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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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52
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Laskar BA, Kumar V, Kundu S, Darshan A, Tyagi K, Chandra K. DNA barcoding of fishes from River Diphlu within Kaziranga National Park in northeast India. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:126-134. [PMID: 29669453 DOI: 10.1080/24701394.2018.1463373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
DNA barcoding technique has been gaining importance in biodiversity research for its easy and rapid ability of delineating organisms' partial DNA sequences into molecular operational taxonomic units (MOTUs), and identification based on referral sequences from expert identified species. We generated mtCOI barcode sequences from morphologically identified fishes from River Diphlu in northeast India. A portion of this river falls within an important rhinoceros and tiger conservation site, the Kaziranga National Park. Partial mtCOI sequences for 103 fish specimens belonging to six orders, 19 families, 37 genera and 47 a priori identified species, were delineated into 48 MOTUs based on reciprocal monophyly criteria in maximum likelihood and Bayesian tree, and 49 groups by automatic barcode gap discovery (ABGD). Morphological and molecular basis of species identification was congruent for around 80% straightforward cases. We contributed barcodes for eight species which either had no barcodes in databases or are having ambiguous barcodes. We detected four 'near threatened' and two data deficient species as per the IUCN Red List status, besides a few 'least concerned' species. We also observed a wide scope of barcoding studies on fishes from northeast India to cover the endemic species and to resolve the prevailing taxonomic problems.
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Affiliation(s)
- Boni Amin Laskar
- a Freshwater Biology Regional Centre, Zoological Survey of India , Hyderabad , India
| | - Vikas Kumar
- b Molecular Systematics Division , Centre for DNA Taxonomy, Zoological Survey of India , Kolkata , India
| | - Shantanu Kundu
- b Molecular Systematics Division , Centre for DNA Taxonomy, Zoological Survey of India , Kolkata , India
| | - Achom Darshan
- c Center with Potential for Excellence in Biodiversity, Rajiv Gandhi University , Doimukh , India
| | - Kaomud Tyagi
- b Molecular Systematics Division , Centre for DNA Taxonomy, Zoological Survey of India , Kolkata , India
| | - Kailash Chandra
- b Molecular Systematics Division , Centre for DNA Taxonomy, Zoological Survey of India , Kolkata , India
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53
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Adeoba MI, Kabongo R, der Bank HV, Yessoufou K. Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae). Zookeys 2018:105-121. [PMID: 29674898 PMCID: PMC5906743 DOI: 10.3897/zookeys.746.13502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 12/14/2017] [Indexed: 12/02/2022] Open
Abstract
Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.
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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
| | - Ronny Kabongo
- African Centre for DNA Barcoding, University of Johannesburg, Kingsway Campus, PO Box 524, Auckland Park 2006, South Africa
| | - Herman Van der Bank
- Department of Zoology, University of Johannesburg, Kingsway Campus PO Box 524, Auckland Park 2006, 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
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54
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Adeoba MI, Kabongo R, Van der Bank H, Yessoufou K. Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae). Zookeys 2018. [DOI: 10.3897/zookeys.744.13502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for comparative phylogenetic analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.
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55
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Adeoba MI, Kabongo R, Van der Bank H, Yessoufou K. Re-evaluation of the discriminatory power of DNA barcoding on some specimens of African Cyprinidae (subfamilies Cyprininae and Danioninae). Zookeys 2018. [DOI: 10.3897/zookeys.740.13502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Specimen identification in the absence of diagnostic morphological characters (e.g., larvae) can be problematic even for experts. The goal of the present study was to assess the performance of COI in discriminating specimens of the fish family Cyprinidae in Africa, and to explore whether COI-phylogeny can be reliably used for phylogenetic comparative analysis. The main objective was to analyse a matrix of COI sequences for 315 specimens from 15 genera of African Cyprinidae using various distance-based identification methods alongside multiple tests of DNA barcode efficacy (barcode gap, species monophyly on NJ tree). Some morphological and biological characters were also mapped on a COI-phylogeny reconstructed using Maximum Parsimony. First, the results indicated the existence of barcode gaps, a discriminatory power of COI ranging from 79 % to 92 %, and that most nodes form well-supported monophyletic clades on an NJ tree. Second, it was found that some morphological and biological characters are clustered on the COI-phylogeny, and this indicates the reliability of these characters for taxonomic discrimination within the family. Put together, our results provide not only an additional support for the COI as a good barcode marker for the African Cyprinidae but it also indicate the utility of COI-based phylogenies for a wide spectrum of ecological questions related to African Cyprinidae.
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56
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Atminarso D, Wibowo A, Kusuma WE, Prianto E, Ahnelt H, Vasemägi A, Kumazawa Y. The complete mitochondrial DNA sequence of Pectenocypris sp. (Actinopterygii: Cyprinidae) from Serkap River, Sumatra, Indonesia. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:122-124. [PMID: 33474089 PMCID: PMC7799607 DOI: 10.1080/23802359.2018.1424585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The whole mitochondrial genome of a small cyprinid freshwater fish Pectenocypris sp. collected from Serkap River, Central Sumatra, Indonesia was sequenced. This mitochondrial genome consisted of 16,589 bp and included 37 genes in the same order as in many other vertebrates including the human. Phylogenetic analysis suggested that this taxon clusters with Boraras maculatus among several Rasbora species.
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Affiliation(s)
- Dwi Atminarso
- Research Institute for Inland Fisheries, Agency for Research and Human Resource Development, Ministry of Marine Affairs and Fisheries, Palembang, Indonesia.,Inland Fishery Resources Development and Management Department, Southeast Asian Fisheries Development Center, Palembang, Indonesia
| | - Arif Wibowo
- Research Institute for Inland Fisheries, Agency for Research and Human Resource Development, Ministry of Marine Affairs and Fisheries, Palembang, Indonesia.,Inland Fishery Resources Development and Management Department, Southeast Asian Fisheries Development Center, Palembang, Indonesia
| | - Wahyu Endra Kusuma
- Department of Aquaculture, Faculty of Fisheries and Marine Science, University of Brawijaya, Malang, Indonesia
| | - Eko Prianto
- Research Center for Fisheries, Agency for Research and Human Resource Development, Ministry of Marine Affairs and Fisheries, Jakarta, Indonesia
| | - Harald Ahnelt
- Department of Theoretical Biology, University of Vienna, Vienna, Austria
| | - Anti Vasemägi
- Department of Biology, Division of Genetics and Physiology, University of Turku, Turku, Finland.,Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Yoshinori Kumazawa
- Department of Information and Basic Science and Research Center for Biological Diversity, Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
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57
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Huang SP, Wang FY, Wang TY. Molecular Phylogeny of the Opsariichthys Group (Teleostei: Cypriniformes) Based On Complete Mitochondrial Genomes. Zool Stud 2017; 56:e40. [PMID: 31966239 PMCID: PMC6517700 DOI: 10.6620/zs.2017.56-40] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 12/06/2017] [Indexed: 11/18/2022]
Abstract
Shih-Pin Huang, Feng-Yu Wang, and Tzi-Yuan Wang (2017) The complete mitochondrial genomes of 76 species from 43 genera under Cyprinidae sensu lato were collected to reassess the molecular phylogeny of Opsariichthyinae sensu Liao et al. 2011. The mitogenomes of three species, Candidia barbata, Opsariichthys evolans, and Opsariichthys pachycephalus, were newly sequenced. Phylogenetic trees were reconstructed based on 13 concatenated multiple protein-coding genes with two ribosomal RNA genes. The concatenated dataset provided a new perspective on systematics and relationships. Tree topologies show that a monophyletic group containing Parazacco, Candidia, Nipponocypris, Zacco, and Opsariichthys should belong to the Opsariichthys group. In addition, the present results also strongly support that Candidia and Nipponocypris should be regarded as distinct genera within the Opsariichthys group. Aphyocypris, Yaoshanicus, Nicholsicypris, and Pararasbora form a monophyletic group within Xenocyprididae, distinct from the Opsariichthys group. Furthermore, Hemigrammocypris is nested with four species of Metzia, a genus of ex-Cultrinae in Xenocyprididae. In addition, two major types of distinct stripes - longitudinal and vertical - were observed among species of the Opsariichthys group and were highly correlated with molecular phylogenetic relationships. Such types of vertical and longitudinal stripes presented in the Opsariichthys group might have originated in an ancestor species, after which distinct vertical stripes might have been lost among these cyprinids but retained in the Opsariichthys group.
