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Múrria C, Wangensteen OS, Somma S, Väisänen L, Fortuño P, Arnedo MA, Prat N. Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173243. [PMID: 38761946 DOI: 10.1016/j.scitotenv.2024.173243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 04/04/2024] [Accepted: 05/12/2024] [Indexed: 05/20/2024]
Abstract
Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources - tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding - for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community - benthic versus water column, respectively - and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.
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Affiliation(s)
- Cesc Múrria
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Zoological Systematics & Evolution (ZooSysEvo), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | - Owen S Wangensteen
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain; Norwegian College of Fishery Science, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Simona Somma
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Leif Väisänen
- Stream Ecology Research Group, Department of Ecology and Genetics, University of Oulu, Finland
| | - Pau Fortuño
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Freshwater Ecology, Hydrology and Management (FEHM), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Miquel A Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Zoological Systematics & Evolution (ZooSysEvo), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Narcís Prat
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Grup de Recerca Freshwater Ecology, Hydrology and Management (FEHM), Universitat de Barcelona, Barcelona, Catalonia, Spain
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2
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Macko P, Derka T, Čiamporová-Zaťovičová Z, Grabowski M, Čiampor F. Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries. Mol Ecol Resour 2024; 24:e13954. [PMID: 38520175 DOI: 10.1111/1755-0998.13954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/25/2024]
Abstract
Mayflies (Ephemeroptera) are among the crucial water and habitat quality bioindicators. However, despite their intensive long-term use in various studies, more reliable mayfly DNA barcode data have been produced in a negligible number of countries, and only ~40% of European species had been barcoded with less than 50% of families covered. Despite being carried out in a small area, our study presents the second-most species-rich DNA reference library of mayflies from Europe and the first comprehensive view from an important biodiversity hotspot such as the Western Carpathians. Within 1153 sequences, 76 morphologically determined species were recorded and added to the Barcode of Life Data System (BOLD) database. All obtained sequences were assigned to 97 BINs, 11 of which were unique and three represented species never barcoded before. Sequences of 16 species with high intraspecific variability were divided into 40 BINs, confirming the presence of cryptic lineages. Due to the low interspecific divergence and the non-existing barcoding gap, sequences of six species were assigned to three shared BINs. Delimitation analyses resulted in 79 and 107 putative species respectively. Bayesian and maximum-likelihood phylogenies confirmed the monophyly of almost all species and complexes of cryptic taxa and proved that DNA barcoding distinguishes almost all studied mayfly species. We have shown that it is still sufficient to thoroughly investigate the fauna of a small but geographically important area to enrich global databases greatly. In particular, the insights gained here transcend the local context and may have broader implications for advancing barcoding efforts.
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Affiliation(s)
- Patrik Macko
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Tomáš Derka
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Zuzana Čiamporová-Zaťovičová
- Department of Ecology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Michal Grabowski
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Fedor Čiampor
- ZooLab, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
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3
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El Alami M, Vuataz L, El Yaagoubi S, Sartori M. Another new species of the genus Habrophlebia Eaton, 1881 (Ephemeroptera, Leptophlebiidae) from the Maghreb. Zookeys 2023; 1186:47-70. [PMID: 38115829 PMCID: PMC10729008 DOI: 10.3897/zookeys.1186.112796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/30/2023] [Indexed: 12/21/2023] Open
Abstract
A new species belonging to the genus Habrophlebia Eaton, 1881 is described at the nymphal stage from the Rif Mountains of Morocco. This species presents unique features, such as the chorionic arrangement of the egg and the ornamentation of the posterior margin of abdominal tergites. It is compared to all west European Habrophlebia species and a table with discriminating characters is given. A phylogenetic reconstruction based on COI sequences fully supports the hypothesis of a new species in the Rif Mountains, with possible further distribution in southern Spain.
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Affiliation(s)
- Majida El Alami
- Université Abdelmalek Essaâdi, Faculté des Sciences, Département de Biologie, Laboratoire Ecologie, Systématique et Conservation de la Biodiversité (LESB), Unité de Recherche Labellisée CNRST N°18. B.P.2121. Tétouan 93002, MoroccoUniversité Abdelmalek EssaâdiTétouanMorocco
| | - Laurent Vuataz
- Muséum Cantonal des Sciences Naturelles, Département de Zoologie, Palais de Rumine, Place Riponne 6, CH-1005, Lausanne, SwitzerlandMuséum Cantonal des Sciences Naturelles, Département de ZoologieLausanneSwitzerland
- University of Lausanne (UNIL), Department of Ecology and Evolution, CH-1015 Lausanne, SwitzerlandUniversity of Lausanne (UNIL)LausanneSwitzerland
| | - Sara El Yaagoubi
- Université Abdelmalek Essaâdi, Faculté des Sciences, Département de Biologie, Laboratoire Ecologie, Systématique et Conservation de la Biodiversité (LESB), Unité de Recherche Labellisée CNRST N°18. B.P.2121. Tétouan 93002, MoroccoUniversité Abdelmalek EssaâdiTétouanMorocco
| | - Michel Sartori
- Muséum Cantonal des Sciences Naturelles, Département de Zoologie, Palais de Rumine, Place Riponne 6, CH-1005, Lausanne, SwitzerlandMuséum Cantonal des Sciences Naturelles, Département de ZoologieLausanneSwitzerland
- University of Lausanne (UNIL), Department of Ecology and Evolution, CH-1015 Lausanne, SwitzerlandUniversity of Lausanne (UNIL)LausanneSwitzerland
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4
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Dambri BM, Godunko RJ, Benhadji N. Baetidae (Insecta: Ephemeroptera) of Aurès Mountains (Algeria): A New Species of the Baetis alpinus Species Group, with Notes on Baetis Laech, 1815 Biogeography within Maghreb. INSECTS 2023; 14:899. [PMID: 37999098 PMCID: PMC10672397 DOI: 10.3390/insects14110899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023]
Abstract
A new species, Baetis (Baetis) dihyaesp. nov., belonging to the Baetis alpinus species group, is described and illustrated based on larval material collected in the Aurès Mountains (northeastern Algeria) in 2020-2021. This new species is closely related to three European species, e.g., Baetis (B.) alpinus (Pictet, 1843); B. (B.) nubecularis Eaton, 1898; and B. (B.) pasquetorum Righetti & Thomas, 2002 by the combination of the following characteristics: (i) more than one short, stout bristle at the tip of segment II of the maxillary palp and (ii) a well-developed paracercus. However, the new species clearly differs from all congeners of the Baetis alpinus species group primarily by the (a) structure of mouthparts-with 14-18 long submarginal setae arranged in a single irregular row on the dorsal surface of the labrum; 2-6 short, stout bristles at the tip of segment II of the maxillary palp; and segment II of the labial palp without a considerably developed apico-internal lobe); (b) setation of abdominal terga, with a few triangular-shaped scales sparsely scattered near the posterior margin only; and (c) a well-developed paracercus, comprised of more than 50 segments. Primary data on the biology and distribution of this new species are provided, and molecular affinities are verified by the analysis of COI (barcode) sequences. Detailed notes on the distribution of mayfly species belonging to the Baetis alpinus species group common in Western Europe and the western part of North Africa are presented. The historical movement of Baetis representatives between Europe, North West Africa, and subsequently Algeria, with the land bridges 'Strait of Gibraltar' and 'Strait of Sicily' as colonization routes, is discussed in detail and identified in the present study as the Western Algeria colonization path and Eastern Algeria colonization path, respectively.
