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Diaz-Recio Lorenzo C, Tran Lu Y A, Brunner O, Arbizu PM, Jollivet D, Laurent S, Gollner S. Highly structured populations of copepods at risk to deep-sea mining: Integration of genomic data with demogenetic and biophysical modelling. Mol Ecol 2024; 33:e17340. [PMID: 38605683 DOI: 10.1111/mec.17340] [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: 09/21/2023] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 04/13/2024]
Abstract
Copepoda is the most abundant taxon in deep-sea hydrothermal vents, where hard substrate is available. Despite the increasing interest in seafloor massive sulphides exploitation, there have been no population genomic studies conducted on vent meiofauna, which are known to contribute over 50% to metazoan biodiversity at vents. To bridge this knowledge gap, restriction-site-associated DNA sequencing, specifically 2b-RADseq, was used to retrieve thousands of genome-wide single-nucleotide polymorphisms (SNPs) from abundant populations of the vent-obligate copepod Stygiopontius lauensis from the Lau Basin. SNPs were used to investigate population structure, demographic histories and genotype-environment associations at a basin scale. Genetic analyses also helped to evaluate the suitability of tailored larval dispersal models and the parameterization of life-history traits that better fit the population patterns observed in the genomic dataset for the target organism. Highly structured populations were observed on both spatial and temporal scales, with divergence of populations between the north, mid, and south of the basin estimated to have occurred after the creation of the major transform fault dividing the Australian and the Niuafo'ou tectonic plate (350 kya), with relatively recent secondary contact events (<20 kya). Larval dispersal models were able to predict the high levels of structure and the highly asymmetric northward low-level gene flow observed in the genomic data. These results differ from most studies conducted on megafauna in the region, elucidating the need to incorporate smaller size when considering site prospecting for deep-sea exploitation of seafloor massive sulphides, and the creation of area-based management tools to protect areas at risk of local extinction, should mining occur.
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Affiliation(s)
- Coral Diaz-Recio Lorenzo
- Adaptation et Diversité en Milieu Marin (AD2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Adrien Tran Lu Y
- UMR MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Sète, France
| | - Otis Brunner
- Okinawa Institute for Science and Technology, Kunigami-gun, Okinawa, Japan
| | - Pedro Martínez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research, Wilhelmshaven, Germany
| | - Didier Jollivet
- Adaptation et Diversité en Milieu Marin (AD2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - Sabine Gollner
- NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, 't Horntje (Texel), The Netherlands
- Utrecht University, Utrecht, The Netherlands
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2
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Lopes GP, Rohe F, Bertuol F, Polo E, Lima IJ, Valsecchi J, Santos TCM, Nash SD, da Silva MNF, Boubli JP, Farias IP, Hrbek T. Taxonomic review of Saguinus mystax (Spix, 1823) (Primates, Callitrichidae), and description of a new species. PeerJ 2023; 11:e14526. [PMID: 36647446 PMCID: PMC9840391 DOI: 10.7717/peerj.14526] [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: 03/16/2022] [Accepted: 11/15/2022] [Indexed: 01/13/2023] Open
Abstract
Although the Amazon has the greatest diversity of primates, there are still taxonomic uncertainties for many taxa, such as the species of the Saguinus mystax group. The most geographically broadly distributed and phenotypically diverse species in this group is S. mystax, and its phenotypic diversity has been recognized as three subspecies-S. mystax mystax, S. mystax pileatus and S. mystax pluto-with non-overlapping geographic distributions. In this sense, we carried out an extensive field survey in their distribution areas and used a framework of taxonomic hypothesis testing of genomic data combined with an integrative taxonomic decision-making framework to carry out a taxonomic revision of S. mystax. Our tests supported the existence of three lineages/species. The first species corresponds to Saguinus mystax mystax from the left bank of the Juruá River, which was raised to the species level, and we also discovered and described animals from the Juruá-Tefé interfluve previously attributed to S. mystax mystax as a new species. The subspecies S. m. pileatus and S. m. pluto are recognized as a single species, under a new nomenclatural combination. However, given their phenotypic distinction and allopatric distribution, they potentially are a manifestation of an early stage of speciation, and therefore we maintain their subspecific designations.
