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Hoang HD, Pham HM, Tran NT, Durand JD, Wu L, Pfeiffer J, Chen XY, Page LM. Taxonomic revision of the Southeast Asian brook barb genus Poropuntius Smith, 1931 (Teleostei, Cyprinidae) with description of a new species from Vietnam. Zookeys 2024; 1204:199-222. [PMID: 38882566 PMCID: PMC11176814 DOI: 10.3897/zookeys.1204.120873] [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: 02/14/2024] [Accepted: 05/04/2024] [Indexed: 06/18/2024] Open
Abstract
Molecular data from samples encompassing 22 nominal species of Poropuntius indicate that the species-level diversity in the genus has been vastly overestimated, likely due to inadequate taxon and geographic sampling and reliance on morphological characters that vary intra-specifically. The latter includes discrete mouth morphologies related to alternate feeding strategies (ecomorphs) within populations. One new species is described, Poropuntiusanlaoensis Hoàng, Phạm & Trần, sp. nov., and 17 synonyms of six valid species names of Poropuntius, P.krempfi, P.alloiopleurus, P.huangchuchieni, P.laoensis, P.kontumensis, and P.deauratus, are recognised. Additional taxonomic changes in this widespread and generally poorly known genus are likely as more molecular and morphological data become available.
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Affiliation(s)
- Huy Duc Hoang
- Department of Ecology and Evolutionary Biology, University of Science, Ho Chi Minh City, Vietnam University of Science Ho Chi Minh City Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam Vietnam National University Ho Chi Minh City Vietnam
| | - Hung Manh Pham
- Department of Ecology and Evolutionary Biology, University of Science, Ho Chi Minh City, Vietnam University of Science Ho Chi Minh City Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam Vietnam National University Ho Chi Minh City Vietnam
| | - Ngan Trong Tran
- Department of Ecology and Evolutionary Biology, University of Science, Ho Chi Minh City, Vietnam University of Science Ho Chi Minh City Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam Vietnam National University Ho Chi Minh City Vietnam
| | - Jean-Dominique Durand
- IRD, MARBEC (University of Montpellier, CNRS, Ifremer, IRD), Montpellier, France University of Montpellier Montpellier France
| | - Ling Wu
- Southeast Asia Wildlife Biodiversity Research Group, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650223, China Kunming Institute of Zoology, the Chinese Academy of Sciences Kunming China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Science, Yezin, Nay Pyi Taw 05282, Myanmar Southeast Asia Biodiversity Research Institute, Chinese Academy of Science Yezin Myanmar
| | - John Pfeiffer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, Washington, DC 20560, USA National Museum of Natural History Washington, DC United States of America
| | - Xiao-Yong Chen
- Southeast Asia Wildlife Biodiversity Research Group, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming, Yunnan 650223, China Kunming Institute of Zoology, the Chinese Academy of Sciences Kunming China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Science, Yezin, Nay Pyi Taw 05282, Myanmar Southeast Asia Biodiversity Research Institute, Chinese Academy of Science Yezin Myanmar
| | - Lawrence M Page
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA University of Florida Gainesville United States of America
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Khensuwan S, de Menezes Cavalcante Sassi F, Rosa de Moraes RL, Rab P, Liehr T, Supiwong W, Seetapan K, Tanomtong A, Tantisuwichwong N, Arunsang S, Buasriyot P, Tongnunui S, Cioffi MDB. Chromosomes of Asian cyprinid fishes: Novel insight into the chromosomal evolution of Labeoninae (Teleostei, Cyprinidae). PLoS One 2024; 19:e0292689. [PMID: 38324533 PMCID: PMC10849230 DOI: 10.1371/journal.pone.0292689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/26/2023] [Indexed: 02/09/2024] Open
Abstract
The Labeoninae subfamily is a highly diversified but demonstrably monophyletic lineage of cyprinid fishes comprising five tribes and six incertae sedis genera. This widely distributed assemblage contains some 48 genera and around 480 recognized species distributed in freshwaters of Africa and Asia. In this study, the karyotypes and other chromosomal properties of five Labeoninae species found in Thailand Labeo chrysophekadion (Labeonini) and Epalzeorhynchos bicolor, Epalzeorhynchos munense, Henicorhynchus siamensis, Thynnichthys thynnoides (´Osteochilini´) were examined using conventional and molecular cytogenetic protocols. Our results confirmed a diploid chromosome number (2n) invariably 2n = 50, but the ratio of uni- and bi-armed chromosomes was highly variable among their karyotypes, indicating extensive structural chromosomal rearrangements. Karyotype of L. chrysophekadion contained 10m+6sm+20st+14a, 32m+10sm+8st for H. siamensis, 20m+12sm+10st+8a in E. bicolor, 20m+8sm+8st+14a in E. munense, and 18m+24sm+8st in T. thynnoides. Except for H. siamensis, which had four sites of 5S rDNA sites, other species under study had only one chromosome pair with those sites. In contrast, only one pair containing 18S rDNA sites were found in the karyotypes of three species, whereas two sites were found in that of E. bicolor. These cytogenetic patterns indicated that the cytogenomic divergence patterns of these labeonine species largely corresponded to the inferred phylogenetic tree. In spite of the 2n stability, diverse patterns of rDNA and microsatellite distribution as well as their various karyotype structures demonstrated significant evolutionary differentiation of Labeoninae genomes as exemplified in examined species. Labeoninae offers a traditional point of view on the evolutionary forces fostering biological diversity, and the recent findings add new pieces to comprehend the function of structural chromosomal rearrangements in adaption and speciation.
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Affiliation(s)
- Sudarat Khensuwan
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen, Thailand
| | | | - Renata Luiza Rosa de Moraes
- Departamento de Genética e Evolução, Laboratório de Citogenética de Peixes, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Petr Rab
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, Czech Academy of Sciences, Rumburská, Liběchov, Czech Republic
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Weerayuth Supiwong
- Faculty of Interdisciplinary Studies, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai, Thailand
| | - Kriengkrai Seetapan
- School of Agriculture and Natural Resources, University of Phayao, Tumbol Maeka, Muang, Phayao, Thailand
| | - Alongklod Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen, Thailand
| | | | - Satit Arunsang
- Program in Animal Science, Faculty of Agricultural Technology and Agro-Industry, Rajamangala University of Technology Suvarnabhumi, Phra Nakhon Si Ayutthaya, Ayutthaya, Thailand
| | - Phichaya Buasriyot
- Faculty of Science and Technology, Rajamangala University of Technology Suvarnabhumi, Mueang Nonthaburi, Nonthaburi, Thailand
| | - Sampun Tongnunui
- Department of Conservation Biology, Mahidol University, Kanchanburi Campus, Sai Yok, Kanchanaburi Province, Thailand
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Laboratório de Citogenética de Peixes, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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3
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Meuser AV, Pitura AR, Mandeville EG. A high-quality reference genome for the common creek chub, Semotilus atromaculatus. G3 (BETHESDA, MD.) 2024; 14:jkad283. [PMID: 38128526 PMCID: PMC10849318 DOI: 10.1093/g3journal/jkad283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 12/23/2023]
Abstract
Creek chub (Semotilus atromaculatus) is a leuciscid minnow species commonly found in anthropogenically disturbed environments, making it an excellent model organism to study human impacts on aquatic systems. Genomic resources for creek chub and other leuciscid species are currently limited. However, advancements in DNA sequencing now allow us to create genomic resources at a historically low cost. Here, we present a high quality, 239 contig reference genome for the common creek chub, created with PacBio HiFi sequencing. We compared the assembly quality of two pipelines: Pacific Biosciences' Improved Phase Assembly (873 contigs) and Hifiasm (239 contigs). Quality and completeness of this genome is comparable to the zebrafish (Danioninae) and fathead minnow (Leuciscidae) genomes. The creek chub genome is highly syntenic to the zebrafish and fathead minnow genomes, and while our assembly does not resolve into the expected 25 chromosomes, synteny with zebrafish suggests that each creek chub chromosome is likely represented by 1-4 large contigs in our assembly. This reference genome is a valuable resource that will enhance genomic biodiversity studies of creek chub and other nonmodel leuciscid species common to disturbed environments.
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Affiliation(s)
- Amanda V Meuser
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Amy R Pitura
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Elizabeth G Mandeville
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
- Department of Biology, Northern Michigan University, 1401 Presque Isle Avenue, Marquette, MI 49855, USA
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4
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Řehulková E, Seifertová M, Francová K, Šimková A. Nearctic Dactylogyrus species (Platyhelminthes, Monogenea) parasitizing cypriniform fishes in the context of morphology and phylogeny, with descriptions of seven new species. Parasite 2023; 30:30. [PMID: 37589452 PMCID: PMC10433842 DOI: 10.1051/parasite/2023032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/16/2023] [Indexed: 08/18/2023] Open
Abstract
Ribosomal DNA sequences are currently available for 32 morphologically recognized species of Dactylogyrus parasitizing Nearctic cypriniforms, but only 16 of them are assigned to nominal species. Herein, morphological data on 28 of the 32 species are provided, together with comments on their phylogenetic relationships in the context of the morphology of taxonomically important structures. Seven new species of Dactylogyrus are described from five species of leuciscids and one species of catostomids, as follows: D. aduncus n. sp. from Campostoma spadiceum, D. cloutmani n. sp. from Luxilus chrysocephalus isolepis, D. cornifrons n. sp. from Cyprinella venusta, D. fimbratus n. sp. from Rhinichthys cataractae, D. mcallisteri n. sp. from Semotilus atromaculatus, and D. chieni n. sp. and D. haneki n. sp. from Hypentelium nigricans. Four previously described species of Dactylogyrus, D. atromaculatus from S. atromaculatus, D. eos from C. neogaeus, D. parvicirrus from Notemigonus crysoleucas and D. perlus from L. c. isolepis, are redescribed and/or figured. As for the remaining 17 species, only the male copulatory organs (MCOs) taken from the respective hologenophores are illustrated. On the basis of phylogenetic analyses, two main clades of Nearctic Dactylogyrus were recognized and supported by the different morphology of the MCO. The first one included 22 strictly Nearctic species sharing the same MCO type with Dactylogyrus spp. parasitizing cyprinids likely of Asian origin. The second clade encompassed Dactylogyrus spp. with diverse MCO morphology and was placed in the sister position to Dactylogyrus spp. parasitizing European leuciscids and North-West African cyprinids.
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Affiliation(s)
- Eva Řehulková
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
| | - Mária Seifertová
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
| | - Kateřina Francová
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University Kotlářská 2 611 37 Brno Czech Republic
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5
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Molokomme PS, Benovics M, Luus-Powell WJ, Lukhele LP, Přikrylová I. Dactylogyrus spp. (Dactylogyridae, Monogenea) from tinfoil barb, Barbonymus schwanenfeldii imported into South Africa: morphometric and molecular characterisation. Parasite 2023; 30:29. [PMID: 37565987 PMCID: PMC10416761 DOI: 10.1051/parasite/2023031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/16/2023] [Indexed: 08/12/2023] Open
Abstract
This study reports on three species of Dactylogyrus Diesing, 1850 (Dactylogyridae) collected from tinfoil barb, Barbonymus schwanenfeldii (Bleeker) which were imported into South Africa as ornamental fish from Sri Lanka and Thailand. Supplementary morphometric characterisation and molecular data (partial 18S and 28S rDNA, and ITS1 region sequences) are presented for Dactylogyrus lampam (Lim & Furtado, 1986), Dactylogyrus tapienensis Chinabut & Lim, 1993 and Dactylogyrus viticulus Chinabut & Lim, 1993. Prevalence of Dactylogyrus spp. infection was 87% and 80% for fish from Sri Lanka and Thailand, respectively. Composition of the parasites between the fish of each origin differed. All three species were found to infect fish from Thailand, but only D. lampam was present on the fish received from Sri Lanka. Phylogenetic analysis revealed the position of studied species, with D. lampam clustering within the lineages of varicorhini-type species, while D. tapienensis and D. viticulus form a sister lineage to Dactylogyrus spp. associated with Cyprinus carpio L. and Carassius spp., species parasitising central African large cyprinids (Labeo Cuvier), and species parasitising African and Middle Eastern Carasobarbus spp.