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Affiliation(s)
- Shih-Pin Huang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan. E-mail:
| | - Feng-Yu Wang
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung, Taiwan. E-mail:
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan. E-mail:
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58
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Ito T, Fukuda T, Morimune T, Hosoya K. Evolution of the connection patterns of the cephalic lateral line canal system and its use to diagnose opsariichthyin cyprinid fishes (Teleostei, Cyprinidae). Zookeys 2017:115-131. [PMID: 29290716 PMCID: PMC5740415 DOI: 10.3897/zookeys.718.13574] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 10/28/2017] [Indexed: 11/12/2022] Open
Abstract
The cephalic lateral line canal systems were compared among 12 species of the cyprinid tribe Opsariichthyini. All species were characterized by the separation of the supraorbital canal from both the infraorbital and the temporal canals, and the left side of the supratemporal canal from the right side of the canal. In species of Candidia, Opsariichthys, Parazacco, and Zacco, and Nipponocyprissieboldii the temporal canal was separated from the preoperculomandibular canal. In Nipponocypristemminckii and N.koreanus, the temporal canal was connected to the preoperculomandibular canal. Separation of the left and right sides of the supratemporal canal is a possible synapomorphy of the opsariichthyin cyprinids. Opsariichthysuncirostris and O.bidens are unique among the opsariichthyins in that the connection between the infraorbital and temporal canals is retarded. The variation in arrangement of the cephalic lateral line canal system can be used as diagnostic characters for the opsariichthyin species.
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Affiliation(s)
- Taiki Ito
- Wetlands International Japan, 2F Jono Building II 17-1, Odenma-cho, Nihonbashi, Chuo-ku, Tokyo, 103-0011, Japan
| | - Toyoaki Fukuda
- Tezukayama Junior & Senior High School, Gakuen-minami 3-1-3, Nara 631-0034, Japan
| | - Toshihiko Morimune
- Department of Environmental Management, Faculty of Agriculture, Kindai University, Nakamachi 3327-204, Nara 631-8505, Japan
| | - Kazumi Hosoya
- Department of Environmental Management, Faculty of Agriculture, Kindai University, Nakamachi 3327-204, Nara 631-8505, Japan
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59
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Kullander SO, Rahman MM, Norén M, Mollah AR. Devario in Bangladesh: Species diversity, sibling species, and introgression within danionin cyprinids (Teleostei: Cyprinidae: Danioninae). PLoS One 2017; 12:e0186895. [PMID: 29166410 PMCID: PMC5699798 DOI: 10.1371/journal.pone.0186895] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/27/2017] [Indexed: 11/26/2022] Open
Abstract
Four species of Devario are recorded from Bangladesh: D. aequipinnatus, D. anomalus, D. coxi, new species, and D. devario. Devario aequipinnatus has a wide distribution in northern India and Bangladesh. Devario coxi, from southeastern Bangladesh near Cox's Bazar, differs from D. aequipinnatus in mtDNA (COI, p-distance 1.8%), colouration, proportional measurements, and meristics. The minor morphological differences and low frequency of overlapping meristics suggest relatively recent separation of D. coxi from other D. aequipinnatus. Devario anomalus occurs only in southeastern Bangladesh and is here reported from localities in addition to the type locality. It differs from the similar D. xyrops in adjacent Myanmar by slender body shape and by 2.3% p-distance in the COI gene. Specimens of D. anomalus from the Sangu River were found to have the mitochondrial genome of D. aequipinnatus from Bangladesh, but agree with other D. anomalus in the nuclear RAG1 gene. Devario devario has a wide distribution on the Indian Peninsula and border regions; in Bangladesh it is restricted in distribution to the Ganga, Brahmaputra, and Meghna drainages. Reports of D. assamensis and D. malabaricus from Bangladesh are misidentifications. Perilampus ostreographus M'Clelland, 1839, is tentatively synonymized with D. aequipinnatus. Phylogenetic analysis of 14 species of striped devarios based on the COI gene results in a polytomy with four unresolved clades. Devario deruptotalea from the Chindwin basin is the sister group of D. aequipinnatus+D. coxi. Devario devario is the sistergroup of D. xyrops+D. anomalus.
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Affiliation(s)
- Sven O. Kullander
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Michael Norén
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
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60
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McMenamin S, Carter C, Cooper WJ. Thyroid Hormone Stimulates the Onset of Adult Feeding Kinematics in Zebrafish. Zebrafish 2017; 14:517-525. [PMID: 28933679 DOI: 10.1089/zeb.2017.1453] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The physical demands for swimming and feeding change dramatically over the course of development for many aquatic animals. Indeed, in teleosts, the transition from larva to adult involves major shifts in both trophic morphology and feeding behavior. A spike in thyroid hormone (TH) coordinates many developmental processes that occur during this adult transition in numerous vertebrate species. Using mutant and transgenic zebrafish, we tested the hypothesis that TH is essential for the transition from larval to adult feeding kinematic profiles. We found that every measured kinematic variable that distinguished larvae from adults also differentiated hypothyroid from wild-type (WT) euthyroid adults, suggesting that TH is indeed necessary for the onset of mature feeding behaviors. In contrast, feeding kinematics in hyperthyroid adults were extremely similar to those measured in euthyroid adults. Altered TH signaling underlies pedomorphosis in some amphibian species, and Danionella is a pedomorphic danionin genus. We therefore tested whether feeding kinematics of adult Danionella would more closely match larval zebrafish (and hypothyroid adults) than WT adult zebrafish. We found Danionella feeding kinematics resemble those of larval (and hypothyroid) zebrafish in multiple respects. Overall, we conclude that TH is essential in stimulating the onset of adult feeding kinematics in zebrafish, and that some of the underlying developmental pathways may have been lost in Danionella.