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Affiliation(s)
- Gerson Paulino Lopes
- Programa em Pós-Graduação em Zoologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Grupo de Pesquisa em Ecologia e Conservação de Primatas, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil,Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
| | - Fábio Rohe
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Fabrício Bertuol
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Erico Polo
- Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Ivan Junqueira Lima
- Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil,Programa de Pós-Graduação em Ecologia Aplicada, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - João Valsecchi
- Grupo de Pesquisa em Ecologia e Conservação de Primatas, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil,Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil,Rede de Pesquisa em Diversidade, Conservação e Uso da Fauna da Amazônia, Manaus, Amazonas, Brazil,Comunidad de Manejo de Fauna Silvestre en América Latina, Iquitos, Peru
| | - Tamily Carvalho Melo Santos
- Grupo de Pesquisa em Ecologia de Vertebrados Terrestres, Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Amazonas, Brazil
| | - Stephen D. Nash
- Department of Anatomical Sciences/Health Sciences Center, Stony Brook University, New York, United States of America
| | | | - Jean P. Boubli
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil,School of Science, Engineering and the Environment, University of Salford, Salford, United Kingdom
| | - Izeni Pires Farias
- Programa em Pós-Graduação em Zoologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Tomas Hrbek
- Programa em Pós-Graduação em Zoologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Laboratório de Evolução e Genética Animal/Departamento de Genética/Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil,Department of Biology, Trinity University, San Antonio, Texas, United States
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3
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Costa-Araújo R, Silva-Jr JS, Boubli JP, Rossi RV, Canale GR, Melo FR, Bertuol F, Silva FE, Silva DA, Nash SD, Sampaio I, Farias IP, Hrbek T. An integrative analysis uncovers a new, pseudo-cryptic species of Amazonian marmoset (Primates: Callitrichidae: Mico) from the arc of deforestation. Sci Rep 2021; 11:15665. [PMID: 34341361 PMCID: PMC8328995 DOI: 10.1038/s41598-021-93943-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/23/2021] [Indexed: 12/03/2022] Open
Abstract
Amazonia has the richest primate fauna in the world. Nonetheless, the diversity and distribution of Amazonian primates remain little known and the scarcity of baseline data challenges their conservation. These challenges are especially acute in the Amazonian arc of deforestation, the 2500 km long southern edge of the Amazonian biome that is rapidly being deforested and converted to agricultural and pastoral landscapes. Amazonian marmosets of the genus Mico are little known endemics of this region and therefore a priority for research and conservation efforts. However, even nascent conservation efforts are hampered by taxonomic uncertainties in this group, such as the existence of a potentially new species from the Juruena-Teles Pires interfluve hidden within the M. emiliae epithet. Here we test if these marmosets belong to a distinct species using new morphological, phylogenomic, and geographic distribution data analysed within an integrative taxonomic framework. We discovered a new, pseudo-cryptic Mico species hidden within the epithet M. emiliae, here described and named after Horacio Schneider, the pioneer of molecular phylogenetics of Neotropical primates. We also clarify the distribution, evolutionary and morphological relationships of four other Mico species, bridging Linnean, Wallacean, and Darwinian shortfalls in the conservation of primates in the Amazonian arc of deforestation.
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Affiliation(s)
- Rodrigo Costa-Araújo
- Museu Paraense Emílio Goeldi, Mastozoology Collection, Belém, 66077-830, Brazil.
- Laboratory of Evolution and Animal Genetics, Federal University of Amazonas, Manaus, 69077-000, Brazil.
| | - José S Silva-Jr
- Museu Paraense Emílio Goeldi, Mastozoology Collection, Belém, 66077-830, Brazil
| | - Jean P Boubli
- School of Science, Engineering and Environment, University of Salford, Salford, M54WT, UK
| | - Rogério V Rossi
- Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, 78060-900, Brazil
| | - Gustavo R Canale
- Institute of Natural, Human and Social Sciences, Federal University of Mato Grosso, Sinop, 78557-267, Brazil
| | - Fabiano R Melo
- Department of Forest Engineering, Federal University of Viçosa, Viçosa, 36570-900, Brazil
| | - Fabrício Bertuol
- Laboratory of Evolution and Animal Genetics, Federal University of Amazonas, Manaus, 69077-000, Brazil
| | - Felipe E Silva
- Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Tefé, 69553-225, Brazil
| | - Diego A Silva
- Graduate Program in Ecology and Conservation, State University of Mato Grosso, Nova Xavantina, 78690-000, Brazil
| | - Stephen D Nash
- Departments of Anatomical Sciences and Art, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Iracilda Sampaio
- Institute of Coastal Studies, Federal University of Pará, Bragança, 68600-000, Brazil
| | - Izeni P Farias
- Laboratory of Evolution and Animal Genetics, Federal University of Amazonas, Manaus, 69077-000, Brazil
| | - Tomas Hrbek
- Laboratory of Evolution and Animal Genetics, Federal University of Amazonas, Manaus, 69077-000, Brazil.
- Department of Biology, Trinity University, San Antonio, 78212, USA.
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Ortiz D, Pekár S, Bilat J, Alvarez N. Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider. Mol Phylogenet Evol 2020; 154:106997. [PMID: 33164854 DOI: 10.1016/j.ympev.2020.106997] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 11/28/2022]
Abstract
Genomic data provide unprecedented power for species delimitation. However, current implementations are still time and resource consuming. In addition, bioinformatic processing is contentious and its impact on downstream analyses is insufficiently understood. Here we employ ddRAD sequencing and a thorough sampling for species delimitation in Zodarion styliferum, a widespread Iberian ant-eating spider. We explore the influence of the loci filtering strategy on the downstream phylogenetic analyses, genomic clustering and coalescent species delimitation. We also assess the accuracy of one mitochondrial (COI) and one nuclear (ITS) barcode for fast and inexpensive species delineation in the group. Our genomic data strongly support two morphologically cryptic but ecologically divergent lineages, mainly restricted to the central-eastern and western parts of the Iberian Peninsula, respectively. Larger matrices with more missing data showed increased genomic diversity, supporting that bioinformatic strategies to maximize matrix completion disproportionately exclude loci with the highest mutation rates. Moderate loci filtering gave the best results across analyses: although larger matrices returned concatenated phylogenies with higher support, middle-sized matrices performed better in genetic structure analyses. COI displayed high diversity and a conspicuous barcode gap, revealing 13 mitochondrial lineages. Mitonuclear discordance is consistent with ancestral isolation in multiple groups, probably in glacial refugia, followed by range expansion and secondary contact that produced genomic homogenization. Several apparently (unidirectionally) introgressed specimens further challenge the accuracy of species identification through mitochondrial barcodes in the group. Conversely, ITS failed to separate both lineages of Z. styliferum. This study shows an extreme case of mitonuclear discordance that highlights the limitations of single molecular barcodes for species delimitation, even in presence of distinct barcode gaps, and brings new light on the effects of parameterization on shallow-divergence studies using RAD data.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Julia Bilat
- Geneva Natural History Museum, Geneva, Switzerland
| | - Nadir Alvarez
- Geneva Natural History Museum, Geneva, Switzerland; Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
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