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Schwob G, Cabrol L, Saucède T, Gérard K, Poulin E, Orlando J. Unveiling the co-phylogeny signal between plunderfish Harpagifer spp. and their gut microbiomes across the Southern Ocean. Microbiol Spectr 2024; 12:e0383023. [PMID: 38441978 PMCID: PMC10986581 DOI: 10.1128/spectrum.03830-23] [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: 11/01/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
Understanding the factors that sculpt fish gut microbiome is challenging, especially in natural populations characterized by high environmental and host genomic complexity. However, closely related hosts are valuable models for deciphering the contribution of host evolutionary history to microbiome assembly, through the underscoring of phylosymbiosis and co-phylogeny patterns. Here, we propose that the recent diversification of several Harpagifer species across the Southern Ocean would allow the detection of robust phylogenetic congruence between the host and its microbiome. We characterized the gut mucosa microbiome of 77 individuals from four field-collected species of the plunderfish Harpagifer (Teleostei, Notothenioidei), distributed across three biogeographic regions of the Southern Ocean. We found that seawater physicochemical properties, host phylogeny, and geography collectively explained 35% of the variation in bacterial community composition in Harpagifer gut mucosa. The core microbiome of Harpagifer spp. gut mucosa was characterized by a low diversity, mostly driven by selective processes, and dominated by a single Aliivibrio Operational Taxonomic Unit (OTU) detected in more than 80% of the individuals. Nearly half of the core microbiome taxa, including Aliivibrio, harbored co-phylogeny signal at microdiversity resolution with host phylogeny, indicating an intimate symbiotic relationship and a shared evolutionary history with Harpagifer. The clear phylosymbiosis and co-phylogeny signals underscore the relevance of the Harpagifer model in understanding the role of fish evolutionary history in shaping the gut microbiome assembly. We propose that the recent diversification of Harpagifer may have led to the diversification of Aliivibrio, exhibiting patterns that mirror the host phylogeny. IMPORTANCE Although challenging to detect in wild populations, phylogenetic congruence between marine fish and its microbiome is critical, as it highlights intimate associations between hosts and ecologically relevant microbial symbionts. Our study leverages a natural system of closely related fish species in the Southern Ocean to unveil new insights into the contribution of host evolutionary trajectory on gut microbiome assembly, an underappreciated driver of the global marine fish holobiont. Notably, we unveiled striking evidence of co-diversification between Harpagifer and its microbiome, demonstrating both phylosymbiosis of gut bacterial communities and co-phylogeny of some specific bacterial symbionts, mirroring the host diversification patterns. Given Harpagifer's significance as a trophic resource in coastal areas and its vulnerability to climatic and anthropic pressures, understanding the potential evolutionary interdependence between the hosts and its microbiome provides valuable microbial candidates for future monitoring, as they may play a pivotal role in host species acclimatization to a rapidly changing environment.
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Affiliation(s)
- Guillaume Schwob
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
| | - Léa Cabrol
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France, Marseille, France
| | - Thomas Saucède
- UMR 6282 Biogeosciences, University Bourgogne Franche-Comté, CNRS, EPHE, Dijon, France
| | - Karin Gérard
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Laboratory of Antarctic and Subantarctic Marine Ecosystems, Faculty of Sciences, University of Magallanes, Punta Arenas, Chile
- Cape Horn International Center, Puerto Williams, Chile
| | - Elie Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
- Institute of Ecology and Biodiversity, Santiago, Chile
| | - Julieta Orlando
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Department of Ecological Sciences, Faculty of Sciences, University of Chile, Santiago, Chile
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Phylogeography and evolutionary history of the Panamic Clingfish Gobiesox adustus in the Tropical Eastern Pacific. Mol Phylogenet Evol 2022; 173:107496. [PMID: 35569809 DOI: 10.1016/j.ympev.2022.107496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/26/2022] [Accepted: 04/18/2022] [Indexed: 11/20/2022]
Abstract
The Panamic Clingfish Gobiesox adustus is widely distributed in the Tropical Eastern Pacific (TEP), from the central Gulf of California, Mexico to Ecuador, including the oceanic Revillagigedo Archipelago, and Isla del Coco. This cryptobenthic species is restricted to very shallow rocky-reef habitats. Here, we used one mitochondrial and three nuclear DNA markers from 155 individuals collected across the distribution range of the species in order to evaluate if geographically structured populations exist and to elucidate its evolutionary history. Phylogenetic analyses recovered a monophyletic group, with four well-supported, allopatric subgroups. Each subgroup corresponded to one of the following well-known biogeographic regions/provinces: 1) the Revillagigedo Archipelago, 2) the Cortez + Mexican provinces (Mexico), 3) the Panamic province (from El Salvador to Ecuador), and 4) Isla del Coco. A molecular-clock analysis showed a mean date for the divergence between clade I (the Revillagigedos and Cortez + Mexican provinces) and clade II (Panamic province and Isla del Coco) in the Pliocene, at ca. 5.33 Mya. Within clade I, the segregation between the Revillagigedos and Cortez + Mexican province populations was dated at ca. 1.18 Mya, during the Pleistocene. Within clade II, the segregation between samples of Isla del Coco and the Panamic province samples was dated at ca. 0.77 Mya, during the Pleistocene. The species tree, Bayesian species delimitation tests (BPP and STACEY), the ΦST, AMOVA, and the substantial genetic distances that exist between those four subgroups, indicate that they are independent evolutionary units. These cladogenetic events seem to be related to habitat discontinuities, and oceanographic and geological processes that produce barriers to gene flow for G. adustus, effects of which are enhanced by the intrinsic ecological characteristics of this species.