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Affiliation(s)
- Prince S. Molokomme
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DSI-NRF SARChI Chair (Ecosystem Health), Department of Biodiversity, University of Limpopo Sovenga 0727 South Africa
| | - Michal Benovics
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Department of Botany and Zoology, Faculty of Science, Masaryk University 611 37 Brno Czech Republic
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Department of Zoology, Faculty of Sciences, Comenius University in Bratislava 841 04 Bratislava Slovakia
| | - Wilmien J. Luus-Powell
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DSI-NRF SARChI Chair (Ecosystem Health), Department of Biodiversity, University of Limpopo Sovenga 0727 South Africa
| | - Linda P. Lukhele
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DSI-NRF SARChI Chair (Ecosystem Health), Department of Biodiversity, University of Limpopo Sovenga 0727 South Africa
| | - Iva Přikrylová
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DSI-NRF SARChI Chair (Ecosystem Health), Department of Biodiversity, University of Limpopo Sovenga 0727 South Africa
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Water Research Group, Unit for Environmental Sciences and Development, North-West University Potchefstroom 2520 South Africa
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6
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Hao C, Liu Y, Wei N, Arken K, Shi C, Yue C. The complete mitochondrial genomes of the Leuciscus baicalensis and Rutilus rutilus: a detailed genomic comparison among closely related species of the Leuciscinae subfamily. Gene 2023:147535. [PMID: 37328078 DOI: 10.1016/j.gene.2023.147535] [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: 01/09/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/18/2023]
Abstract
Cyprinidae is the largest family in the order of freshwater fish Cypriniformes. Increased subfamily members of Cyprinidae have been suggested to be re-classified for decades. In this study, we sequenced the mitochondrial genomes (mitogenomes) of Leuciscus baicalensis and Rutilus rutilus collected from northwest China and compared with other closely related species to determine their associated family or subfamily. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of Leuciscus baicalensis and Rutilus rutilus and characterized the mitogenomes by the gene structure, gene order, and the secondary structures of the 22 tRNA genes. We compared mitogenome features of Leuciscinae with other subfamilies in Cyprinidae. We used the analytic Bayesian Information and Maximum Likelihood methods to determine phylogenetic trees of 13 PCGs. The mitogenomes of Leuciscus baicalensis and Rutilus rutilus were 16,607 bp and 16,606 bp, respectively. Organization and location of these genes were consistent with already studied Leuciscinae fishes. Synonymous codon usage was conservative in Leuciscinae as compared with other subfamilies in Cyprinidae. Phylogenetic analysis indicated that Leuciscinae was a monophyletic group, and genus Leuciscus was a paraphyletic group. Our approach, for the first time, of studying comparative mitochondrial genomics and phylogenetics together provided a supportive platform to the analysis of population genetics and phylogeny for Leuciscinae. Our results indicated a promising potential of comparative mitochondrial genomics in the manifestation of phylogenetic relationships between fishes, leading us to a suggestion that mitogenomes should be routinely considered in clarifying phylogenetics of family and subfamily members of fish.
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Affiliation(s)
- Cuilan Hao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China.
| | - Yanjun Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Nianwen Wei
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Kadirden Arken
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Caixia Shi
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Cheng Yue
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
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7
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Li C, Xiao H, Zhang X, Lin H, Elmer KR, Zhao J. Deep genome-wide divergences among species in White Cloud Mountain minnow Tanichthys albonubes (Cypriniformes: Tanichthyidae) complex: Conservation and species management implications. Mol Phylogenet Evol 2023; 182:107734. [PMID: 36804428 DOI: 10.1016/j.ympev.2023.107734] [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: 09/08/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Identifying cryptic species is important for the assessments of biodiversity. Further, untangling mechanisms underlying the origins of cryptic species can facilitate our understanding of evolutionary processes. Advancements in genomic approaches for non-model systems have offered unprecedented opportunities to investigate these areas. The White Cloud Mountain minnow (Tanichthys albonubes) is a popular freshwater pet fish worldwide but its wild populations in China are critically endangered. Recent research based on a few molecular markers suggested that this species in fact comprised seven cryptic species, of which six were previously unknown. Here, we tested six of these cryptic species and quantified genomic interspecific divergences between species in the T. albonubes complex by analyzing genome-wide restriction site-associated DNA sequencing (RADseq) data generated from 189 individuals sampled from seven populations (including an outgroup congeneric species, T. micagemmae). We found that six cryptic species previously suggested were well supported by RADseq data. The genetic diversity of each species in the T. albonubes complex was low compared with T. micagemmae and the contemporary effective population sizes (Ne) of each cryptic species were small. Phylogenetic analysis showed seven clades with high support values confirmed with Neighbor-Net trees. The pairwise divergences between species in T. albonubes complex were deep and the highly differentiated loci were evenly distributed across the genome. We proposed that the divergence level of T. albonubes complex is at a late stage of cryptic speciation and lacking gene flow. Our findings provide new insights into cryptic speciation and have important implications for conservation and species management of T. albonubes complex.
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Affiliation(s)
- Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Han Xiao
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Xiuxia Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Hungdu Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China.
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8
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Yang T, Tan C, Sun W, Li D, Zhao L, Li F. Characterization of the complete mitochondrial genome sequence of Tanichthys albiventris and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:207-210. [PMID: 36755877 PMCID: PMC9901433 DOI: 10.1080/23802359.2023.2171244] [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] [Indexed: 02/05/2023] Open
Abstract
In this study, we sequenced, annotated, and characterized the mitogenome of Tanichthys albiventris for the first time. The complete mitogenome is 16,544 bp in length, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. We found nine genetic overlaps and 17 intergenic spacer regions throughout the mitogenome of T. albiventris. The A + T content of the mitogenome is 60.93%. All PCGs have the same start codon of the standard ATG, excepting for that of cytochrome c oxidase 1 (cox1) which is the GTG. A phylogenetic analysis with another 15 species of the Cyprinidae was performed using MrBayes and IQtree, based on the amino acid sequences of 13 mitochondrial PCGs. The results indicated that T. albiventris shares a close ancestry with Tanichthys albonubes.
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Affiliation(s)
- Tiezhu Yang
- College of Fisheries, Xinyang Agriculture and Forestry University, Xinyang, China,Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang, China
| | - Chenxi Tan
- College of Fisheries, Xinyang Agriculture and Forestry University, Xinyang, China,Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang, China
| | - Wenhao Sun
- College of Fisheries, Xinyang Agriculture and Forestry University, Xinyang, China,Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang, China
| | - Dongpu Li
- College of Fisheries, Xinyang Agriculture and Forestry University, Xinyang, China,Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang, China
| | - Liangjie Zhao
- College of Fisheries, Xinyang Agriculture and Forestry University, Xinyang, China,Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang, China,Liangjie Zhao College of Fisheries, Xinyang Agriculture and Forestry University, Xinyang464000, China
| | - Fan Li
- Branch of Shanghai Science and Technology Museum, Shanghai Natural History Museum, Shanghai, China,Institute of Hydrobiology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, China,CONTACT Fan Li Branch of Shanghai Science and Technology Museum, Shanghai Natural History Museum, Shanghai200041, China
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9
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Benovics M, Vukić J, Šanda R, Nejat F, Charmpila EA, Buj I, Shumka S, Porcelloti S, Tarkan SA, Aksu S, Emiroğlu O, Šimková A. Monogeneans and chubs: Ancient host-parasite system under the looking glass. Mol Phylogenet Evol 2023; 179:107667. [PMID: 36400419 DOI: 10.1016/j.ympev.2022.107667] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Host-parasite coevolution is one of the fundamentals of evolutionary biology. Due to the intertwined evolutionary history of two interacting species and reciprocal coadaptation processes of hosts and parasites, we can expect that studying parasites will shed more light onto the evolutionary processes of their hosts. Monogenea (ectoparasitic Platyhelminthes) and their cyprinoid fish hosts represent one of the best models for studying host-parasite evolutionary relationships using a cophylogenetic approach. These parasites have developed remarkably high host specificity, where each host species often serves as a potential host for its own host-specific monogenean species. Here, the cophylogenetic relationships in the Dactylogyrus-Squalius system was investigated, as Squalius is one of several cyprinoid genera with puzzling phylogeography and inhabits all four major peri-Mediterranean peninsulas. Of 29 endemic Squalius species examined for the presence of Dactylogyrus parasites, a total of 13 Dactylogyrus species were collected from the gills of 20 Squalius species across a wide range of distribution. Phylogenetic reconstruction revealed a polyphyletic origin for Dactylogyrus species parasitizing congeneric Squalius, with four major clades being recognized. On the basis of the delimitation of host specificity, strict specialists parasitizing single host species, geographic specialists parasitizing congeners in a limited geographical region, and true generalists parasitizing congeners in various geographical regions were recognized in Dactylogyrus species parasitizing Squalius. The phylogenetic reconstruction of Squalius hosts revealed two major clades, the first encompassing only peri-Mediterranean species and the second including species from other Euro-Asian regions. Distance-based cophylogenetic methods did not reveal a statistically significant global cophylogenetic structure in the studied system; however, several host-parasite links among Iberian endemic species contributed significantly to the overall structure. The widest host range and associated genetic variability were recorded for D. folkmanovae, parasitizing nine Squalius species, and D. vistulae, parasitizing 13 Squalius species. Two different dispersion mechanisms and morphological adaptations to Squalius hosts were clearly reflected in the contrasting cophylogenetic patterns for these two species with different levels of host specificity. While host-parasite cospeciation plays an important role in diversification within D. folkmanovae, diversification within D. vistulae is driven mainly by host switching.
