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Xu CH, Song L, Wang Q, Chen XJ. Complete mitochondrial genome of Devario shanensis (Cypriniformes: Danionidae: Danioninae): genome characterization and phylogenetic consideration. Mitochondrial DNA B Resour 2024; 9:797-801. [PMID: 38895506 PMCID: PMC11185080 DOI: 10.1080/23802359.2024.2363367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
In this study, a comprehensive analysis is presented on the complete mitochondrial genome and phylogenetic relationships of Devario shanensis, an endemic species to the Irrawaddy drainage in southwestern China. The complete mitogenome sequence of D. shanensis was sequenced to be 16,860 bp long and encompassed 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a non-coding control region. The overall AT content (61.1%) was much higher than GC content (38.9%). Phylogenetic analyses employing maximum-likelihood and Bayesian inference methods on the complete mitogenomes, including D. shanensis and 13 other species, unveiled a close genomic relationship between D. shanensis and Devario interruptus. This work will contribute to the genetic resource enrichment and phylogenetic researches on genus Devario.
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Affiliation(s)
- Chun Hui Xu
- College of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College. Taizhou, Jiangsu Province, P.R. China
| | - Lin Song
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu Province, P.R. China)
| | - Quan Wang
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu Province, P.R. China)
| | - Xiao Jiang Chen
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu Province, P.R. China)
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2
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Fam YQ, Jamaluddin JAF, Muhammad-Rasul AH, Ilham-Norhakim ML, Rosely NFN, Lavoué S. Contrasting genetic and morphological differentiation among geographical lineages of a stenotopic miniature rasborine, Boraras maculatus, in Peninsular Malaysia. JOURNAL OF FISH BIOLOGY 2024; 104:171-183. [PMID: 37775959 DOI: 10.1111/jfb.15572] [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: 07/05/2023] [Revised: 09/12/2023] [Accepted: 09/26/2023] [Indexed: 10/01/2023]
Abstract
The variability in the stenotopic miniature rasborine Boraras maculatus (Cypriniformes: Danionidae: Rasborinae) across acidic-water habitats of Peninsular Malaysia (PM) was investigated using two molecular markers (the mitochondrial cytochrome c oxidase subunit I [COI] gene and the nuclear rhodopsin gene), as well as morphological evidence. Molecular phylogenetic analyses revealed differentiation among populations of B. maculatus in PM with the distinction of four allopatric lineages. Each of them was recognized as a putative species by automatic species delimitation methods. These lineages diverged from each other between 7.4 and 1.9 million years ago. A principal component analysis (PCA) was conducted to examine the multivariate variation in 11 morphometric measurements among three of these lineages. PCA results showed a significant overlap in morphological characteristics among these lineages. Additionally, a photograph-based machine learning approach failed to fully differentiate these lineages, suggesting limited morphological differentiation. B. maculatus represents a case of morphological stasis in a stenotopic miniature species. Strong habitat preference, coupled with long-term habitat fragmentation, may explain why each lineage of B. maculatus has a restricted distribution and did not disperse to other regions within and outside of PM, despite ample possibilities when the Sunda shelf was emerged and drained by large paleodrainages for most of the past 7 million years. The conservation status of B. maculatus and its peat swamp habitats are discussed, and it is concluded that peat swamps comprise several evolutionary units. Each of these units is considered a conservation unit and deserves appropriate protection.
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Affiliation(s)
- Yi Qing Fam
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | | | | | - Mohd Lokman Ilham-Norhakim
- Environmental Management and Conservation Research Unit (eNCORe), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), Johor, Malaysia
- Kim Ichthyologist Centre, Kg Parit Samsu, Jalan Temenggong Ahmad, Johor, Malaysia
| | - Nik Fadzly N Rosely
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang, Malaysia
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Ke Z, Zhou K, Hou M, Luo H, Li Z, Pan X, Zhou J, Jing T, Ye H. Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae. Animals (Basel) 2023; 13:3841. [PMID: 38136877 PMCID: PMC10740543 DOI: 10.3390/ani13243841] [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: 10/25/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
The elongate loach is an endemic fish in China. Previous studies have provided some insights into the mitochondrial genome composition and the phylogenetic relationships of the elongate loach inferred using protein-coding genes (PCGs), yet detailed information about it remains limited. Therefore, in this study we sequenced the complete mitochondrial genome of the elongate loach and analyzed its structural characteristics. The PCGs and mitochondrial genome were used for selective stress analysis and genomic comparative analysis. The complete mitochondrial genome of the elongate loach, together with those of 35 Cyprinidae species, was used to infer the phylogenetic relationships of the Cobitidae family through maximum likelihood (ML) reconstruction. The results showed that the genome sequence has a full length of 16,591 bp, which includes 13 PCGs, 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 2 non-coding regions (CR D-loop and light chain sub-chain replication origin OL). Overall, the elongate loach shared the same gene arrangement and composition of the mitochondrial genes with other teleost fishes. The Ka/Ks ratios of all mitochondrial PCGs were less than 1, indicating that all of the PCGs were evolving under purifying selection. Genome comparison analyses showed a significant sequence homology of species of Leptobotia. A significant identity between L. elongata and the other five Leptobotia species was observed in the visualization result, except for L. mantschurica, which lacked the tRNA-Arg gene and had a shorter tRNA-Asp gene. The phylogenetic tree revealed that the Cobitidae species examined here can be grouped into two clades, with the elongate loach forming a sister relationship with L. microphthalma. This study could provide additional inferences for a better understanding of the phylogenetic relationships among Cobitidae species.
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Affiliation(s)
- Zhenlin Ke
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
| | - Kangqi Zhou
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (K.Z.); (Z.L.); (X.P.)
| | - Mengdan Hou
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
| | - Hui Luo
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
| | - Zhe Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (K.Z.); (Z.L.); (X.P.)
| | - Xianhui Pan
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China; (K.Z.); (Z.L.); (X.P.)
| | - Jian Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China
| | - Tingsen Jing
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
| | - Hua Ye
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, College of Fisheries, Southwest University, Chongqing 402460, China; (Z.K.); (M.H.); (H.L.); (T.J.)
- Key Laboratory of Aquatic Science of Chongqing, Chongqing 400175, China
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Gong Y, Yang T, Su C, Zhao L, Li F. The complete mitochondrial genome of the Tanichthys flavianalis (Cypriniformes: Tanichthyidae) and its phylogeny. Mitochondrial DNA B Resour 2023; 8:1325-1329. [PMID: 38196797 PMCID: PMC10776059 DOI: 10.1080/23802359.2023.2282794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/08/2023] [Indexed: 01/11/2024] Open
Abstract
In the present study, we have sequenced, annotated and characterized the complete mitogenome of Tanichthys flavianalis Li, Liao & Shen, 2022, which is an endemic minnow to Hainan Province, China. The entire mitogenome size is 16,545 bp, containing 37 genes coding for 13 mitochondrial proteins, 22 tRNAs, 2 rRNAs, and one putative control region. It has the typical fish mitochondrial gene arrangement, though with 9 gene overlaps and 17 intergenic spacers scattering throughout the mitogenome, and a high A + T bias (60.8%) comparing to other Cyprinids. ATG is used as the start codon in most mitochondrial protein coding genes (PCGs) except for cox1 which uses GTG, whereas the canonical TAA/TAG are prevailing stop codons except for cox2, cox3, nad4 and cytb. Phylogenetic analyses with other reported species from Tanichyidae were conducted using IQ-TREE and MrBayes, based on the concatenated 13 PCGs. The results clustered T. flavinalis with the newly described T. albiventris Li Bohlen & Liao, 2022, and proved the reciprocally monophyletic relationship between Chinese and Vietnamese Tanichthys.
