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Pino-Bodas R, Ahti T, Stenroos S, Martín MP, Burgaz AR. Multilocus approach to species recognition in the Cladonia humilis complex (Cladoniaceae, Ascomycota). AMERICAN JOURNAL OF BOTANY 2013; 100:664-678. [PMID: 23507737 DOI: 10.3732/ajb.1200162] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY The members of the Cladonia humilis complex are characterized by a well-developed primary thallus and broadly scyphose podetia. In the present study, this complex was phylogenetically analyzed to test the boundaries between the species and to determine the usefulness of the phenotypic characters to distinguish them. The species C. conista, C. cyathomorpha, C. hammeri, C. humilis, C. kurokawae, C. nashii, C. pulvinella, and C. subconistea were examined. METHODS Four DNA loci were sequenced and analyzed to test the monophyly of the species. For the phylogenetic reconstructions, maximum parsimony, maximum likelihood, and Bayesian methods were employed. The genealogical sorting index was used to quantify the exclusive ancestry of the nonmonophyletic species on the tree. KEY RESULTS The performed phylogenetic analyses showed that the C. humilis complex is not monophyletic. Cladonia nashii is not closely related to the remaining taxa within the complex. Seven monophyletic lineages were identified, most of which comprise specimens belonging to more than one chemotype. Cladonia hammeri and C. pulvinella are conspecific, and this taxon is not present in Europe. CONCLUSIONS This study suggests that morphological characters and secondary metabolites have less taxonomical value than thought in the Cladonia humilis complex. Use of multilocus phylogeny is recommended to delimit species.
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Affiliation(s)
- Raquel Pino-Bodas
- Departamento Biología Vegetal 1, Universidad Complutense de Madrid, Spain.
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Santini F, Nguyen MTT, Sorenson L, Waltzek TB, Lynch Alfaro JW, Eastman JM, Alfaro ME. Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae). J Evol Biol 2013; 26:1003-18. [DOI: 10.1111/jeb.12112] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 12/18/2012] [Accepted: 12/19/2012] [Indexed: 11/28/2022]
Affiliation(s)
- F. Santini
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
| | - M. T. T. Nguyen
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
| | - L. Sorenson
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
| | - T. B. Waltzek
- Department of Infectious Diseases and Pathology; College of Veterinary Medicine, University of Florida; Gainesville FL USA
| | - J. W. Lynch Alfaro
- Institute for Society and Genetics & Department of Anthropology; University of California Los Angeles; Los Angeles CA USA
| | - J. M. Eastman
- Department of Biological Sciences & the Institute of Bioinformatics and Evolutionary Study; University of Idaho; Moscow ID USA
| | - M. E. Alfaro
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
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53
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Tao W, Mayden RL, He S. Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses. Mol Phylogenet Evol 2013; 66:603-16. [DOI: 10.1016/j.ympev.2012.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 09/18/2012] [Accepted: 09/21/2012] [Indexed: 11/16/2022]
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54
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Imoto JM, Saitoh K, Sasaki T, Yonezawa T, Adachi J, Kartavtsev YP, Miya M, Nishida M, Hanzawa N. Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis. Gene 2013; 514:112-24. [DOI: 10.1016/j.gene.2012.10.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 09/10/2012] [Accepted: 10/19/2012] [Indexed: 10/27/2022]
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Du J, Yan J, Zhou K. Isolation of microsatellite markers for Pelophylax nigromaculata and a tentative application in detecting interspecific introgression. Gene 2012; 508:130-4. [PMID: 22967873 DOI: 10.1016/j.gene.2012.07.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 07/14/2012] [Accepted: 07/30/2012] [Indexed: 12/12/2022]
Abstract
Twenty-seven microsatellite markers were obtained from the black-spotted frog, Pelophylax nigromaculata,using the FIASCO (Fast Isolation by AFLP of Sequences containing repeats) protocol. Genotyping of 60 individuals showed that the number of alleles ranged from 4 to 25 with an average of 12.78 alleles per locus. The observed and expected heterozygosities ranged from 0.137 to 0.956 and 0.594 to 0.948, with averages of 0.531 and 0.809, respectively. Many of these loci were successfully cross-amplified in five other ranid species. The introgression between P. nigromaculata and Pelophylax plancyi was assessed using 5 microsatellite loci on 159 individuals collected from Liaoning, northeast China. Two distinct genetic clusters (pure species) as well as seven unassigned individuals were identified by factorial correspondence analysis (FCA), New Hybrids and Structure. The unassigned individuals, which are likely the product of interspecific hybridization, indicate the usefulness of these microsatellite loci for future studies of hybridization and introgression between these two ranid species.