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Affiliation(s)
- Besma M. Dambri
- Department of Ecology and Environment, Faculty of Natural and Life Sciences, University of Batna 2, Fesdis 05078, Batna, Algeria;
| | - Roman J. Godunko
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 37005 České Budějovice, Czech Republic;
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90237 Lodz, Poland
- State Museum of Natural History, National Academy of Sciences of Ukraine, Teatralna 18, 79008 Lviv, Ukraine
| | - Nadhira Benhadji
- Institute of Technology and Life Sciences–National Research Institute, Falenty, Hrabska Avenue 3, 05090 Raszyn, Poland
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5
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El Yaagoubi S, Vuataz L, El Alami M, Gattolliat JL. A new species of the Baetisfuscatus group (Ephemeroptera, Baetidae) from Morocco. Zookeys 2023; 1180:27-50. [PMID: 37744949 PMCID: PMC10517345 DOI: 10.3897/zookeys.1180.109298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
Baetisrifensissp. nov. is the first representative of the Baetisfuscatus group to be described from the Maghreb. It was collected from streams in the Rif region of northern Morocco. All species of the B.fuscatus group are morphologically very similar, with slight differences in colour. Thus, in addition to morphological description, species delimitation based on genetic evidence was carried out. The new species was compared with other members of the B.fuscatus group from the Palaearctic region.
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Affiliation(s)
- Sara El Yaagoubi
- Laboratoire Ecologie, Systématique, Conservation de la Biodiversité (LESCB), Unité de Recherche Labellisée CNRST N°18, Université Abdelmalek Essaâdi, Faculté des Sciences, Département de Biologie, B.P.2121 93002 Tétouan, MoroccoUniversité Abdelmalek EssaâdiTetouanMorocco
| | - Laurent Vuataz
- Muséum Cantonal des Sciences Naturelles, Palais de Rumine, Place Riponne 6, CH-1005 Lausanne, SwitzerlandMuséum Cantonal des Sciences Naturelles, Palais de RumineLausanneSwitzerland
- University of Lausanne (UNIL), Department of Ecology and Evolution, CH-1015 Lausanne, SwitzerlandUniversity of Lausanne (UNIL)LausanneSwitzerland
| | - Majida El Alami
- Laboratoire Ecologie, Systématique, Conservation de la Biodiversité (LESCB), Unité de Recherche Labellisée CNRST N°18, Université Abdelmalek Essaâdi, Faculté des Sciences, Département de Biologie, B.P.2121 93002 Tétouan, MoroccoUniversité Abdelmalek EssaâdiTetouanMorocco
| | - Jean-Luc Gattolliat
- Muséum Cantonal des Sciences Naturelles, Palais de Rumine, Place Riponne 6, CH-1005 Lausanne, SwitzerlandMuséum Cantonal des Sciences Naturelles, Palais de RumineLausanneSwitzerland
- University of Lausanne (UNIL), Department of Ecology and Evolution, CH-1015 Lausanne, SwitzerlandUniversity of Lausanne (UNIL)LausanneSwitzerland
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6
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Ranasinghe UGSL, Eberle J, Benjamin SP, Ahrens D. Local stochastics and ecoclimatic situation shape phytophagous chafer assemblage composition. Ecol Evol 2023; 13:e10091. [PMID: 37187965 PMCID: PMC10175718 DOI: 10.1002/ece3.10091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 04/20/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023] Open
Abstract
Very little is known about factors determining the assemblage structure of megadiverse polyphagous-herbivore scarab chafers in the tropics (Coleoptera: Scarabaeidae). Here, we examined the composition of Sri Lankan chafer assemblages and investigated whether it is influenced more by the general ecoclimatic situation, macrohabitat, or indetermined stochastic biotic and abiotic factors of each locality. We also explored the influence of the latter on separate lineages and general body size. Based on dedicated field surveys conducted during the dry and wet seasons, we examined 4847 chafer individuals of 105 species sampled using multiple UV-light traps in 11 localities covering different forest types and altitudinal zones. Assemblages were assessed for compositional similarity, species diversity, and abundance within four major eco-spatial partitions: forest types, elevational zones, localities, and macrohabitats. Our results revealed that assemblages were shaped mainly by locality stochastics (i.e., multi-factor ensemble of all biotic and abiotic environmental conditions at local scale), and to a minor extent by ecoclimatic conditions. Macrohabitat had little effect on the assemblage composition. This was true for the entire chafer assemblage as well as for all single lineages or different body size classes. However, in medium and large species the contrasts between localities were less pronounced, which was not the case for individual lineages of the assemblage. Contrasts of assemblage similarity between localities were much more evident than those for forest types and elevation zones. Significant correlation between species composition and geographic distance was found only for the assemblage of small-bodied specimens. Seasonal change (dry-wet) in species composition was minor and only measurable in a few localities. The strong turnover between examined localities corroborates with the high degree of endemism in many phytophagous chafers, particularly in Sericini. Connected with their hypothetic poor habitat specificity and polyphagy, this might also explain why so many chafer crop pests in the Asian tropics are endemics.