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Affiliation(s)
- Sarah McMenamin
- 1 Biology Department, Boston College , Chestnut Hill, Massachusetts
| | - Casey Carter
- 2 School of Biological Sciences, Washington State University Tri-cities , Richland, Washington
| | - Wiliam James Cooper
- 2 School of Biological Sciences, Washington State University Tri-cities , Richland, Washington
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61
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Hirt MV, Arratia G, Chen WJ, Mayden RL, Tang KL, Wood RM, Simons AM. Effects of gene choice, base composition and rate heterogeneity on inference and estimates of divergence times in cypriniform fishes. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- M. Vincent Hirt
- University of Minnesota, Ecology, Evolution, and Behavior Graduate Program, St. Paul, MN 55108, USA
- University of Minnesota, Bell Museum of Natural History, Minneapolis, MN 55455, USA
| | - Gloria Arratia
- Biodiversity Research Center, University of Kansas, Lawrence, KS 66045, USA
| | - Wei-Jen Chen
- National Taiwan University, Institute of Oceanography, Taipei 10617, Taiwan
| | - Richard L. Mayden
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Kevin L. Tang
- Department of Biology, University of Michigan-Flint, Flint, MI 48502, USA
| | - Robert M. Wood
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Andrew M. Simons
- University of Minnesota, Bell Museum of Natural History, Minneapolis, MN 55455, USA
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, MN 55108, USA
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62
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Sungani H, Ngatunga BP, Koblmüller S, Mäkinen T, Skelton PH, Genner MJ. Multiple colonisations of the Lake Malawi catchment by the genus Opsaridium (Teleostei: Cyprinidae). Mol Phylogenet Evol 2017; 107:256-265. [DOI: 10.1016/j.ympev.2016.09.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 09/13/2016] [Accepted: 09/29/2016] [Indexed: 01/19/2023]
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63
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Riddin MA, Bills IR, Villet MH. Phylogeographic, morphometric and taxonomic re-evaluation of the river sardine, Mesobola brevianalis (Boulenger, 1908) (Teleostei, Cyprinidae, Chedrini). Zookeys 2016:121-150. [PMID: 28138294 PMCID: PMC5240351 DOI: 10.3897/zookeys.641.10434] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/08/2016] [Indexed: 11/29/2022] Open
Abstract
The river sardine, Mesobolabrevianalis (Boulenger, 1908), is the type species of Mesobola Howes, 1984. Standard phylogenetic analyses of partial sequences of the cytochrome oxidase I gene of individuals from populations across southern Africa that are currently identified as Mesobolabrevianalis showed that these populations represent four genetically distinct allopatric lineages. Furthermore, Engraulicyprissardella (Günther, 1868), the type species of Engraulicypris Günther, 1894, was convincingly nested amongst these clades. These findings support synonymisation of Engraulicypris and Mesobolasyn. n.; restoration of Engraulicyprisgariepinus (Barnard, 1943), stat. rev. for the lower Orange River population; description of two new species, Engraulicyprisngalalasp. n. and Engraulicyprishowesisp. n. from the Rovuma and Kunene river systems, respectively; affirmation of the synonymy of Engraulicyprisbrevianalis (Boulenger, 1908), comb. n. sensu stricto and Engraulicypriswhitei van der Horst, 1934; and restoration of Engraulicyprisbredoi Poll, 1945, stat. rev. and Engraulicyprisspinifer Bailey & Matthes, 1971, stat. rev. from Mesobola. Discriminant function analysis of a truss network of five traditional morphometric measurements and 21 morphometric measurements that characterised the shape of the fishes was used to seek morphological markers for the genetically distinct populations. Only Engraulicyprisgariepinus was morphometrically distinctive, but live colouration differed between the lineages. Detailed taxonomic descriptions and an identification key for the species are provided.
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Affiliation(s)
- Megan A Riddin
- Department of Zoology & Entomology, Rhodes University, African Street, PO Box 94, Grahamstown, 6140 South Africa
| | - I Roger Bills
- South African Institute for Aquatic Biodiversity, Somerset Street, Grahamstown, 6140 South Africa
| | - Martin H Villet
- Department of Zoology & Entomology, Rhodes University, African Street, PO Box 94, Grahamstown, 6140 South Africa
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64
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Molecular phylogeny and historical biogeography of the Indonesian freshwater fish Rasbora lateristriata species complex (Actinopterygii: Cyprinidae): Cryptic species and west-to-east divergences. Mol Phylogenet Evol 2016; 105:212-223. [DOI: 10.1016/j.ympev.2016.08.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/27/2016] [Accepted: 08/22/2016] [Indexed: 12/19/2022]
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65
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Kenthao A, Wangsomnuk PP, Jearranaiprepame P. Genetic variations and population structure in three populations of beardless barb, Cyclocheilichthys apogon (Valenciennes, 1842) inferred from mitochondrial cytochrome b sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:82-90. [PMID: 27838941 DOI: 10.1080/24701394.2016.1242581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
This study aimed to investigate the relation of dispersal barrier and genetic diversity, population structure, and demographic history of 46 samples of beardless barb, Cyclocheilichthys apogon (Valenciennes, 1842) collected from three different locations in North-eastern Thailand. The analysis of molecular variance (AMOVA) was employed in order to determine the genetic variability within and among populations of this fish. The neutrality tests and mismatch distribution analysis were additionally applied to assess the neutrality and demographic expansion of the populations, respectively. Contiguous sequences within range from 1100 to1140 bp were obtained with varying 16 different haplotypes with high-haplotype diversity (0.8773 ± 0.0327) and low-nucleotide diversity (0.00215 ± 0.00020). The variations within and among populations accounted for 98.98 and 1.02% of the total variation, respectively. The low level of pairwise Fst estimations indicated a possible gene flow among populations and a suggestion of genetic homogeneity at this geographical range. A supportive idea of having a single-maternal lineage and past demographic expansion or selection experiencing has distinctly appeared among these populations. The current data suggests that all three populations distinctly exist as a single stock unit and that is an important factor in identifying genetic variation of C. apogon in this geographical area to be used in establishing effective plans and strategies for a conservation and management.
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Affiliation(s)
- Anan Kenthao
- a Department of Biology, Faculty of Science , Khon Kaen University , Khon Kaen , Thailand
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66
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Stout CC, Tan M, Lemmon AR, Lemmon EM, Armbruster JW. Resolving Cypriniformes relationships using an anchored enrichment approach. BMC Evol Biol 2016; 16:244. [PMID: 27829363 PMCID: PMC5103605 DOI: 10.1186/s12862-016-0819-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp). RESULTS Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae. CONCLUSIONS Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.
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Affiliation(s)
- Carla C. Stout
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Milton Tan
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306 USA
| | - Emily Moriarty Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306 USA
| | - Jonathan W. Armbruster
- Department of Biological Sciences, Auburn University, 101 Rouse Life Sciences Building, Auburn, AL 36849 USA
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67
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Ebach MC, Michael MS. From Correlation to Causation: What Do We Need in the Historical Sciences? Acta Biotheor 2016; 64:241-62. [PMID: 27364751 DOI: 10.1007/s10441-016-9282-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 06/19/2016] [Indexed: 10/21/2022]
Abstract
Changes in the methodology of the historical sciences make them more vulnerable to unjustifiable speculations being passed off as scientific results. The integrity of historical science is in peril due the way speculative and often unexamined causal assumptions are being used to generate data and underpin the identification of correlations in such data. A step toward a solution is to distinguish between plausible and speculative assumptions that facilitate the inference from measured and observed data to causal claims. One way to do that is by comparing these assumptions against a well-attested set of aspects of causation, such as the so-called "Bradford Hill Criteria" (BHC). The BHC do not provide a test for causation or necessary and sufficient conditions for causation but do indicate grounds for further investigation. By revising the BHC to reflect the needs and focus of historical sciences, it will be possible to assess the cogency of methods of investigation. These will be the Historical Sciences Bradford Hill Criteria (HSBHC). An application to one area in historical science is used to demonstrate the effectiveness of the HSBHC, namely biogeography. Four methods are assessed in order to show how the HSBHC can be used to examine the assumptions between our data and the causal biogeographical processes we infer.