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Biogeography of the coastal fishes of the Socotra Archipelago: Challenging current ecoregional concepts. PLoS One 2022; 17:e0267086. [PMID: 35486578 PMCID: PMC9053782 DOI: 10.1371/journal.pone.0267086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 04/03/2022] [Indexed: 11/19/2022] Open
Abstract
The Socotra Archipelago, located in the eastern Gulf of Aden, has a unique marine environment, which combines tropical and ‘pseudo-temperate’ elements. An updated species inventory recently considered its coastal fish diversity the highest among Arabian ecoregions, necessitating to re-assess the ichthyogeographic position of the island group. The main aim of this study is to describe the distributional biogeography of its coastal fish fauna in relation to contemporary ichthyogeographic and ecoregional concepts. Inferences are drawn with regard to the marine biogeographic arrangement and ecoregional partitioning of the Arabian region. The main datasets comprise eight and twenty selected families including 404 and 898 species, respectively, from Arabian ecoregions. The Socotra Archipelago has close affinities to a putative ecoregion in the eastern Gulf of Aden that extends to southern Oman. It is more closely related to the Arabian Sea coast of Oman than to ecoregions in the Red Sea and a putative ecoregion in the western Gulf of Aden. The Gulf of Aden does not represent a consistent ecoregion in ichthyogeographic terms, because its eastern and western parts are less closely related to one another than to other ecoregions. The Socotra Archipelago and the eastern Gulf of Aden should therefore not be assigned to a joined province with Red Sea ecoregions. The coastal fish faunas of the southern Red Sea have close affinities with those of the western Gulf of Aden. The Arabian/Persian Gulf is least related to the other Arabian ecoregions. The authors posit the Socotra Archipelago as a distinct ecoregion, either on its own or in combination with affiliated mainland areas. This best reflects the ichthyogeographic data and the exceptionally high levels of fish and overall marine diversity. Two alternative ecoregional delineations are proposed, serving as working hypotheses for onward research.
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Torres-Hernández E, Betancourt-Resendes I, Angulo A, Robertson DR, Barraza E, Espinoza E, Díaz-Jaimes P, Domínguez-Domínguez O. A multi-locus approach to elucidating the evolutionary history of the clingfish Tomicodon petersii (Gobiesocidae) in the Tropical Eastern Pacific. Mol Phylogenet Evol 2021; 166:107316. [PMID: 34537324 DOI: 10.1016/j.ympev.2021.107316] [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: 02/24/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Marine species that are widely distributed in the Tropical Eastern Pacific (TEP) has served as a model for studying biogeographic patterns resulting from the effects of intraregional habitat discontinuities and oceanographic processes on the diversification and evolution of cryptobenthic reef fishes. Tomicodon petersii, a clingfish (Gobiesocidae) endemic to the TEP, is found on very shallow rocky reefs from central Mexico to northern Peru, and in the Cocos and Galapagos islands. We evaluated the effect of likely biogeographic barriers in different parts of the TEP on the diversification process of this species. We used one mitochondrial and three nuclear DNA markers from 112 individuals collected across the distribution range of T. petersii. Our phylogenetic results showed the samples constituted a monophyletic group, with three well-supported, allopatric subgroups: in the Mexican province, the Panamic province (from El Salvador to Ecuador), and the Galapagos Islands. The split between the Mexican and more southerly clades was estimated to occur at the end of the Miocene ca. 5.74 Mya, and the subsequent cladogenetic event separating the Galapagos population from the Panamic population at the junction of the Pliocene and Pleistocene, ca. 2.85 Mya. The species tree, Bayesian species delimitation tests (BPP), STACEY, and substantial genetic distances separating these three populations indicate that these three independent evolutionary units likely include two unnamed species. The cladogenetic events that promoted the formation of those genetically differentiated groups are consistent with disruptive effects on gene flow of habitat discontinuities and oceanographic processes along the mainland shoreline in the TEP and of ocean-island isolation, in conjunction with the species intrinsic life-history characteristics.