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Affiliation(s)
- Yuzhou Gong
- Branch of Shanghai Science and Technology Museum, Shanghai Natural History Museum, Shanghai, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, China
| | - Tiezhu Yang
- College of Fisheries, Xinyang Agriculture and Forestry University, Xinyang, China
- Fishery Biological Engineering Technology Research Center of Henan Province, Xinyang, China
| | - Chaoqun Su
- 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
| | - Fan Li
- Branch of Shanghai Science and Technology Museum, Shanghai Natural History Museum, Shanghai, China
- Institute of Hydrobiology, The Key Laboratory of Aquatic Biodiverstiy and Conservation of Chinese Academy of Sciences, Chinese Academy of Sciences, Wuhan, China
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Nguyen S, Lee RS, Mohlmann E, Petrullo G, Blythe J, Ranieri I, McMenamin S. Craniofacial diversity across Danionins and the effects of TH status on craniofacial morphology of two Danio species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.09.552728. [PMID: 37609193 PMCID: PMC10441423 DOI: 10.1101/2023.08.09.552728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The model zebrafish ( Danio rerio ) belongs to the Danioninae subfamily with a range of informative phenotypes. However, the craniofacial diversity across the subfamily is not fully described. To better understand craniofacial phenotypes across Danioninae we used microCT and 3D geometric morphometrics to capture skull shapes from nine species. The Danio species examined showed largely similar skull shapes, although D. aesculapii , the sister species to D. rerio showed a unique morphology. Two non- Danio species examined, Chela dadiburjori and Devario aequipinnatus showed distinct skull morphologies unique from those of other species examined. Thyroid hormone regulates skeletal development and remodeling, and we asked if changes in developmental thyroid hormone metabolism could underlie some of the craniofacial diversity across Danioninae. We reared two Danio species under altered thyroid profiles, finding that hypothyroid individuals from both species showed corresponding morphological shifts in skull shape. Hypothyroid Danios showed skull morphologies closer to that of Chela and unlike any of the examined wild-type Danio species. We provide an examination of the evolved craniofacial diversity across Danioninae, and demonstrate that alterations to thyroid hormone have the capacity to create unique skull phenotypes.
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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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Chen XJ, Liu WZ, Song L, Liu HX. Assembly and phylogenetic analysis of the complete mitogenome of Devario interruptus (Teleostei, Cypriniformes, Danionidae). Mitochondrial DNA B Resour 2023; 8:187-191. [PMID: 36755879 PMCID: PMC9901436 DOI: 10.1080/23802359.2022.2151831] [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] [Indexed: 02/05/2023] Open
Abstract
The complete mitochondrial DNA genome of Devario interruptus was sequenced on the Illumina HiSeq platform and found to be 16,735 bp and included 37 genes encoding 13 proteins, 22 tRNAs, two rRNAs, and two non-coding regions. The proportion of nucleotides in mitochondrial genome was T (27.9%), C (23.7%), A (33%), G (15.4%), and the deviation of AT was 60.9%. A Maximum-Likelihood phylogenetic tree was reconstructed using the concatenated mitochondrial protein-coding genes of D. interruptus and other 18 species of fishes. Phylogenetic analysis results supported that D. interruptus was closely related to Devario shanensis. Fundamental genetic data of D. interruptus will be essential for further genetic studies.
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Affiliation(s)
- Xiao Jiang Chen
- College of Fisheries Science and Technology, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou City, Jiangsu Province, P. R. China,CONTACT Xiao Jiang Chen Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, 225300, China
| | - Wen Zhao Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian City, Liaoning Province, P. R. China
| | - Lin Song
- College of Fisheries Science and Technology, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou City, Jiangsu Province, P. R. China
| | - Hai Xia Liu
- College of Fisheries Science and Technology, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou City, Jiangsu Province, P. R. 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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Chen IS, Jang-Liaw NH. Phylogeography of Aphyocypris normalis Nichols and Pope, 1927 at Hainan Island and adjacent areas based on mitochondrial DNA data. PLoS One 2023; 18:e0282460. [PMID: 36854024 PMCID: PMC9974131 DOI: 10.1371/journal.pone.0282460] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
We investigated the genetic structure of the freshwater fish Aphyocypris normalis, in 33 populations around Hainan Island and southern mainland China. Sequencing of the mitochondrial DNA (mtDNA) cytochrome b from 127 specimens yielded 47 haplotypes, from which we inferred a Bayesian tree. This revealed three major divergences: a principal clade of specimens with widespread geographic distribution, plus two clades with limited distribution. We estimated that these diverged between 1.05-0.16 Ma. Additionally, based on molecular data and comparing with the climate patterns of Hainan Island, eight phylogeographic ranges (populations) of A. normalis were constructed: the eastern plain (E), northeastern hills and plain (NE), northwestern hills and lowlands (NW), central mountains (C), southeastern hills and plain (SE), southern mountains and hills (S), southwestern mountains and lowlands (SW), and western lowlands (W). The patterns of geographical divergence in this species do not reflect the isolation caused by the Qiongzhou (Hainan) Strait, which would generally be experienced by terrestrial animals on isolated islands. The present results indicate that the major clades within A. normalis have diverged before the temporary land bridge existed across the strait during the Last Glacial Maximum.
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Affiliation(s)
- I-Shiung Chen
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Nian-Hong Jang-Liaw
- Conservation Genetics Laboratory, Conservation and Research Center, Taipei Zoo, Taipei, Taiwan
- * E-mail:
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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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Chen XJ, Song L, Cao YW, Wang Q. Phylogenetic relationship and characterization of the complete mitochondrial genome sequence of Opsarius caudiocellatus (Cypriniformes: Danionidae: Chedrinae). Mitochondrial DNA B Resour 2022; 7:2051-2055. [DOI: 10.1080/23802359.2022.2151324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Xiao Jiang Chen
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China
| | - Lin Song
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China
| | - You Wen Cao
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China
| | - Quan Wang
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, China
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12
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Chen XJ, Song L, Song Y, Wang Q. Determination and analysis of the complete mitochondrial genome of Barilius barila (Cypriniformes: Danionidae: Chedrinae). MITOCHONDRIAL DNA PART B 2022; 7:2002-2005. [PMID: 36451966 PMCID: PMC9704074 DOI: 10.1080/23802359.2022.2148824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cyprinid fish Barilius barila found in the Irrawaddy water system is a valuable fishery resource and has been listed as Least Concern by the IUCN. This study determined the complete mitochondrial genome of B. barila from Yunnan, China, for the first time. Circular molecule of B. barila mitogenome was sequenced to be 16,560 bp in length, with the typical gene structure of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and two noncoding areas (control region and the origin of L-strand replication). Overall nucleotides composition appeared to be 27.5% A, 24.8% T, 19.2% G, and 28.6% C, with a slight AT (52.3%) bias. The topology of the phylogenetic tree showed that B. barila was well grouped with Opsarius caudiocellatus, and clustered together with the genus Opsarius instead of Barilius, revealing that it was more reasonable for Barilius barila to belong to Opsarius rather than Barilius.
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Affiliation(s)
- Xiao Jiang Chen
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, P.R. China
| | - Lin Song
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, P.R. China
| | - Yang Song
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, P.R. China
| | - Quan Wang
- College of Fisheries Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, P.R. China
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13
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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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14
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Lindemann N, Kalix L, Possiel J, Stasch R, Kusian T, Köster RW, von Trotha JW. A comparative analysis of Danionella cerebrum and zebrafish (Danio rerio) larval locomotor activity in a light-dark test. Front Behav Neurosci 2022; 16:885775. [PMID: 35990722 PMCID: PMC9385977 DOI: 10.3389/fnbeh.2022.885775] [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: 02/28/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
The genus Danionella comprises some of the smallest known vertebrate species and is evolutionary closely related to the zebrafish, Danio rerio. With its optical translucency, rich behavioral repertoire, and a brain volume of just 0.6 mm3, Danionella cerebrum (Dc) holds great promise for whole-brain in vivo imaging analyses with single cell resolution of higher cognitive functions in an adult vertebrate. Little is currently known, however, about the basic locomotor activity of adult and larval Danionella cerebrum and how it compares to the well-established zebrafish model system. Here, we provide a comparative developmental analysis of the larval locomotor activity of Dc and AB wildtype as well as crystal zebrafish in a light-dark test. We find similarities but also differences in both species, most notably a striking startle response of Dc following a sudden dark to light switch, whereas zebrafish respond most strongly to a sudden light to dark switch. We hypothesize that the different startle responses in both species may stem from their different natural habitats and could represent an opportunity to investigate how neural circuits evolve to evoke different behaviors in response to environmental stimuli.