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68
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Tingström O, Wesula Lwande O, Näslund J, Spyckerelle I, Engdahl C, Von Schoenberg P, Ahlm C, Evander M, Bucht G. Detection of Sindbis and Inkoo Virus RNA in Genetically Typed Mosquito Larvae Sampled in Northern Sweden. Vector Borne Zoonotic Dis 2016; 16:461-7. [PMID: 27159120 PMCID: PMC4931352 DOI: 10.1089/vbz.2016.1940] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Introduction: Mosquito-borne viruses have a widespread distribution across the globe and are known to pose serious threats to human and animal health. The maintenance and dissemination of these viruses in nature are driven through horizontal and vertical transmission. In the temperate climate of northern Sweden, there is a dearth of knowledge on whether mosquito-borne viruses that occur are transmitted transovarially. To gain a better understanding of mosquito-borne virus circulation and maintenance, mosquito larvae were sampled in northern Sweden during the first and second year after a large outbreak of Ockelbo disease in 2013 caused by Sindbis virus (SINV). Materials and Methods: A total of 3123 larvae were sampled during the summers of 2014 and 2015 at multiple sites in northern Sweden. The larvae were homogenized and screened for viruses using RT-PCR and sequencing. Species identification of selected larvae was performed by genetic barcoding targeting the cytochrome C oxidase subunit I gene. Results and Discussion: SINV RNA was detected in mosquito larvae of three different species, Ochlerotatus (Oc.) communis, Oc. punctor, and Oc. diantaeus. Inkoo virus (INKV) RNA was detected in Oc. communis larvae. This finding suggested that these mosquitoes could support transovarial transmission of SINV and INKV. Detection of virus in mosquito larva may serve as an early warning for emerging arboviral diseases and add information to epidemiological investigations before, during, and after outbreaks. Furthermore, our results demonstrated the relevance of genetic barcoding as an attractive and effective method for mosquito larva typing. However, further mosquito transmission studies are needed to ascertain the possible role of different mosquito species and developmental stages in the transmission cycle of arboviruses.
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Affiliation(s)
- Olov Tingström
- 1 Swedish Defence Research Agency , CBRN Defence and Security, Umeå, Sweden .,2 Department of Clinical Microbiology, Virology, Umeå University , Umeå, Sweden .,3 Department of Clinical Microbiology, Infectious Diseases, Umeå University , Umeå, Sweden
| | | | - Jonas Näslund
- 1 Swedish Defence Research Agency , CBRN Defence and Security, Umeå, Sweden
| | - Iris Spyckerelle
- 2 Department of Clinical Microbiology, Virology, Umeå University , Umeå, Sweden .,3 Department of Clinical Microbiology, Infectious Diseases, Umeå University , Umeå, Sweden
| | - Cecilia Engdahl
- 1 Swedish Defence Research Agency , CBRN Defence and Security, Umeå, Sweden
| | | | - Clas Ahlm
- 3 Department of Clinical Microbiology, Infectious Diseases, Umeå University , Umeå, Sweden
| | - Magnus Evander
- 2 Department of Clinical Microbiology, Virology, Umeå University , Umeå, Sweden
| | - Göran Bucht
- 1 Swedish Defence Research Agency , CBRN Defence and Security, Umeå, Sweden
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69
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Daane JM, Rohner N, Konstantinidis P, Djuranovic S, Harris MP. Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies. Mol Biol Evol 2015; 33:162-73. [PMID: 26452532 DOI: 10.1093/molbev/msv208] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The identification of genetic mechanisms underlying evolutionary change is critical to our understanding of natural diversity, but is presently limited by the lack of genetic and genomic resources for most species. Here, we present a new comparative genomic approach that can be applied to a broad taxonomic sampling of nonmodel species to investigate the genetic basis of evolutionary change. Using our analysis pipeline, we show that duplication and divergence of fgfr1a is correlated with the reduction of scales within fishes of the genus Phoxinellus. As a parallel genetic mechanism is observed in scale-reduction within independent lineages of cypriniforms, our finding exposes significant developmental constraint guiding morphological evolution. In addition, we identified fixed variation in fgf20a within Phoxinellus and demonstrated that combinatorial loss-of-function of fgfr1a and fgf20a within zebrafish phenocopies the evolved scalation pattern. Together, these findings reveal epistatic interactions between fgfr1a and fgf20a as a developmental mechanism regulating skeletal variation among fishes.
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Affiliation(s)
- Jacob M Daane
- Department of Genetics, Harvard Medical School, Boston, MA Department of Orthopaedic Research, Boston Children's Hospital, Boston, MA
| | - Nicolas Rohner
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Peter Konstantinidis
- Department of Fisheries Science, Virginia Institute of Marine Science, Gloucester Point, VA
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University, Saint Louis
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, MA Department of Orthopaedic Research, Boston Children's Hospital, Boston, MA
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70
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Kusuma WE, Kumazawa Y. Complete mitochondrial genome sequences of two Indonesian rasboras (Rasbora aprotaenia and Rasbora lateristriata). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4222-4223. [PMID: 26061337 DOI: 10.3109/19401736.2015.1022749] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Complete mitochondrial genome sequences were determined for two Indonesian freshwater fishes, Rasbora aprotaenia and Rasbora lateristriata. These genomes are 16,541 bp and 16,539 bp in length, respectively and encode 37 genes in the typical vertebrate gene arrangement. Phylogenetic analyses supported a view that these species are very closely related to each other.
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Affiliation(s)
- Wahyu Endra Kusuma
- a Department of Information and Biological Sciences and Research Center for Biological Diversity , Graduate School of Natural Sciences, Nagoya City University , Nagoya , Japan and.,b Department of Aquaculture, Faculty of Fisheries and Marine Science , University of Brawijaya Indonesia
| | - Yoshinori Kumazawa
- a Department of Information and Biological Sciences and Research Center for Biological Diversity , Graduate School of Natural Sciences, Nagoya City University , Nagoya , Japan and
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71
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Parichy DM. Advancing biology through a deeper understanding of zebrafish ecology and evolution. eLife 2015; 4:e05635. [PMID: 25807087 PMCID: PMC4373672 DOI: 10.7554/elife.05635] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/06/2015] [Indexed: 01/02/2023] Open
Abstract
Over the last two decades, the zebrafish has joined the ranks of premier model organisms for biomedical research, with a full suite of tools and genomic resources. Yet we still know comparatively little about its natural history. Here I review what is known about the natural history of the zebrafish, where significant gaps in our knowledge remain, and how a fuller appreciation of this organism's ecology and behavior, population genetics, and phylogeny can inform a variety of research endeavors.
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Affiliation(s)
- David M Parichy
- Department of Biology, University of Washington, Seattle, United States
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72
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Ahnelt H, Herdina AN, Metscher BD. Unusual pharyngeal dentition in the African Chedrin fishes (Teleostei: Cyprinindae): Significance for phylogeny and character evolution. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2015.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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73
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Hubert N, Kadarusman, Wibowo A, Busson F, Caruso D, Sulandari S, Nafiqoh N, Pouyaud L, Rüber L, Avarre JC, Herder F, Hanner R, Keith P, Hadiaty RK. DNA Barcoding Indonesian freshwater fishes: challenges and prospects. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/dna-2015-0018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractWith 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.
