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Zhu C, Pan Z, Chang G, Wang H, Ding H, Wu N, Qiang X, Yu X, Wang L, Zhang J. Polymorphisms of the growth hormone gene and their association with growth traits and sex in Sarcocheilichthys sinensis. Mol Genet Genomics 2020; 295:1477-1488. [PMID: 32700104 DOI: 10.1007/s00438-020-01714-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 07/15/2020] [Indexed: 11/27/2022]
Abstract
The growth hormone gene (gh) of Sarcocheilichthys sinensis was cloned and characterized in this study. The cDNA length of gh was 973 bp, containing a 5'-UTR of 15 bp, a 3'-UTR of 325 bp and an open reading frame of 633 bp. The genomic DNA of gh was 2135 bp in length containing five exons and four introns. The precursor peptide of gh contained 210 amino acids (aa), including a signal peptide of 22 aa (Met1-Ala22) and a mature region of 188 aa (Ser23-Leu210). The similarity and identity ranges of the gh precursor peptide with those of other cyprinids were 88.6%-99.0% and 84.8%-98.6%, respectively. The gh of S. sinensis expressed at the highest level in the pituitary, and its expression was also detected in muscle and brain. Six polymorphic sites were detected in intron 1 (g.51InDel, g.64InDel and g.242InDel), intron 2 (g.864T>C), intron 3 (g.1017InDel) and intron 4 (g.1541A>G). Among these sites, g.242InDel was significantly associated with condition factor, g.1541A>G was associated with all six growth traits, while g.864T>C was associated with sex. The data obtained herein provide useful information for further studies on the regulation mechanisms of growth and sexual growth differences in S. sinensis.
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Affiliation(s)
- Chuankun Zhu
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, China.
| | - Zhengjun Pan
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Guoliang Chang
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Hui Wang
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Huaiyu Ding
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Nan Wu
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Xiaogang Qiang
- Huai'an Fishery Technology Guidance Station, Huai'an, China
| | - Xiangsheng Yu
- Huai'an Fishery Technology Guidance Station, Huai'an, China
| | - Long Wang
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, China
- Fisheries and Life Science College, Shanghai Ocean University, Shanghai, China
| | - Ji Zhang
- Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, China
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Corona-Santiago DK, Domínguez-Domínguez O, Tovar-Mora L, Pardons-Blas JR, Herrerías-Diego Y, Pérez-Rodríguez R, Doadrio I. Historical biogeography reveals new independent evolutionary lineages in the Pantosteus plebeius-nebuliferus species-group (Actinopterygii: Catostomidae). BMC Evol Biol 2018; 18:173. [PMID: 30453887 PMCID: PMC6245702 DOI: 10.1186/s12862-018-1286-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 10/31/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The Pantosteus plebeius-nebuliferus species-group is a group of freshwater fishes distributed in endo- and exorheic drainage basins in the Mexican Sierra Madre Occidental mountain range system and central North Mexico. The geological history of this region is considered an important factor in explaining the evolutionary history of low vagility animals like freshwaters fishes. The aim of this study was to examine the phylogenetic relationships and describe the evolutionary history of the species-group. We hypothesized that the genetic structure and distribution of the main clades of Pantosteus plebeius-nebuliferus are associated with the geological history of Northern Mexico. To this end, we obtained DNA sequences of mitochondrial and nuclear genes and performed phylogenetic and phylogeographic analyses. Divergence time estimation and ancestral area reconstruction were also carried out to propose a biogeographical hypothesis, and species boundaries within the species-group were also tested. RESULTS We identified four clades within the Pantosteus plebeius-nebuliferus species-group in both markers. Divergence ranged from 5.9% to 9.2% for cytb and 0.1% to 0.9% for GHI. We observed significant genetic structure and no shared haplotypes between clades. We estimated that the clades diverged during the last 5.1 Myr, with a biogeographic scenario suggesting eight vicariant and four dispersal events through the historic range of the species-group. We found that the best species-delimitation model is when four species are assumed, which correspond to the main clades. We identified nine evolutionary significance units (ESUs), pertinent to the conservation of the group, each representing populations present in distinct drainage basins. CONCLUSIONS The evolutionary history of the Pantosteus plebeius-nebuliferus species-group is characterized by vicariant post-dispersal processes, linked to geological changes in the Sierra Madre Occidental and central Northern Mexico since the Pliocene. This is congruent with biogeographic patterns described for other co-distributed fish species. We propose a new phylogenetic hypothesis for the species-group, clarifying the taxonomy of this evolutionarily complex group. Our results suggest that the species-group consists of at least four clades with independent evolutionary histories, two of which may represent new undescribed species. Our identification of ESUs provides a basis upon which conservation measures can be developed for the species-group.