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Affiliation(s)
- Eloísa Torres-Hernández
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, Mexico; Instituto Nacional de Biodiversidad (INABIO), Colección de Peces Calle Rumipamba 341, Av. De los Shyris, Parque "La Carolina", Quito, Ecuador.
| | - Isai Betancourt-Resendes
- CONACYT-Laboratorio de Zoología, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Av. De las Ciencias s/n, Juriquilla, C.P 76230, Delegación Santa Rosa Jáuregui, Santiago de Querétaro, Mexico.
| | - Arturo Angulo
- Museo de Zoología/ Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET) y Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San Pedro de Montes de Oca, 11501-2060 San José, Costa Rica.
| | - D Ross Robertson
- Naos Marine Laboratory, Smithsonian Tropical Research Institute, Balboa, Panama.
| | - Enrique Barraza
- Universidad Francisco Gavidia, Instituto de Ciencia, Tecnología e Inovación, Segundo Nivel, Calle El Progreso N°2748, San Salvador, El Salvador.
| | - Eduardo Espinoza
- Dirección del Parque Nacional Galápagos, Puerto Ayora, Islas Galápagos, Ecuador.
| | - Píndaro Díaz-Jaimes
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, Mexico.
| | - Omar Domínguez-Domínguez
- Instituto Nacional de Biodiversidad (INABIO), Colección de Peces Calle Rumipamba 341, Av. De los Shyris, Parque "La Carolina", Quito, Ecuador; Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" Planta Baja, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico.
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Tang KL, Stiassny MLJ, Mayden RL, DeSalle R. Systematics of Damselfishes. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/i2020105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin L. Tang
- University of Michigan–Flint, Department of Biology, 303 East Kearsley St., Flint, Michigan 48502; . Send reprint requests to this address
| | - Melanie L. J. Stiassny
- American Museum of Natural History, Department of Ichthyology, Central Park West at 79th St., New York, New York 10024;
| | - Richard L. Mayden
- Saint Louis University, Department of Biology, 3507 Laclede Ave., St. Louis, Missouri 63103;
| | - Robert DeSalle
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York, New York 10024;
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Rengifo‐Correa L, Abad‐Franch F, Martínez‐Hernández F, Salazar‐Schettino PM, Téllez‐Rendón JL, Villalobos G, Morrone JJ. A biogeographic–ecological approach to disentangle reticulate evolution in the
Triatoma phyllosoma
species group (Heteroptera: Triatominae), vectors of Chagas disease. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12409] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Laura Rengifo‐Correa
- Departamento de Biología Evolutiva Facultad de Ciencias Museo de Zoología ‘Alfonso L. Herrera’Universidad Nacional Autónoma de México Mexico City Mexico
| | - Fernando Abad‐Franch
- Programa de Pós‐graduação em Medicina Tropical Núcleo de Medicina Tropical Facultade Medicina Universidade de Brasília Brasília Brazil
| | | | - Paz M. Salazar‐Schettino
- Laboratorio de Biología de Parásitos Departamento de Microbiología y Parasitología Facultad de Medicina Universidad Nacional Autónoma de México Mexico City Mexico
| | | | - Guiehdani Villalobos
- Departamento de Ecología de Agentes Patógenos Hospital General Dr. Manuel Gea González Mexico City Mexico
| | - Juan J. Morrone
- Departamento de Biología Evolutiva Facultad de Ciencias Museo de Zoología ‘Alfonso L. Herrera’Universidad Nacional Autónoma de México Mexico City Mexico
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Wang E, Zhang D, Braun MS, Hotz-Wagenblatt A, Pärt T, Arlt D, Schmaljohann H, Bairlein F, Lei F, Wink M. Can Mitogenomes of the Northern Wheatear (Oenanthe oenanthe) Reconstruct Its Phylogeography and Reveal the Origin of Migrant Birds? Sci Rep 2020; 10:9290. [PMID: 32518318 PMCID: PMC7283232 DOI: 10.1038/s41598-020-66287-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/15/2020] [Indexed: 11/09/2022] Open
Abstract
The Northern Wheatear (Oenanthe oenanthe, including the nominate and the two subspecies O. o. leucorhoa and O. o. libanotica) and the Seebohm’s Wheatear (Oenanthe seebohmi) are today regarded as two distinct species. Before, all four taxa were regarded as four subspecies of the Northern Wheatear. Their classification has exclusively been based on ecological and morphological traits, while their molecular characterization is still missing. With this study, we used next-generation sequencing to assemble 117 complete mitochondrial genomes covering O. o. oenanthe, O. o. leucorhoa and O. seebohmi. We compared the resolution power of each individual mitochondrial marker and concatenated marker sets to reconstruct the phylogeny and estimate speciation times of three taxa. Moreover, we tried to identify the origin of migratory wheatears caught on Helgoland (Germany) and on Crete (Greece). Mitogenome analysis revealed two different ancient lineages that separated around 400,000 years ago. Both lineages consisted of a mix of subspecies and species. The phylogenetic trees, as well as haplotype networks are incongruent with the present morphology-based classification. Mitogenome could not distinguish these presumed species. The genetic panmixia among present populations and taxa might be the consequence of mitochondrial introgression between ancient wheatear populations.