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74
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Conway KW, Britz R, Shrestha J, Manimekalan A, Rüber L. Molecular systematics of the Asian torrent minnows (Ostariophysi: Psilorhynchidae) inferred from nuclear and mitochondrial DNA sequence data. J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin W. Conway
- Department of Wildlife and Fisheries Sciences and Biodiversity Research and Teaching Collections; Texas A&M University; College Station TX USA
| | - Ralf Britz
- Department of Zoology; The Natural History Museum; London UK
| | - Jiwan Shrestha
- Nepal Academy for Science and Technology (NAST); Khumaltar; Lalitpur Kathmandu Nepal
| | | | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern; Bern Switzerland
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75
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Zhang J, Zhou C, Fei W, Ma L, Kong X. Complete mitochondrial genome of Danio myersi (Teleostei: Cypriniformes: Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:3913-3914. [PMID: 25484168 DOI: 10.3109/19401736.2014.987262] [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: 11/13/2022]
Abstract
The complete mitochondrial genome (mitogenome) of Danio myersi (Teleostei: Cypriniformes: Cyprinidae) has been sequenced, and it is a circular molecule of 16,565 bp in length and contains the typical complement of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 12 non-coding regions. The order and orientation of the genes are identical to the typical arrangement in vertebrates, and most of the genes were encoded on the H-strand except for ND6 and eight tRNA genes. The AT content of the overall base composition of H-strand is 63.4% (T, 26.8%; C, 25.3%; A, 31.6%; G, 16.4%) and the length of control region is 925 bp with 65.5% AT content. The mitogenome sequenced in the present study will be an important step forward in completely resolving phylogenetic relationships of the subfamily Danioninae in the future.
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Affiliation(s)
- Jie Zhang
- a College of Life Science and.,b College of Fisheries, Henan Normal University , Xinxiang , Henan Province , China
| | - Chuanjiang Zhou
- b College of Fisheries, Henan Normal University , Xinxiang , Henan Province , China
| | - Wei Fei
- a College of Life Science and.,b College of Fisheries, Henan Normal University , Xinxiang , Henan Province , China
| | - Longyang Ma
- a College of Life Science and.,b College of Fisheries, Henan Normal University , Xinxiang , Henan Province , China
| | - Xianghui Kong
- b College of Fisheries, Henan Normal University , Xinxiang , Henan Province , China
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76
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McCluskey BM, Postlethwait JH. Phylogeny of zebrafish, a "model species," within Danio, a "model genus". Mol Biol Evol 2014; 32:635-52. [PMID: 25415969 DOI: 10.1093/molbev/msu325] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Zebrafish (Danio rerio) is an important model for vertebrate development, genomics, physiology, behavior, toxicology, and disease. Additionally, work on numerous Danio species is elucidating evolutionary mechanisms for morphological development. Yet, the relationships of zebrafish and its closest relatives remain unclear possibly due to incomplete lineage sorting, speciation with gene flow, and interspecies hybridization. To clarify these relationships, we first constructed phylogenomic data sets from 30,801 restriction-associated DNA (RAD)-tag loci (483,026 variable positions) with clear orthology to a single location in the sequenced zebrafish genome. We then inferred a well-supported species tree for Danio and tested for gene flow during the diversification of the genus. An approach independent of the sequenced zebrafish genome verified all inferred relationships. Although identification of the sister taxon to zebrafish has been contentious, multiple RAD-tag data sets and several analytical methods provided strong evidence for Danio aesculapii as the most closely related extant zebrafish relative studied to date. Data also displayed patterns consistent with gene flow during speciation and postspeciation introgression in the lineage leading to zebrafish. The incorporation of biogeographic data with phylogenomic analyses put these relationships in a phylogeographic context and supplied additional support for D. aesculapii as the sister species to D. rerio. The clear resolution of this study establishes a framework for investigating the evolutionary biology of Danio and the heterogeneity of genome evolution in the recent history of a model organism within an emerging model genus for genetics, development, and evolution.
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77
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Patterson LB, Bain EJ, Parichy DM. Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution. Nat Commun 2014; 5:5299. [PMID: 25374113 PMCID: PMC4224114 DOI: 10.1038/ncomms6299] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/18/2014] [Indexed: 01/22/2023] Open
Abstract
Fishes have diverse pigment patterns, yet mechanisms of pattern evolution remain poorly understood. In zebrafish, Danio rerio, pigment-cell autonomous interactions generate dark stripes of melanophores that alternate with light interstripes of xanthophores and iridophores. Here, we identify mechanisms underlying the evolution of a uniform pattern in D. albolineatus in which all three pigment cell classes are intermingled. We show that in this species xanthophores differentiate precociously over a wider area, and that cis regulatory evolution has increased expression of xanthogenic Colony Stimulating Factor-1 (Csf1). Expressing Csf1 similarly in D. rerio has cascading effects, driving the intermingling of all three pigment cell classes and resulting in the loss of stripes, as in D. albolineatus. Our results identify novel mechanisms of pattern development and illustrate how pattern diversity can be generated when a core network of pigment-cell autonomous interactions is coupled with changes in pigment cell differentiation.
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Affiliation(s)
- Larissa B Patterson
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
| | - Emily J Bain
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
| | - David M Parichy
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
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78
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Britz R, Conway KW, Rüber L. Miniatures, morphology and molecules: Paedocypris and its phylogenetic position (Teleostei, Cypriniformes). Zool J Linn Soc 2014. [DOI: 10.1111/zoj12184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ralf Britz
- Department of Zoology, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Kevin W. Conway
- Department of Wildlife and Fisheries Sciences and Biodiversity Research and Teaching Collections, Texas A&M University, College Station, TX, 77843, USA
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005, Bern, Switzerland
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79
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Britz R, Conway KW, Rüber L. Miniatures, morphology and molecules:Paedocyprisand its phylogenetic position (Teleostei, Cypriniformes). Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12184] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ralf Britz
- Department of Zoology; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Kevin W. Conway
- Department of Wildlife and Fisheries Sciences and Biodiversity Research and Teaching Collections; Texas A&M University; College Station TX 77843 USA
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern; Bernastrasse 15 3005 Bern Switzerland
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80
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Abstract
Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RAD-tag population genomics to identify sex-linked polymorphisms. After verifying this "RAD-sex" method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, "male genotypes" became males and some "female genotypes" also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture.
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81
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Chang CH, Li F, Shao KT, Lin YS, Morosawa T, Kim S, Koo H, Kim W, Lee JS, He S, Smith C, Reichard M, Miya M, Sado T, Uehara K, Lavoué S, Chen WJ, Mayden RL. Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: evidence for necessary taxonomic revision in the family and the identification of cryptic species. Mol Phylogenet Evol 2014; 81:182-94. [PMID: 25238947 DOI: 10.1016/j.ympev.2014.08.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 10/24/2022]
Abstract
Bitterlings are relatively small cypriniform species and extremely interesting evolutionarily due to their unusual reproductive behaviors and their coevolutionary relationships with freshwater mussels. As a group, they have attracted a great deal of attention in biological studies. Understanding the origin and evolution of their mating system demands a well-corroborated hypothesis of their evolutionary relationships. In this study, we provide the most comprehensive phylogenetic reconstruction of species relationships of the group based on partitioned maximum likelihood and Bayesian methods using DNA sequence variation of nuclear and mitochondrial genes on 41 species, several subspecies and three undescribed species. Our findings support the monophyly of the Acheilognathidae. Two of the three currently recognized genera are not monophyletic and the family can be subdivided into six clades. These clades are further regarded as genera based on both their phylogenetic relationships and a reappraisal of morphological characters. We present a revised classification for the Acheilognathidae with five genera/lineages: Rhodeus, Acheilognathus (new constitution), Tanakia (new constitution), Paratanakia gen. nov., and Pseudorhodeus gen. nov. and an unnamed clade containing five species currently referred to as "Acheilognathus". Gene trees of several bitterling species indicate that the taxa are not monophyletic. This result highlights a potentially dramatic underestimation of species diversity in this family. Using our new phylogenetic framework, we discuss the evolution of the Acheilognathidae relative to classification, taxonomy and biogeography.