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Affiliation(s)
- M Benovics
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic; Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - J Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2 128 44, Czech Republic.
| | - R Šanda
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2 128 44, Czech Republic; Department of Zoology, National Museum, Václavské Náměstí 68, Prague 1 110 00, Czech Republic.
| | - F Nejat
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
| | - E A Charmpila
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2 128 44, Czech Republic.
| | - I Buj
- Department of Zoology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 100 00 Zagreb, Croatia.
| | - S Shumka
- Department of Biotechnology and Food, Faculty of Biotechnology and Food, Agricultural University of Tirana, Tirana, Albania.
| | - S Porcelloti
- Associazione Ichthyos Italia, Via. A Cecchi 12, 52100 Arezzo, Italy.
| | - S A Tarkan
- Faculty of Fisheries, Muğla Sıtkı Koçman University, Menteşe 480 00, Muğla, Turkey; Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.
| | - S Aksu
- Vocational School of Health Services, Eskişehir Osmangazi University, Büyükdere Meşelik Yerleşkesi, 26040 Eskişehir, Turkey.
| | - O Emiroğlu
- Vocational School of Health Services, Eskişehir Osmangazi University, Büyükdere Meşelik Yerleşkesi, 26040 Eskişehir, Turkey.
| | - A Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
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10
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Literman R, Windsor AM, Bart HL, Hunter ES, Deeds JR, Handy SM. Using low-coverage whole genome sequencing (genome skimming) to delineate three introgressed species of buffalofish (Ictiobus). Mol Phylogenet Evol 2023; 182:107715. [PMID: 36707011 DOI: 10.1016/j.ympev.2023.107715] [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: 05/06/2022] [Revised: 11/03/2022] [Accepted: 01/21/2023] [Indexed: 01/26/2023]
Abstract
Consumption of buffalofish has been sporadically associated with Haff disease-like illnesses involving sudden onset muscle pain and weakness due to skeletal muscle rhabdomyolysis, but determination of precisely which species are associated with these illnesses has been impeded by a lack of species-specific DNA-based markers. Here, three closely related species of buffalofish native to the Mississippi River Basin (Ictiobus bubalus, Ictiobus cyprinellus and Ictiobus niger) that have previously proven genetically indistinguishable using both mitochondrial and nuclear single-locus sequencing were reliably discriminated using low-coverage whole genome sequencing ('genome skimming'). Using 44 specimens representing the three species collected from the mid/upper (Missouri) and lower (Louisiana) regions of the species' native ranges, the SISRS (Site Identification from Short Read Sequences) bioinformatics pipeline was adapted to (1) identify over 620Mbp of putatively homologous nuclear sequence data and (2) isolate over 140,000 single-nucleotide polymorphisms (SNPs) that supported accurate species delimitation, all without the use of a reference genome or annotation data. These sites were used to classify Ictiobus spp. samples with genome-skim data, along with a larger set (n = 67) where ultraconserved elements (UCEs) were sequenced. Analyses of whole mitochondrial data revealed more limited signal. Nearly all samples matched their purported species based on morphologic identification, but two Missouri samples morphologically identified as I. niger grouped with samples of I. bubalus, albeit with significant enrichment of I. niger SNPs. To our knowledge this is the first report of a DNA-based tool to reliably discriminate these three morphologically distinct species.
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Affiliation(s)
- Robert Literman
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA.
| | - Amanda M Windsor
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA
| | - Henry L Bart
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
| | - Elizabeth Sage Hunter
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA
| | - Jonathan R Deeds
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD, USA
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11
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Conith MR, Ringo D, Conith AJ, Deleon A, Wagner M, McMenamin S, Cason C, Cooper WJ. The Evolution of Feeding Mechanics in the Danioninae, or Why Giant Danios Don't Suck Like Zebrafish. Integr Org Biol 2022; 4:obac049. [PMID: 36518182 PMCID: PMC9730500 DOI: 10.1093/iob/obac049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/11/2022] [Accepted: 11/11/2022] [Indexed: 08/24/2023] Open
Abstract
By linking anatomical structure to mechanical performance we can improve our understanding of how selection shapes morphology. Here we examined the functional morphology of feeding in fishes of the subfamily Danioninae (order Cypriniformes) to determine aspects of cranial evolution connected with their trophic diversification. The Danioninae comprise three major lineages and each employs a different feeding strategy. We gathered data on skull form and function from species in each clade, then assessed their evolutionary dynamics using phylogenetic-comparative methods. Differences between clades are strongly associated with differences in jaw protrusion. The paedomorphic Danionella clade does not use jaw protrusion at all, members of the Danio clade use jaw protrusion for suction production and prey capture, and members of the sister clade to Danio (e.g., Devario and Microdevario) use jaw protrusion to retain prey after capture. The shape of the premaxillary bone is a major determinant of protrusion ability, and premaxilla morphology in each of these lineages is consistent with their protrusion strategies. Premaxilla shapes have evolved rapidly, which indicates that they have been subjected to strong selection. We compared premaxilla development in giant danio (Devario aequipinnatus) and zebrafish (Danio rerio) and discuss a developmental mechanism that could shift danionine fishes between the feeding strategies employed by these species and their respective clades. We also identified a highly integrated evolutionary module that has been an important factor in the evolution of trophic mechanics within the Danioninae.
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Affiliation(s)
- M R Conith
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - D Ringo
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - A J Conith
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - A Deleon
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - M Wagner
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - S McMenamin
- Biology Department, Boston College, Chestnut Hill, MA 02467, USA
| | - C Cason
- Marine and Coastal Science, Western Washington University, Bellingham, WA 98225, USA
| | - W J Cooper
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
- Marine and Coastal Science, Western Washington University, Bellingham, WA 98225, USA
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12
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Mitogenome of a monotypic genus, Oliotius Kottelat, 2013 (Cypriniformes: Cyprinidae): Genomic characterization and phylogenetic position. Gene 2022; 851:147035. [DOI: 10.1016/j.gene.2022.147035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022]
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13
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Schedel FDB, Musilova Z, Indermaur A, Bitja‐Nyom AR, Salzburger W, Schliewen UK. Towards the phylogenetic placement of the enigmatic African genus Prolabeops Schultz, 1941. JOURNAL OF FISH BIOLOGY 2022; 101:1333-1342. [PMID: 36053860 PMCID: PMC9826184 DOI: 10.1111/jfb.15205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
The small cyprinid genus Prolabeops Schultz, 1941 is restricted to the Nyong and Sanaga River systems in Cameroon. In the past, the genus had been suggested to be either a member of the Labeoninae, Torinae or the Smiliogastrinae mainly on the basis of morphological similarities, and it is nowadays considered as incertae sedis within the Cypriniformes. This study provides the first attempt to reveal the phylogenetic position of Prolabeops using molecular data. For this purpose, the authors sequenced a large fraction of the mitochondrial genome (c. 13,600 bp), including all mitochondrial protein coding genes, of two Prolabeops melanhypopterus specimens and an additional four Enteromius specimens. The large-scale phylogenetic analysis was based on an alignment including all mitochondrial protein coding genes of 902 specimens representing c. 899 cypriniform species. Prolabeops was clearly recovered within the African Smiliogastrinae, forming a weakly supported clade together with Enteromius jae, Enteromius hulstaerti and Barboides gracilis. The study data underline the urgent need of a thorough taxonomic revision of the small African barbs collectively placed in the genus Enteromius.
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Affiliation(s)
- Frederic D. B. Schedel
- Zoological InstituteUniversity of BaselBaselSwitzerland
- Faculty of Biology, Division of Evolutionary BiologyLMU MunichMartinsriedGermany
| | - Zuzana Musilova
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Arnold Roger Bitja‐Nyom
- Department of Biological SciencesUniversity of NgaoundéréNgaoundéréCameroon
- Department of Management of Fisheries and Aquatic EcosystemsUniversity of DoualaDoualaCameroon
| | | | - Ulrich K. Schliewen
- Department of IchthyologySNSB‐Bavarian State Collection Zoology (ZSM)MunichGermany
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14
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Fuke Y, Kano Y, Tun S, Yun L, Win SS, Watanabe K. Cryptic genetic divergence of the red dwarf rasbora, Microrasbora rubescens, in and around Inle Lake: implications for the origin of endemicity in the ancient lake in Myanmar. JOURNAL OF FISH BIOLOGY 2022; 101:1235-1247. [PMID: 36059127 DOI: 10.1111/jfb.15195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Inle Lake, an ancient lake located in the Shan Plateau of Myanmar, is a biogeographically attractive region with high fish endemism. Some endemic species inhabit the lake as well as the surrounding areas. The genetic and ecological relationships between populations in the lake and surrounding areas provide important insights into the process underlying ichthyofaunal formation in Inle Lake. In this study, the authors focused on red dwarf rasbora Microrasbora rubescens, an endemic genus and species in this region, and estimated its population structure and evolutionary scenario based on genome-wide polymorphism, mtDNA and geometric morphometric analyses using samples from Inle Lake and three areas surrounding the lake. The results showed that M. rubescens comprises at least three genetically divergent lineages (Inle, Heho and Hopong) with distinct geographic structures consistent with nuclear and mtDNA data. In contrast, there was no clear regional differentiation in morphology. The divergence time estimation based on mtDNA suggests that the Hopong lineage diverged at 2.7 Ma and the Inle and Heho lineages diverged at 1.9 Ma - consistent with the nuclear DNA results. The deep divergence observed in the endemic species supports the ancient history of ichthyofaunal development in this region. The distinct regional differentiation and morphological conservatism of this species might have been shaped by niche conservatism in stagnant water environments that limit dispersal and morphological diversification. Future comprehensive genetic and morphological analyses and comparisons for other native species should reveal the geographic and ecological processes that shaped the ichthyofauna in this region.
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Affiliation(s)
- Yusuke Fuke
- Laboratory of Animal Ecology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yuichi Kano
- Institute of Decision Science for Sustainable Society, Kyushu University, Fukuoka, Japan
| | - Sein Tun
- Inlay Lake Wildlife Sanctuary, Nature and Wildlife Conservation Division, Forest Department, Ministry of Natural Resources and Environmental Conservation, Myanmar, Nyaung Shwe, Myanmar
- Natma Taung National Park, Kanpalet Township, Myanmar
| | - Lkc Yun
- Inlay Lake Wildlife Sanctuary, Nature and Wildlife Conservation Division, Forest Department, Ministry of Natural Resources and Environmental Conservation, Myanmar, Nyaung Shwe, Myanmar
- Hkakaborazi National Park, Putao, Myanmar
| | - Seint Seint Win
- Department of Zoology, Taunggyi University, Taunggyi, Myanmar
- Department of Zoology, Kyaing Tong University, Keng Tung, Myanmar
| | - Katsutoshi Watanabe
- Laboratory of Animal Ecology, Graduate School of Science, Kyoto University, Kyoto, Japan
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15
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Mu X, Yang Y, Sun J, Yi liu, Xu M, Shao C, Chu KH, Li W, Liu C, Gu D, Fang M, Zhang C, Liu F, Song H, Wang X, Chen J, Ma KY. FishPIE: a universal phylogenetically informative exon markers set for ray-finned fishes. iScience 2022; 25:105025. [PMID: 36105587 PMCID: PMC9464953 DOI: 10.1016/j.isci.2022.105025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/11/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
Understanding the evolutionary history of the highly diverse ray-finned fishes has been challenging, and the development of more universal primers for phylogenetic analyses may help overcoming these challenges. We developed FishPIE, a nested PCR primer set of 82 phylogenetically informative exon markers, and tested it on 203 species from 31 orders of Actinopterygii. We combined orthologous sequences of the FishPIE markers obtained from published genomes and transcriptomes and constructed the phylogeny of 710 species belonging to 190 families and 60 orders. The resulting phylogenies had topologies comparable to previous phylogenomic studies. We demonstrated that the FishPIE markers could address phylogenetic questions across broad taxonomic levels. By incorporating the newly sequenced taxa, we were able to shed new light on the phylogeny of the highly diverse Cypriniformes. Thus, FishPIE holds great promise for generating genetic data for broad taxonomic groups and accelerating our understanding of the fish tree of life. FishPIE is a nested PCR primer set of 82 markers for fish phylogenetic analysis The markers can be broadly applied to all orders of ray-finned fishes Their phylogenetic performance is comparable to that of genomic analyses
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16
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Li F, Smith C, Kawamura K, Vetešník L, Arai R, Reichard M. Unusual egg shape diversity in bitterling fishes. Ecology 2022; 103:e3816. [DOI: 10.1002/ecy.3816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/01/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Fan Li
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
- Shanghai Natural History Museum, Branch of Shanghai Science and Technology Museum Shanghai China
| | - Carl Smith
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
- Department of Ecology and Vertebrate Zoology University of Łódź Łódź Poland
| | | | - Lukáš Vetešník
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
| | - Ryoichi Arai
- Department of Zoology, University Museum University of Tokyo Tokyo Japan
| | - Martin Reichard
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
- Department of Ecology and Vertebrate Zoology University of Łódź Łódź Poland
- Department of Botany & Zoology, Faculty of Science Masaryk University Brno Czech Republic
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17
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Yang X, Ni X, Fu C. Phylogeographical Analysis of the Freshwater Gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) in Southern China. Life (Basel) 2022; 12:1024. [PMID: 35888112 PMCID: PMC9318155 DOI: 10.3390/life12071024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/17/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023] Open
Abstract
The freshwater gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) is a small fish endemic to southern China. In this study, we used mitochondrial cytochrome b gene (Cytb), from wide-ranging samplings of H. chenhsienensis from the Ou River (the central of southern China) to the Yangtze River Basin (the northernmost part of southern China) to explore genetic variations and the evolutionary history of H. chenhsienensis in southern China. In total, 66 haplotypes were identified from Cytb sequences of 142 H. chenhsienensis individuals, which could be divided into lineages A, B, and C with divergence times of ~4.24 Ma and ~3.03 Ma. Lineage A was distributed in the lower reaches of the Yangtze River, the Oujiang River, and the Jiao River, lineage B was distributed in the Qiantang River and the Cao'e River, whereas lineage C was restricted to the Poyang Lake drainage from the middle reaches of the Yangtze River. Lineage A could be subdivided into sub-lineages A-I, A-II, A-III, and A-IV, with divergence times of 1.30, 0.97, and 0.44 Ma. Lineage C could be subdivided into sub-lineages C-I and C-II, with a divergence time of 0.85 Ma. Our findings indicate that climate change during the Pliocene and Pleistocene eras, as well as the limited dispersal ability of H. chenhsienensis, have been major drivers for shaping the phylogeographical patterns of H. chenhsienensis.