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15
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Liu Y, Cao L, Zhang E. Re-description of the loach species Homatula variegata (Dabry de Thiersant, 1874) (Pisces: Nemacheilidae) from the middle Huang-He basin in Shaanxi Province of Central China. JOURNAL OF FISH BIOLOGY 2022; 101:154-167. [PMID: 35524971 DOI: 10.1111/jfb.15080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Despite the wide recognition of Homatula variegata (Dabry de Thiersant, 1874) as a valid Chinese loach, its type locality, identity and distribution still remain contentious. A molecular phylogenetic analysis based on the mitochondrial cytochrome b (cyt b) gene for samples from all known range of the species showed that three distinct species are involved. Morphological comparisons, coupled with examination on the types, confirmed that H. variegata s. str. is characterized by having a sparsely scaled predorsal body, an adipose crest along the dorsal midline of the caudal peduncle that extends forward to the vertical through the posterior end of the anal-fin base and a broadly rounded caudal fin. It is found merely in the Wei-He of the Huang-He basin. The Jinsha-Jiang population, previously misidentified as H. variegata, represents a distinct species, for which Homatula oxygnathra is the available name. Homatula laxiclathra, endemic to the Wei-He, is also a valid species distinct from H. variegata.
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Affiliation(s)
- Yi Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Liang Cao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - E Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
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16
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Jin J, Li C, Zhao J. Descriptions of six new species in White Cloud Mountain minnow Tanichthys albonubes complex (Cypriniformes: Tanichthyidae) in southern China. JOURNAL OF FISH BIOLOGY 2022; 100:1062-1087. [PMID: 35174507 DOI: 10.1111/jfb.15012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Tanichthys albonubes is a critically endangered freshwater fish in South China and is classified as a second-class state-protected animal in China. It is also a colourful ornamental fish and has been introduced into many countries and regions around the world. Previous studies have revealed that there are seven cryptic species in the T. albonubes complex. Here, six new species of these cryptic species were diagnosed and described based on external morphology, colour patterns and osteological characteristics: Tanichthys shenzhenensis sp. nov., Tanichthys huidongensis sp. nov., Tanichthys luheensis sp. nov., Tanichthys dongxingensis sp. nov., Tanichthys guipingensis sp. nov. and Tanichthys hainanensis sp. nov. In addition, an identification key to the genus Tanichthys was provided. The key diagnosable characteristics of six new species in T. albonubes complex include the margin colour of dorsal and anal fins, the number of branched dorsal and anal fins, the relative position of the orbitosphenoid to the parasphenoid, the states of the neural complex, the states of the neural spine of the fourth vertebra and the anterior process of the innominatum. These six new species were also well supported by the phylogenetic tree and uncorrected p-distances based on Cyt b sequences. The distribution pattern of the genus Tanichthys is characterized by point-like, discontinuous distribution and geographically isolated on a large scale with narrow distribution ranges of each species. This study provides scientific data for the taxonomy, conservation status assessment and evolution of Tanichthys.
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Affiliation(s)
- Jinjin Jin
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chao Li
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jun Zhao
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
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17
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Hussin N, Azmir IA, Esa Y, Ahmad A, Salleh FM, Jahari PNS, Munian K, Gan HM. Characterization of the first mitogenomes of the smallest fish in the world, Paedocypris progenetica, from peat swamp of Peninsular Malaysia, Selangor, and Perak. Genomics Inform 2022; 20:e12. [PMID: 35399011 PMCID: PMC9001995 DOI: 10.5808/gi.21081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/17/2022] [Indexed: 11/20/2022] Open
Abstract
The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.
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Affiliation(s)
- NorJasmin Hussin
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), 40450 Shah Alam, Malaysia.,School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM) Negeri Sembilan, Kampus Kuala Pilah, Pekan Parit Tinggi, 72000 Kuala Pilah, Malaysia
| | - Izzati Adilah Azmir
- School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM) Negeri Sembilan, Kampus Kuala Pilah, Pekan Parit Tinggi, 72000 Kuala Pilah, Malaysia
| | - Yuzine Esa
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Malaysia
| | - Amirrudin Ahmad
- School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Malaysia.,Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Johor Bahru 81310, Malaysia
| | - Puteri Nur Syahzanani Jahari
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Johor Bahru 81310, Malaysia
| | - Kaviarasu Munian
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong 52109, Malaysia
| | - Han Ming Gan
- GeneSEQ Sdn Bhd, Bukit Beruntung, 48300 Rawang, Malaysia
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18
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KULLANDER SVEN, NORÉN MICHAEL. The real Devario browni from the Irrawaddy River basin, and the new Devario ahlanderi from the Salween River basin in Myanmar (Teleostei: Cyprinidae: Danioninae). Zootaxa 2022; 5100:54-72. [DOI: 10.11646/zootaxa.5100.1.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Indexed: 11/04/2022]
Abstract
Specimens of Devario from a tributary to the Salween River in Myanmar initially identified as Devario browni but with a different colour pattern, were subjected to a comparative morphological analysis with syntypes and other specimens of D. browni from near its putative type locality. The Salween sample was recognised as representing a distinct species, here named Devario ahlanderi. No significant morphometric differences were found between D. ahlanderi and D. browni. The type series of Devario ahlanderi differed from D. browni and most other species of Devario in the presence of 14 vs 12 circumpeduncular scale rows. Devario ahlanderi, D. browni, and D. fangae shared subadult colour pattern. Adult D. ahlanderi differed from adult D. browni in the trunk colour pattern, consisting of rows of dark blotches or short vertical bars. In D. browni, the flank colour pattern consisted of horizontal dark stripes, the middle of which (the P stripe) frequently diverged anteriorly, enclosing a small light blotch. Specimens previously reported as D. browni from the upper Salween River basin in Yunnan differed slightly in colour pattern, and may represent a distinct species. Devario ahlanderi shared spotted colour pattern with that of one ontogenetic state in D. kysonensis, except that a row of spots marking the P-1 stripe in D. kysonensis was absent in D. ahlanderi. The minimum genetic distance between D. ahlanderi and congeneric species varied from 2.1 to 5% in the mt-coI gene.
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19
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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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20
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Li W, Qiu N, Du H. Complete mitochondrial genome of Rhodeuscyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis. Zookeys 2022; 1081:111-125. [PMID: 35087298 PMCID: PMC8776718 DOI: 10.3897/zookeys.1081.77043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/14/2021] [Indexed: 11/12/2022] Open
Abstract
Rhodeuscyanorostris Li, Liao & Arai, 2020 is a freshwater fish that is endemic to China and restricted to Chengdu City in Sichuan Province. This study is the first to sequence and characterize the complete mitochondrial genome of R.cyanorostris. The mitogenome of R.cyanorostris is 16580 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region (D-loop). The base composition of the sequence is 28.5% A, 27.6% C, 26.4% T, and 17.5% G, with a bias toward A+T. The genome structure, nucleotide composition, and codon usage of the mitogenome of R.cyanorostris are consistent with those of other species of Rhodeus. To verify the molecular phylogeny of the genus Rhodeus, we provide new insights to better understand the taxonomic status of R.cyanorostris. The phylogenetic trees present four major clades based on 19 mitogenomic sequences from 16 Rhodeus species. Rhodeuscyanorostris exhibits the closest phylogenetic relationship with R.pseudosericeus, R.amarus, and R.sericeus. This study discloses the complete mitochondrial genome sequence of R.cyanorostris for the first time and provides the most comprehensive phylogenetic reconstruction of the genus Rhodeus based on whole mitochondrial genome sequences. The information obtained in this study will provide new insights for conservation, phylogenetic analysis, and evolutionary biology research.