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Affiliation(s)
- Chia-Hao Chang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan; Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Fan Li
- Department of Oceanography, National Sun Yet-sen University, Kaohsiung 80424, Taiwan; Institute of Biodiversity Science, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai 200433, China
| | - Kwang-Tsao Shao
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yeong-Shin Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan; Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan
| | | | - Sungmin Kim
- School of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Hyeyoung Koo
- Department of Biological Science, Sangji University, Wonju 220-702, Republic of Korea
| | - Won Kim
- School of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Carl Smith
- School of Biology, University of St Andrews, St Andrews, Fife KY16 8LB, UK; Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
| | - Martin Reichard
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65 Brno, Czech Republic
| | - Masaki Miya
- Natural History Museum & Institute, Chiba 260-8682, Japan
| | - Tetsuya Sado
- Natural History Museum & Institute, Chiba 260-8682, Japan
| | - Kazuhiko Uehara
- Aquatic Life Conservation Research Center, Research Institute of Environment, Agriculture and Fisheries, Osaka 572-0088, Japan
| | - Sébastien Lavoué
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan.
| | - Richard L Mayden
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
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82
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Chen IS, Tsai WL, Huang SP, Chen HM. The complete mitochondrial genome of Temminck's minnow Nipponocypris temminckii (Cypriniformes, Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1542-4. [PMID: 25162706 DOI: 10.3109/19401736.2014.953129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Temminck's minnow Nipponocypris temminckii (Temminck & Schlegel, 1846) which is endemic to Japan and Korean Peninsula has been amplified and sequenced in this study. The complete mitochondrial genome is 16,618 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region (CR) and 1 light-strand replication origin (OL). The overall base composition of N. temminckii is 30.5% for A, 26.5% for T, 26.4% for C, 16.6% for G, with higher AT content 57.0%. This study will be rather beneficial for understanding the phylogenetic approach of Nipponocypris species and other related genera of cyprinid fishes.
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Affiliation(s)
- I-Shiung Chen
- a Institute of Marine Biology, National Taiwan Ocean University , Keelung , Taiwan , ROC and
| | - Wei-Lun Tsai
- a Institute of Marine Biology, National Taiwan Ocean University , Keelung , Taiwan , ROC and.,b Department of Aquaculture , National Taiwan Ocean University , Keelung , Taiwan , ROC
| | - Shih-Pin Huang
- a Institute of Marine Biology, National Taiwan Ocean University , Keelung , Taiwan , ROC and
| | - Hong-Ming Chen
- b Department of Aquaculture , National Taiwan Ocean University , Keelung , Taiwan , ROC
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83
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Chen IS, Liu GD, Shen CN, Prokofiev AM. The complete mitochondrial genome of altai osman Oreoleuciscus humilis Warpachowski (Cypriniformes, Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:953-5. [PMID: 24963765 DOI: 10.3109/19401736.2014.926502] [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: 11/13/2022]
Abstract
The complete mitochondrial genome of altai osman Oreoleuciscus humilis Warpachowski collected from Mongolia has been amplified and sequenced in this study. The complete mitochondrial genome is 16,606 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region (CR) and 1 light-strand replication origin (OL). The overall base composition of Oreoleuciscus humilis is 27.6% for A, 26.4% for T, 27.2% for C, 18.8% for G, with higher AT content 54.0%. This study will be rather beneficial for understanding the phylogenetic approach of Oreoleuciscus species and other related genera of cyprinid fishes.
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Affiliation(s)
- I-Shiung Chen
- a Institute of Marine Biology, National Taiwan Ocean University , Keelung , Taiwan
| | - Guo-Di Liu
- a Institute of Marine Biology, National Taiwan Ocean University , Keelung , Taiwan .,b School of Marine Science, Ningbo University, Ningbo , Zhejiang , PR China
| | - Chia-Ning Shen
- c Genomic Research Center, Academia Sinica , Taipei , Taiwan , and
| | - Artem M Prokofiev
- d Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences , Moscow , Russia
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84
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Chen IS, Liu YW, Huang SP, Shen CN. The complete mitochondrial genome of the Korean minnow Nipponocypris koreanus (Cypriniformes, Cyprinidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:708-10. [PMID: 24779599 DOI: 10.3109/19401736.2014.913153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the Korean minnow Nipponocypris koreanus (Kim et al., 2005) which is endemic to Korean Peninsula has been amplified and sequenced in this study. The complete mitochondrial genome is 16,615 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region (CR) and 1 light-strand replication origin (OL). The overall base composition of N. koreanus is 30.0% for A, 26.8% for T, 26.1% for C, 17.1% for G, with higher AT content 56.8%. This study will be rather beneficial for understanding the phylogenetic approach of Nipponocypris species and other related genera of cyprinid fishes.
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Affiliation(s)
| | - Yu-Wei Liu
- b Institute of Aquaculture, National Taiwan Ocean University , Keelung , Taiwan , ROC , and
| | | | - Chia-Ning Shen
- c Genomic Research Center, Academia Sinica , Taipei , Taiwan , ROC
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85
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Cheng P, Yu D, Liu S, Tang Q, Liu H. Molecular Phylogeny and Conservation Priorities of the Subfamily Acheilognathinae (Teleostei: Cyprinidae). Zoolog Sci 2014; 31:300-8. [DOI: 10.2108/zs130069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Peilin Cheng
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, P. R. China
| | - Dan Yu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, P. R. China
| | - Siqing Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, P. R. China
| | - Qiongying Tang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, P. R. China
| | - Huanzhang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, P. R. China
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86
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Engdahl C, Larsson P, Näslund J, Bravo M, Evander M, Lundström JO, Ahlm C, Bucht G. Identification of Swedish mosquitoes based on molecular barcoding of the COI gene and SNP analysis. Mol Ecol Resour 2013; 14:478-88. [PMID: 24215491 DOI: 10.1111/1755-0998.12202] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/30/2013] [Accepted: 10/30/2013] [Indexed: 11/30/2022]
Abstract
Mosquito-borne infectious diseases are emerging in many regions of the world. Consequently, surveillance of mosquitoes and concomitant infectious agents is of great importance for prediction and prevention of mosquito-borne infectious diseases. Currently, morphological identification of mosquitoes is the traditional procedure. However, sequencing of specified genes or standard genomic regions, DNA barcoding, has recently been suggested as a global standard for identification and classification of many different species. Our aim was to develop a genetic method to identify mosquitoes and to study their relationship. Mosquitoes were captured at collection sites in northern Sweden and identified morphologically before the cytochrome c oxidase subunit I (COI) gene sequences of 14 of the most common mosquito species were determined. The sequences obtained were then used for phylogenetic placement, for validation and benchmarking of phenetic classifications and finally to develop a hierarchical PCR-based typing scheme based on single nucleotide polymorphism sites (SNPs) to enable rapid genetic identification, circumventing the need for morphological characterization. The results showed that exact phylogenetic relationships between mosquito taxa were preserved at shorter evolutionary distances, but at deeper levels, they could not be inferred with confidence using COI gene sequence data alone. Fourteen of the most common mosquito species in Sweden were identified by the SNP/PCR-based typing scheme, demonstrating that genetic typing using SNPs of the COI gene is a useful method for identification of mosquitoes with potential for worldwide application.
