within three locations in southwest UK, by collecting in situ quadrat samples (2,518 in total) during 328 dives. Seagrass shoot density and meadow fragmentation was comparable across locations but was highly variable among sites. Faunal abundance and assemblage structure varied between areas with or without seagrass shoots; this pattern was largely consistent between locations and years. Overall, increased seagrass density was related to increased faunal abundance and explained shifts in faunal assemblage structure, although individual faunal groups were affected differently. More broadly, our study shows that well-funded and orchestrated citizen science projects can, to some extent, gather fundamental information needed to benchmark ecological structure in poorly studied nearshore marine habitats.
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Affiliation(s)
- Dan A. Smale
- Marine Biological Association of the United Kingdom, The LaboratoryPlymouthUK
| | - Graham Epstein
- Marine Biological Association of the United Kingdom, The LaboratoryPlymouthUK
- Ocean and Earth Science, National Oceanography Centre SouthamptonUniversity of SouthamptonSouthamptonUK
| | | | - Martin J. Attrill
- School of Biological and Marine SciencesUniversity of PlymouthPlymouthUK
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Lacoursière‐Roussel A, Howland K, Normandeau E, Grey EK, Archambault P, Deiner K, Lodge DM, Hernandez C, Leduc N, Bernatchez L. eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity. Ecol Evol 2018; 8:7763-7777. [PMID: 30250661 PMCID: PMC6144963 DOI: 10.1002/ece3.4213] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 12/21/2022] Open
Abstract
Because significant global changes are currently underway in the Arctic, creating a large-scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio-temporal distribution of eDNA in two locations. We extracted and amplified eDNA using two COI primer pairs from ~80 water samples that were collected across two Canadian Arctic ports, Churchill and Iqaluit, based on optimized sampling and preservation methods for remote regions surveys. Results demonstrate that aquatic eDNA surveys have the potential to document large-scale Arctic biodiversity change by providing a rapid overview of coastal metazoan biodiversity, detecting nonindigenous species, and allowing sampling in both open water and under the ice cover by local northern-based communities. We show that DNA sequences of ~50% of known Canadian Arctic species and potential invaders are currently present in public databases. A similar proportion of operational taxonomic units was identified at the species level with eDNA metabarcoding, for a total of 181 species identified at both sites. Despite the cold and well-mixed coastal environment, species composition was vertically heterogeneous, in part due to river inflow in the estuarine ecosystem, and differed between the water column and tide pools. Thus, COI-based eDNA metabarcoding may quickly improve large-scale Arctic biomonitoring using eDNA, but we caution that aquatic eDNA sampling needs to be standardized over space and time to accurately evaluate community structure changes.
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Affiliation(s)
| | - Kimberly Howland
- Central and Arctic RegionFisheries and Oceans CanadaFreshwater InstituteWinnipegMBCanada
| | - Eric Normandeau
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Erin K. Grey
- Division of Science, Mathematics and TechnologyGovernors State UniversityUniversity ParkILUSA
| | | | - Kristy Deiner
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZürichSwitzerland
| | - David M. Lodge
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - Cecilia Hernandez
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Noémie Leduc
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Louis Bernatchez
- Department of BiologyInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
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Santamaria CA, Mateos M, DeWitt TJ, Hurtado LA. Constrained body shape among highly genetically divergent allopatric lineages of the supralittoral isopod Ligia occidentalis (Oniscidea). Ecol Evol 2016; 6:1537-54. [PMID: 26900449 PMCID: PMC4747314 DOI: 10.1002/ece3.1984] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/28/2015] [Accepted: 01/03/2016] [Indexed: 11/06/2022] Open
Abstract
Multiple highly divergent lineages have been identified within Ligia occidentalis sensu lato, a rocky supralittoral isopod distributed along a ~3000 km latitudinal gradient that encompasses several proposed marine biogeographic provinces and ecoregions in the eastern Pacific. Highly divergent lineages have nonoverlapping geographic distributions, with distributional limits that generally correspond with sharp environmental changes. Crossbreeding experiments suggest postmating reproductive barriers exist among some of them, and surveys of mitochondrial and nuclear gene markers do not show evidence of hybridization. Populations are highly isolated, some of which appear to be very small; thus, the effects of drift are expected to reduce the efficiency of selection. Large genetic divergences among lineages, marked environmental differences in their ranges, reproductive isolation, and/or high isolation of populations may have resulted in morphological differences in L. occidentalis, not detected yet by traditional taxonomy. We used landmark‐based geometric morphometric analyses to test for differences in body shape among highly divergent lineages of L. occidentalis, and among populations within these lineages. We analyzed a total of 492 individuals from 53 coastal localities from the southern California Bight to Central Mexico, including the Gulf of California. We conducted discriminant function analyses (DFAs) on body shape morphometrics to assess morphological variation among genetically differentiated lineages and their populations. We also tested for associations between phylogeny and morphological variation, and whether genetic divergence is correlated to multivariate morphological divergence. We detected significant differences in body shape among highly divergent lineages, and among populations within these lineages. Nonetheless, neither lineages nor populations can be discriminated on the basis of body shape, because correct classification rates of cross‐validated DFAs were low. Genetic distance and phylogeny had weak to no effect on body shape variation. The supralittoral environment appears to exert strong stabilizing selection and/or strong functional constraints on body shape in L. occidentalis, thereby leading to morphological stasis in this isopod.
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Affiliation(s)
- Carlos A Santamaria
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas; Biology Faculty College of Arts and Sciences University of South Florida Sarasota-Manatee Sarasota Florida
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Thomas J DeWitt
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Luis A Hurtado
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
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