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Affiliation(s)
- Jie Du
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
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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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57
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Liu SQ, Mayden RL, Zhang JB, Yu D, Tang QY, Deng X, Liu HZ. Phylogenetic relationships of the Cobitoidea (Teleostei: Cypriniformes) inferred from mitochondrial and nuclear genes with analyses of gene evolution. Gene 2012; 508:60-72. [PMID: 22868207 DOI: 10.1016/j.gene.2012.07.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 06/15/2012] [Accepted: 07/23/2012] [Indexed: 02/08/2023]
Abstract
The superfamily Cobitoidea of the order Cypriniformes is a diverse group of fishes, inhabiting freshwater ecosystems across Eurasia and North Africa. The phylogenetic relationships of this well-corroborated natural group and diverse clade are critical to not only informing scientific communities of the phylogeny of the order Cypriniformes, the world's largest freshwater fish order, but are key to every area of comparative biology examining the evolution of traits, functional structures, and breeding behaviors to their biogeographic histories, speciation, anagenetic divergence, and divergence time estimates. In the present study, two mitochondrial gene sequences (COI, ND4+5) and four single-copy nuclear gene segments (RH1, RAG1, EGR2B, IRBP) were used to infer the phylogenetic relationships of the Cobitoidea as reconstructed from maximum likelihood (ML) and partitioned Bayesian Analysis (BA). Analyses of the combined mitochondrial/nuclear gene datasets revealed five strongly supported monophyletic Cobitoidea families and their sister-group relationships: Botiidae+(Vaillantellidae+(Cobitidae+(Nemacheilidae+Balitoridae))). These recovered relationships are in agreement with previous systematic studies on the order Cypriniformes and/or those focusing on the superfamily Cobitoidea. Using these relationships, our analyses revealed pattern lineage- or ecological-group-specific evolution of these genes for the Cobitoidea. These observations and results corroborate the hypothesis that these group-specific-ancestral ecological characters have contributed in the diversification and/or adaptations within these groups. Positive selections were detected in RH1 of nemacheilids and in RAG1 of nemacheilids and genus Vaillantella, which indicated that evolution of RH1 (related to eye's optic sense) and RAG1 (related to immunity) genes appeared to be important for the diversification of these groups. The balitorid lineage (those species inhabiting fast-flowing riverine habitats) had, as compared with other cobitoid lineages, significantly different dN/dS, dN and dS values for ND4 and IRBP genes. These significant differences are usually indicative of weaker selection pressure, and lineage-specific evolution on genes along the balitorid lineage. Furthermore, within Cobitoidea, excluding balitorids, species living in subtropics had significantly higher dN/dS values in RAG1 and IRBP genes than those living in temperate and tropical zones. Among tropical cobitoids, genes COI, ND5, EGR2B, IRBP and RH1, had a significantly higher mean dS value than those species in subtropical and temperate groups. These findings suggest that the evolution of these genes could also be ecological-group-specific and may have played an important role in the adaptive evolution and diversification of these groups. Thus, we hypothesize that the genes included in the present study were actively involved in lineage- and/or ecological-group-specific evolutionary processes of the highly diverse Cobitoidea. These two evolutionary patterns, both subject to further testing, are hypothesized as integral in the diversification with this major clade of the world's most diverse group of freshwater fishes.
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Affiliation(s)
- Si-Qing Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, PR China.
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Lei R, Rowley TW, Zhu L, Bailey CA, Engberg SE, Wood ML, Christman MC, Perry GH, Louis EE, Lu G. PhyloMarker–-A Tool for Mining Phylogenetic Markers through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny. Evol Bioinform Online 2012. [DOI: 10.4137/ebo.s9886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker /.
