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Yusuf LH, Lemus YS, Thorpe P, Garcia CM, Ritchie MG. Evidence for gene flow and trait reversal during radiation of Mexican Goodeid fish. Heredity (Edinb) 2024:10.1038/s41437-024-00694-1. [PMID: 38858547 DOI: 10.1038/s41437-024-00694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/12/2024] Open
Abstract
Understanding the phylogeographic history of a group and identifying the factors contributing to speciation is an important challenge in evolutionary biology. The Goodeinae are a group of live-bearing fishes endemic to Mexico. Here, we develop genomic resources for species within the Goodeinae and use phylogenomic approaches to characterise their evolutionary history. We sequenced, assembled and annotated the genomes of four Goodeinae species, including Ataeniobius toweri, the only matrotrophic live-bearing fish without a trophotaenia in the group. We estimated timings of species divergence and examined the extent and timing of introgression between the species to assess if this may have occurred during an early radiation, or in more recent episodes of secondary contact. We used branch-site models to detect genome-wide positive selection across Goodeinae, and we specifically asked whether this differs in A. toweri, where loss of placental viviparity has recently occurred. We found evidence of gene flow between geographically isolated species, suggesting vicariant speciation was supplemented by limited post-speciation gene flow, and gene flow may explain previous uncertainties about Goodeid phylogeny. Genes under positive selection in the group are likely to be associated with the switch to live-bearing. Overall, our studies suggest that both volcanism-driven vicariance and changes in reproductive mode influenced radiation in the Goodeinae.
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Affiliation(s)
- Leeban H Yusuf
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK.
| | - Yolitzi Saldívar Lemus
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
- Department of Biology, Texas State University, San Marcos, TX, USA
| | - Peter Thorpe
- School of Life Sciences, University of Dundee, Dundee, UK
| | - Constantino Macías Garcia
- Instituto de Ecologia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito exterior s/n anexo al Jardín Botánico C. P. 04510, Mexico City CdMx, Mexico
| | - Michael G Ritchie
- Centre for Biological Diversity, School of Biology, University of St Andrews, St Andrews, UK
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Compositional turnover in ecto- and endoparasite assemblages of an African bat, Miniopterus natalensis (Chiroptera, Miniopteridae): effects of hierarchical scale and host sex. Parasitology 2020; 147:1728-1742. [PMID: 32867864 DOI: 10.1017/s0031182020001602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We studied the compositional turnover in infracommunities and component communities of ecto- and endoparasites infesting a bat, Miniopterus natalensis (Chiroptera, Miniopteridae), across seven sampling sites using the zeta diversity metric (measuring similarity between multiple communities) and calculating zeta decline and retention rate (both scales) and zeta decay (component communities). We asked whether the patterns of zeta diversity differ between (a) infracommunities and component communities; (b) ecto- and endoparasites and (c) subsets of communities infecting male and female bats. The pattern of compositional turnover differed between infracommunities and component communities in endoparasites only. The shape of zeta decline for infracommunities indicated that there were approximately equal probabilities of ecto- and endoparasitic species to occur on/in any bat individual within a site. The shape of zeta decline for component communities suggested the stochasticity of ectoparasite turnover, whereas the turnover of endoparasites was driven by niche-based processes. Compositional turnover in component communities of ectoparasites was more spatially dependent than that of endoparasites. Spatial independence of compositional turnover in endoparasites was due to subcommunities harboured by female bats. We conclude that the patterns of compositional turnover in infracommunities were similar in ecto- and endoparasites, whereas the patterns of turnover in component communities differed between these groups.
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Taxonomic status of Rhabdochona ictaluri (Nematoda: Rhabdochonidae) based on molecular and morphological evidence. Parasitol Res 2019; 118:441-452. [PMID: 30631928 DOI: 10.1007/s00436-018-6189-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
Abstract
The genus Rhabdochona includes more than 100 species infecting freshwater fishes in all zoogeographical regions of the world. In Mexico, 12 nominal species of Rhabdochona have been recorded. Of these, Rhabdochona ictaluri was originally described as a parasite of endemic catfishes of the family Ictaluridae; however, the species was later considered on morphological grounds as a junior synonym of Rhabdochona kidderi. In this study, newly sampled specimens of R. ictaluri were obtained from the type host and type locality and were used to perform a detailed morphological analysis and molecular phylogenetic inferences through one mitochondrial and two nuclear genes; data were used in an integrative taxonomy context to test the taxonomic status of R. ictaluri. This approach proved to be very useful to confirm the validity of this species, and robust species limits were established between these two putative species considering morphology, molecular data, host association, and biogeography.