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18
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Singh P, Irisarri I, Torres-Dowdall J, Thallinger GG, Svardal H, Lemmon EM, Lemmon AR, Koblmüller S, Meyer A, Sturmbauer C. Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and repeated trophic transitions. Ecol Evol 2022; 12:e9077. [PMID: 35866021 PMCID: PMC9288888 DOI: 10.1002/ece3.9077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/12/2022] Open
Abstract
Cichlid fishes of the tribe Tropheini are a striking case of adaptive radiation, exemplifying multiple trophic transitions between herbivory and carnivory occurring in sympatry with other established cichlid lineages. Tropheini evolved highly specialized eco-morphologies to exploit similar trophic niches in different ways repeatedly and rapidly. To better understand the evolutionary history and trophic adaptations of this lineage, we generated a dataset of 532 targeted loci from 21 out of the 22 described Tropheini species. We resolved the Tropheini into seven monophyletic genera and discovered one to be polyphyletic. The polyphyletic genus, Petrochromis, represents three convergent origins of the algae grazing trophic specialization. This repeated evolution of grazing may have been facilitated by adaptive introgression as we found evidence for gene flow among algae grazing genera. We also found evidence of gene flow among algae browsing genera, but gene flow was restricted between herbivorous and carnivorous genera. Furthermore, we observed no evidence supporting a hybrid origin of this radiation. Our molecular evolutionary analyses suggest that opsin genes likely evolved in response to selection pressures associated with trophic ecology in the Tropheini. We found surprisingly little evidence of positive selection in coding regions of jaw-shaping genes in this trophically diverse lineage. This suggests low degrees of freedom for further change in these genes, and possibly a larger role for regulatory variation in driving jaw adaptations. Our study emphasizes Tropheini cichlids as an important model for studying the evolution of trophic specialization and its role in speciation.
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Affiliation(s)
- Pooja Singh
- Institute of Biology University of Graz Graz Austria.,Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany.,Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Iker Irisarri
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany.,Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum Hamburg Hamburg Germany
| | - Julián Torres-Dowdall
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany
| | - Gerhard G Thallinger
- Institute of Biomedical Informatics Graz University of Technology Graz Austria.,OMICS Center Graz, BioTechMed Graz Graz Austria
| | - Hannes Svardal
- Department of Biology University of Antwerp Antwerp Belgium.,Naturalis Biodiversity Center Leiden The Netherlands
| | - Emily Moriarty Lemmon
- Department of Biological Science Florida State University, Biomedical Research Facility Tallahassee Florida USA
| | - Alan R Lemmon
- Department of Biological Science Florida State University, Biomedical Research Facility Tallahassee Florida USA
| | | | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology University of Konstanz Constance Germany
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19
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Zhang C, Zhang K, Peng Y, Zhou J, Liu Y, Liu B. Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae. Front Genet 2022; 13:922634. [PMID: 35754812 PMCID: PMC9213810 DOI: 10.3389/fgene.2022.922634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 12/04/2022] Open
Abstract
Complete mitochondrial genomes (mitogenomes) can provide valuable information for phylogenetic relationships, gene rearrangement, and molecular evolution. Here, we report the mitochondrial whole genomes of three Garra species and explore the mechanisms of rearrangements that occur in their mitochondrial genomes. The lengths of the mitogenomes’ sequences of Garra dengba, Garra tibetana, and Garra yajiangensis were 16,876, 16,861, and 16,835, respectively. They contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genomes of three Garra species were rearranged compared to other fish mitochondrial genomes. The tRNA-Thr, tRNA-Pro and CR (T-P-CR) genes undergo replication followed by random loss of the tRNA-Thr and tRNA-Pro genes to form tRNA-Thr, CR1, tRNA-Pro and CR2 (T-CR-P-CR). Tandem duplication and random loss best explain this mitochondrial gene rearrangement. These results provide a foundation for future characterization of the mitochondrial gene arrangement of Labeoninae and further phylogenetic studies.
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Affiliation(s)
- Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Kun Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Ying Peng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
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20
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Ligula intestinalis infection in a native Leuciscid hybrid ( Alburnus derjugini x Squalius orientalis) in the Kürtün Dam Lake, Northeast Anatolia. Helminthologia 2022; 59:83-93. [PMID: 35601768 PMCID: PMC9075872 DOI: 10.2478/helm-2022-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/09/2022] [Indexed: 11/20/2022] Open
Abstract
Taxonomic evaluations are needed to accurately determine the host selection of fish parasites. The present study is a multidisciplinary research in the field of basic and fish diseases sciences. The description of the hybrid species of Squalius orientalis and Alburnus derjugini and infection of Ligula intestinalis in these hybrid fish were reported for the first time from the Kürtün Dam Lake in northeast Turkey. A total of 450 fish were sampled in March, August, and October in 2020 using gillnets. Detailed morphological characteristics (n = 24) were compared to determine the difference among ancestors and hybrid species. The prevalence of L. intestinalis between the sampling periods and the size groups of fish (0 – 10, 11 – 15, and ≥16 cm in length) were examined. Moreover, the highest prevalence of the parasite was observed in October (78.94 %), with a size range of 0 – 10 cm in length (77.8 %). In addition, the total prevalence of the parasite was 48.44 %. The results revealed that most of the diagnostic metric and meristic features of hybrid fish were ranging between the data of S. orientalis and A. derjugini. According to previous reports, when hybrid individuals were compared with their ancestors in terms of prevalence, hybrid individuals were more susceptible to L. intestinalis infections. This study was unique as it provided the first record of L. intestinalis in a hybrid fish population.
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21
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Mitochondrial genetic diversity, phylogeography and historical demography of Moroccan native freshwater fishes: a case study of the genus Luciobarbus Heckel, 1843. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01107-6] [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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22
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Piller KR, Parker E, Lemmon AR, Moriarty Lemmon E. Investigating the utility of Anchored Hybrid Enrichment data to investigate the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes. Mol Phylogenet Evol 2022; 173:107482. [PMID: 35452841 DOI: 10.1016/j.ympev.2022.107482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 10/18/2022]
Abstract
The Killifishes (Cyprinodontiformes) are a diverse and well-known group of fishes that contains sixteen families inclusive of Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae, Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae, Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae, and Valenciidae and more than 1,200 species that are globally distributed in tropical and temperate, freshwater and estuarine habitats. The evolutionary relationships among the families within the group, based on different molecular and morphological data sets, have remained uncertain. Therefore, the objective of this study was to use a targeted approach, anchored hybrid enrichment, to investigate the phylogenetic relationships among the families within the Cyprindontiformes. This study included more than 100 individuals, representing all sixteen families within the Cyprinodontiformes, including many recently diagnosed families. We recovered an average of 244 loci per individual. These data were submitted to phylogenetic analyses (RaxML and ASTRAL) and although we recovered many of the same relationships as in previous studies of the group, several novel sets of relationships for other families also were recovered. In addition, two well-established clades (Suborders Cyprinodontoidei and Aplocheilodei) were recovered as monophyletic and are in agreement with most previous studies. We also assessed the degree of gene tree discordance in our dataset to evaluate support for alternative topological hypotheses for interfamilial relationships within the Cyprinodontiformes using a variety of different analyses. The results from this study will provide a robust, historical framework needed to investigate a plethora of biogeographic, taxonomic, ecological, and physiological questions for this group of fishes.
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Affiliation(s)
- Kyle R Piller
- Department of Biological Science, Southeastern Louisiana University, Hammond, LA 70402, USA.
| | - Elyse Parker
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, FL, 32306-4295, USA
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23
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Keer S, Storch JD, Nguyen S, Prado M, Singh R, Hernandez LP, McMenamin SK. Thyroid hormone shapes craniofacial bones during postembryonic zebrafish development. Evol Dev 2022; 24:61-76. [PMID: 35334153 PMCID: PMC8976723 DOI: 10.1111/ede.12399] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 01/12/2023]
Abstract
Changing the shape of craniofacial bones can profoundly alter ecological function, and understanding how developmental conditions sculpt skeletal phenotypes can provide insight into evolutionary adaptations. Thyroid hormone (TH) stimulates metamorphosis and regulates skeletal morphogenesis across vertebrates. To assess the roles of this hormone in sculpting the craniofacial skeleton of a non-metamorphic vertebrate, we tested zebrafish for developmental periods of TH-induced craniofacial shape change. We analyzed shapes of specific bones that function in prey detection, capture and processing. We quantified these elements from late-larval through adult stages under three developmental TH profiles. Under wild-type conditions, each bone progressively grows allometrically into a mature morphology over the course of postembryonic development. In three of the four bones, TH was required to sculpt an adult shape: hypothyroidism inhibited aspects of shape change, and allowed some components of immature shape to be retained into adulthood. Excess developmental TH stimulated aspects of precocious shape change leading to abnormal morphologies in some bones. Skeletal features with functional importance showed high sensitivities to TH, including the transformator process of the tripus, the mandibular symphysis of the lower jaw, the scutiform lamina of the hyomandibula, and the anterior arm of the pharyngeal jaw. In all, we found that TH is necessary for shaping mature morphology of several essential skeletal elements; this requirement is particularly pronounced during larval development. Altered TH titer leads to abnormal morphologies with likely functional consequences, highlighting the potential of TH and downstream pathways as targets for evolutionary change.