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Affiliation(s)
- Runhua Lei
- Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, United States
| | - Thaine W. Rowley
- Department of Biology, University of Nebraska at Omaha, NE 68135, United States
| | - Lifeng Zhu
- College of Life Science, Nanjing Normal University, Jiangsu 210097, China
| | - Carolyn A. Bailey
- Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, United States
| | - Shannon E. Engberg
- Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, United States
| | - Mindy L. Wood
- Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, United States
| | - Mary C. Christman
- Department of Biology, University of Nebraska at Omaha, NE 68135, United States
| | - George H. Perry
- Department of Anthropology, Pennsylvania State University, PA 16802, United States
| | - Edward E. Louis
- Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, United States
| | - Guoqing Lu
- Department of Biology, University of Nebraska at Omaha, NE 68135, United States
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Walker DM, Castlebury LA, Rossman AY, White JF. New molecular markers for fungal phylogenetics: two genes for species-level systematics in the Sordariomycetes (Ascomycota). Mol Phylogenet Evol 2012; 64:500-12. [PMID: 22626621 DOI: 10.1016/j.ympev.2012.05.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 03/05/2012] [Accepted: 05/04/2012] [Indexed: 10/28/2022]
Abstract
Although significant progress has been made resolving deep branches of the fungal tree of life, many fungal systematists are interested in species-level questions to both define species and assess fungal biodiversity. Fungal genome sequences are a useful resource to systematic biologists for developing new phylogenetic markers that better represent the whole genome. Here we report primers for two newly identified single-copy protein-coding genes, FG1093 and MS204, for use with ascomycetes. Although fungi were the focus of this study, this methodological approach could be easily applied to marker development for studies of other organisms. The tests used here to assess phylogenetic informativeness are computationally rapid, require only rudimentary datasets to evaluate existing or newly developed markers, and can be applied to other non-model organisms to assist in experimental design of phylogenetic studies. Phylogenetic utility of the markers was tested in two genera, Gnomoniopsis and Ophiognomonia (Gnomoniaceae, Diaporthales). The phylogenetic performance of β-tubulin, ITS, and tef-1α was compared with FG1093 and MS204. Phylogenies inferred from FG1093 and MS204 were largely in agreement with β-tubulin, ITS, and tef-1α although some topological conflict was observed. Resolution and support for branches differed based on the combination of markers used for each genus. Based on two independent tests of phylogenetic performance, FG1093 and MS204 were determined to be equal to or better than β-tubulin, ITS, and tef-1α in resolving species relationships. Differences were found in site-specific rate of evolution in all five markers. In addition, isolates from 15 orders and 22 families of Ascomycota were screened using primers for FG1093 and MS204 to demonstrate primer utility across a wide diversity of ascomycetes. The primer sets for the newly identified genes FG1093 and MS204 and methods used to develop them are useful additions to the ascomycete systematists' toolbox.
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Affiliation(s)
- Donald M Walker
- Department of Plant Biology and Pathology, Rutgers University, 59 Dudley Rd, New Brunswick, NJ 08901, USA
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60
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Collins RA, Armstrong KF, Meier R, Yi Y, Brown SDJ, Cruickshank RH, Keeling S, Johnston C. Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. PLoS One 2012; 7:e28381. [PMID: 22276096 PMCID: PMC3262790 DOI: 10.1371/journal.pone.0028381] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 11/07/2011] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Poorly regulated international trade in ornamental fishes poses risks to both biodiversity and economic activity via invasive alien species and exotic pathogens. Border security officials need robust tools to confirm identifications, often requiring hard-to-obtain taxonomic literature and expertise. DNA barcoding offers a potentially attractive tool for quarantine inspection, but has yet to be scrutinised for aquarium fishes. Here, we present a barcoding approach for ornamental cyprinid fishes by: (1) expanding current barcode reference libraries; (2) assessing barcode congruence with morphological identifications under numerous scenarios (e.g. inclusion of GenBank data, presence of singleton species, choice of analytical method); and (3) providing supplementary information to identify difficult species. METHODOLOGY/PRINCIPAL FINDINGS We sampled 172 ornamental cyprinid fish species from the international trade, and provide data for 91 species currently unrepresented in reference libraries (GenBank/Bold). DNA barcodes were found to be highly congruent with our morphological assignments, achieving success rates of 90-99%, depending on the method used (neighbour-joining monophyly, bootstrap, nearest neighbour, GMYC, percent threshold). Inclusion of data from GenBank (additional 157 spp.) resulted in a more comprehensive library, but at a cost to success rate due to the increased number of singleton species. In addition to DNA barcodes, our study also provides supporting data in the form of specimen images, morphological characters, taxonomic bibliography, preserved vouchers, and nuclear rhodopsin sequences. Using this nuclear rhodopsin data we also uncovered evidence of interspecific hybridisation, and highlighted unrecognised diversity within popular aquarium species, including the endangered Indian barb Puntius denisonii. CONCLUSIONS/SIGNIFICANCE We demonstrate that DNA barcoding provides a highly effective biosecurity tool for rapidly identifying ornamental fishes. In cases where DNA barcodes are unable to offer an identification, we improve on previous studies by consolidating supplementary information from multiple data sources, and empower biosecurity agencies to confidently identify high-risk fishes in the aquarium trade.