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Affiliation(s)
- Wenjing Li
- YANGTZE Eco-Environment Engineering Research Center, China Three Gorges Corporation, Beijing 100038, ChinaYANGTZE Eco-Environment Engineering Research CenterBeijingChina
| | - Ning Qiu
- Key Laboratory of Environmental Protection Technology on Water Transport, Ministry of Transport, Tianjin research institute for water transport engineering, M.O.T., Tianjin 300456, ChinaMinistry of Transport, Tianjin research institute for water transport engineeringTianjinChina
| | - Hejun Du
- Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, Hubei 443100, ChinaChinese Sturgeon Research InstituteYichangChina
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21
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Diversification and biogeography of Dawkinsia (Teleostei: Cyprinidae) in the Western Ghats-Sri Lanka biodiversity hotspot. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00515-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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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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23
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Huang D, Lewis VM, Foster TN, Toomey MB, Corbo JC, Parichy DM. Development and genetics of red coloration in the zebrafish relative Danio albolineatus. eLife 2021; 10:70253. [PMID: 34435950 PMCID: PMC8416024 DOI: 10.7554/elife.70253] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/25/2021] [Indexed: 12/11/2022] Open
Abstract
Animal pigment patterns play important roles in behavior and, in many species, red coloration serves as an honest signal of individual quality in mate choice. Among Danio fishes, some species develop erythrophores, pigment cells that contain red ketocarotenoids, whereas other species, like zebrafish (D. rerio) only have yellow xanthophores. Here, we use pearl danio (D. albolineatus) to assess the developmental origin of erythrophores and their mechanisms of differentiation. We show that erythrophores in the fin of D. albolineatus share a common progenitor with xanthophores and maintain plasticity in cell fate even after differentiation. We further identify the predominant ketocarotenoids that confer red coloration to erythrophores and use reverse genetics to pinpoint genes required for the differentiation and maintenance of these cells. Our analyses are a first step toward defining the mechanisms underlying the development of erythrophore-mediated red coloration in Danio and reveal striking parallels with the mechanism of red coloration in birds.
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Affiliation(s)
- Delai Huang
- Department of Biology, University of Virginia, Charlottesville, United States
| | - Victor M Lewis
- Department of Biology, University of Virginia, Charlottesville, United States
| | - Tarah N Foster
- Department of Biological Science, University of Tulsa, Tulsa, United States
| | - Matthew B Toomey
- Department of Biological Science, University of Tulsa, Tulsa, United States.,Department of Pathology and Immunology, Washington University School of Medicine, St Louis, United States
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, United States
| | - David M Parichy
- Department of Biology, University of Virginia, Charlottesville, United States.,Department of Cell Biology, University of Virginia, Charlottesville, United States
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24
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Tang KL, Stiassny MLJ, Mayden RL, DeSalle R. Systematics of Damselfishes. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/i2020105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin L. Tang
- University of Michigan–Flint, Department of Biology, 303 East Kearsley St., Flint, Michigan 48502; . Send reprint requests to this address
| | - Melanie L. J. Stiassny
- American Museum of Natural History, Department of Ichthyology, Central Park West at 79th St., New York, New York 10024;
| | - Richard L. Mayden
- Saint Louis University, Department of Biology, 3507 Laclede Ave., St. Louis, Missouri 63103;
| | - Robert DeSalle
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York, New York 10024;
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25
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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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26
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The new chimeric chiron genes evolved essential roles in zebrafish embryonic development by regulating NAD + levels. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1929-1948. [PMID: 33521859 DOI: 10.1007/s11427-020-1851-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
The origination of new genes is important for generating genetic novelties for adaptive evolution and biological diversity. However, their potential roles in embryonic development, evolutionary processes into ancient networks, and contributions to adaptive evolution remain poorly investigated. Here, we identified a novel chimeric gene family, the chiron family, and explored its genetic basis and functional evolution underlying the adaptive evolution of Danioninae fishes. The ancestral chiron gene originated through retroposition of nampt in Danioninae 48-54 million years ago (Mya) and expanded into five duplicates (chiron1-5) in zebrafish 1-4 Mya. The chiron genes (chirons) likely originated in embryonic development and gradually extended their expression in the testis. Functional experiments showed that chirons were essential for zebrafish embryo development. By integrating into the NAD+ synthesis pathway, chirons could directly catalyze the NAD+ rate-limiting reaction and probably impact two energy metabolism genes (nmnat1 and naprt) to be under positive selection in Danioninae fishes. Together, these results mainly demonstrated that the origin of new chimeric chiron genes may be involved in adaptive evolution by integrating and impacting the NAD+ biosynthetic pathway. This coevolution may contribute to the physiological adaptation of Danioninae fishes to widespread and varied biomes in Southeast Asian.
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27
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Characterization of the complete mitochondrial genome of Macrotocinclus affinis (Siluriformes; Loricariidae) and phylogenetic studies of Siluriformes. Mol Biol Rep 2021; 48:677-689. [PMID: 33442829 DOI: 10.1007/s11033-020-06120-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
The vertebrate mitochondrial genome is typically circular molecules made up of 14,000 to 16,000 bp, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (12 s rRNA and 16 s rRNA) and a control region. Compared with nuclear DNA, mitochondrial DNA has a higher mutation rate, so it is one of the most effective and reliable molecular markers in fish phylogeny. Macrotocinclus affinis was the only species in Macrotocinclus (it was classified as Otocinclus in the past) and currently lacks genetic information. Most of the current researches are based on the mitochondrial Cytb gene and RAG1 and RAG2 nuclear genes to study the phylogenetic analysis of Siluriformes. So, the study provides the characteristic features of the Macrotocinclus affinis mitochondrial genome and this is the first time that the phylogenetic relationship of Siluriformes has been reconstructed based on COI. We aimed to sequence the entire mitochondrial genome of Macrotocinclus affinis using conventional PCR techniques and to clarify its phylogenetic status in Siluriformes by using the COI sequence of mitochondria. In this study, we sequenced the whole mitochondrial genome of this species yielding a 16,632 bp circular assembly composed of the typical vertebrate mitochondrial features. It contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region, and one origin of replication on the light-strand. The overall base composition includes A (30.07%), T (24.43%), C (29.43%) and G (16.01%). The genome composition is A + T biased (54.5%), and exhibits AT-skew (0.1036) and GC-skew (-0.2962). Moreover, the 13 PCGs encode 3850 amino acids in total. The result of the phylogenetic tree supports Macrotocinclus affinis has a closest relationship with Otocinclus cf. hoppei far. These results will help to understand the characteristics of the mitochondrial genome of Macrotocinclus affinis and provide molecular basis for the evolutionary relationship of Loricariidae.
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28
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On the Challenge to Correctly Identify Rasboras (Teleostei: Cyprinidae: Danioninae) Inhabiting the Mesangat Wetlands, East Kalimantan, Indonesia. DIVERSITY 2020. [DOI: 10.3390/d13010008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Within the subfamily Danioninae, rasborine cyprinids are known as a ‘catch-all’ group, diagnosed by only a few characteristics. Most species closely resemble each other in morphology. Species identification is therefore often challenging. In this study, we attempted to determine the number of rasborine species occurring in samples from the Mesangat wetlands in East Kalimantan, Indonesia, by using different approaches. Morphological identification resulted in the distinction of five species (Trigonopoma sp., Rasbora cf. hubbsi Brittan, 1954, R. rutteni Weber and de Beaufort, 1916, R. trilineata Steindachner, 1870, and R. vaillantii, Popta 1905). However, genetic species delimitation methods (Poisson tree processes (PTP) and multi-rate PTP (mPTP)) based on DNA barcodes and principal component analysis (PCA) based on homologous geometric morphometric landmarks, revealed a single cluster for Trigonopoma sp. and R. trilineata, respectively, whereas the remaining traditionally identified species were distinguished neither by DNA barcodes nor by the morphometry approach. A k-mean clustering based on the homologous landmarks divided the sample into 13 clusters and was thus found to be inappropriate for landmark data from species extremely resembling each other in morphology. Due to inconsistent results between the applied methods we refer to the traditional identifications and distinguish five rasborine species for the Mesangat wetlands.