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Affiliation(s)
- Stephanie Keer
- Department of Biological Sciences, The George Washington University, Science and Engineering Hall, 800 22nd Street NW, Suite 6000, Washington, DC 20052 USA
| | - Joshua D. Storch
- Department of Biological Sciences, The George Washington University, Science and Engineering Hall, 800 22nd Street NW, Suite 6000, Washington, DC 20052 USA
| | - Stacy Nguyen
- Biology Department, Boston College, 140 Commonwealth Ave, Higgins Hall Room 360, Chestnut Hill MA 02467 USA
| | - Mia Prado
- Department of Biological Sciences, The George Washington University, Science and Engineering Hall, 800 22nd Street NW, Suite 6000, Washington, DC 20052 USA
| | - Rajendra Singh
- Biology Department, Boston College, 140 Commonwealth Ave, Higgins Hall Room 360, Chestnut Hill MA 02467 USA
| | - L. Patricia Hernandez
- Department of Biological Sciences, The George Washington University, Science and Engineering Hall, 800 22nd Street NW, Suite 6000, Washington, DC 20052 USA
| | - Sarah K. McMenamin
- Biology Department, Boston College, 140 Commonwealth Ave, Higgins Hall Room 360, Chestnut Hill MA 02467 USA
- corresponding author: Sarah K. McMenamin:
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Shkil FN, Borisov V, Seleznev D, Kapitanova D, Abdissa B, Dzerzhinskii K, Smirnov S. Intra- and interspecific variability of the cranial ossification sequences in Barbus sensu lato. Evol Biol 2022. [DOI: 10.1007/s11692-022-09563-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Kojima KK. Diversity and Evolution of DNA Transposons Targeting Multicopy Small RNA Genes from Actinopterygian Fish. BIOLOGY 2022; 11:biology11020166. [PMID: 35205033 PMCID: PMC8869645 DOI: 10.3390/biology11020166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary DNA transposons are parasitic DNA segments that can move or duplicate themselves from one site to another in the genome. Dada is a unique group of DNA transposons, which specifically insert themselves into multicopy RNA genes such as transfer RNA (tRNA) genes or small nuclear RNA (snRNA) genes to avoid the disruption of single-copy functional genes. However, only a few Dada families have been characterized along with their target sequences. Here, vertebrate genomes were surveyed to characterize new Dada transposons, and over 120 Dada families were characterized from diverse fishes. They were classified into 12 groups with confirmed target specificities. Various tRNA genes, as well as 5S ribosomal RNA (rRNA) genes were inserted by Dada transposons. Phylogenetic analysis revealed that Dada transposons inserted in the same RNA genes are closely related. Phylogenetically related Dada transposons inserted in different RNA genes show the sequence similarity around their insertion sites, indicating Dada proteins recognize DNA nucleotide sequences to find their targets. Understanding how Dada discovers the targets would help develop target-specific insertions of foreign DNA segments. Abstract Dada is a unique superfamily of DNA transposons, inserted specifically in multicopy RNA genes. The zebrafish genome harbors five families of Dada transposons, whose targets are U6 and U1 snRNA genes, and tRNA-Ala and tRNA-Leu genes. Dada-U6, which is inserted specifically in U6 snRNA genes, is found in four animal phyla, but other target-specific lineages have been reported only from one or two species. Here, vertebrate genomes and transcriptomes were surveyed to characterize Dada families with new target specificities, and over 120 Dada families were characterized from the genomes of actinopterygian fish. They were classified into 12 groups with confirmed target specificities. Newly characterized Dada families target tRNA genes for Asp, Asn, Arg, Gly, Lys, Ser, Tyr, and Val, and 5S rRNA genes. Targeted positions inside of tRNA genes are concentrated in two regions: around the anticodon and the A box of RNA polymerase III promoter. Phylogenetic analysis revealed the relationships among actinopterygian Dada families, and one domestication event in the common ancestor of carps and minnows belonging to Cyprinoidei, Cypriniformes. Sequences targeted by phylogenetically related Dada families show sequence similarities, indicating that the target specificity of Dada is accomplished through the recognition of primary nucleotide sequences.
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Affiliation(s)
- Kenji K Kojima
- Genetic Information Research Institute, Cupertino, CA 95014, USA
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26
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Xu X, Guan W, Niu B, Guo D, Xie QP, Zhan W, Yi S, Lou B. Chromosome-Level Assembly of the Chinese Hooksnout Carp (Opsariichthys bidens) Genome Using PacBio Sequencing and Hi-C Technology. Front Genet 2022; 12:788547. [PMID: 35126459 PMCID: PMC8807397 DOI: 10.3389/fgene.2021.788547] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Xiaojun Xu
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wenzhi Guan
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baolong Niu
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Dandan Guo
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qing-Ping Xie
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wei Zhan
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shaokui Yi
- School of Life Sciences, Huzhou University, Huzhou, China
- *Correspondence: Shaokui Yi, ; Bao Lou,
| | - Bao Lou
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Shaokui Yi, ; Bao Lou,
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27
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Buj I, Knjaz M, Ćaleta M, Marčić Z, Ivić L, Onorato L, Šanda R, Vukić J, Horvatić S, Zanella D, Mustafić P. Phylogeographic pattern, genetic diversity, and evolutionary history of the enigmatic freshwater fish species
Aulopyge huegelii
(Actinopterygii: Cyprinidae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ivana Buj
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Mia Knjaz
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Marko Ćaleta
- Faculty of Teacher Education University of Zagreb Zagreb Croatia
| | - Zoran Marčić
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Lucija Ivić
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Lucija Onorato
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | | | - Jasna Vukić
- Department of Ecology Faculty of Science Charles University Prague Czech Republic
| | - Sven Horvatić
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Davor Zanella
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | - Perica Mustafić
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
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28
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Zhang Z, Li S, Zhang J, Song W, Yang J, Mu J. The complete mitochondrial genome of an endangered minnow Aphyocypris lini (Cypriniformes: Xenocyprididae): genome characterization and phylogenetic consideration. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00811-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Kim SK, Cho HW. Characterization of the complete mitochondrial genome of Aphyocypris chinensis (Cypriniformes, Xenocyprididae), and its phylogenetic position in Cypriniformes. Mitochondrial DNA B Resour 2021; 6:2531-2533. [PMID: 34377819 PMCID: PMC8330764 DOI: 10.1080/23802359.2021.1959460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Sang Ki Kim
- Department of Zoology, Nakdonggang National Institute of Biological Resources, Sangju, South Korea
| | - Hee-Wook Cho
- Department of Zoology, Nakdonggang National Institute of Biological Resources, Sangju, South Korea
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30
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Viñuela Rodríguez N, Šanda R, Zogaris S, Vukić J. Evolutionary history of the Pelasgus minnows (Teleostei: Leuciscidae), an ancient endemic genus from the Balkan Peninsula. Mol Phylogenet Evol 2021; 164:107274. [PMID: 34333114 DOI: 10.1016/j.ympev.2021.107274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 10/20/2022]
Abstract
The Balkans are one of the European biodiversity hotspots, hosting outstandingly rich, yet threatened, flora and fauna. This region hosts one of the richest endemic freshwater ichthyofauna in Europe, including several genera occurring exclusively here. One of these is the genus of the primary freshwater minnows Pelasgus, which was designated only in 2007. The genus is one of the most ancient genera of the family Leuciscidae and comprises seven small-bodied species, inhabiting slower, well-vegetated courses of rivers. This work is the first molecular multilocus phylogeny of the genus, based on one mitochondrial and three nuclear markers. In total, 305 individuals across almost entire distribution range of the genus were analysed. We inferred the evolutionary history of the species by comparing the results of our calibrated multilocus coalescent species-tree to palaeogeological events. The diversification of the genus started in the early Miocene and continued through to the beginning of Pleistocene. We identified the regions of the oldest colonization by Pelasgus, the drainages of the ancient lakes Ohrid and Prespa, and the southernmost part of the Peloponnese, hosting Pelasgus minutus, P. prespensis and P. laconicus, respectively. We showed that P. prespensis is not endemic to Lake Prespa, as previously thought; it occurs also in the Albanian River Devoll. This corroborates the emerging opinion that the endemic taxa of ancient lakes evolved within larger-scale historic drainages and not only within the lakes. Our results showed that the species with the most recent common ancestor of the early Pliocene origin, P. thesproticus, P. epiroticus, P. stymphalicus and P. marathonicus, have neighbouring distribution ranges. Pelasgus epiroticus is especially interesting, not only for its pronounced genetic diversity with a geographic pattern, but also for being found at three localities within the native distribution range of P. stymphalicus as a result of a translocation. At two of these localities, we identified hybrids between the two species, and at one of them, the genetically pure native species was not found at all. This points to a threat of the loss of the native ichthyofauna due to unintentional translocations.
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Affiliation(s)
- Nuria Viñuela Rodríguez
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic
| | - Radek Šanda
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic; Department of Zoology, National Museum, Václavské nám. 68, Prague 1, 11000, Czech Republic
| | - Stamatis Zogaris
- Hellenic Centre for Marine Research, Institute of Marine Biological Sciences and Inland Waters, Athinon-Souniou Ave., Anavissos, Attica, 19013, Greece
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, 12844, Czech Republic.
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Abstract
Mavericks are virus-like mobile genetic elements found in the genomes of eukaryotes. Although Mavericks encode capsid morphogenesis homologs, their viral particles have not been observed. Here, we provide new evidence supporting the viral nature of Mavericks and the potential existence of virions. To this end, we conducted a phylogenomic analysis of Mavericks in hundreds of vertebrate genomes, discovering 134 elements with an intact coding capacity in 17 host species. We reveal an extensive genomic fossil record in 143 species and date three groups of elements to the Late Cretaceous. Bayesian phylogenetic analysis using genomic fossil orthologs suggests that Mavericks have infected osteichthyans for ∼419 My. They have undergone frequent cross-species transmissions in cyprinid fish and all core genes are subject to strong purifying selection. We conclude that vertebrate Mavericks form an ancient lineage of aquatic dsDNA viruses which are probably still functional in some vertebrate lineages.
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Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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32
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Sam KK, Lau NS, Shu-Chien AC, Muchlisin ZA, Nugroho RA. Complete Mitochondrial Genomes of Paedocypris micromegethes and Paedocypris carbunculus Reveal Conserved Gene Order and Phylogenetic Relationships of Miniaturized Cyprinids. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.662501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Helminth communities of endemic cyprinoids of the Apennine Peninsula, with remarks on ectoparasitic monogeneans, and a description of four new Dactylogyrus Diesing, 1850 species. Parasitology 2021; 148:1003-1018. [PMID: 33843503 PMCID: PMC10090784 DOI: 10.1017/s0031182021000615] [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] [Indexed: 12/13/2022]
Abstract
The fauna of the Apennine Peninsula is, in comparison to other southern European peninsulas, relatively species-poor regarding the number of endemic cyprinoid species. Nonetheless, the recent introduction of non-native species has significantly increased the total number of freshwater species in this region. Such invasive species may represent a threat to the native fauna, associated among other things with the introduction of non-native parasites with their original hosts.In the present study, we investigated endemic cyprinoid species for the presence of helminth parasites. A total of 36 ectoparasitic monogenean species and five endoparasitic helminth species were collected from ten cyprinoid species in five localities in northern Italy. Out of 20 Dactylogyrus species (gill monogeneans specific to cyprinoids), four were identified as new to science and herein described: Dactylogyrus opertus n. sp. and Dactylogyrus sagittarius n. sp. from Telestes muticellus, Dactylogyrus conchatus n. sp. from T. muticellus and Protochondrostoma genei, and Dactylogyrus globulatus n. sp. from Chondrostoma soetta. All new Dactylogyrus species appear to be endemic to the Apennine Peninsula; however, they share a common evolutionary history with the endemic Dactylogyrus parasitizing cyprinoids of the Balkans. This common origin of cyprinoid-specific parasites supports a historical connection between these two (currently separated) geographical regions.