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Affiliation(s)
- Rupert A Collins
- Bio-Protection Research Centre, Lincoln University, Canterbury, New Zealand.
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61
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Gante HF, Alves MJ, Dowling TE. Paralog-specific primers for the amplification of nuclear Loci in tetraploid barbels (barbus: cypriniformes). ACTA ACUST UNITED AC 2011; 102:617-21. [PMID: 21705490 DOI: 10.1093/jhered/esr059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Thirty paralog-specific primers were developed, following an intron-primed exon-crossing strategy, for S7 and growth hormone genes in Barbus (subgenera Barbus and Luciobarbus). We found that paralog-specific amplification requires the use of only one paralog-specific primer, allowing their simultaneous use with universal exon-primed intron-crossing primers of broad taxonomic applicability. This hybrid annealing strategy guarantees both specificity and generality of amplification reactions and represents a step forward in the amplification of duplicated nuclear loci in polyploid organisms and members of multigene families. Assays of several representative taxa identified high levels of segregating single nucleotide polymorphisms (SNPs) and nucleotide diversity within each of these subgenera. Additionally, several insertions-deletions (indels) that are diagnostic across species are found in intronic regions. Therefore, these primers provide a reliable source of valuable nuclear SNP and indel data for population and species level studies of barbels, such as applied conservation and basic evolutionary studies.
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Affiliation(s)
- Hugo F Gante
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4601, USA.
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CONWAY KEVINW. Osteology of the South Asian Genus Psilorhynchus McClelland, 1839 (Teleostei: Ostariophysi: Psilorhynchidae), with investigation of its phylogenetic relationships within the order Cypriniformes. Zool J Linn Soc 2011. [DOI: 10.1111/j.1096-3642.2011.00698.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Nakatani M, Miya M, Mabuchi K, Saitoh K, Nishida M. Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation. BMC Evol Biol 2011; 11:177. [PMID: 21693066 PMCID: PMC3141434 DOI: 10.1186/1471-2148-11-177] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Accepted: 06/22/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. RESULTS Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. CONCLUSIONS The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100-112 Ma, creating an over 100 million year time span without fossil evidence. This formidable ghost range partially reflects a genuine difference between the estimated ages of stem group origin (molecular divergence time) and crown group morphological diversification (fossil divergence time); the ghost range, however, would be filled with discoveries of older fossils that can be used as more reasonable time constraints as well as with developments of more realistic models that capture the rates of molecular sequences accurately.
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Affiliation(s)
- Masanori Nakatani
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5Kashiwanoha, Kashiwa-shi, Chiba 277-8564, Japan
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Tang KL, Agnew MK, Chen WJ, Vincent Hirt M, Raley ME, Sado T, Schneider LM, Yang L, Bart HL, He S, Liu H, Miya M, Saitoh K, Simons AM, Wood RM, Mayden RL. Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae). Mol Phylogenet Evol 2011; 61:103-24. [PMID: 21672635 DOI: 10.1016/j.ympev.2011.05.022] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 05/24/2011] [Accepted: 05/30/2011] [Indexed: 11/18/2022]
Abstract
The members of the cyprinid subfamily Gobioninae, commonly called gudgeons, form one of the most well-established assemblages in the family Cyprinidae. The subfamily is a species-rich group of fishes, these fishes display diverse life histories, appearances, and behavior. The phylogenetic relationships of Gobioninae are examined using sequence data from four loci: cytochrome b, cytochrome c oxidase I, opsin, and recombination activating gene 1. This investigation produced a data matrix of 4114 bp for 162 taxa that was analyzed using parsimony, maximum likelihood, and Bayesian inference methods. The phylogenies our analyses recovered corroborate recent studies on the group. The subfamily Gobioninae is monophyletic and composed of three major lineages. We find evidence for a Hemibarbus-Squalidus group, and the tribes Gobionini and Sarcocheilichthyini, with the Hemibarbus-Squalidus group sister to a clade of Gobionini-Sarcocheilichthyini. The Hemibarbus-Squalidus group includes those two genera; the tribe Sarcocheilichthyini includes Coreius, Coreoleuciscus, Gnathopogon, Gobiocypris, Ladislavia, Paracanthobrama, Pseudorasbora, Pseudopungtungia, Pungtungia, Rhinogobio, and Sarcocheilichthys; the tribe Gobionini includes Abbottina, Biwia, Gobio, Gobiobotia, Huigobio, Microphysogobio, Platysmacheilus, Pseudogobio, Romanogobio, Saurogobio, and Xenophysogobio. The monotypic Acanthogobio is placed into the synonymy of Gobio. We tentatively assign Belligobio to the Hemibarbus-Squalidus group and Mesogobio to Gobionini; Paraleucogobio and Parasqualidus remain incertae sedis. Based on the topologies presented, the evolution of swim bladder specializations, a distinctive feature among cyprinids, has occurred more than once within the subfamily.