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29
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Sequencing and characterisation of complete mitogenome DNA for Rasbora sarawakensis (Cypriniformes: Cyprinidae: Rasbora) with phylogenetic consideration. Comput Biol Chem 2020; 89:107403. [PMID: 33120127 DOI: 10.1016/j.compbiolchem.2020.107403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/18/2020] [Accepted: 10/11/2020] [Indexed: 11/23/2022]
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30
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Li C, Jiang S, Schneider K, Jin J, Lin H, Wang J, Elmer KR, Zhao J. Cryptic species in White Cloud Mountain minnow, Tanichthys albonubes: Taxonomic and conservation implications. Mol Phylogenet Evol 2020; 153:106950. [PMID: 32889137 DOI: 10.1016/j.ympev.2020.106950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
Cryptic species describe two or more species that had mistakenly been considered to be a single species, a phenomenon that has been found throughout the tree of life. Recognizing cryptic species is key to estimating the real biodiversity of the world and understanding evolutionary processes. Molecular methods present an unprecedented opportunity for biologists to question whether morphologically similar populations are actually cryptic species. The minnow Tanichthys albonubes is a critically endangered freshwater fish and was classified as a second-class state-protected animal in China. Previous studies have revealed highly divergent lineages with similar morphological characters in this species. Herein, we tested for cryptic species across the ranges of all known wild populations of this minnow. Using multilocus molecular (one mitochondrial gene, two nuclear genes and 13 microsatellite loci) and morphological data for 230 individuals from eight populations, we found deep genetic divergence among these populations with subtle morphological disparity. Morphological examination found variance among these populations in the number of branched anal-fin rays. Based on genetic data, we inferred eight monophyletic groups that were well supported by haplotype network and population clustering analyses. Species delimitation methods suggested eight putative species in the T. albonubes complex. Molecular dating suggested that these cryptic species diverged in the period from the Pliocene to the Pleistocene. Based on these findings, we propose the existence of seven cryptic species in the T. albonubes complex. Our results highlight the need for a taxonomic revision of Tanichthys. What is more, the conservation status of and conservation strategies for the T. albonubes complex should be reassessed as soon as possible.
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Affiliation(s)
- Chao Li
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Shuying Jiang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Kevin Schneider
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Jinjin Jin
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Hungdu Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Junjie Wang
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Jun Zhao
- Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China.
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31
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Sudasinghe H, Pethiyagoda R, Raghavan R, Dahanukar N, Rüber L, Meegaskumbura M. Diversity, phylogeny and biogeography ofSystomus(Teleostei, Cyprinidae) in Sri Lanka. ZOOL SCR 2020. [DOI: 10.1111/zsc.12445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiranya Sudasinghe
- Evolutionary Ecology and Systematics Lab Department of Molecular Biology and Biotechnology University of Peradeniya Peradeniya Sri Lanka
- Postgraduate Institute of Science University of Peradeniya Peradeniya Sri Lanka
| | | | - Rajeev Raghavan
- Department of Fisheries Resource Management Kerala University of Fisheries and Ocean Studies (KUFOS) Kochi India
| | - Neelesh Dahanukar
- Indian Institute of Science Education and Research (IISER) Pune India
| | - Lukas Rüber
- Naturhistorisches Museum Bern Bern Switzerland
- Aquatic Ecology and Evolution Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory of Forest Ecology & Conservation College of Forestry Guangxi University Nanning China
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32
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Chung HH, Kamar CKA, Lim LWK, Roja JS, Liao Y, Lam TTY, Chong YL. Sequencing and characterization of complete mitogenome DNA of Rasbora tornieri (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance. J Genet 2020. [DOI: 10.1007/s12041-020-01221-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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33
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Sudasinghe H, Pethiyagoda R, Meegaskumbura M. A molecular phylogeny of the genusLaubuka(Teleostei: Cyprinidae) in Sri Lanka reveals multiple origins and a cryptic species. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1771468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Hiranya Sudasinghe
- Evolutionary Ecology and Systematics Lab, Department of Molecular Biology and Biotechnology, University of Peradeniya, Peradeniya, Sri Lanka
- Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Rohan Pethiyagoda
- Ichthyology Section, Australian Museum, 6 College Street, Sydney, 2010, NSW, Australia
| | - Madhava Meegaskumbura
- Guangxi Key Laboratory of Forest Ecology & Conservation, College of Forestry, Guangxi University, Nanning, P.R. China
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34
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Chung HH, Lim LWK, Liao Y, Lam TTY, Chong YL. Sequencing and Characterisation of Complete Mitochondrial DNA Genome for Trigonopoma pauciperforatum (Cypriniformes: Cyprinidae: Danioninae) with Phylogenetic Consideration. Trop Life Sci Res 2020; 31:107-121. [PMID: 32963714 PMCID: PMC7485528 DOI: 10.21315/tlsr2020.31.1.7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Trigonopoma pauciperforatum or the redstripe rasbora is a cyprinid commonly found in marshes and swampy areas with slight acidic tannin-stained water in the tropics. In this study, the complete mitogenome sequence of T. pauciperforatum was first amplified in two parts using two pairs of overlapping primers and then sequenced. The size of the mitogenome is 16,707 bp, encompassing 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organisation was detected between this species and other family members. The heavy strand accommodates 28 genes while the light strand houses the remaining nine genes. Most protein-coding genes utilise ATG as start codon except for COI gene which uses GTG instead. The terminal associated sequence (TAS), central conserved sequence block (CSB-F, CSB-D and CSB-E) as well as variable sequence block (CSB-1, CSB-2 and CSB-3) are conserved in the control region. The maximum likelihood phylogenetic tree revealed the divergence of T. pauciperforatum from the basal region of the major clade, where its evolutionary relationships with Boraras maculatus, Rasbora cephalotaenia and R. daniconius are poorly resolved as suggested by the low bootstrap values. This work contributes towards the genetic resource enrichment for peat swamp conservation and comprehensive in-depth comparisons across other phylogenetic researches done on the Rasbora-related genus.
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Affiliation(s)
- Hung Hui Chung
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Leonard Whye Kit Lim
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Yunshi Liao
- School of Public Health, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong
| | - Tommy Tsan-Yuk Lam
- School of Public Health, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong
| | - Yee Ling Chong
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
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35
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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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36
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Characterization of the complete mitochondrial genome of Barilius malabaricus and its phylogenetic implications. Genomics 2019; 112:2154-2163. [PMID: 31843505 DOI: 10.1016/j.ygeno.2019.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/11/2019] [Accepted: 12/12/2019] [Indexed: 11/22/2022]
Abstract
Bariliine fishes are important components of the ornamental as well as subsistence fishery sectors in India. Many of the species in the genus Barilius are threatened by habitat loss and therefore need to be met with conservation initiatives. Effective conservation measures, however, require clarification of species identities and resolution of the validity of many species currently treated as synonymous or sub-species. The complete mitochondrial genome data provide better insight into phylogenetic information than the short fragment or single gene based analysis. Thus, we have sequenced the complete mitochondrial genome of Barilius malabaricus, one of the important fish species in the fresh water ornamental sector, for better understanding its phylogenetic status. The 16,519 bp mitochondrial genome consists of 37 genes which classifies as 22 tRNA, 13 protein coding and 2 ribosomal RNA genes and a control region. Overall, the mitochondrial genome bears the typical gene order and composition as in other fishes. Further, the COI, cytochrome b and 16S rRNA gene sequences revealed that, B. malabaricus is genetically closer to B. canarensis and B. bakeri compared to other Barilius species. Also, the Barilius species of west flowing rivers in Western Ghats were consistently recovered as a clade distinct from other species. We therefore suggest to retain the genus name Barilius for the species from the Western Ghats until a comprehensive analysis based on both morphological and molecular markers reveals the relationship between species now variously placed in the genera Barilius and Opsarius in greater detail.