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34
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Cornman RS, McKenna JE, Fike JA. Composition and distribution of fish environmental DNA in an Adirondack watershed. PeerJ 2021; 9:e10539. [PMID: 33680576 PMCID: PMC7919543 DOI: 10.7717/peerj.10539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/19/2020] [Indexed: 11/24/2022] Open
Abstract
Background Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration. Methods We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. Results We found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/µL DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson’s R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish (Ictalurus punctatus) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error.
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Affiliation(s)
- Robert S Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | - James E McKenna
- U.S. Geological Survey, Great Lakes Science Center, Cortland, NY, USA
| | - Jennifer A Fike
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
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35
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Bishani A, Prokopov DY, Romanenko SA, Molodtseva AS, Perelman PL, Interesova EA, Beklemisheva VR, Graphodatsky AS, Trifonov VA. Evolution of Tandemly Arranged Repetitive DNAs in Three Species of Cyprinoidei with Different Ploidy Levels. Cytogenet Genome Res 2021; 161:32-42. [PMID: 33677437 DOI: 10.1159/000513274] [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: 04/15/2020] [Accepted: 08/10/2020] [Indexed: 11/19/2022] Open
Abstract
Polyploid species represent a challenge for both cytogenetic and genomic studies due to their high chromosome numbers and the morphological similarity between their paralogous chromosomes. This paper describes the use of low-coverage high-throughput sequencing to identify the 14 most abundant tandemly arranged repetitive elements in the paleotetraploid genome of the crucian carp (Carassius carassius, 2n = 100). These repetitive elements were then used for molecular cytogenetic studies of a closely related functionally triploid form of the Prussian carp (Carassius gibelio, 3n = 150 + Bs) and a relatively distant diploid species, the tench (Tinca tinca, 2n = 48). According to their distribution on the chromosomes of the 3 aforementioned species, the repetitive elements here identified can be divided into 5 groups: (1) those specific to a single genomic locus in both Carassius species, despite the recent carp-specific genome duplication; (2) those located in a single genomic locus of T. tinca, but amplified in one or both Carassius species; (3) those massively amplified in the B chromosomes of C. gibelio; (4) those located in a single locus in C. gibelio, but amplified in many blocks in C. carassius; and (5) those located in multiple pericentromeric loci in both Carassius species. Our data indicate that some of the repetitive elements are highly conserved in cyprinoid species and may serve as good cytogenetic and genomic markers for discriminating paralogous chromosomes, while others are evolutionarily recent, and their amplification may be related to the last whole-genome duplication event.
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Affiliation(s)
- Ali Bishani
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation, .,Novosibirsk State University, Novosibirsk, Russian Federation,
| | - Dmitry Y Prokopov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation
| | - Svetlana A Romanenko
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation
| | - Anna S Molodtseva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation
| | - Elena A Interesova
- Department of Ichthyology and Hydrobiology, Tomsk State University, Tomsk, Russian Federation
| | | | | | - Vladimir A Trifonov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
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36
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Banker SE, Lemmon AR, Hassinger AB, Dye M, Holland SD, Kortyna ML, Ospina OE, Ralicki H, Lemmon EM. Hierarchical Hybrid Enrichment: Multitiered Genomic Data Collection Across Evolutionary Scales, With Application to Chorus Frogs (Pseudacris). Syst Biol 2021; 69:756-773. [PMID: 31886503 PMCID: PMC7302053 DOI: 10.1093/sysbio/syz074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/26/2019] [Accepted: 11/04/2019] [Indexed: 01/25/2023] Open
Abstract
Determining the optimal targets of genomic subsampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for subsampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first, we compare the benefits of target loci developed for deep- and shallow scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography), and within a hybrid zone (population genomics). Specifically, we target evolutionarily conserved loci that are appropriate for deeper phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple-locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer key evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels: we 1) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; 2) estimate the phylogeographic history of Pseudacris feriarum, which reveals up to five independent invasions leading to sympatry with congener Pseudacris nigrita to form replicated reinforcement contact zones with ongoing gene flow into sympatry; and 3) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is lower than microsatellite-based estimates. We find that the hierarchical hybrid enrichment approach offers an efficient, multitiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales. [Anchored hybrid enrichment; heat map; hybridization; phylogenetics; phylogeography; population genomics; reinforcement; reproductive character displacement.].
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Affiliation(s)
- Sarah E Banker
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Integrative Biology, University of California, Berkeley, #3160 Berkeley, CA 94720-3160, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Alyssa Bigelow Hassinger
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12th Avenue, 300 Aronoff Laboratory, Columbus, OH 43210, USA
| | - Mysia Dye
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Sean D Holland
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Oscar E Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Hannah Ralicki
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Biological Science, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06268, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
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37
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Hughes LC, Ortí G, Saad H, Li C, White WT, Baldwin CC, Crandall KA, Arcila D, Betancur-R R. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Mol Ecol Resour 2020; 21:816-833. [PMID: 33084200 DOI: 10.1111/1755-0998.13287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022]
Abstract
Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.
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Affiliation(s)
- Lily C Hughes
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Guillermo Ortí
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Hadeel Saad
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Chenhong Li
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - William T White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Keith A Crandall
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA
| | - Dahiana Arcila
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Sam Noble Oklahoma Museum of Natural History, Norman, OK, USA.,Department of Biology, University of Oklahoma, Norman, OK, USA
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Saenjundaeng P, Supiwong W, Sassi FMC, Bertollo LAC, Rab P, Kretschmer R, Tanomtong A, Suwannapoom C, Reungsing M, Cioffi MDB. Chromosomes of Asian cyprinid fishes: Variable karyotype patterns and evolutionary trends in the genus Osteochilus (Cyprinidae, Labeoninae, "Osteochilini"). Genet Mol Biol 2020; 43:e20200195. [PMID: 33156892 PMCID: PMC7783954 DOI: 10.1590/1678-4685-gmb-2020-0195] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/29/2020] [Indexed: 11/22/2022] Open
Abstract
The Cyprinidae family is a highly diversified but demonstrably monophyletic lineage of cypriniform fishes. Among them, the genus Osteochilus contains 35 recognized valid species distributed from India, throughout Myanmar, Laos, Thailand, Malaysia, Indonesian archipelago to southern China. In this study, karyotypes and other chromosomal characteristics of five Osteochilus species occurring in Thailand, namely O. lini, O. melanopleura, O. microcephalus, O. vittatus and O. waandersii were examined using conventional and molecular cytogenetic protocols. Our results showed they possessed diploid chromosome number (2n) invariably 2n = 50, but the ratio of uni- and bi-armed chromosomes was highly variable among their karyotypes, indicating extensive chromosomal rearrangements. Only one chromosome pair bearing 5S rDNA sites occurred in most species, except O. melanopleura, where two sites were detected. In contrast, only one chromosomal pair bearing 18S rDNA sites were observed among their karyotypes, but in different positions. These cytogenetic patterns indicated that the cytogenomic divergence patterns of these Osteochilus species were largely corresponding to the inferred phylogenetic tree. Similarly, different patterns of the distributions of rDNAs and microsatellites across genomes of examined species as well as their different karyotype structures indicated significant evolutionary differentiation of Osteochilus genomes.
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Affiliation(s)
- Pasakorn Saenjundaeng
- Faculty of Interdisciplinary Studies, Khon Kaen University, Nong
Khai Campus, Nong Khai 43000, Thailand
| | - Weerayuth Supiwong
- Faculty of Interdisciplinary Studies, Khon Kaen University, Nong
Khai Campus, Nong Khai 43000, Thailand
| | - Francisco M. C. Sassi
- Universidade Federal de São Carlos, Departamento de Genética e
Evolução, São Carlos, SP, Brazil
| | - Luiz A. C. Bertollo
- Universidade Federal de São Carlos, Departamento de Genética e
Evolução, São Carlos, SP, Brazil
| | - Petr Rab
- Czech Academy of Sciences, Institute of Animal Physiology and
Genetics, Laboratory of Fish Genetics, Rumburská 89, Libechov 277 21, Czech
Republic
| | - Rafael Kretschmer
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação
em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Alongklod Tanomtong
- KhonKaen University, Faculty of Science, Department of Biology,
Muang, KhonKaen 40002, Thailand
| | - Chatmongkon Suwannapoom
- University of Phayao, School of Agriculture and Natural Resources,
Department of Fishery, Muang, Phayao 56000, Thailand
| | - Montri Reungsing
- Rajamangala University of Technology Tawan-ok, Faculty of Science
and Technology, Department of Biotechnology, Siracha, Chonburi 20110, Thailand
| | - Marcelo de Bello Cioffi
- Universidade Federal de São Carlos, Departamento de Genética e
Evolução, São Carlos, SP, Brazil
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Soltani AR, Motamedi M, Teimori A. Adult neuronal regeneration in the telencephalon of the killifish Aphaniops hormuzensis. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:350-361. [PMID: 33107185 DOI: 10.1002/jez.b.23008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/16/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022]
Abstract
The potential of central nervous system regeneration was evaluated for the first time in the injured brain of the old world killifish Aphaniops hormuzensis. The histomorphological organization in the regeneration procedure was evaluated using the hematoxylin and eosin (H&E) staining and the bromodeoxyuridine (BrdU) immunohistochemistry technique. The histological tissue sections were sampled daily for 10 days. Based on the H&E staining, a large gliosis reaction was detected along with vacuolization and telencephalon deformation on 1-day post-lesion (dpl). The vacuolated zone declined fast and the telencephalon hemisphere recovered on 3 dpl. The symptoms of injured telencephalon nervous tissue were resolved within 7 dpl in both genders. In the BrdU test of the control group, BrdU-labeled cells were observed in the ventricular zone (VZ), pallium (Pa), and lateral pallium (LPa). On 1 dpl, the BrdU+ cells accumulated in the VZ, Pa, and LPa (located near the injury area). From 3 dpl onwards, the BrdU+ cells were reduced in the telencephalic VZ, Pa, and LPa. Based on the BrdU+ results, the adult brain in A. hormuzensis possesses a remarkable capacity for neuronal regeneration. By taking into account the high neural regeneration potency of A. hormuzensis and its relatively short lifespan, it could be concluded that besides the currently known models, the members of aphaniid fishes could probably be valuable animals to study the regeneration phenomenon in the vertebrates.