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Affiliation(s)
- Kevin L Tang
- Saint Louis University, Department of Biology, St. Louis, MO 63103, USA.
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Parallel evolution in eight-barbel loaches of the genus Lefua (Balitoridae, Cypriniformes) revealed by mitochondrial and nuclear DNA phylogenies. Mol Phylogenet Evol 2011; 60:416-27. [PMID: 21609774 DOI: 10.1016/j.ympev.2011.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 05/05/2011] [Accepted: 05/05/2011] [Indexed: 11/21/2022]
Abstract
The evolutionary history of eight-barbel loaches of the genus Lefua contains important phylogenetic information that will aid in resolution of the faunal formations and evolutionary histories of Japanese and East Asian freshwater fishes. Our sequencing of the mitochondrial D-loop region in a large number of samples allowed construction of the most comprehensive phylogeny of these loaches to date; we demonstrated monophyly of five Lefua species and identified populations of Lufua. sp. and Lefua echigonia. Loaches inhabiting the Tokai region in Japan were morphologically and ecologically indistinguishable from Lefua sp. However, they were included in the L. echigonia lineage. We determined a novel phylogeny by sequencing the nuclear ribosomal S7 subunit and showed that nuclear DNA phylogeny essentially matched the mitochondrial DNA phylogeny. Loaches from the Tokai region were part of the L. echigonia lineage, indicating parallel evolution between Tokai loaches and Lefua sp. in western Japan. We presented the most robust phylogeny to date using concatenated mitochondrial and nuclear sequences. The wealth of molecular information allowed us to speculate on evolutionary processes in the genus Lefua.
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Arroyave J, Stiassny MLJ. Phylogenetic relationships and the temporal context for the diversification of African characins of the family Alestidae (Ostariophysi: Characiformes): evidence from DNA sequence data. Mol Phylogenet Evol 2011; 60:385-97. [PMID: 21550408 DOI: 10.1016/j.ympev.2011.04.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 04/15/2011] [Accepted: 04/20/2011] [Indexed: 01/20/2023]
Abstract
Phylogenetic relationships within the family Alestidae were investigated using parsimony, maximum likelihood, and Bayesian approaches based on a molecular dataset that included both nuclear and mitochondrial markers. Multiple representatives of all but two of the recognized alestid genera were included, which allowed for testing previous hypotheses of intergeneric relationships and the monophyly of several genera. The phylogenetic position of the Neotropical genus Chalceus with respect to the family Alestidae was also examined. In order to understand the temporal context of alestid diversification, Bayesian methods of divergence time estimation using fossil data in the form of calibration priors were used to date the nodes of the phylogenetic tree. Our results rejected the monophyly of the family as currently recognized (Alestidae sensu lato) and revealed several instances of poly- and paraphyly among genera. The genus Chalceus was recovered well nested within Neotropical characiforms, thus rejecting the hypothesis that this taxon is the most basal alestid. The estimated mean divergence time for the alestid clade (Alestidae sensu stricto) was 54 Mya with a 95% credibility interval of 63-49 Mya. These results are incongruent with the hypothesis that the origin of the family Alestidae predates the African-South American Drift-Vicariance event.
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Affiliation(s)
- Jairo Arroyave
- Department of Ichthyology, Division of Vertebrate Zoology, American Museum of Natural History, Central Park West at 79th St., New York, NY 10024, USA.