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37
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Lim LWK, Roja JS, Kamar CKA, Chung HH, Liao Y, Lam TTY, Chong YL. Sequencing and characterization of complete mitogenome DNA for Rasbora myersi (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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38
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Galindo D, Sweet E, DeLeon Z, Wagner M, DeLeon A, Carter C, McMenamin SK, Cooper WJ. Thyroid hormone modulation during zebrafish development recapitulates evolved diversity in danionin jaw protrusion mechanics. Evol Dev 2019; 21:231-246. [PMID: 31374588 PMCID: PMC6815664 DOI: 10.1111/ede.12299] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protrusile jaws are a highly useful innovation that has been linked to extensive diversification in fish feeding ecology. Jaw protrusion can enhance the performance of multiple functions, such as suction production and capturing elusive prey. Identifying the developmental factors that alter protrusion ability will improve our understanding of fish diversification. In the zebrafish protrusion arises postmetamorphosis. Fish metamorphosis typically includes significant changes in trophic morphology, accompanies a shift in feeding niche and coincides with increased thyroid hormone production. We tested whether thyroid hormone affects the development of zebrafish feeding mechanics. We found that it affected all developmental stages examined, but that effects were most pronounced after metamorphosis. Thyroid hormone levels affected the development of jaw morphology, feeding mechanics, shape variation, and cranial ossification. Adult zebrafish utilize protrusile jaws, but an absence of thyroid hormone impaired development of the premaxillary bone, which is critical to jaw protrusion. Premaxillae from early juvenile zebrafish and hypothyroid adult zebrafish resemble those from adults in the genera Danionella, Devario, and Microdevario that show little to no jaw protrusion. Our findings suggest that evolutionary changes in how the developing skulls of danionin minnows respond to thyroid hormone may have promoted diversification into different feeding niches.
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Affiliation(s)
- Demi Galindo
- School of Biological Sciences, Washington State University, Pullman, Washington
| | - Elly Sweet
- School of Biological Sciences, Washington State University, Pullman, Washington
| | - Zoey DeLeon
- School of Biological Sciences, Washington State University, Pullman, Washington
| | - Mitchel Wagner
- School of Biological Sciences, Washington State University, Pullman, Washington
| | - Adrian DeLeon
- School of Biological Sciences, Washington State University, Pullman, Washington
| | - Casey Carter
- School of Biological Sciences, Washington State University, Pullman, Washington
| | | | - W. James Cooper
- School of Biological Sciences, Washington State University, Pullman, Washington
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39
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Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group. Gene 2019; 713:143967. [DOI: 10.1016/j.gene.2019.143967] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 06/12/2019] [Accepted: 07/03/2019] [Indexed: 11/18/2022]
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40
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Huang XX, Hsu KC, Kang B, Kuo PH, Tsai WH, Liang CM, Lin HD, Wang WK. Population structure of Aphyocypris normalis: phylogeography and systematics. Zookeys 2019; 872:77-90. [PMID: 31528116 PMCID: PMC6718371 DOI: 10.3897/zookeys.872.33105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/23/2019] [Indexed: 11/30/2022] Open
Abstract
Aphyocyprisnormalis (Teleostei: Cyprinidae) is an endemic species in South China, but little is known about its genetic structure. This study examined the population structure of A.normalis using sequences of the mitochondrial DNA control region and cytochrome b gene (2,086 bp). In total, 107 specimens were collected from nine populations. All 105 mtDNA haplotypes were identified as belonging to two allopatric phylogroups. The results of a statistical dispersal-vicariance analysis (S-DIVA) suggested that the ancestral populations of A.normalis were distributed widely on Hainan Island and east of the Leizhou Peninsula. A comparison of the fixation indices NST (0.532) and GST (0.004) revealed that the phylogeny and geography had a significant relationship. Our study found that (1) the Wuzhishan and Yinggeling Mountain Range was an important barrier limiting gene exchange between populations on both sides; (2) cyclic climate changes may have shaped migrations and population differentiations; and (3) different colonization times caused different population diversities between codistributed species. In addition, the inter- and intraspecific diversities of the genus Aphyocypris were estimated.
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Affiliation(s)
- Xiao-Xia Huang
- Key laboratory of atmospheric environment and processes in the boundary layer over the low-latitude plateau region, Yunnan University, Kunming, 650091, China Yunnan University Kunming China
| | - Kui-Ching Hsu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China Guangdong Ocean University Zhanjiang China
| | - Bin Kang
- College of Fisheries, Ocean University of China, Qingdao 266003, China Ocean University of China Qingdao China
| | - Po-Hsun Kuo
- Department of Industrial Management, National Taiwan University of Science and Technology, Taipei 106, Taiwan National Taiwan University of Science and Technology Taipei Taiwan
| | - Wan-Hsin Tsai
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, Taiwan Feng Chia University Taichung Taiwan
| | - Chih-Ming Liang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, Taiwan Feng Chia University Taichung Taiwan
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, Tainan 701, Taiwan The Affiliated School of National Tainan First Senior High School Tainan Taiwan
| | - Wei-Kuang Wang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung 407, Taiwan Feng Chia University Taichung Taiwan
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41
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Phylogenetic relationships of Cypriniformes and plasticity of pharyngeal teeth in the adaptive radiation of cyprinids. SCIENCE CHINA-LIFE SCIENCES 2019; 62:553-565. [DOI: 10.1007/s11427-019-9480-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/01/2018] [Indexed: 12/23/2022]
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42
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Adeoba M, Tesfamichael SG, Yessoufou K. Preserving the tree of life of the fish family Cyprinidae in Africa in the face of the ongoing extinction crisis. Genome 2019; 62:170-182. [DOI: 10.1139/gen-2018-0023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Our understanding of how the phylogenetic tree of fishes might be affected by the ongoing extinction risk is poor. This is due to the unavailability of comprehensive DNA data, especially for many African lineages. In addition, the ongoing taxonomic confusion within some lineages, e.g., Cyprinidae, makes it difficult to contribute to the debate on how the fish tree of life might be shaped by extinction. Here, we combine COI sequences and taxonomic information to assemble a fully sampled phylogeny of the African Cyprinidae and investigate whether we might lose more phylogenetic diversity (PD) than expected if currently threatened species go extinct. We found evidence for phylogenetic signal in extinction risk, suggesting that some lineages might be at higher risk than others. Based on simulated extinctions, we found that the loss of all threatened species, which approximates 37% of total PD, would lead to a greater loss of PD than expected, although highly evolutionarily distinct species are not particularly at risk. Pending the reconstruction of an improved multi-gene phylogeny, our results suggest that prioritizing high-EDGE species (evolutionary distinct and globally endangered species) in conservation programmes, particularly in some geographic regions, would contribute significantly to safeguarding the tree of life of the African Cyprinidae.
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Affiliation(s)
- Mariam Adeoba
- Department of Zoology, University of Johannesburg, Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa
| | - Solomon G. Tesfamichael
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa
| | - Kowiyou Yessoufou
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa
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43
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Kálmán M, Lőrincz DL, Sebők OM, Ari C, Oszwald E, Somiya H, Jancsik V. Cerebrovascular β-dystroglycan immunoreactivity in vertebrates: not detected in anurans and in the teleosts Ostariophysi and Euteleostei. Integr Zool 2019; 15:16-31. [PMID: 30811839 DOI: 10.1111/1749-4877.12384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The aim of the present paper was to check for the presence of cerebrovascular dystroglycan in vertebrates, because dystroglycan, which is localized in the vascular astroglial end-feet, has a pivotal function in glio-vascular connections. In mammalian brains, the immunoreactivity of β-dystroglycan subunit delineates the vessels. The results of the present study demonstrate similar patterns in other vertebrates, except for anurans and the teleost groups Ostariophysi and Euteleostei. In this study, we investigated 1 or 2 representative species of the main groups of Chondrichthyes, teleost and non-teleost ray-finned fishes, urodeles, anurans, and reptiles. We also investigated 5 mammalian and 3 bird species. Animals were obtained from breeders or fishermen. The presence of β-dystroglycan was investigated immunohistochemically in free-floating sections. Pre-embedding electron microscopical immunohistochemistry on Heterodontus japonicus shark brains demonstrated that in Elasmobranchii, β-dystroglycan is also localized in the perivascular glial end-feet despite the different construction of their blood-brain barrier. The results indicated that the cerebrovascular β-dystroglycan immunoreactivity disappeared separately in anurans, and in teleosts, in the latter group before its division to Ostariophysi and Euteleostei. Immunohistochemistry in muscles and western blots from brain homogenates, however, detected the presence of β-dystroglycan, even in anurans and all teleosts. A possible explanation is that in the glial end-feet, β-dystroglycan is masked in these animals, or disappeared during adaptation to the freshwater habitat.