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Affiliation(s)
- U. G. Sasanka L. Ranasinghe
- Zoological Research Museum A. Koenig, BonnLeibniz Institute for the Analysis of Biodiversity Change (LIB)BonnGermany
- National Institute of Fundamental StudiesKandySri Lanka
| | - Jonas Eberle
- Zoological Research Museum A. Koenig, BonnLeibniz Institute for the Analysis of Biodiversity Change (LIB)BonnGermany
- University of SalzburgSalzburgAustria
| | - Suresh P. Benjamin
- Zoological Research Museum A. Koenig, BonnLeibniz Institute for the Analysis of Biodiversity Change (LIB)BonnGermany
- National Institute of Fundamental StudiesKandySri Lanka
| | - Dirk Ahrens
- Zoological Research Museum A. Koenig, BonnLeibniz Institute for the Analysis of Biodiversity Change (LIB)BonnGermany
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7
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Gattolliat JL, Samraoui B, Benhadji N, Kechemir L, Zrelli S, El Yaagoubi S, El Moutaouakil MEA, Sartori M. Baetidae (Baetidae, Ephemeroptera) in the Maghreb: state of the art, key, and perspectives. Zookeys 2023; 1139:137-163. [PMID: 36761280 PMCID: PMC9860507 DOI: 10.3897/zookeys.1139.94586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/30/2022] [Indexed: 01/15/2023] Open
Abstract
Among mayflies, Baetidae are often considered as easy to recognise at the family level, but difficult to identify at lower level. In several faunistic or ecological studies, the identification remains at the family level; Baetidae are generally considered as widespread and ubiquitous, therefore as poorly informative for ecological studies or bioassessments. Here, a straightforward identification key is offered to larvae of the ten genera of Baetidae reported from Maghreb based on easily observable and understandable characters. The diversity, ecology, and distribution of each taxonomic unit (genera or subgenera) are discussed and the main difficulties for deeper identification are pointed out. Future challenges and remaining taxonomic riddles for Maghrebian Baetidae are detailed.
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Affiliation(s)
- Jean-Luc Gattolliat
- Museum of Zoology, Palais de Rumine, Place Riponne 6, CH-1014 Lausanne, SwitzerlandMuseum of ZoologyLausanneSwitzerland,Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, SwitzerlandUniversity of LausanneLausanneSwitzerland
| | - Boudjéma Samraoui
- Laboratoire de Conservation des Zones Humides, University 8 mai 1945, Guelma, AlgeriaUniversité 8 Mai 1945GuelmaAlgeria,Department of Biology, University Badji Mokhtar Annaba, Annaba, AlgeriaUniversity Badji Mokhtar AnnabaAnnabaAlgeria
| | - Nadhira Benhadji
- Laboratoire de Recherche Valorisation des Actions de L’homme Pour la Protection de L’environnement et Application en Santé Publique, University of Tlemcen, BP 119, 13000 Tlemcen, AlgeriaUniversity of TlemcenTlemcenAlgeria,Department of Hydrobiology, Institute of Biology, University of Szczecin, Felczaka street 3 c, 71- 412 Szczecin, PolandUniversity of SzczecinSzczecinPoland
| | - Lina Kechemir
- Faculté des Sciences agronomiques et des sciences biologiques, University of Mouloud Mammeri, Tizi-Ouzou, AlgeriaUniversity of Mouloud MammeriTizi-OuzouAlgeria
| | - Sonia Zrelli
- Unit of Hydrobiology, Laboratory of Environment Biomonitoring (LBE), Faculty of Sciences of Bizerta, University of Bizerta, 7021 Jarzouna, TunisiaUniversity of BizertaJarzounaTunisia,Honoris United Universities, Ecole Polytechnique Centrale, Avenue Mohamed V, 1002 Tunis, TunisiaHonoris United UniversitiesTunisTunisia
| | - Sara El Yaagoubi
- Laboratory of Ecology, Systematics and Conservation of the Biodiversity, department of Biology, Faculty of Science, University of Abdelmalek Essaadi, Avenue Sebta, 93002 Tetouan, MoroccoUniversity of Abdelmalek EssaadiTetouanMorocco
| | - Majida El Alami El Moutaouakil
- Laboratory of Ecology, Systematics and Conservation of the Biodiversity, department of Biology, Faculty of Science, University of Abdelmalek Essaadi, Avenue Sebta, 93002 Tetouan, MoroccoUniversity of Abdelmalek EssaadiTetouanMorocco
| | - Michel Sartori
- Museum of Zoology, Palais de Rumine, Place Riponne 6, CH-1014 Lausanne, SwitzerlandMuseum of ZoologyLausanneSwitzerland,Department of Ecology and Evolution, Biophore, University of Lausanne, CH-1015 Lausanne, SwitzerlandUniversity of LausanneLausanneSwitzerland
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8
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Novaković BB, Raković MB, Čiampor Jr F, Teofilova TM, Živić IM. Genetic variability of the riffle beetle Elmis maugetii Latreille, 1802 (Coleoptera: Elmidae) in Europe and North Africa. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01206-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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9
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Ishii NI, Hirota SK, Matsuo A, Sato MP, Sasaki T, Suyama Y. Species–genetic diversity correlations depend on ecological similarity between multiple moorland plant species. OIKOS 2022. [DOI: 10.1111/oik.09023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Naohiro I. Ishii
- Field Science Center, Graduate School of Agricultural Science, Tohoku Univ., Naruko‐onsen Osaki Miyagi Japan
- Graduate School of Environment and Information Sciences, Yokohama National Univ., Hodogaya Yokohama Kanagawa Japan
| | - Shun K. Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku Univ., Naruko‐onsen Osaki Miyagi Japan
| | - Ayumi Matsuo
- Field Science Center, Graduate School of Agricultural Science, Tohoku Univ., Naruko‐onsen Osaki Miyagi Japan
| | - Mitsuhiko P. Sato
- Field Science Center, Graduate School of Agricultural Science, Tohoku Univ., Naruko‐onsen Osaki Miyagi Japan
| | - Takehiro Sasaki
- Graduate School of Environment and Information Sciences, Yokohama National Univ., Hodogaya Yokohama Kanagawa Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku Univ., Naruko‐onsen Osaki Miyagi Japan
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10
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Diversity and Distribution of Mayflies from Morocco (Ephemeroptera, Insecta). DIVERSITY 2022. [DOI: 10.3390/d14060498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Recent research in various Moroccan areas allowed an update and a revision of the Moroccan Ephemeroptera checklist. In this case, 54 species are now listed, belonging to 10 families and 26 genera. The distribution of all studied species is discussed, as well as their biogeographical affinities. Moroccan Mayflies are characterized by a clear dominance of Mediterranean elements with a strong rate of endemism (33.4%).