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Affiliation(s)
- Amir Reza Soltani
- Department of Biology, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mina Motamedi
- Department of Biology, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Azad Teimori
- Department of Biology, Shahid Bahonar University of Kerman, Kerman, Iran
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40
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Dalziel AC, Tirbhowan S, Drapeau HF, Power C, Jonah LS, Gbotsyo YA, Dion‐Côté A. Using asexual vertebrates to study genome evolution and animal physiology: Banded ( Fundulus diaphanus) x Common Killifish ( F. heteroclitus) hybrid lineages as a model system. Evol Appl 2020; 13:1214-1239. [PMID: 32684956 PMCID: PMC7359844 DOI: 10.1111/eva.12975] [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: 12/17/2019] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/27/2022] Open
Abstract
Wild, asexual, vertebrate hybrids have many characteristics that make them good model systems for studying how genomes evolve and epigenetic modifications influence animal physiology. In particular, the formation of asexual hybrid lineages is a form of reproductive incompatibility, but we know little about the genetic and genomic mechanisms by which this mode of reproductive isolation proceeds in animals. Asexual lineages also provide researchers with the ability to produce genetically identical individuals, enabling the study of autonomous epigenetic modifications without the confounds of genetic variation. Here, we briefly review the cellular and molecular mechanisms leading to asexual reproduction in vertebrates and the known genetic and epigenetic consequences of the loss of sex. We then specifically discuss what is known about asexual lineages of Fundulus diaphanus x F. heteroclitus to highlight gaps in our knowledge of the biology of these clones. Our preliminary studies of F. diaphanus and F. heteroclitus karyotypes from Porter's Lake (Nova Scotia, Canada) agree with data from other populations, suggesting a conserved interspecific chromosomal arrangement. In addition, genetic analyses suggest that: (a) the same major clonal lineage (Clone A) of F. diaphanus x F. heteroclitus has remained dominant over the past decade, (b) some minor clones have also persisted, (c) new clones may have recently formed, and iv) wild clones still mainly descend from F. diaphanus ♀ x F. heteroclitus ♂ crosses (96% in 2017-2018). These data suggest that clone formation may be a relatively rare, but continuous process, and there are persistent environmental or genetic factors causing a bias in cross direction. We end by describing our current research on the genomic causes and consequences of a transition to asexuality and the potential physiological consequences of epigenetic variation.
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Affiliation(s)
| | - Svetlana Tirbhowan
- Department of BiologySaint Mary's UniversityHalifaxNSCanada
- Département de biologieUniversité de MonctonMonctonNBCanada
| | | | - Claude Power
- Département de biologieUniversité de MonctonMonctonNBCanada
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41
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Benovics M, Vukić J, Šanda R, Rahmouni I, Šimková A. Disentangling the evolutionary history of peri-Mediterranean cyprinids using host-specific gill monogeneans. Int J Parasitol 2020; 50:969-984. [PMID: 32619430 DOI: 10.1016/j.ijpara.2020.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/01/2020] [Accepted: 05/15/2020] [Indexed: 11/29/2022]
Abstract
The diversification of Mediterranean fish appears to be far more complex than could be explained by a single dispersion model. Cyprinids represent one of the most species-rich groups of freshwater fishes living in this region. The current distribution of several highly divergent cyprinid taxa is most likely the result of multiple dispersion events. Cyprinid fish serve as hosts for the highly diversified and host-specific monogenean parasites of the genus Dactylogyrus. On the assumption that the distribution of Dactylogyrus spp. reflects the biogeography and evolutionary history of their hosts, we used these parasites as an additional tool to shed new light on the evolutionary history of peri-Mediterranean cyprinids of the subfamily Barbinae. The degree of congruence between host and parasite phylogenies was investigated using 29 Dactylogyrus spp. and 34 Barbinae hosts belonging to the genera Aulopyge, Barbus and Luciobarbus. We showed that the morphological adaptation of Dactylogyrus (i.e. of the ventral bar, representing the most variable morphological character of the attachment organ) is linked with parasite phylogeny. By applying distance-based and event-based cophylogenetic approaches, we revealed a significant global coevolutionary signal. A total of 62% of individual host-parasite links contributed significantly to the coevolutionary structure evidenced between hosts of Barbus spp. and Iberian Luciobarbus spp., and their host-specific Dactylogyrus spp. The host switching of parasites was revealed as the most important coevolutionary event in the Dactylogyrus-Barbinae system in the peri-Mediterranean region. Cophylogenetic analyses and the mapping of the morphological character of the parasite attachment organ onto the phylogeny of Dactylogyrus indicate that endemic southern European Dactylogyrus spp. parasitizing cyprinids of Barbinae have multiple origins. We suggest that continental bridges connecting southern Europe and North Africa played a crucial role in the dispersion of cyprinids, affecting the distribution of their host-specific gill parasites.
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Affiliation(s)
- Michal Benovics
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic.
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague, Czech Republic
| | - Radek Šanda
- National Museum, Václavské Náměstí 68, 115 79 Prague, Czech Republic
| | - Imane Rahmouni
- Laboratory of Biodiversity, Ecology and Genome, Mohammed V University, Rabat, Morocco
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
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42
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Cao M, Tang L, Chen J, Zhang X, Easy RH, You P. The mitogenome of freshwater loach Homatula laxiclathra (Teleostei: Nemacheilidae) with phylogenetic analysis of Nemacheilidae. Ecol Evol 2020; 10:5990-6000. [PMID: 32607206 PMCID: PMC7319148 DOI: 10.1002/ece3.6338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 11/11/2022] Open
Abstract
The complete mitogenome can provide valuable genetic information to reconstruct relationships between species. In this study, we sequenced a stone loach, Homatula laxiclathra (Teleostei: Nemacheilidae), which is found in the northern region of the Qinling Mountains in China. The size of the H. laxiclathra mitogenome is 16,570 bp, which contains 37 typical mitochondrial genes including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a control region (D-loop) with a total AT content of 55.8%. This is similar to other Nemacheilidae sequences published in GenBank. Furthermore, a mito-phylogenomic analysis of 46 Nemacheilidae species places H. laxiclathra in a robust monophyletic Homatula cluster with other Homatula species. Our results contribute toward a better understanding of a true phylogeny of these species based on large-scale taxonomic samplings as well as to help grasp the evolution of fish mitogenomes.
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Affiliation(s)
- Mengfei Cao
- School of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Ling Tang
- School of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Juan Chen
- School of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Xiaoyu Zhang
- School of Life SciencesShaanxi Normal UniversityXi'anChina
| | | | - Ping You
- School of Life SciencesShaanxi Normal UniversityXi'anChina
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43
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Raby L, Völkel P, Le Bourhis X, Angrand PO. The Polycomb Orthologues in Teleost Fishes and Their Expression in the Zebrafish Model. Genes (Basel) 2020; 11:genes11040362. [PMID: 32230868 PMCID: PMC7230241 DOI: 10.3390/genes11040362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/18/2020] [Accepted: 03/26/2020] [Indexed: 01/25/2023] Open
Abstract
The Polycomb Repressive Complex 1 (PRC1) is a chromatin-associated protein complex involved in transcriptional repression of hundreds of genes controlling development and differentiation processes, but also involved in cancer and stem cell biology. Within the canonical PRC1, members of Pc/CBX protein family are responsible for the targeting of the complex to specific gene loci. In mammals, the Pc/CBX protein family is composed of five members generating, through mutual exclusion, different PRC1 complexes with potentially distinct cellular functions. Here, we performed a global analysis of the cbx gene family in 68 teleost species and traced the distribution of the cbx genes through teleost evolution in six fish super-orders. We showed that after the teleost-specific whole genome duplication, cbx4, cbx7 and cbx8 are retained as pairs of ohnologues. In contrast, cbx2 and cbx6 are present as pairs of ohnologues in the genome of several teleost clades but as singletons in others. Furthermore, since zebrafish is a widely used vertebrate model for studying development, we report on the expression of the cbx family members during zebrafish development and in adult tissues. We showed that all cbx genes are ubiquitously expressed with some variations during early development.
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44
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Sholihah A, Delrieu-Trottin E, Sukmono T, Dahruddin H, Risdawati R, Elvyra R, Wibowo A, Kustiati K, Busson F, Sauri S, Nurhaman U, Dounias E, Zein MSA, Fitriana Y, Utama IV, Muchlisin ZA, Agnèse JF, Hanner R, Wowor D, Steinke D, Keith P, Rüber L, Hubert N. Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes. Sci Rep 2020; 10:2818. [PMID: 32071342 PMCID: PMC7028728 DOI: 10.1038/s41598-020-59544-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/20/2020] [Indexed: 11/25/2022] Open
Abstract
Sundaland constitutes one of the largest and most threatened biodiversity hotspots; however, our understanding of its biodiversity is afflicted by knowledge gaps in taxonomy and distribution patterns. The subfamily Rasborinae is the most diversified group of freshwater fishes in Sundaland. Uncertainties in their taxonomy and systematics have constrained its use as a model in evolutionary studies. Here, we established a DNA barcode reference library of the Rasborinae in Sundaland to examine species boundaries and range distributions through DNA-based species delimitation methods. A checklist of the Rasborinae of Sundaland was compiled based on online catalogs and used to estimate the taxonomic coverage of the present study. We generated a total of 991 DNA barcodes from 189 sampling sites in Sundaland. Together with 106 previously published sequences, we subsequently assembled a reference library of 1097 sequences that covers 65 taxa, including 61 of the 79 known Rasborinae species of Sundaland. Our library indicates that Rasborinae species are defined by distinct molecular lineages that are captured by species delimitation methods. A large overlap between intraspecific and interspecific genetic distance is observed that can be explained by the large amounts of cryptic diversity as evidenced by the 166 Operational Taxonomic Units detected. Implications for the evolutionary dynamics of species diversification are discussed.
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Affiliation(s)
- Arni Sholihah
- Instut Teknologi Bandung, School of Life Sciences and Technology, Bandung, Indonesia.,UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France
| | - Erwan Delrieu-Trottin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.,Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Invalidenstrasse 43, Berlin, 10115, Germany
| | - Tedjo Sukmono
- Universitas Jambi, Department of Biology, Jalan Lintas Jambi - Muara Bulian Km15, 36122, Jambi, Sumatra, Indonesia
| | - Hadi Dahruddin
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.,Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Renny Risdawati
- Department of Biology Education, STKIP PGRI Sumatera Barat, Jl Gunung Pangilun, Padang, 25137, Indonesia
| | - Roza Elvyra
- Universitas Riau, Department of Biology, Simpang Baru, Tampan, Pekanbaru, 28293, Indonesia
| | - Arif Wibowo
- Southeast Asian Fisheries Development Center, Inland Fisheries Resources Development and Management Department, 8 Ulu, Seberang Ulu I, Palembang, 30267, Indonesia.,Research Institute for Inland Fisheries and Fisheries extensions, Agency for Marine and Fisheries Research, Ministry of Marine Affairs and Fisheries., Jl. H.A. Bastari No. 08, Jakabaring, Palembang, 30267, Indonesia
| | - Kustiati Kustiati
- Universitas Tanjungpura, Department of Biology, Jalan Prof. Dr. H. Hadari Nawawi, Pontianak, 78124, Indonesia
| | - Frédéric Busson
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.,UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN), Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231, Paris, cedex, 05, France
| | - Sopian Sauri
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Ujang Nurhaman
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Edmond Dounias
- UMR 5175 CEFE (IRD, UM, CNRS, EPHE), 1919 route de Mende, 34293, Montpellier, cedex, 05, France
| | - Muhamad Syamsul Arifin Zein
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Yuli Fitriana
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Ilham Vemendra Utama
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | | | - Jean-François Agnèse
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France
| | - Robert Hanner
- Department of Integrative Biology, Centre for Biodiversity Genomics, 50 Stone Rd E, Guelph, ON, N1G2W1, Canada
| | - Daisy Wowor
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor Km 46, Cibinong, 16911, Indonesia
| | - Dirk Steinke
- Department of Integrative Biology, Centre for Biodiversity Genomics, 50 Stone Rd E, Guelph, ON, N1G2W1, Canada
| | - Philippe Keith
- UMR 7208 BOREA (MNHN-CNRS-UPMC-IRD-UCBN), Muséum National d'Histoire Naturelle, 43 rue Cuvier, 75231, Paris, cedex, 05, France
| | - Lukas Rüber
- Naturhistorisches Museum Bern, Bernastrasse 15, Bern, 3005, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, cedex, 05, France.