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Affiliation(s)
- Mihály Kálmán
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - David L Lőrincz
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary.,University of Leicester, Dept. of Neuroscience, Psychology and Behaviour, Leicester, United Kingdom
| | - Olivér M Sebők
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Csilla Ari
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary.,Hyperbaric Neuroscience Research Lab., Dept of Psychology, University of South Florida, Tampa, Florida, USA
| | - Erzsébet Oszwald
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Hiroaki Somiya
- Department of Environmental Biology, Chubu University, Chubu, Japan
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44
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Adeoba MI, Yessoufou K. Analysis of temporal diversification of African Cyprinidae (Teleostei, Cypriniformes). Zookeys 2018:141-161. [PMID: 30588160 PMCID: PMC6302146 DOI: 10.3897/zookeys.806.25844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 10/02/2018] [Indexed: 11/12/2022] Open
Abstract
Recent evidence that freshwater fishes diversify faster than marine fishes signifies that the evolutionary history of biodiversity in freshwater system is of particular interest. Here, the evolutionary diversification events of African Cyprinidae, a freshwater fish family with wide geographic distribution, were reconstructed and analysed. The overall diversification rate of African Cyprinidae is 0.08 species per million year (when extinction rate is very high, i.e., ε = 0.9) and 0.11 species per million year (when ε = 0). This overall rate is lower than the rate reported for African Cichlids, suggesting that African freshwaters might be less conducive for a rapid diversification of Cyprinidae. However, the observed diversification events of African Cyprinidae occurred in the last 10 million years. The temporal pattern of these events follows a non-constant episodic birth-death model (Bayes Factor > 28) and the rate-constant model never outperformed any of the non-constant models tested. The fact that most diversification events occurred in the last 10 million years supports the pattern reported for Cyprinidae in other continent, e.g., Asia, perhaps pointing to concomitant diversification globally. However, the diversification events coincided with major geologic and paleo-climatic events in Africa, suggesting that geological and climatic events may have mediated the diversification patterns of Cyprinidae on the continent.
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Affiliation(s)
- Mariam I Adeoba
- Department of Zoology, University of Johannesburg, Kingsway Campus PO Box 524, Auckland Park 2006, South Africa University of Johannesburg Johannesburg South Africa
| | - Kowiyou Yessoufou
- Department of Geography, Environmental management and Energy studies, University of Johannesburg, Kingsway Campus PO Box 524, Auckland Park 2006, South Africa University of Johannesburg Johannesburg South Africa
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45
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Sousa-Santos C, Jesus TF, Fernandes C, Robalo JI, Coelho MM. Fish diversification at the pace of geomorphological changes: evolutionary history of western Iberian Leuciscinae (Teleostei: Leuciscidae) inferred from multilocus sequence data. Mol Phylogenet Evol 2018; 133:263-285. [PMID: 30583043 DOI: 10.1016/j.ympev.2018.12.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/12/2018] [Accepted: 12/15/2018] [Indexed: 01/05/2023]
Abstract
The evolutionary history of western Iberian Leuciscinae, obligatory freshwater fish, is directly linked to the evolution of the hydrographic network of the Iberian Peninsula after its isolation from the rest of Europe, which involved dramatic rearrangements such as the transition from endorheic lakes to open basins draining to the Atlantic. Previous phylogenetic research on western Iberian leuciscines, using mainly mitochondrial DNA and more recently one or two nuclear genes, has found contradictory results and there remain many unresolved issues regarding species relationships, taxonomy, and evolutionary history. Moreover, there is a lack of integration between phylogenetic and divergence time estimates and information on the timing of geomorphological changes and paleobasin rearrangements in the Iberian Peninsula. This study presents the first comprehensive fossil-calibrated multilocus coalescent species tree of western Iberian Leuciscinae (including 14 species of Achondrostoma, Iberochondrostoma, Pseudochondrostoma and Squalius endemic to the Iberian Peninsula, seven of which endemic to Portugal) based on seven nuclear genes, and from which we infer their biogeographic history by comparing divergence time estimates to known dated geological events. The phylogenetic pattern suggests slow-paced evolution of leuciscines during the Early-Middle Miocene endorheic phase of the main Iberian river basins, with the shift to exorheism in the late Neogene-Quaternary allowing westward dispersals that resulted in many cladogenetic events and a high rate of endemism in western Iberia. The results of this study also: (i) confirm the paraphyly of S. pyrenaicus with respect to S. carolitertii, and thus the possible presence of a new taxon in the Portuguese Tagus currently assigned to S. pyrenaicus; (ii) support the taxonomic separation of the Guadiana and Sado populations of S. pyrenaicus; (iii) show the need for further population sampling and taxonomic research to clarify the phylogenetic status of A. arcasii from the Minho basin and of the I. lusitanicum populations in the Sado and Tagus basins; and (iv) indicate that A. occidentale, I. olisiponensis and P. duriensis are the most ancient lineages within their respective genera.
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Affiliation(s)
- C Sousa-Santos
- MARE - Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal.
| | - T F Jesus
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egaz Moniz, 1649-028 Lisbon, Portugal(2).
| | - C Fernandes
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal.
| | - J I Robalo
- MARE - Marine and Environmental Sciences Centre, ISPA-Instituto Universitário, Rua Jardim do Tabaco 34, 1149-041 Lisbon, Portugal.
| | - M M Coelho
- cE3c - Center for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal.
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46
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Malmstrøm M, Britz R, Matschiner M, Tørresen OK, Hadiaty RK, Yaakob N, Tan HH, Jakobsen KS, Salzburger W, Rüber L. The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes. Genome Biol Evol 2018; 10:1088-1103. [PMID: 29684203 PMCID: PMC5906920 DOI: 10.1093/gbe/evy058] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2018] [Indexed: 12/20/2022] Open
Abstract
The world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.