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11
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Rahman MM, Burian A, Creedy TJ, Vogler AP. DNA
‐based assessment of environmental degradation in an unknown fauna: the freshwater macroinvertebrates of the
Indo‐Burmese
hotspot. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Md. Mizanur Rahman
- Department of Life Sciences, Natural History Museum London UK
- Department of Life Sciences, Silwood Park Campus Imperial College London Ascot UK
- Department of Zoology University of Dhaka Dhaka Bangladesh
| | - Alfred Burian
- Marine Ecology Department Lurio University Nampula Mozambique
- Department of Computational Landscape Ecology, UFZ–Helmholtz Centre for Environmental Research Leipzig Germany
| | - Thomas J. Creedy
- Department of Life Sciences, Natural History Museum London UK
- Department of Life Sciences, Silwood Park Campus Imperial College London Ascot UK
| | - Alfried P. Vogler
- Department of Life Sciences, Natural History Museum London UK
- Department of Life Sciences, Silwood Park Campus Imperial College London Ascot UK
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12
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Martins FMS, Feio MJ, Porto M, Filipe AF, Bonin A, Serra SRQ, Alves PC, Taberlet P, Beja P. Assessing changes in stream macroinvertebrate communities across ecological gradients using morphological versus DNA metabarcoding approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149030. [PMID: 34311381 DOI: 10.1016/j.scitotenv.2021.149030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Freshwater macroinvertebrates provide valuable indicators for biomonitoring ecosystem change in relation to natural and anthropogenic drivers. DNA metabarcoding is an efficient approach for estimating such indicators, but its results may differ from morphotaxonomic approaches traditionally used in biomonitoring. Here we test the hypothesis that despite differences in the number and identity of taxa recorded, both approaches may retrieve comparable patterns of community change, and detect similar ecological gradients influencing such changes. We compared results obtained with morphological identification at family level of macroinvertebrates collected at 80 streams under a Water Framework Directive biomonitoring program in Portugal, with results obtained with metabarcoding from the ethanol preserving the bulk samples, using either single (COI-M19BR2, 16S-Inse01, 18S-Euka02) or multiple markers. Metabarcoding recorded less families and different communities compared to morphotaxonomy, but community sensitivities to disturbance estimated with the IASPT index were more similar across approaches. Spatial variation in local community metrics and the factors influencing such variation were significantly correlated between morphotaxonomy and metabarcoding. After reducing random noise in the dissimilarity matrices, the spatial variation in community composition was also significantly correlated across methods. A dominant gradient of community change was consistently retrieved, and all methods identified a largely similar set of anthropogenic stressors strongly influencing such gradient. Overall, results confirm our initial hypothesis, suggesting that morphotaxonomy and metabarcoding can estimate consistent spatial patterns of community variation and their main drivers. These results are encouraging for macroinvertebrate biomonitoring using metabarcoding approaches, suggesting that they can be intercalibrated with morphotaxonomic approaches to recover equivalent spatial and temporal gradients of ecological change.
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Affiliation(s)
- Filipa M S Martins
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal.
| | - Maria J Feio
- Universidade de Coimbra, MARE, Centro de Ciências do Mar e do Ambiente, Departamento de Ciência da Vida, Coimbra, Portugal
| | - Miguel Porto
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Ana F Filipe
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Aurélie Bonin
- Université Grenoble Alpes, CNRS, Laboratoire d'Ecologie Alpine (LECA), Grenoble, France
| | - Sónia R Q Serra
- Universidade de Coimbra, MARE, Centro de Ciências do Mar e do Ambiente, Departamento de Ciência da Vida, Coimbra, Portugal
| | - Paulo C Alves
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal
| | - Pierre Taberlet
- Université Grenoble Alpes, CNRS, Laboratoire d'Ecologie Alpine (LECA), Grenoble, France; UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
| | - Pedro Beja
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vila do Conde, Portugal; CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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13
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Overcast I, Ruffley M, Rosindell J, Harmon L, Borges PAV, Emerson BC, Etienne RS, Gillespie R, Krehenwinkel H, Mahler DL, Massol F, Parent CE, Patiño J, Peter B, Week B, Wagner C, Hickerson MJ, Rominger A. A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities. Mol Ecol Resour 2021; 21:2782-2800. [PMID: 34569715 PMCID: PMC9297962 DOI: 10.1111/1755-0998.13514] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 11/30/2022]
Abstract
Biodiversity accumulates hierarchically by means of ecological and evolutionary processes and feedbacks. Within ecological communities drift, dispersal, speciation, and selection operate simultaneously to shape patterns of biodiversity. Reconciling the relative importance of these is hindered by current models and inference methods, which tend to focus on a subset of processes and their resulting predictions. Here we introduce massive ecoevolutionary synthesis simulations (MESS), a unified mechanistic model of community assembly, rooted in classic island biogeography theory, which makes temporally explicit joint predictions across three biodiversity data axes: (i) species richness and abundances, (ii) population genetic diversities, and (iii) trait variation in a phylogenetic context. Using simulations we demonstrate that each data axis captures information at different timescales, and that integrating these axes enables discriminating among previously unidentifiable community assembly models. MESS is unique in generating predictions of community‐scale genetic diversity, and in characterizing joint patterns of genetic diversity, abundance, and trait values. MESS unlocks the full potential for investigation of biodiversity processes using multidimensional community data including a genetic component, such as might be produced by contemporary eDNA or metabarcoding studies. We combine MESS with supervised machine learning to fit the parameters of the model to real data and infer processes underlying how biodiversity accumulates, using communities of tropical trees, arthropods, and gastropods as case studies that span a range of data availability scenarios, and spatial and taxonomic scales.