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SAITOH KENJI, SADO TETSUYA, DOOSEY MICHAELH, BART Jr HENRYL, INOUE JUNG, NISHIDA MUTSUMI, MAYDEN RICHARDL, MIYA MASAKI. Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi). Zool J Linn Soc 2011. [DOI: 10.1111/j.1096-3642.2010.00651.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Tao W, Zou M, Wang X, Gan X, Mayden RL, He S. Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes). PLoS One 2010; 5:e13508. [PMID: 20976012 PMCID: PMC2958143 DOI: 10.1371/journal.pone.0013508] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 09/21/2010] [Indexed: 11/19/2022] Open
Abstract
Despite their great diversity and biological importance, evolutionary relationships among the endemic clade of East Asian Cyprinidae remain ambiguous. Understanding the phylogenetic history of this group involves many challenges. For instance, ecomorphological convergence may confound morphology-based phylogenetic inferences, and previous molecular phylogenetic studies based on single genes have often yielded contradictory and poorly supported trees. We assembled a comprehensive data matrix of 100 nuclear gene segments (∼ 71132 base pairs) for representative species of the endemic East Asian cyprinid fauna and recovered a robust phylogeny from this genome-wide signal supported by multiple analytical methods, including maximum parsimony, maximum likelihood and Bayesian inference. Relaxed molecular clock analyses indicated species radiations of this clade concentrated at approximately 1.9–7.6 MYA. We provide evidence that the bursts of diversification in this fauna are directly linked to major paleoenvironmental events associated with monsoon evolution occurring from late Miocene to Pliocene. Ancestral state reconstruction reveals convergent morphological characters are hypothesized to be independent products of similar selective pressures in ecosystems. Our study is the first comprehensive phylogenetic study of the enigmatic East-Asian cyprinids. The explicit molecular phylogeny provides a valuable framework for future research in genome evolution, adaptation and speciation of cyprinids.
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Affiliation(s)
- Wenjing Tao
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Ming Zou
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xuzhen Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xiaoni Gan
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Richard L. Mayden
- Laboratory of Integrated Genomics, Biodiversity, and Conservation, Department of Biology, Saint Louis University, Saint Louis, Missouri, United States of America
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, People's Republic of China
- * E-mail:
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Mayden RL, Chen WJ. The world’s smallest vertebrate species of the genus Paedocypris: A new family of freshwater fishes and the sister group to the world’s most diverse clade of freshwater fishes (Teleostei: Cypriniformes). Mol Phylogenet Evol 2010; 57:152-75. [DOI: 10.1016/j.ympev.2010.04.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2009] [Revised: 03/29/2010] [Accepted: 04/02/2010] [Indexed: 11/25/2022]
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70
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Palandačić A, Zupančič P, Snoj A. Revised classification of former genus Phoxinellus using nuclear DNA sequences. BIOCHEM SYST ECOL 2010. [DOI: 10.1016/j.bse.2010.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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71
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Saitoh K, Chen WJ, Mayden RL. Extensive hybridization and tetrapolyploidy in spined loach fish. Mol Phylogenet Evol 2010; 56:1001-10. [DOI: 10.1016/j.ympev.2010.04.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 04/14/2010] [Accepted: 04/16/2010] [Indexed: 12/15/2022]
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Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). Mol Phylogenet Evol 2010; 57:189-214. [PMID: 20553898 DOI: 10.1016/j.ympev.2010.05.021] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 05/20/2010] [Accepted: 05/20/2010] [Indexed: 11/20/2022]
Abstract
The members of the cyprinid subfamily Danioninae form a diverse and scientifically important group of fishes, which includes the zebrafish, Danio rerio. The diversity of this assemblage has attracted much scientific interest but its monophyly and the relationships among its members are poorly understood. The phylogenetic relationships of the Danioninae are examined herein using sequence data from mitochondrial cytochrome b, mitochondrial cytochrome c oxidase I, nuclear opsin, and nuclear recombination activating gene 1. A combined data matrix of 4117 bp for 270 taxa was compiled and analyzed. The resulting topology supports some conclusions drawn by recent studies on the group and certain portions of the traditional classification, but our results also contradict key aspects of the traditional classification. The subfamily Danioninae is not monophyletic, with putative members scattered throughout Cyprinidae. Therefore, we restrict Danioninae to the monophyletic group that includes the following genera: Amblypharyngodon, Barilius, Cabdio, Chela, Chelaethiops, Danio, Danionella, Devario (including Inlecypris), Esomus, Horadandia, Laubuca, Leptocypris, Luciosoma, Malayochela, Microdevario, Microrasbora, Nematabramis, Neobola, Opsaridium, Opsarius, Paedocypris, Pectenocypris, Raiamas, Rasbora (including Boraras and Trigonostigma), Rasboroides, Salmostoma, Securicula, and Sundadanio. This Danioninae sensu stricto is divided into three major lineages, the tribes Chedrini, Danionini, and Rasborini, where Chedrini is sister to a Danionini-Rasborini clade. Each of these tribes is monophyletic, following the restriction of Danioninae. The tribe Chedrini includes a clade of exclusively African species and contains several genera of uncertain monophyly (Opsarius, Raiamas, Salmostoma). Within the tribe Rasborini, the species-rich genus Rasbora is rendered non-monophyletic by the placement of two monophyletic genera, Boraras and Trigonostigma, hence we synonymize those two genera with Rasbora. In the tribe Danionini, the miniature genus Danionella is recovered as the sister group of Danio, with D. nigrofasciatus sister to D. rerio.