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45
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Bird NC, Abels JR, Richardson SS. Histology and structural integration of the major morphologies of the Cypriniform Weberian apparatus. J Morphol 2019; 281:273-293. [PMID: 31886901 DOI: 10.1002/jmor.21097] [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: 07/16/2019] [Revised: 10/31/2019] [Accepted: 12/06/2019] [Indexed: 11/05/2022]
Abstract
The Weberian apparatus, a diagnostic feature of otophysan fishes, is a novel hearing adaptation integrating several developmental and morphological systems (ear-vertebral column-swim bladder). Otophysan fishes are one of the largest and most successful freshwater clades, with over 10,000 species across most continents. The largest otophysan order, Cypriniformes, dominates the freshwaters of Asia, Europe, North America, and Africa. Spanning such a wide variety of environments, the Weberian apparatus undergoes morphological modifications to maintain functionality. Within Cypriniformes, we propose three distinct morphological classes of the Weberian apparatus based on the level of skeletal expansion around the swim bladder: simple (typical of most Cyprinidae), anterior plate (found in families such as Gyrinocheilidae, Catostomidae, and Botiidae), and encapsulated (either single-capsule as found, e.g., in Gobionidae and Cobitidae, or double-capsule as found, e.g., in Nemacheilidae and Balitoridae). Little ontological or comparative data exists regarding the construction or integration of these different morphologies, and less is known about the tissue level integration and variation within these morphologies. We used paraffin histology to document the hard and soft tissue anatomy of the Weberian apparatus in six species representing all morphological classes. We found sites of similarity across the morphologies including size and structure of the saccule, aspects of ossicle ossification, and swim bladder tunica composition, indicating potential sites of developmental and functional constraint. In contrast, we found differences across both auditory and nonauditory features in otic chamber size, ossification within ossicles and other vertebral elements, and composition of ligaments, indicating likely sites of adaptability. Some of these changes are likely evolutionary (taxonomic), but may be influenced by the environmental niche occupied by the clade. These results show a clear need for increased ontological and comparative study of the complete cypriniform Weberian apparatus, particularly histologically, as well as increased auditory studies across morphological types.
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Affiliation(s)
- Nathan C Bird
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa
| | - Jeremy R Abels
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa
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46
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Buj I, Marčić Z, Čavlović K, Ćaleta M, Tutman P, Zanella D, Duplić A, Raguž L, Ivić L, Horvatić S, Mustafić P. Multilocus phylogenetic analysis helps to untangle the taxonomic puzzle of chubs (genus Squalius: Cypriniformes: Actinopteri) in the Adriatic basin of Croatia and Bosnia and Herzegovina. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractFish of the genus Squalius inhabit various freshwater habitats across Europe and Asia, with a particularly high diversity in the Mediterranean area, but the taxonomic status of many populations is still a matter of debate. This study aims to resolve the taxonomic uncertainties of chubs distributed in the Adriatic basin of Croatia and Bosnia and Herzegovina. Phylogenetic reconstruction based on the mitochondrial gene for cytochrome b and two nuclear genes, the recombination activating gene 1 and the rhodopsin gene, reveal high diversity of chubs in the investigated area. Two evolutionary independent groups are revealed: the first comprising the species Squalius illyricus, S. microlepis, S. svallize, S. tenellus and S. zrmanjae, and a second group corresponding with S. squalus. Genetic distinctiveness of species belonging to different groups is high due to their divergence that began in the Middle Miocene. In addition to allopatric speciation as the main force of divergence of Adriatic Squalius species, several instances of natural hybridizations were detected, contributing to the observed diversity. A comparison of phylogenetic scenarios using Bayesian factors corroborated the molecular basis for recognition of six Squalius species in the Adriatic basin, while Squalius janae is confirmed to be a junior synonym of S. squalus.
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Affiliation(s)
- Ivana Buj
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Zoran Marčić
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Kristina Čavlović
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Marko Ćaleta
- Faculty of Teacher Education, University of Zagreb, Zagreb, Croatia
| | - Pero Tutman
- Institute of Oceanography and Fisheries, Split, Croatia
| | - Davor Zanella
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Aljoša Duplić
- Croatian Agency for Environment and Nature, Zagreb, Croatia
| | - Lucija Raguž
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Lucija Ivić
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Sven Horvatić
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Perica Mustafić
- Department of Zoology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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47
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Zangl L, Daill D, Gessl W, Friedrich T, Koblmüller S. Austrian gudgeons of the genusGobio(Teleostei: Gobionidae): A mixture of divergent lineages. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Lukas Zangl
- Institute of Biology University of Graz Graz Austria
| | - Daniel Daill
- Institute of Biology University of Graz Graz Austria
- Consultants in Aquatic Ecology and Engineering –blattfisch e.U. Wels Austria
| | | | - Thomas Friedrich
- Institute of Hydrobiology and Aquatic Ecosystem Management University of Natural Resources and Life Sciences Vienna Vienna Austria
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48
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Rocha S, Azevedo C, Alves Â, Antunes C, Casal G. Morphological and molecular characterization of myxobolids (Cnidaria, Myxozoa) infecting cypriniforms (Actinopterygii, Teleostei) endemic to the Iberian Peninsula. Parasite 2019; 26:48. [PMID: 31414983 PMCID: PMC6694745 DOI: 10.1051/parasite/2019049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/30/2019] [Indexed: 11/21/2022] Open
Abstract
The Iberian Peninsula provides a unique freshwater ecosystem for native and endemic cypriniforms to thrive. Despite cypriniforms being hosts to multiple myxobolids worldwide, little research has been performed in this geographic location. In this study, the examination of three Iberian endemic cypriniforms showed that myxosporean richness in the Iberian Peninsula is underestimated, with three new and one known myxobolid species being reported based on morphological and molecular data (SSU). Myxobolus arcasii n. sp. is described from the kidney and gonads of the "bermejuela" Achondrostoma arcasii, M. duriensis n. sp. from the gills of the Northern straight-mouth nase Pseudochondrostoma duriense, and Thelohanellus paludicus n. sp. from the intestine of the Southern Iberian spined-loach Cobitis paludica. Myxobolus pseudodispar Gorbunova, 1936 is further reported from several organs of P. duriense, and from the spleen of A. arcasii. The occurrence of M. pseudodispar in endemic Iberian species reveals that host-shift followed its co-introduction with central European leuciscids into this geographic location. Several other myxobolids originally described from barbels in central Europe have also been reported from the Iberian endemic cypriniform Luciobarbus bocagei. Nonetheless, except for M. musculi, the identification of these myxobolids in L. bocagei is here shown to be dubious and require molecular confirmation. Phylogenetic analyses reveal M. arcasii n. sp. and M. duriensis n. sp. clustering within different lineages of leuciscid-infecting species, showing that myxobolids entered Leuciscidae as hosts multiple times during their evolution. Constituting the first myxobolid reported from the subfamily Cobitinae, Thelohanellus paludicus n. sp. stands alone in the tree topology.
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Affiliation(s)
- Sónia Rocha
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Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS/UP) Rua Jorge Viterbo Ferreira No. 228 4050-313 Porto Portugal
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Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros de Leixões Av. General Norton de Matos s/n 4450-208 Matosinhos Portugal
| | - Carlos Azevedo
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Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS/UP) Rua Jorge Viterbo Ferreira No. 228 4050-313 Porto Portugal
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Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros de Leixões Av. General Norton de Matos s/n 4450-208 Matosinhos Portugal
| | - Ângela Alves
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Institute of Biomedical Sciences Abel Salazar, University of Porto (ICBAS/UP) Rua Jorge Viterbo Ferreira No. 228 4050-313 Porto Portugal
| | - Carlos Antunes
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Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros de Leixões Av. General Norton de Matos s/n 4450-208 Matosinhos Portugal
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Aquamuseu do Rio Minho Parque do Castelinho 4920-290 Vila Nova de Cerveira Portugal
| | - Graça Casal
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University Institute of Health Sciences & Institute of Research and Advanced Training in Health Sciences and Technologies, CESPU Rua Central da Gandra No. 1317 4585-116 Gandra Portugal
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49
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Yang K, Jiang W, Wang X, Zhang Y, Pan X, Yang J. Evolution of the intermuscular bones in the Cyprinidae (Pisces) from a phylogenetic perspective. Ecol Evol 2019; 9:8555-8566. [PMID: 31410261 PMCID: PMC6686301 DOI: 10.1002/ece3.5374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 01/15/2023] Open
Abstract
Intermuscular bones (IBs) are widely present in morphologically generalized teleost fishes and are commonly found in the Cyprinidae. Intermuscular bones are small, hard spicules of bone that are formed by ossification in the myosepta between neighboring myomeres. Why fish have IBs, and whether there is any evolutionary pattern to their occurrence, has been poorly understood. However, the presence of IBs does substantially affect the meat quality and commercial values of many cyprinid fishes in aquaculture. In this study, we sampled 592 individuals of cyprinid fishes to systematically investigate the evolution of IBs from a phylogenetic point of view. We found that the total number of IBs in the Cyprinidae ranged from 73 to 169, and we clarified that only two categories of IBs (epineural and epipleural) were present in all examined cyprinids. Most of the IBs were distributed in the posterior region of the fish, which might be an optimal target for selecting fewer IB strains in aquaculture. There was a positive correlation between IBs and the number of vertebrae, thus making it possible to predict the approximate number of IBs by counting the number of vertebrae. Although the IBs displayed some correlation with phylogenetic relationships in some lineages and to ecological factors such as diet (especially carnivore), in an overall view the variations of IBs in cyprinids were extremely diverse. The number and patterns of IBs in these fishes may reflect their phylogenetic history, but have been shaped by multiple environment factors. In this study, we also confirmed that X-ray photography remains an optimal and reliable method for the study of IBs.
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Affiliation(s)
- Kunfeng Yang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Wansheng Jiang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Xiaoai Wang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Yuanwei Zhang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Xiaofu Pan
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Junxing Yang
- Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
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50
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Pfeiffer JM, Breinholt JW, Page LM. Unioverse: A phylogenomic resource for reconstructing the evolution of freshwater mussels (Bivalvia, Unionoida). Mol Phylogenet Evol 2019; 137:114-126. [DOI: 10.1016/j.ympev.2019.02.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/25/2019] [Accepted: 02/18/2019] [Indexed: 10/27/2022]
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