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Affiliation(s)
- Martin Malmstrøm
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway.,Zoological Institute, University of Basel, Switzerland
| | - Ralf Britz
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Michael Matschiner
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway.,Zoological Institute, University of Basel, Switzerland
| | - Ole K Tørresen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway
| | - Renny Kurnia Hadiaty
- Ichthyology Laboratory, Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Norsham Yaakob
- Forest Research Institute Malaysia (FRIM), Kepong, Selangor Darul Ehsan, Malaysia
| | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Kjetill Sigurd Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway
| | - Walter Salzburger
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway.,Zoological Institute, University of Basel, Switzerland
| | - Lukas Rüber
- Naturhistorisches Museum Bern, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Switzerland
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47
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Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes. PLoS Genet 2018; 14:e1007538. [PMID: 30226839 PMCID: PMC6161917 DOI: 10.1371/journal.pgen.1007538] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/28/2018] [Accepted: 08/13/2018] [Indexed: 12/13/2022] Open
Abstract
Fishes of the genus Danio exhibit diverse pigment patterns that serve as useful models for understanding the genes and cell behaviors underlying the evolution of adult form. Among these species, zebrafish D. rerio exhibit several dark stripes of melanophores with sparse iridophores that alternate with light interstripes of dense iridophores and xanthophores. By contrast, the closely related species D. nigrofasciatus has an attenuated pattern with fewer melanophores, stripes and interstripes. Here we demonstrate species differences in iridophore development that presage the fully formed patterns. Using genetic and transgenic approaches we identify the secreted peptide Endothelin-3 (Edn3)—a known melanogenic factor of tetrapods—as contributing to reduced iridophore proliferation and fewer stripes and interstripes in D. nigrofasciatus. We further show the locus encoding this factor is expressed at lower levels in D. nigrofasciatus owing to cis-regulatory differences between species. Finally, we show that functions of two paralogous loci encoding Edn3 have been partitioned between skin and non-skin iridophores. Our findings reveal genetic and cellular mechanisms contributing to pattern differences between these species and suggest a model for evolutionary changes in Edn3 requirements for pigment patterning and its diversification across vertebrates. Neural crest derived pigment cells generate the spectacular variation in skin pigment patterns among vertebrates. Mammals and birds have just a single skin pigment cell, the melanocyte, whereas ectothermic vertebrates have several pigment cells including melanophores, iridophores and xanthophores, that together organize into a diverse array of patterns. In the teleost zebrafish, Danio rerio, an adult pattern of stripes depends on interactions between pigment cell classes and between pigment cells and their tissue environment. The close relative D. nigrofasciatus has fewer stripes and prior analyses suggested a difference between these species that lies extrinsic to the pigment cells themselves. A candidate for mediating this difference is Endothelin-3 (Edn3), essential for melanocyte development in warm-blooded animals, and required by all three classes of pigment cells in an amphibian. We show that Edn3 specifically promotes iridophore development in Danio, and that differences in Edn3 expression contribute to differences in iridophore complements, and striping, between D. rerio and D. nigrofasciatus. Our study reveals a novel function for Edn3 and provides new insights into how changes in gene expression yield morphogenetic outcomes to effect diversification of adult form.
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48
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Arumugam S, Ramaiah S. Concentrations of toxic metals (Pb, Cd, Cr) in the tissues and their effects on diversification of Devario aequipinnatus populations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2018; 28:379-390. [PMID: 29869528 DOI: 10.1080/09603123.2018.1479516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Recently, momentous consideration has being given to our natural ecosystems due to toxic metals, insidious to our environment execute as pollutants to the freshwater ecosystems. The accumulations of metals were encompassed with lead, cadmium and chromium in organs of Devario aequipinnatus. Although, the microscopic scrutinization from the gill and liver of the fish species were explored, the crucial conditions of the ecosystem. The histological study plays a key role in determining the effects of pollution. In the length-weight relationships of the regression parameters of coefficient value r2, 'a' value and 'b' value were showed the negative allometric growth rate of species D. aequipinnatus. However, the nucleotide sequence blast search was performed in NCBI database. In that the species of D.aequipinnatus were closely associated with other sub-species but within same genus, and it showed the similarity range between 100% and 90% in reference to other species for phylogenetic analysis.
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Affiliation(s)
- Sabaridasan Arumugam
- a PG and Research Department of Biotechnology , Sri Vinayaga College of Arts and Science , Ulundurpet, Villupuram District , Tamilnadu , India
| | - Soranam Ramaiah
- b Department of Environmental Sciences , Sri Paramakalyani Centre of Excellence in Environmental Sciences, Manonmaniam Sundaranar University , Alwarkurichi , Tamil Nadu , India
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49
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Shifatu O, Glasshagel-Chilson S, Nelson HM, Patel P, Tomamichel W, Higginbotham C, Evans PK, Lafontant GS, Burns AR, Lafontant PJ. Heart Development, Coronary Vascularization and Ventricular Maturation in a Giant Danio ( Devario malabaricus). J Dev Biol 2018; 6:jdb6030019. [PMID: 30037066 PMCID: PMC6162710 DOI: 10.3390/jdb6030019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 12/17/2022] Open
Abstract
Giant danios (genus Devario), like zebrafish, are teleosts belonging to the danioninae subfamily of cyprinids. Adult giant danios are used in a variety of investigations aimed at understanding cellular and physiological processes, including heart regeneration. Despite their importance, little is known about development and growth in giant danios, or their cardiac and coronary vessels development. To address this scarcity of knowledge, we performed a systematic study of a giant danio (Devario malabaricus), focusing on its cardiac development, from the segmentation period to ten months post-fertilization. Using light and scanning electron microscopy, we documented that its cardiovascular development and maturation proceed along well defined dynamic and conserved morphogenic patterns. The overall size and cardiovascular expansion of this species was significantly impacted by environmental parameters such as rearing densities. The coronary vasculature began to emerge in the late larval stage. More importantly, we documented two possible loci of initiation of the coronary vasculature in this species, and compared the emergence of the coronaries to that of zebrafish and gourami. This is the first comprehensive study of the cardiac growth in a Devario species, and our findings serve as an important reference for further investigations of cardiac biology using this species.
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Affiliation(s)
- Olubusola Shifatu
- Department of Biology, DePauw University, Greencastle, IN 46135, USA.
| | | | - Hannah M Nelson
- Department of Biology, DePauw University, Greencastle, IN 46135, USA.
| | - Purva Patel
- Department of Biology, DePauw University, Greencastle, IN 46135, USA.
| | - Wendy Tomamichel
- Department of Biology, DePauw University, Greencastle, IN 46135, USA.
| | - Clay Higginbotham
- Department of Biology, DePauw University, Greencastle, IN 46135, USA.
| | - Paula K Evans
- Department of Biology, DePauw University, Greencastle, IN 46135, USA.
| | | | - Alan R Burns
- College of Optometry, University of Houston, Houston, TX 77204, USA.
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50
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Schönhuth S, Vukić J, Šanda R, Yang L, Mayden RL. Phylogenetic relationships and classification of the Holarctic family Leuciscidae (Cypriniformes: Cyprinoidei). Mol Phylogenet Evol 2018; 127:781-799. [PMID: 29913311 DOI: 10.1016/j.ympev.2018.06.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022]
Abstract
The phylogenetic relationships and classification of the freshwater fish order Cypriniformes, like many other species-rich groups of vertebrates, has evolved over time with some consistency and inconsistencies of relationships across various studies. Within Cypriniformes, the Holarctic family Leuciscidae is one of the most widely distributed and highly diverse monophyletic groups of cyprinoids. Despite several studies conducted on this group, alternative hypotheses exist as to the composition and relationships within Leuciscidae. Here we assess the extent, composition, phylogenetic relationships, and taxonomy of this highly diverse group of fishes, using multiple mitochondrial and nuclear loci and a comprehensive and dense taxonomic sampling. Analyses of 418 specimens (410 species) resolve a well-supported Leuciscidae including 362 specimens (358 taxa) in six well-supported subfamilies/major clades: Pseudaspininae/Far East Asian clade (FEA); Laviniinae/North American Western clade (WC); Plagopterinae/North American Creek Chub-Plagopterin clade (CC-P); Leuciscinae/Eurasian Old World clade (OW) (minus Phoxinus) plus North American Notemigonus; Phoxininae/Eurasian Phoxinus clade (PHX); and Pogonichthyinae/North American clade (NA) including all remaining leuciscids. Within Leuciscidae, neither the traditional phoxinins (Phoxinus, FEA, Nearctic genera) nor all Nearctic genera (minus Notemigonus) are resolved as monophyletic; whereas the WC and CC-P form two independent lineages from remaining North American cyprinoids. A close relationship exists between Eurasian Phoxinus, NA, and OW clades, while FEA is the sister group to all remaining Leuciscidae. Major lineages resolved within these six subfamilies are mostly congruent with some previous studies. Our results suggests a complex evolutionary history of this diverse and widespread group of fishes.
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Affiliation(s)
- Susana Schönhuth
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA.
| | - Jasna Vukić
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44 Prague, Czech Republic
| | - Radek Šanda
- Department of Zoology, National Museum, Vaclavske namesti 68, 115 79 Prague, Czech Republic
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, 1659 Museum Rd., Gainesville, FL 32611, USA
| | - Richard L Mayden
- Biology Department, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO 63103, USA
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