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Affiliation(s)
- Diushi Keri Corona-Santiago
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC. c/José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - Llanet Tovar-Mora
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - José Ramón Pardons-Blas
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC. c/José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Yvonne Herrerías-Diego
- Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán Mexico
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC. c/José Gutiérrez Abascal, 2, 28006 Madrid, Spain
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Kamenskaya DN, Pankova MV, Atopkin DM, Brykov VA. Divergence of paralogous growth-hormone-encoding genes and their promoters in salmonidae. Mol Biol 2017. [DOI: 10.1134/s0026893317020121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Pérez-Rodríguez R, Domínguez-Domínguez O, Mar-Silva AF, Doadrio I, Pérez-Ponce de León G. The historical biogeography of the southern group of the sucker genusMoxostoma(Teleostei: Catostomidae) and the colonization of central Mexico. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12383] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rodolfo Pérez-Rodríguez
- Instituto de Ecología Aplicada; UAT; División del Golfo 356; Col. Libertad; Ciudad Victoria Tamaulipas C.P. 87019 México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática; Facultad de Biología; UMSNH; C.P. 58000 Morelia Michoacán México
| | - Adan Fernando Mar-Silva
- Laboratorio de Biología Acuática; Facultad de Biología; UMSNH; C.P. 58000 Morelia Michoacán México
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales; CSIC; c/José Gutiérrez Abascal 2 E-28006 Madrid España México
| | - Gerardo Pérez-Ponce de León
- Departamento de Zoología; Instituto de Biología; UNAM; Circuito exterior s/n Ciudad Universitaria Coyoacán C.P. 04510 México D.F. México
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Kamenskaya DN, Pankova MV, Atopkin DM, Brykov VA. Fish growth-hormone genes: Evidence of functionality of paralogous genes in Levanidov’s charr Salvelinus levanidovi. Mol Biol 2015. [DOI: 10.1134/s002689331505009x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Schmidt RC, Bart HL, Nyingi DW, Gichuki NN. Phylogeny of suckermouth catfishes (Mochokidae: Chiloglanis) from Kenya: the utility of Growth Hormone introns in species level phylogenies. Mol Phylogenet Evol 2014; 79:415-21. [PMID: 25079137 DOI: 10.1016/j.ympev.2014.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 07/18/2014] [Accepted: 07/19/2014] [Indexed: 11/30/2022]
Abstract
African suckermouth catfishes (Mochokidae: Chiloglanis) occur in freshwater throughout tropical Africa. Specimens from all major drainages across Kenya were collected over three field seasons. Here we present a phylogeny inferred from both mitochondrial cytochrome b (cyt b) and introns of the nuclear Growth Hormone gene (GH). The phylogeny inferred from introns is largely congruent with the results from an analysis of cyt b. The length and variability of GH introns make them ideal species level nuclear markers without the problem of introgression commonly encountered with mitochondrial genes. This analysis confirmed the presence of two previously known undescribed Chiloglanis species and also suggests the presence of previously unknown diversity within the Athi River system. The resulting phylogeny also indicates the presence of two separate lineages within C. brevibarbis. The historical biogeography of Chiloglanis within Kenya is discussed. The utility of GH intron for species level phylogenies of Siluriformes is compared to that in other groups.
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Affiliation(s)
- Ray C Schmidt
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Boggs Hall, New Orleans, LA 70118, United States.
| | - Henry L Bart
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Boggs Hall, New Orleans, LA 70118, United States
| | - Dorothy Wanja Nyingi
- Ichthyology Section, National Museums of Kenya, PO Box 40658-00100, Nairobi, Kenya
| | - Nathan Ndegwa Gichuki
- School of Biological Sciences, University of Nairobi, PO Box 30197-00100, Nairobi, Kenya
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Cloning and Characterization of Pangasianodon hypophthalmus Growth Hormone Gene and its Heterologous Expression. Appl Biochem Biotechnol 2014; 173:1446-68. [DOI: 10.1007/s12010-014-0946-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/23/2014] [Indexed: 10/25/2022]
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Unmack PJ, Dowling TE, Laitinen NJ, Secor CL, Mayden RL, Shiozawa DK, Smith GR. Influence of introgression and geological processes on phylogenetic relationships of Western North American mountain suckers (Pantosteus, Catostomidae). PLoS One 2014; 9:e90061. [PMID: 24619087 PMCID: PMC3949674 DOI: 10.1371/journal.pone.0090061] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 01/29/2014] [Indexed: 12/04/2022] Open
Abstract
Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western USA and into northern Mexico. They are typically found in medium gradient, middle-elevation reaches of rivers over rocky substrates. This study (1) compares molecular data with morphological and paleontological data for proposed species of Pantosteus, (2) tests hypotheses of their monophyly, (3) uses these data for phylogenetic inferences of sister-group relationships, and (4) estimates timing of divergence events of identified lineages. Using 8055 base pairs from mitochondrial DNA protein coding genes, Pantosteus and Catostomus are reciprocally monophyletic, in contrast with morphological data. The only exception to a monophyletic Pantosteus is P. columbianus whose mtDNA is closely aligned with C. tahoensis because of introgression. Within Pantosteus, several species have deep genetic divergences among allopatric sister lineages, several of which are diagnosed and elevated to species, bringing the total diversity in the group to 11 species. Conflicting molecular and morphological data may be resolved when patterns of divergence are shown to be correlated with sympatry and evidence of introgression.