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Affiliation(s)
- Cecilia Engdahl
- Swedish Defense Research Agency, CBRN Defense and Security, Umeå, SE-901 82, Sweden; Department of Clinical Microbiology, Virology, Umeå University, Umeå, SE-901 85, Sweden; Department of Clinical Microbiology, Infectious Diseases, Umeå University, Umeå, SE-901 85, Sweden
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87
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Koizumi N, Morioka S, Mori A, Vongvichith B, Shibukawa K, Nishida K, Watabe K, Takemura T. Characterization of twenty-four polymorphic microsatellite loci of Rasbora borapetensis. CONSERV GENET RESOUR 2013. [DOI: 10.1007/s12686-013-9888-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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88
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Froehlich JM, Fowler ZG, Galt NJ, Smith DL, Biga PR. Sarcopenia and piscines: the case for indeterminate-growing fish as unique genetic model organisms in aging and longevity research. Front Genet 2013; 4:159. [PMID: 23967015 PMCID: PMC3743216 DOI: 10.3389/fgene.2013.00159] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 07/30/2013] [Indexed: 01/07/2023] Open
Abstract
Sarcopenia and dynapenia pose significant problems for the aged, especially as life expectancy rises in developed countries. Current therapies are marginally efficacious at best, and barriers to breakthroughs in treatment may result from currently employed model organisms. Here, we argue that the use of indeterminate-growing teleost fish in skeletal muscle aging research may lead to therapeutic advancements not possible with current mammalian models. Evidence from a comparative approach utilizing the subfamily Danioninae suggests that the indeterminate growth paradigm of many teleosts arises from adult muscle stem cells with greater proliferative capacity, even in spite of smaller progenitor populations. We hypothesize that paired-box transcription factors, Pax3/7, are involved with this enhanced self-renewal and that prolonged expression of these factors may allow some fish species to escape, or at least forestall, sarcopenia/dynapenia. Future research efforts should focus on the experimental validation of these genes as key factors in indeterminate growth, both in the context of muscle stem cell proliferation and in prevention of skeletal muscle senescence.
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Affiliation(s)
- Jacob M Froehlich
- Department of Biology, University of Alabama at Birmingham Birmingham, AL, USA
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89
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Soylemez O, Kondrashov FA. Estimating the rate of irreversibility in protein evolution. Genome Biol Evol 2013; 4:1213-22. [PMID: 23132897 PMCID: PMC3542581 DOI: 10.1093/gbe/evs096] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Whether or not evolutionary change is inherently irreversible remains a controversial
topic. Some examples of evolutionary irreversibility are known; however, this question has
not been comprehensively addressed at the molecular level. Here, we use data from 221
human genes with known pathogenic mutations to estimate the rate of irreversibility in
protein evolution. For these genes, we reconstruct ancestral amino acid sequences along
the mammalian phylogeny and identify ancestral amino acid states that match known
pathogenic mutations. Such cases represent inherent evolutionary irreversibility because,
at the present moment, reversals to these ancestral amino acid states are impossible for
the human lineage. We estimate that approximately 10% of all amino acid
substitutions along the mammalian phylogeny are irreversible, such that a return to the
ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes
with high rates of irreversibility, as much as 40% of all amino acid evolution was
estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral
phenotypes, the molecular nature of the high rate of irreversibility in proteins is best
explained by evolution with a high prevalence of compensatory, epistatic interactions
between amino acid sites. Under such mode of protein evolution, once an amino acid
substitution is fixed, the probability of its reversal declines as the protein sequence
accumulates changes that affect the phenotypic manifestation of the ancestral state. The
prevalence of epistasis in evolution indicates that the observed high rate of
irreversibility in protein evolution is an inherent property of protein structure and
function.
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Affiliation(s)
- Onuralp Soylemez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain
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90
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Froehlich JM, Galt NJ, Charging MJ, Meyer BM, Biga PR. In vitro indeterminate teleost myogenesis appears to be dependent on Pax3. In Vitro Cell Dev Biol Anim 2013; 49:371-85. [PMID: 23613306 DOI: 10.1007/s11626-013-9616-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 04/03/2013] [Indexed: 02/06/2023]
Abstract
The zebrafish (Danio rerio) has been used extensively as a model system for developmental studies but, unlike most teleost fish, it grows in a determinate-like manner. A close relative, the giant danio (Devario cf. aequipinnatus), grows indeterminately, displaying both hyperplasia and hypertrophy of skeletal myofibers as an adult. To better understand adult muscle hyperplasia, a postlarval/postnatal process that closely resembles secondary myogenesis during development, we characterized the expression of Pax3/7, c-Met, syndecan-4, Myf5, MyoD1, myogenin, and myostatin during in vitro myogenesis, a technique that allows for the complete progression of myogenic precursor cells to myotubes. Pax7 appears to be expressed only in newly activated MPCs while Pax3 is expressed through most of the myogenic program, as are c-Met and syndecan-4. MyoD1 appears important in all stages of myogenesis, while Myf5 is likely expressed at low to background levels, and myogenin expression is enriched in myotubes. Myostatin, like MyoD1, appears to be ubiquitous at all stages. This is the first comprehensive report of key myogenic factor expression patterns in an indeterminate teleost, one that strongly suggests that Pax3 and/or Myf5 may be involved in the regulation of this paradigm. Further, it validates this species as a model organism for studying adult myogenesis in vitro, especially mechanisms underlying nascent myofiber recruitment.
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91
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Tang KL, Lumbantobing DN, Mayden RL. The Phylogenetic Placement ofOxygastervan Hasselt, 1823 (Teleostei: Cypriniformes: Cyprinidae) and the Taxonomic Status of the Family-Group Name Oxygastrinae Bleeker, 1860. COPEIA 2013. [DOI: 10.1643/cg-10-121] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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92
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Liu QL, Xu BH, Xiao TY, Su JM, Yao YB, Liu YJ. Complete mitochondrial genome of the Xiangjiang barbel chub Squaliobarbus curriculus: comparative analysis of the genetic variation associated with geographical population. MITOCHONDRIAL DNA 2013; 24:654-6. [PMID: 23452330 DOI: 10.3109/19401736.2013.772167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The barbel chub (Squaliobarbus curriculus), a kind of small commercial fish, is widespread in China. In this study, we sequenced the mitochondrial genome of the barbel chub from the Xiangjiang River. The total length of the mitochondrial genome is 16,619 bp, with the base composition of 31.19% A, 25.01% T, 27.68% C, and 16.12% G. The organization and arrangement of these genes are the same as that found in the teleosts, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a major noncoding control region (D-loop region). Compared with the S. curriculus collected from Jiangsu province, there were 29 mutation sites in the mitogenome sequence of Xiangjiang S. curriculus. All the mutation sites were transitions and mainly occurred in protein-coding genes (21/29), two mutation sites occurred in transfer RNA, two occurred in ribosomal RNA, and four occurred in D-loop region. Among the 21 mutation sites in protein-coding genes, 6 mutation sites resulted in amino acid mutation in ND2, ATPase6, COX3, ND4, and Cytb genes, while the others were synonymous substitutions. These results indicated that there was genetic variation in different geographical populations of S. curriculus.
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Affiliation(s)
- Qiao-Lin Liu
- College of Animal Science and Technology, Hunan Agricultural University , Changsha 410128 , People's Republic of China
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93
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Development and characterization of 29 polymorphic microsatellite loci for Esomus metallicus. CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9699-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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94
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Chang CH, Tsai CL, Jang-Liaw NH. Complete mitochondrial genome of the Chinese rasbora Rasbora steineri (Teleostei, Cyprinidae). MITOCHONDRIAL DNA 2012. [PMID: 23194281 DOI: 10.3109/19401736.2012.744977] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We describe the complete mitochondrial genome sequence of the Chinese rasbora, Rasbora steineri, which is a small cyprinid distributed in southeastern Asia. The circle genome (16,530 bp) consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. It has the typical vertebrate mitochondrial gene arrangement.