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Affiliation(s)
- Erjia Wang
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
| | - Dezhi Zhang
- Key laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, UniversityMerops apiaster. J. Divers of Chinese Academy of Sciences, Beijing, China
| | - Markus Santhosh Braun
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Omics IT and Data Management Core Facility, German Cancer Research Center, Heidelberg University, Heidelberg, Germany
| | - Tomas Pärt
- Department of Ecology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Debora Arlt
- Department of Ecology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Heiko Schmaljohann
- Institute of Avian Research "Vogelwarte Helgoland", Wilhelmshaven, Germany.,Institute for Biology und Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Franz Bairlein
- Institute of Avian Research "Vogelwarte Helgoland", Wilhelmshaven, Germany
| | - Fumin Lei
- Key laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, UniversityMerops apiaster. J. Divers of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
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Salas E, Hobbs JA, Bernal MA, Simison WB, Berumen ML, Bernardi G, Rocha LA. Distinct patterns of hybridization across a suture zone in a coral reef fish ( Dascyllus trimaculatus). Ecol Evol 2020; 10:2813-2837. [PMID: 32211158 PMCID: PMC7083663 DOI: 10.1002/ece3.6068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 12/05/2019] [Accepted: 01/07/2020] [Indexed: 11/16/2022] Open
Abstract
Hybrid zones are natural laboratories for investigating the dynamics of gene flow, reproductive isolation, and speciation. A predominant marine hybrid (or suture) zone encompasses Christmas Island (CHR) and Cocos (Keeling) Islands (CKE), where 15 different instances of interbreeding between closely related species from Indian and Pacific Oceans have been documented. Here, we report a case of hybridization between genetically differentiated Pacific and Indian Ocean lineages of the three-spot dascyllus, Dascyllus trimaculatus (Rüppell, 1829). Field observations indicate there are subtle color differences between Pacific and Indian Ocean lineages. Most importantly, population densities of color morphs and genetic analyses (mitochondrial DNA and SNPs obtained via RADSeq) suggest that the pattern of hybridization within the suture zone is not homogeneous. At CHR, both color morphs were present, mitochondrial haplotypes of both lineages were observed, and SNP analyses revealed both pure and hybrid genotypes. Meanwhile, in CKE, the Indian Ocean color morphs were prevalent, only Indian Ocean mitochondrial haplotypes were observed, and SNP analysis showed hybrid individuals with a large proportion (~80%) of their genotypes assigning to the Indian Ocean lineage. We conclude that CHR populations are currently receiving an influx of individuals from both ocean basins, with a greater influence from the Pacific Ocean. In contrast, geographically isolated CKE populations appear to be self-recruiting and with more influx of individuals from the Indian Ocean. Our research highlights how patterns of hybridization can be different at scales of hundreds of kilometers, due to geographic isolation and the history of interbreeding between lineages.
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Affiliation(s)
- Eva Salas
- Ichthyology DepartmentCalifornia Academy of SciencesSan FranciscoCAUSA
- Ecology and Evolutionary Biology DepartmentUniversity of California Santa CruzSanta CruzCAUSA
| | - Jean‐Paul A. Hobbs
- School of Biological SciencesThe University of QueenslandBrisbaneQLDAustralia
| | | | - W. Brian Simison
- Center for Comparative GenomicsCalifornia Academy of SciencesSan FranciscoCAUSA
| | - Michael L. Berumen
- Red Sea Research Center, Biological and Environmental Science and Engineering DivisionKing Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Giacomo Bernardi
- Ecology and Evolutionary Biology DepartmentUniversity of California Santa CruzSanta CruzCAUSA
| | - Luiz A. Rocha
- Ichthyology DepartmentCalifornia Academy of SciencesSan FranciscoCAUSA
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