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Abstract
We need reliable data on the spatial distribution of parasites in order to achieve an inventory of global parasite biodiversity and establish robust conservation initiatives based on regional disease risk. This requires an integrated and spatially consistent effort toward the discovery of new parasite species. Using a large and representative dataset on the geographical coordinates where 4943 helminth species were first discovered, we first test whether the geographical distribution of parasite species reports is spatially congruent across helminth higher taxa; i.e. whether areas, where many trematodes are found, are also areas where many nematodes or cestodes have been discovered. Second, we test whether the global geographical distribution of new helminth species reports has changed significantly over time, i.e. across the last few decades. After accounting for spatial autocorrelation in the data, we find no strong statistical support for either of the patterns we investigated. Overall, our results indicate that helminth species discoveries are both spatially incongruent among higher taxa of helminths, and inconsistent over time. These findings suggest that the global parasite discovery effort is inefficient, spatially biased and subject to idiosyncrasies. Coordinated biodiscovery programmes, involving research teams with expertise in multiple taxonomic groups, seem the best approach to remedy these issues.
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Ennen JR, Matamoros WA, Agha M, Lovich JE, Sweat SC, Hoagstrom CW. Hierarchical, Quantitative Biogeographic Provinces for All North American Turtles and Their Contribution to the Biogeography of Turtles and the Continent. HERPETOLOGICAL MONOGRAPHS 2017. [DOI: 10.1655/herpmonographs-d-16-00013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Joshua R. Ennen
- Tennessee Aquarium Conservation Institute, Tennessee Aquarium, 175 Baylor School Road, Chattanooga, TN 37405, USA
| | - Wilfredo A. Matamoros
- Facultad de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Museo de Zoología, Tuxtla Gutiérrez, Chiapas, México Apartado Postal 29000, México
| | - Mickey Agha
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jeffrey E. Lovich
- U.S. Geological Survey, Southwest Biological Science Center, 2255 North Gemini Drive, Flagstaff, AZ 86001, USA
| | - Sarah C. Sweat
- Tennessee Aquarium Conservation Institute, Tennessee Aquarium, 175 Baylor School Road, Chattanooga, TN 37405, USA
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Quiroz-Martínez B, Álvarez F, Espinosa H, Salgado-Maldonado G. Concordant biogeographic patterns among multiple taxonomic groups in the Mexican freshwater biota. PLoS One 2014; 9:e105510. [PMID: 25136979 PMCID: PMC4138176 DOI: 10.1371/journal.pone.0105510] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/23/2014] [Indexed: 11/18/2022] Open
Abstract
In this paper we analyse the degree of concordance in species richness and taxonomic distinctness (diversity) patterns among different freshwater taxonomic groups in order to test three long held patterns described in Mexican freshwater biogeography: 1. The aquatic biota of Mexico includes two distinct faunas, a rich Neotropical component in the south and a south-eastern region and a less rich Nearctic component towards central and northern latitudes of the country. 2. A hotspot of species richness and diversity has been recorded in the Usumacinta, including the Yucatan Peninsula. 3. The presence of two distinct biotas in Mexico, an eastern one distributed along the Gulf of Mexico slope, and a western one associated to the Pacific versant. We use species richness and taxonomic distinctness to explore patterns of diversity and how these patterns change between zoogeographical regions. This paper points out a clear separation between Neotropical and Nearctic drainage basins but also between eastern (Gulf of Mexico) and western (Pacific) drainage basins. Present data gives additional empirical support from freshwater biota for three long held beliefs regarding distributional patterns of the Mexican biota. The neotropical basins of Mexico are generally host to a richest and more diversified fauna, that includes more families, genera and species, compared to the less rich and less diverse fauna in the nearctic basins.
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Affiliation(s)
- Benjamín Quiroz-Martínez
- Universidad Nacional Autónoma de México, Instituto de Biología, Laboratorio de Helmintología, México D. F., México
- Universidad Nacional Autónoma de México, Instituto de Biología, Colección Nacional de Crustáceos, México D. F., México
| | - Fernando Álvarez
- Universidad Nacional Autónoma de México, Instituto de Biología, Colección Nacional de Crustáceos, México D. F., México
| | - Héctor Espinosa
- Universidad Nacional Autónoma de México, Instituto de Biología, Colección Nacional de Peces, México D.F., México
| | - Guillermo Salgado-Maldonado
- Universidad Nacional Autónoma de México, Instituto de Biología, Laboratorio de Helmintología, México D. F., México
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Taxonomic distinctness and richness of helminth parasite assemblages of freshwater fishes in Mexican hydrological basins. PLoS One 2013; 8:e74419. [PMID: 24086342 PMCID: PMC3785472 DOI: 10.1371/journal.pone.0074419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 08/01/2013] [Indexed: 11/26/2022] Open
Abstract
In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra - host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern - nearctic and southern - neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance - decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis.
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