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Chen WJ, Lheknim V, Mayden RL. Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma resolved with six nuclear genes. JOURNAL OF FISH BIOLOGY 2009; 75:2197-2208. [PMID: 20738682 DOI: 10.1111/j.1095-8649.2009.02398.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Molecular variation in six nuclear genes provides substantive phylogenetic evidence for the recognition of a new cypriniform family, the Ellopostomatidae, to include the enigmatic Southern Asia loach genus Ellopostoma. The current six loach families form a monophyletic group, with the Nemacheilidae as the sister group to Ellopostomatidae; Vaillantellidae forms the sister group to all families exclusive of Botiidae. While the superfamily Cobitoidea includes eight families, the monophyly of this large clade within the Cypriniformes remains a vexing problem despite extensive molecular analyses and is in need of further investigation.
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Affiliation(s)
- W-J Chen
- Department of Biology, Saint Louis University, 3507 Laclede Ave, St. Louis, MO 63103, USA.
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Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the world’s largest clade of freshwater fishes: Further evidence from six nuclear genes. Mol Phylogenet Evol 2009; 52:544-9. [DOI: 10.1016/j.ympev.2009.01.006] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mayden RL, Chen WJ, Bart HL, Doosey MH, Simons AM, Tang KL, Wood RM, Agnew MK, Yang L, Hirt MV, Clements MD, Saitoh K, Sado T, Miya M, Nishida M. Reconstructing the phylogenetic relationships of the earth’s most diverse clade of freshwater fishes—order Cypriniformes (Actinopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome. Mol Phylogenet Evol 2009; 51:500-14. [DOI: 10.1016/j.ympev.2008.12.015] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 12/14/2008] [Accepted: 12/15/2008] [Indexed: 11/28/2022]
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Reducing cloning artifacts for recovery of allelic sequences by T7 endonuclease I cleavage and single re-extension of PCR products--a benchmark. Gene 2008; 423:92-5. [PMID: 18644429 DOI: 10.1016/j.gene.2008.06.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 06/05/2008] [Accepted: 06/23/2008] [Indexed: 11/20/2022]
Abstract
Occurrence of chimeric sequences and related artifacts in PCR cloning procedures gives us risks of over-estimation of haplotypes or alleles. Recombination among haplotypes occurs through template switching during PCR cycles or through random repair of mismatch sites on heteroduplex DNA by the host cell. To eliminate the chimeric cloning artifacts, we tested two alternative protocols using T7 endonuclease I cleavage of mismatch sites and re-extension of nascent strands. Though T7 endonuclease I effectively eliminated chimeric clones in some cases, it produced many short fragments. Protocol with single re-extension of PCR products successfully recovered non-recombinant clones with fewer short fragments. In spite of the improvement of allelic recovery through these two protocols, there were still a few recombinants that remained in both reaction mixtures, and thus interpretation of the results for haplotype diversity in a PCR-amplified DNA population should be cautionary. Because re-extension in a diluted reaction mixture is quick, inexpensive and effective, it is advisable to use this procedure for recovery of chromosomal alleles with PCR cloning.
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