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Affiliation(s)
- Isaac Overcast
- Biology Department, Graduate Center of the City University of New York, New York, New York, USA.,Biology Department, City College of New York, New York, New York, USA.,Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
| | - Megan Ruffley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, Idaho, USA
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, UK
| | - Luke Harmon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Paulo A V Borges
- Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group, Faculdade de Ciências Agrárias e do Ambiente, Universidade dos Açores, Açores, Portugal
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology, IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Rosemary Gillespie
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
| | | | - D Luke Mahler
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Francois Massol
- CNRS, Inserm, CHU Lille, University of Lille, Lille, France.,Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France.,CNRS, Evo-Eco-Paleo, SPICI Group, University of Lille, Lille, France
| | - Christine E Parent
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, Idaho, USA
| | - Jairo Patiño
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology, IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain.,Plant Conservation and Biogeography Group, Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Universidad de La Laguna, Tenerife, Islas Canarias, Spain
| | - Ben Peter
- Group of Genetic Diversity through Space and Time, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bob Week
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Catherine Wagner
- Department of Botany and Biodiversity Institute, University of Wyoming, Laramie, Wyoming, USA
| | - Michael J Hickerson
- Biology Department, Graduate Center of the City University of New York, New York, New York, USA.,Biology Department, City College of New York, New York, New York, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Andrew Rominger
- School of Biology and Ecology, University of Maine, Orono, Maine, USA.,Maine Center for Genetics in the Environment, University of Maine, Orono, Maine, USA
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14
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Gálvez-Reyes N, Arribas P, Andújar C, Emerson BC, Piñero D, Mastretta-Yanes A. Dispersal limitations and long-term persistence drive differentiation from haplotypes to communities within a tropical sky-island: Evidence from community metabarcoding. Mol Ecol 2021; 30:6611-6626. [PMID: 34564919 DOI: 10.1111/mec.16195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 01/04/2023]
Abstract
Neutral theory proposes that dispersal stochasticity is one of the main drivers of local diversity. Haplotypes-level genetic variation can now be efficiently sampled from across whole communities, thus making it possible to test neutral predictions from the genetic to species-level diversity, and higher. However, empirical data is still limited, with the few studies to date coming from temperate latitudes. Here, we focus on a tropical mountain within the Transmexican Volcanic Belt to evaluate spatially fine-scale patterns of arthropod community assembly to understand the role of dispersal limitation and landscape features as drivers of diversity. We sampled whole-communities of arthropods for eight orders at a spatial scale ranging from 50 m to 19 km, using whole community metabarcoding. We explored multiple hierarchical levels, from individual haplotypes to lineages at 0.5, 1.5, 3, 5, and 7.5% similarity thresholds, to evaluate patterns of richness, turnover, and distance decay of similarity with isolation-by-distance and isolation-by-resistance (costs to dispersal given by landscape features) approaches. Our results showed that distance and altitude influence distance decay of similarity at all hierarchical levels. This holds for arthropod groups of contrasting dispersal abilities, but with different strength depending on the spatial scale. Our results support a model where local-scale differentiation mediated by dispersal constraints, combined with long-term persistence of lineages, is an important driver of diversity within tropical sky islands.
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Affiliation(s)
- Nancy Gálvez-Reyes
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Santa Cruz de Tenerife, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Santa Cruz de Tenerife, Spain
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Santa Cruz de Tenerife, Spain
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), CDMX, Mexico.,Consejo Nacional de Ciencia y Tecnología, Benito Juárez (CONACYT), CDMX, Mexico
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15
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Sarremejane R, Cid N, Stubbington R, Datry T, Alp M, Cañedo-Argüelles M, Cordero-Rivera A, Csabai Z, Gutiérrez-Cánovas C, Heino J, Forcellini M, Millán A, Paillex A, Pařil P, Polášek M, Tierno de Figueroa JM, Usseglio-Polatera P, Zamora-Muñoz C, Bonada N. DISPERSE, a trait database to assess the dispersal potential of European aquatic macroinvertebrates. Sci Data 2020; 7:386. [PMID: 33177529 PMCID: PMC7658241 DOI: 10.1038/s41597-020-00732-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/21/2020] [Indexed: 11/09/2022] Open
Abstract
Dispersal is an essential process in population and community dynamics, but is difficult to measure in the field. In freshwater ecosystems, information on biological traits related to organisms' morphology, life history and behaviour provides useful dispersal proxies, but information remains scattered or unpublished for many taxa. We compiled information on multiple dispersal-related biological traits of European aquatic macroinvertebrates in a unique resource, the DISPERSE database. DISPERSE includes nine dispersal-related traits subdivided into 39 trait categories for 480 taxa, including Annelida, Mollusca, Platyhelminthes, and Arthropoda such as Crustacea and Insecta, generally at the genus level. Information within DISPERSE can be used to address fundamental research questions in metapopulation ecology, metacommunity ecology, macroecology and evolutionary ecology. Information on dispersal proxies can be applied to improve predictions of ecological responses to global change, and to inform improvements to biomonitoring, conservation and management strategies. The diverse sources used in DISPERSE complement existing trait databases by providing new information on dispersal traits, most of which would not otherwise be accessible to the scientific community.