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Affiliation(s)
- Chia-Hao Chang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan
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95
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Wang X, Gan X, Li J, Mayden RL, He S. Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data: implications for Cyprinidae systematics. SCIENCE CHINA-LIFE SCIENCES 2012; 55:761-73. [DOI: 10.1007/s11427-012-4366-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/16/2012] [Indexed: 11/29/2022]
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96
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LIAO TEYU, KULLANDER SVENO. Phylogenetic significance of the kinethmoid-associated Y-shaped ligament and long intercostal ligaments in the Cypriniformes (Actinopterygii: Ostariophysi). ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00565.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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97
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Yang L, Arunachalam M, Sado T, Levin BA, Golubtsov AS, Freyhof J, Friel JP, Chen WJ, Hirt MV, Manickam R, Agnew MK, Simons AM, Saitoh K, Miya M, Mayden RL, He S. Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes). Mol Phylogenet Evol 2012; 65:362-79. [PMID: 22728909 DOI: 10.1016/j.ympev.2012.06.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 06/12/2012] [Accepted: 06/14/2012] [Indexed: 10/28/2022]
Abstract
The cyprinid tribe Labeonini (sensuRainboth, 1991) is a large group of freshwater fishes containing around 40 genera and 400 species. They are characterized by an amazing diversity of modifications to their lips and associated structures. In this study, a total of 34 genera and 142 species of putative members of this tribe, which represent most of the generic diversity and more than one third of the species diversity of the group, were sampled and sequenced for four nuclear genes and five mitochondrial genes (totaling 9465bp). Phylogenetic relationships and subdivision of this tribe were investigated and the placement and status of most genera are discussed. Partitioned maximum likelihood analyses were performed based on the nuclear dataset, mitochondrial dataset, combined dataset, and the dataset for each nuclear gene. Inclusion of the genera Paracrossochilus, Barbichthys, Thynnichthys, and Linichthys in the Labeonini was either confirmed or proposed for the first time. None of the genera Labeo, Garra, Bangana, Cirrhinus, and Crossocheilus are monophyletic. Taxonomic revisions of some genera were made: the generic names Gymnostomus Heckel, 1843, Ageneiogarra Garman, 1912 and Gonorhynchus McClelland, 1839 were revalidated; Akrokolioplax Zhang and Kottelat, 2006 becomes a junior synonym of Gonorhynchus; the species Osteochilus nashii was found to be a member of the barbin genus Osteochilichthys. Five historical hypotheses on the classification of the Labeonini were tested and rejected. We proposed to subdivide the tribe, which is strongly supported as monophyletic, into four subtribes: Labeoina, Garraina, Osteochilina, and Semilabeoina. The taxa included in each subtribe were listed and those taxa that need taxonomic revision were discussed.
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Affiliation(s)
- Lei Yang
- Department of Biology, Saint Louis University, 3507 Laclede Ave., St. Louis, MO 63103, USA.
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98
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Staab KL, Ferry LA, Hernandez LP. Comparative kinematics of cypriniform premaxillary protrusion. ZOOLOGY 2012; 115:65-77. [DOI: 10.1016/j.zool.2011.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 08/11/2011] [Accepted: 09/26/2011] [Indexed: 01/08/2023]
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99
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Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription. PLoS Genet 2012; 8:e1002585. [PMID: 22479192 PMCID: PMC3315460 DOI: 10.1371/journal.pgen.1002585] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 01/24/2012] [Indexed: 01/01/2023] Open
Abstract
The intestinal microbiota enhances dietary energy harvest leading to increased fat storage in adipose tissues. This effect is caused in part by the microbial suppression of intestinal epithelial expression of a circulating inhibitor of lipoprotein lipase called Angiopoietin-like 4 (Angptl4/Fiaf). To define the cis-regulatory mechanisms underlying intestine-specific and microbial control of Angptl4 transcription, we utilized the zebrafish system in which host regulatory DNA can be rapidly analyzed in a live, transparent, and gnotobiotic vertebrate. We found that zebrafish angptl4 is transcribed in multiple tissues including the liver, pancreatic islet, and intestinal epithelium, which is similar to its mammalian homologs. Zebrafish angptl4 is also specifically suppressed in the intestinal epithelium upon colonization with a microbiota. In vivo transgenic reporter assays identified discrete tissue-specific regulatory modules within angptl4 intron 3 sufficient to drive expression in the liver, pancreatic islet β-cells, or intestinal enterocytes. Comparative sequence analyses and heterologous functional assays of angptl4 intron 3 sequences from 12 teleost fish species revealed differential evolution of the islet and intestinal regulatory modules. High-resolution functional mapping and site-directed mutagenesis defined the minimal set of regulatory sequences required for intestinal activity. Strikingly, the microbiota suppressed the transcriptional activity of the intestine-specific regulatory module similar to the endogenous angptl4 gene. These results suggest that the microbiota might regulate host intestinal Angptl4 protein expression and peripheral fat storage by suppressing the activity of an intestine-specific transcriptional enhancer. This study provides a useful paradigm for understanding how microbial signals interact with tissue-specific regulatory networks to control the activity and evolution of host gene transcription.
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100
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Engeman JM, Mabee PM. Segmentation and fusion on the midline: basibranchial homologies in cypriniform fishes. J Morphol 2012; 273:725-36. [PMID: 22460806 DOI: 10.1002/jmor.20017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 12/17/2011] [Accepted: 02/05/2012] [Indexed: 11/09/2022]
Abstract
The development and homologies of the median elements of the ventral hyoid and branchial arches of Cypriniformes have been unclear. We compared the developmental morphology of this region across five species (Cycleptus elongatus, Luxilus zonatus, Danio rerio, Devario auropurpureus, and Cobitis striata), representing three of five major clades of cypriniforms. The development of basibranchial 1 is similar in catostomids and cyprinids, where a single, elongate, basihyal + anterior copula divides into separate elements. A gap develops between the posterior end of the basihyal cartilage and the anterior copula in catostomids but in cyprinids (Luxiluszonatus, Danio rerio, and Devarioauropurpureus) there is little separation and the basihyal and basibranchial 1 may grow close together or retain a cartilaginous connection (Danio rerio, several outgroups). In loaches and Gyrinocheilus, the gap posterior to the basihyal has been alternately interpreted as either the absence or posterior displacement of basibranchial 1. Uniquely among examined species, in Cobitis striata, the basihyal cartilage and anterior copula form as separate cartilages and remain distinct throughout development with a prominent gap between the basihyal and most anterior basibranchial, which we interpret as loss of basibranchial 1. In the posterior region associated with branchial arches 4 and 5, all examined species except Danio rerio, which has only a basibranchial 4 cartilage, have separate basibranchial 4 and 5 cartilages in early ontogeny. Basibranchials 4 and 5 remain separate in Cycleptus elongatus, Devario auropurpurea, and Cobitis striata, but fuse in Luxilus zonatus to form a posterior copula. The orientation of basibranchial 4 and 5 cartilages in Cobitis striata is similar to catostomids and cyprinids. The most posterior median element in the branchial arches, the post-ceratobranchial cartilage, generally forms as a separate cartilage in catostomids but in Cobitis striata is connected with basibranchial 5 cartilage from earliest appearance.
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Affiliation(s)
- Jeffrey M Engeman
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
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