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Affiliation(s)
- Peter J. Unmack
- WIDB 401, Department of Biology, Brigham Young University, Provo, Utah, United States of America
- National Evolutionary Synthesis Center, Durham, North Carolina, United States of America
- * E-mail:
| | - Thomas E. Dowling
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Nina J. Laitinen
- WIDB 401, Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Carol L. Secor
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Richard L. Mayden
- Department of Biology, Saint Louis University, St. Louis, Missouri, United States of America
| | - Dennis K. Shiozawa
- WIDB 401, Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Gerald R. Smith
- Museum of Zoology, The University of Michigan, Ann Arbor, Michigan, United States of America
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Wang M, Yang JX, Chen XY. Molecular phylogeny and biogeography of percocypris (Cyprinidae, Teleostei). PLoS One 2013; 8:e61827. [PMID: 23750199 PMCID: PMC3672144 DOI: 10.1371/journal.pone.0061827] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 03/18/2013] [Indexed: 12/05/2022] Open
Abstract
Fierce predatory freshwater fishes, the species of Percocypris (Cyprinidae, Teleostei) inhabit large rivers or lakes, and have a specific distribution pattern. Only a single species or subspecies occurs in each large-scale drainage basin of the Southeastern Tibetan Plateau. In this study, the molecular phylogenetic relationships for all but one of the described subspecies/species of Percocypris were investigated based on three mitochondrial genes (16S; COI; Cyt b) and one nuclear marker (Rag2). The results of Maximum Likelihood and Bayesian Inference analyses show that Percocypris is a strongly supported monophyletic group and that it is the sister group of Schizothorax. Combined with analyses of morphological characters, our results suggest that Percocypris needs to be reclassified, and we propose that six species be recognized, with corresponding distributions in five main drainages (including one lake). In addition, based on the results of the estimation of divergence times and ancestral drainages, we hypothesize that Percocypris likely originated in the early Miocene from a paleo-connected drainage system containing the contemporary main drainages of the Southeastern Tibetan Plateau. This study suggests that vicariance (due to the uplift of the Tibetan Plateau modifying the large-scale morphologies of drainage basins in the Southeastern Tibetan Plateau) has played an important role in the speciation of the genus. Furthermore, external morphological characters (such as the length of the fins) and an internal trait (the position of pterygiophore) appear to be correlated with different habitats in rivers and the lake.
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Affiliation(s)
- Mo Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Xing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- * E-mail: (XYC); (JXY)
| | - Xiao-Yong Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- * E-mail: (XYC); (JXY)
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Ma Q, Liu S, Zhuang Z, Lin L, Sun Z, Liu C, Ma H, Su Y, Tang Q. Genomic structure, polymorphism and expression analysis of the growth hormone (GH) gene in female and male Half-smooth tongue sole (Cynoglossus semilaevis). Gene 2012; 493:92-104. [DOI: 10.1016/j.gene.2011.11.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 10/08/2011] [Accepted: 11/01/2011] [Indexed: 01/28/2023]
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Clements MD, Bart HL, Hurley DL. A different perspective on the phylogenetic relationships of the Moxostomatini (Cypriniformes: Catostomidae) based on cytochrome-b and Growth Hormone intron sequences. Mol Phylogenet Evol 2012; 63:159-67. [PMID: 22266182 DOI: 10.1016/j.ympev.2012.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 12/21/2011] [Accepted: 01/03/2012] [Indexed: 10/14/2022]
Abstract
We have examined phylogenetic relationships of suckers of tribe Moxostomatini (Cypriniformes, Catostomidae) using cytochrome-b and Growth Hormone gene intron sequences. Phylogenies were significantly different from recent estimates of relationships based primarily on morphology (Smith, 1992) and cytochrome-b sequences (Harris et al., 2002). Overall, there was little support for many basal nodes in the phylogeny, however it was clear that Scartomyzon and Moxostoma were not monophyletic, despite morphological evidence provided Robins and Raney (1956, 1957), Jenkins (1970), and Smith (1992). Growth Hormone sequences provided good support for a monophyletic Western Scartomyzon lineage and thus suggested a single ancestral invasion of Scartomyzon-like fishes into drainages of Texas and Mexico. Phylogenetic relationships of Western Scartomyzon are structured geographically and do not conform well to current taxonomy.
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Affiliation(s)
- Mark D Clements
- Tulane University Museum of Natural History, Belle Chasse, LA 70037, USA.
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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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