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Affiliation(s)
- Romain Sarremejane
- School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Núria Cid
- INRAE, UR RiverLy, centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626, Villeurbanne, Cedex, France
- Grup de Recerca Freshwater Ecology, Hydrology and Management (FEHM), Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Rachel Stubbington
- School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Thibault Datry
- INRAE, UR RiverLy, centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626, Villeurbanne, Cedex, France
| | - Maria Alp
- INRAE, UR RiverLy, centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626, Villeurbanne, Cedex, France
| | - Miguel Cañedo-Argüelles
- Grup de Recerca Freshwater Ecology, Hydrology and Management (FEHM), Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Adolfo Cordero-Rivera
- ECOEVO Lab, E.E. Forestal, Univesidade de Vigo, Campus A Xunqueira, 36005, Pontevedra, Spain
| | - Zoltán Csabai
- Department of Hydrobiology, University of Pécs, Ifjúság útja 6, H7624, Pécs, Hungary
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Cayetano Gutiérrez-Cánovas
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Jani Heino
- Finnish Environment Institute, Freshwater Centre, Paavo Havaksen Tie 3, FI-90570, Oulu, Finland
| | - Maxence Forcellini
- INRAE, UR RiverLy, centre de Lyon-Villeurbanne, 5 rue de la Doua CS70077, 69626, Villeurbanne, Cedex, France
| | - Andrés Millán
- Department of Ecology and Hydrology, Biology Faculty, Murcia University, Campus de Espinardo, 30100, Murcia, Spain
| | - Amael Paillex
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Sciences, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
- ECOTEC Environment SA, 1203, Geneva, Switzerland
| | - Petr Pařil
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Marek Polášek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - José Manuel Tierno de Figueroa
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, Avenida Fuente Nueva, s/n, 18071, Granada, Spain
| | - Philippe Usseglio-Polatera
- Université de Lorraine, CNRS, UMR 7360, LIEC, Laboratoire Interdisciplinaire des Environnements Continentaux, F-57070, Metz, France
| | - Carmen Zamora-Muñoz
- Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, Avenida Fuente Nueva, s/n, 18071, Granada, Spain
| | - Núria Bonada
- Grup de Recerca Freshwater Ecology, Hydrology and Management (FEHM), Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Diagonal 643, 08028, Barcelona, Catalonia, Spain
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16
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Benhadji N, Sartori M, Abdellaoui Hassaine K, Gattolliat JL. Reports of Baetidae (Ephemeroptera) species from Tafna Basin, Algeria and biogeographic affinities revealed by DNA barcoding. Biodivers Data J 2020; 8:e55596. [PMID: 32879616 PMCID: PMC7442755 DOI: 10.3897/bdj.8.e55596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/24/2020] [Indexed: 11/13/2022] Open
Abstract
Background The Mediterranean basin is known to be the cradle of many endemic species. Within mayflies (Insecta, Ephemeroptera), North African species belonging to the family Baetidae remain poorly known and, traditionally, affinities to European fauna were proposed. Recent studies, based on molecular reconstructions, showed closer relationships to Mediterranean islands fauna. New information Baetidae were sampled from North-West Algerian wadis (Tafna basin) and involved in COI barcoding reconstructions. Seven species were identified. The subgenus Rhodobaetis is represented by Baetisatlanticus known previously from Macaronesian islands, Europe and Morocco and the Maghrebian endemic Baetissinespinosus. Specimens, previously identified as Cloeoncf.dipterum, correspond to Cloeonperegrinator and, until now, only reported from Macaronesia. Besides the confirmation of endemicity of some species, such as Procloenstagnicola and B.sinespinosus, our molecular study showed quite original results for relationships between European, insular and Algerian species. Baetismaurus stood out as a North African endemic sister clade to an Iberian clade. Furthermore, we found clear interspecific distances between Algerian and European clades for A.cf.sinaica and B.cf.pavidus, suggesting the presence of cryptic species in Algeria. However, additional studies are needed, as, for the moment, no clear morphological characters were found to separate the different clades and support them as valid species.
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Affiliation(s)
- Nadhira Benhadji
- Laboratoire de recherche Valorisation des actions de l'homme pour la protection de l'environnement et application en santé publique, Université de Tlemcen, BP 119 13000, Tlemcen, Algeria Laboratoire de recherche Valorisation des actions de l'homme pour la protection de l'environnement et application en santé publique, Université de Tlemcen, BP 119 13000 Tlemcen Algeria
| | - Michel Sartori
- Département d'Ecologie et Evolution, Université de Lausanne, Lausanne, Switzerland Département d'Ecologie et Evolution, Université de Lausanne Lausanne Switzerland.,Musée cantonal de zoologie, Lausanne, Switzerland Musée cantonal de zoologie Lausanne Switzerland
| | - Karima Abdellaoui Hassaine
- Laboratoire de recherche Valorisation des actions de l'homme pour la protection de l'environnement et application en santé publique, Université de Tlemcen, BP 119 13000, Tlemcen, Algeria Laboratoire de recherche Valorisation des actions de l'homme pour la protection de l'environnement et application en santé publique, Université de Tlemcen, BP 119 13000 Tlemcen Algeria
| | - Jean-Luc Gattolliat
- Département d'Ecologie et Evolution, Université de Lausanne, Lausanne, Switzerland Département d'Ecologie et Evolution, Université de Lausanne Lausanne Switzerland.,Musée cantonal de zoologie, Lausanne, Switzerland Musée cantonal de zoologie Lausanne Switzerland
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17
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Arribas P, Andújar C, Salces-Castellano A, Emerson BC, Vogler AP. The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding. Mol Ecol 2020; 30:48-61. [PMID: 32772446 DOI: 10.1111/mec.15591] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023]
Abstract
Soil arthropod communities are highly diverse and critical for ecosystem functioning. However, our knowledge of spatial structure and the underlying processes of community assembly are scarce, hampered by limited empirical data on species diversity and turnover. We implement a high-throughput sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra-specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multihierarchical approach was performed using haplotype-level COI metabarcoding of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1,000 codistributed species and nearly 3,000 haplotypes. Local assemblage composition differed greatly between grasslands and forests and, within each habitat, showed strong spatial structure and high endemicity. Distance decay was high at all levels, even at the scale of a few kilometres or less. The local distance decay patterns were self-similar for the haplotypes and higher hierarchical entities, and this fractal structure was similar in all regions, suggesting that uniform processes of limited dispersal determine local-scale community assembly. Our results from whole-community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod diversity on Earth.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research Group (IPNA-CSIC), La Laguna, Spain.,Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group (IPNA-CSIC), La Laguna, Spain.,Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
| | | | - Brent C Emerson
- Island Ecology and Evolution Research Group (IPNA-CSIC), La Laguna, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
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18
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Drivers of Benthic Macroinvertebrate Assemblages in Equatorial Alpine Rivers of the Rwenzoris (Uganda). WATER 2020. [DOI: 10.3390/w12061668] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The Sub-Saharan alpine freshwater biodiversity is currently impacted by human settlements, climate change, agriculture, and mining activities. Because of the limited biodiversity studies in the region, a better understanding is needed of the important environmental variables affecting macroinvertebrate assemblages. In this paper, macroinvertebrate diversity responses to 18 environmental variables were studied at 30 sites along unique Rwenzori rivers at the equator in Uganda. We hypothesized that anthropogenic disturbance and local environmental variables affect macroinvertebrate diversity, irrespective of altitudinal gradients. Based on altitude and climate, the sites were subdivided into three altitude groups consisting of 10 sites each: upstream (US) 1400–1600 m.a.s.l.; midstream (MS) 1091–1399 m.a.s.l., and downstream (DS) 900–1090 m.a.s.l. A total of 44 macroinvertebrate families and 1623 individuals were identified. The macroinvertebrate diversity patterns were influenced by temperature, altitude, and latitude. Regression analysis revealed that temperature and nickel, were negative predictors of taxa richness. Nickel, which is released by mining activity, is detrimental to aquatic communities in Sub-Saharan alpine ecosystems. Significant longitudinal variation in macroinvertebrate diversity was observed between the sites, which were also affected by mineral and temperature gradients. Our study highlights the need for long-term monitoring in this region to detect and reduce the threats to river biodiversity from anthropogenic activity.
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19
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Barros MJF, Silva-Arias GA, Segatto ALA, Reck-Kortmann M, Fregonezi JN, Diniz-Filho JAF, Freitas LB. Phylogenetic niche conservatism and plant diversification in South American subtropical grasslands along multiple climatic dimensions. Genet Mol Biol 2020; 43:e20180291. [PMID: 32353100 PMCID: PMC7197982 DOI: 10.1590/1678-4685-gmb-2018-0291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 07/31/2019] [Indexed: 11/22/2022] Open
Abstract
Phylogenetic niche conservatism can be investigated at multiple scales on an explicit geographical context. Haplotype-based comparative analyses of lineages occupying the same region, and thus subjected to similar environmental factors, allow decoupling shared evolutionary and ecological patterns, as well as multiple dimensions of adaptive diversification. Here we aimed to assess the role of environmental drivers on diversification of subtropical grassland, based on haplotypic diversity of two plant genera. We sampled two closely related and co-distributed grassland plant genera, Petunia and Calibrachoa, across their entire distribution area. Eigenvectors extracted from pairwise distances based on chloroplast DNA haplotypes were used to fit Phylogenetic Signal-Representation (PSR) curves to estimate evolutionary patterns in 19 bioclimatic variables and altitude. The PSR curves showed that altitude, precipitation, and temperature variables changed at different rates with haplotype differentiation. Altitude and temperature traits evolved under conditions closer to a neutral dynamics, whereas precipitation traits differentiated following more complex models. Our results indicated that the diversification in the two genera was more limited by precipitation conditions. Based on these novel findings, we suggest that future studies should test the possible impact of precipitation variables on the process of ecological differentiation in these genera.
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Affiliation(s)
- Michel J F Barros
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Gustavo A Silva-Arias
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Ana Lúcia Anversa Segatto
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Maikel Reck-Kortmann
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Jeferson N Fregonezi
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | | | - Loreta B Freitas
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
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20
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Characteristics, Main Impacts, and Stewardship of Natural and Artificial Freshwater Environments: Consequences for Biodiversity Conservation. WATER 2020. [DOI: 10.3390/w12010260] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this overview (introductory article to a special issue including 14 papers), we consider all main types of natural and artificial inland freshwater habitas (fwh). For each type, we identify the main biodiversity patterns and ecological features, human impacts on the system and environmental issues, and discuss ways to use this information to improve stewardship. Examples of selected key biodiversity/ecological features (habitat type): narrow endemics, sensitive (groundwater and GDEs); crenobionts, LIHRes (springs); unidirectional flow, nutrient spiraling (streams); naturally turbid, floodplains, large-bodied species (large rivers); depth-variation in benthic communities (lakes); endemism and diversity (ancient lakes); threatened, sensitive species (oxbow lakes, SWE); diverse, reduced littoral (reservoirs); cold-adapted species (Boreal and Arctic fwh); endemism, depauperate (Antarctic fwh); flood pulse, intermittent wetlands, biggest river basins (tropical fwh); variable hydrologic regime—periods of drying, flash floods (arid-climate fwh). Selected impacts: eutrophication and other pollution, hydrologic modifications, overexploitation, habitat destruction, invasive species, salinization. Climate change is a threat multiplier, and it is important to quantify resistance, resilience, and recovery to assess the strategic role of the different types of freshwater ecosystems and their value for biodiversity conservation. Effective conservation solutions are dependent on an understanding of connectivity between different freshwater ecosystems (including related terrestrial, coastal and marine systems).
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21
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Rincon-Sandoval M, Betancur-R R, Maldonado-Ocampo JA. Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers. Mol Ecol 2019; 28:1096-1115. [PMID: 30714250 DOI: 10.1111/mec.15036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/17/2019] [Accepted: 01/23/2019] [Indexed: 01/06/2023]
Abstract
The Neotropical region represents one of the greatest biodiversity hot spots on earth. Despite its unparalleled biodiversity, regional comparative phylogeographic studies are still scarce, with most focusing on model clades (e.g. birds) and typically examining a handful of loci. Here, we apply a genome-wide comparative phylogeographic approach to test hypotheses of codiversification of freshwater fishes in the trans-Andean region. Using target capture methods, we examined exon data for over 1,000 loci combined with complete mitochondrial genomes to study the phylogeographic history of five primary fish species (>150 individuals) collected from eight major river basins in Northwestern South America and Lower Central America. To assess their patterns of genetic structure, we inferred genealogical concordance taking into account all major aspects of phylogeography (within loci, across multiple genes, across species and among biogeographic provinces). Based on phylogeographic concordance factors, we tested four a priori biogeographic hypotheses, finding support for three of them and uncovering a novel, unexpected pattern of codiversification. The four emerging inter-riverine patterns are as follows: (a) Tuira + Atrato, (b) Ranchería + Catatumbo, (c) Magdalena system and (d) Sinú + Atrato. These patterns are interpreted as shared responses to the complex uplifting and orogenic processes that modified or sundered watersheds, allowing codiversification and speciation over geological time. We also find evidence of cryptic speciation in one of the species examined and instances of mitochondrial introgression in others. These results help further our knowledge of the historical geographic factors shaping the outstanding biodiversity of the Neotropics.
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Affiliation(s)
- Melissa Rincon-Sandoval
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.,Department of Biology, University of Puerto Rico, San Juan, Puerto Rico
| | - Ricardo Betancur-R
- Department of Biology, University of Puerto Rico, San Juan, Puerto Rico.,Department of Biology, The University of Oklahoma, Norman, Oklahoma
| | - Javier A Maldonado-Ocampo
- Laboratorio de Ictiología, Unidad de Ecología y Sistemática (UNESIS), Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
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22
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Whelan NV, Galaska MP, Sipley BN, Weber JM, Johnson PD, Halanych KM, Helms BS. Riverscape genetic variation, migration patterns, and morphological variation of the threatened Round Rocksnail, Leptoxis ampla. Mol Ecol 2019; 28:1593-1610. [PMID: 30697854 DOI: 10.1111/mec.15032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/10/2019] [Accepted: 01/23/2019] [Indexed: 12/14/2022]
Abstract
Within riverine systems, headwater populations are hypothesized to harbour higher amounts of genetic distinctiveness than populations in the main stem of a river and display increased genetic diversity in large, downstream habitats. However, these hypotheses were mostly developed with insects and fish, and they have not been tested on many invertebrate lineages. Pleuroceridae gastropods are of particular ecological importance to rivers of eastern North America, sometimes comprising over 90% of macroinvertebrate biomass. Yet, virtually nothing is known of pleurocerid landscape genetics, including whether genetic diversity follows predictions made by hypotheses developed on more mobile species. Moreover, the commonly repeated hypothesis that intraspecific morphological variation in gastropods results from ecophenotypic plasticity has not been well tested on pleurocerids. Using 2bRAD-seq to discover single nucleotide polymorphisms, we show that the threatened, Cahaba River endemic pleurocerid, Leptoxis ampla, has limited gene flow among populations and that migration is downstream-biased, conflicting with previous hypotheses. Both tributary and main stem populations harbour unique genomic profiles, and genetic diversity was highest in downstream populations. Furthermore, L. ampla shell morphology was more correlated with genetic differences among individuals and populations than habitat characteristics. We anticipate similar genetic and demographic patterns to be seen in other pleurocerids, and hypotheses about gene flow and population demographics that were based on more mobile taxa often, but not always, apply to freshwater gastropods. From a conservation standpoint, genetic structure of L. ampla populations suggests distinctive genetic diversity is lost with localized extirpation, a phenomenon common across the range of Pleuroceridae.
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Affiliation(s)
- Nathan V Whelan
- Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, United States Fish and Wildlife Service, Auburn, Alabama.,School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, Auburn, Alabama
| | - Matthew P Galaska
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
| | - Breanna N Sipley
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Jennifer M Weber
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Paul D Johnson
- Alabama Department of Conservation and Natural Resources, Alabama Aquatic Biodiversity Center, Marion, Alabama
| | | | - Brian S Helms
- Department of Biological and Environmental Sciences, Troy University, Troy, Alabama
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23
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Reisch C, Schmid C. Species and genetic diversity are not congruent in fragmented dry grasslands. Ecol Evol 2019; 9:664-671. [PMID: 30680146 PMCID: PMC6342089 DOI: 10.1002/ece3.4791] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 10/15/2018] [Accepted: 11/09/2018] [Indexed: 01/19/2023] Open
Abstract
Biological diversity comprises both species diversity (SD) and genetic diversity (GD), and it has been postulated that both levels of diversity depend on similar mechanisms. Species-genetic diversity correlations (SGDC) are therefore supposed to be generally positive. However, in contrast to theory, empirical data are contradictory. Furthermore, there is a pronounced lack of multispecies studies including also the ecological factors potentially driving species and genetic diversity. We analyzed the relationship between the species diversity of dry grasslands and the genetic diversity of several dry grassland plant species, therefore, in the context of habitat fragmentation and habitat conditions. Our study revealed a lack of correlation between species and genetic diversity. We demonstrated previously that SD mainly depends on habitat conditions (vegetation height and cover of litter), whereas GD is significantly affected by habitat fragmentation (distance to the nearest dry grassland in 1830 and connectivity in 2013). This seems to be the main reason why SD and GD are not congruent in fragmented grasslands. Our results support, hence, the observation that positive SGDCs can mainly be found in natural, island-like study systems in equilibrium and at similar levels of heterogeneity. In fragmented dry grassland ecosystems, which differ in heterogeneity, this state of equilibrium may not have been reached mitigating the positive relationship between SD and GD. From our study, it can be concluded that in fragmented dry grasslands, the protection of SD does not necessarily ensure the conservation of GD.
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Affiliation(s)
- Christoph Reisch
- Institute of Plant SciencesUniversity of RegensburgRegensburgGermany
| | - Christoph Schmid
- Research Unit Comparative Microbiome AnalysisGerman Research Center for Environmental HealthNeuherbergGermany
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