1
|
Torsabo D, Ishak SD, Noordin NM, Waiho K, Koh ICC, Yazed MA, Abol-Munafi AB. Optimizing reproductive performance in pangasius catfish broodstock: A review of dietary and molecular strategies. Vet Anim Sci 2024; 25:100375. [PMID: 39005967 PMCID: PMC11245938 DOI: 10.1016/j.vas.2024.100375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024] Open
Abstract
Pangasius catfish, a significant player in the global whitefish market, encounters challenges in aquaculture production sustainability. Quality broodstock maintenance and seed production are impeded by growth, maturation, and fecundity issues. This review investigates the efficacy of strategic nutrient composition and molecular strategies in enhancing broodstock conditions and reproductive performance across various fish species. A notable knowledge gap for Pangasius catfish hampers aquaculture progress. The review assesses nutrient manipulation's impact on reproductive physiology, emphasizing pangasius broodstock. A systematic review analysis following PRISMA guidelines was conducted to identify research trends and hotspots quantitatively, revealing a focus on P. bocourti and fertilization techniques. Addressing this gap, the review offers insights into dietary nutrients manipulation and genetic tool utilization for improved seed production, contributing to pangasius catfish aquaculture sustainability.
Collapse
Affiliation(s)
- Donald Torsabo
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Department of Fisheries and Aquaculture, Joseph Sarwuan Tarka University, Makurdi, Makurdi, Benue State, Nigeria
| | - Sairatul Dahlianis Ishak
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Noordiyana Mat Noordin
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity and Conservation, College of Marine Sciences, Beibu Gulf University, Guangxi, China
- Center for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Ivan Chong Chu Koh
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Muhammad Abduh Yazed
- Faculty of Fisheries and Food Science Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Ambok Bolong Abol-Munafi
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| |
Collapse
|
2
|
Rodríguez-Machado S, Elías DJ, McMahan CD, Gruszkiewicz-Tolli A, Piller KR, Chakrabarty P. Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements. Mol Phylogenet Evol 2024; 190:107965. [PMID: 37977500 DOI: 10.1016/j.ympev.2023.107965] [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: 07/07/2023] [Revised: 10/18/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Poeciliids (Cyprinodontiformes: Poeciliidae), commonly known as livebearers, are popular fishes in the aquarium trade (e.g., guppies, mollies, swordtails) that are widely distributed in the Americas, with 274 valid species in 27 genera. This group has undergone various taxonomic changes recently, spurred by investigations using traditional genetic markers. Here we used over 1,000 ultraconserved loci to infer the relationships within Poeciliidae in the first attempt at understanding their diversification based on genome-scale data. We explore gene tree discordance and investigate potential incongruence between concatenation and coalescent inference methods. Our aim is to examine the influence of incomplete lineage sorting and reticulate evolution on the poeciliids' evolutionary history and how these factors contribute to the observed gene tree discordace. Our concatenated and coalescent phylogenomic inferences recovered four major clades within Poeciliidae. Most supra-generic level relationships we inferred were congruent with previous molecular studies, but we found some disagreements; the Middle American taxa Phallichthys and Poecilia (Mollienesia) were recovered as non-monophyletic, and unlike other recent molecular studies, we recovered Brachyrhaphis as monophyletic. Our study is the first to provide signatures of reticulate evolution in Poeciliidae at the family level; however, continued finer-scale investigations are needed to understand the complex evolutionary history of the family along with a much-needed taxonomic re-evaluation.
Collapse
Affiliation(s)
- Sheila Rodríguez-Machado
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States.
| | - Diego J Elías
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States; Field Museum of Natural History, Chicago, IL 60605, United States
| | - Caleb D McMahan
- Field Museum of Natural History, Chicago, IL 60605, United States
| | - Anna Gruszkiewicz-Tolli
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA 70402, United States
| | - Kyle R Piller
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA 70402, United States
| | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States
| |
Collapse
|
3
|
Yang X, Song Y, Zhang R, Yu M, Guo X, Guo H, Du X, Sun S, Li C, Mao X, Fan G, Liu X. Unravelling the genomic features, phylogeny and genetic basis of tooth ontogenesis in Characiformes through analysis of four genomes. DNA Res 2023; 30:dsad022. [PMID: 37788574 PMCID: PMC10590162 DOI: 10.1093/dnares/dsad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/05/2023] Open
Abstract
Characiformes is a diverse and evolutionarily significant order of freshwater fish encompassing over 2,300 species. Despite its diversity, our understanding of Characiformes' evolutionary relationships and adaptive mechanisms is limited due to insufficient genome sequences. In this study, we sequenced and assembled the genomes of four Characiformes species, three of which were chromosome-level assemblies. Our analyses revealed dynamic changes in gene family evolution, repeat sequences and variations in chromosomal collinearity within these genomes. With the assembled genomes, we were not only able to elucidate the evolutionary relationship of the four main orders in Otophysi but also indicated Characiformes as the paraphyletic group. Comparative genomic analysis with other available fish genomes shed light on the evolution of genes related to tooth development in Characiformes. Notably, variations in the copy number of secretory calcium-binding phosphoproteins (SCPP) genes were observed among different orders of Otophysi, indicating their potential contribution to the diversity of tooth types. Our study offers invaluable genome sequences and novel insights into Characiformes' evolution, paving the way for further genomic and evolutionary research in fish.
Collapse
Affiliation(s)
- Xianwei Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Song
- BGI Research, Qingdao 266555, China
| | | | | | | | | | - Xiao Du
- BGI Research, Qingdao 266555, China
- BGI Research, Shenzhen 518083, China
| | - Shuai Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Qingdao 266555, China
| | | | | | - Guangyi Fan
- BGI Research, Qingdao 266555, China
- BGI Research, Shenzhen 518083, China
| | - Xin Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI Research, Shenzhen 518083, China
| |
Collapse
|
4
|
Nogueira AF, Oliveira C, Langeani F, Netto-Ferreira AL. Phylogenomics, evolution of trophic traits and divergence times of hemiodontid fishes (Ostariophysi: Characiformes). Mol Phylogenet Evol 2023:107864. [PMID: 37343656 DOI: 10.1016/j.ympev.2023.107864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
The South American characiform family Hemiodontidae comprises five genera and 34 species. The family lacks comprehensive phylogenetic hypotheses resolving its species relationships. The studies that addressed these questions exhibited a narrow taxon sampling or used single-locus markers. Herein we surveyed hundreds of ultraconserved elements (UCEs) loci to provide the first molecular phylogenetic hypothesis and divergence time estimates for hemiodontids encompassing all its genera and most species (27 of the 34 valid species). We also tracked the history of the protractile upper jaw in the genera Argonectes and Bivibranchia across the recovered phylogenies through ancestral state reconstruction. Our results corroborate the monophyly of Hemiodontidae and the genera Argonectes and Bivibranchia in all phylogenetic methods with maximum clade support. The genera Anodus and Hemiodus were not monophyletic because Anodus elongatus was sister to the monotypic Micromischodus instead of A. orinocensis, and H. immaculatus did not form a clade with its other congeners, but instead was sister to the clade including Anodus and Micromischodus. All remaining species of Hemiodus were placed together into a monophyletic group, where they were arranged into four major subclades. The relationship in the family is summarised as: (Bivibranchia, (Argonectes, ((H. immaculatus, (Anodus, Micromischodus)), Hemiodus clade))), in discordance with the morphological phylogeny that placed all genera monophyletic and resolved the family as: ((Anodus, Micromischodus), (Hemiodus, (Argonectes, Bivibranchia))). The origin of Hemiodontidae was estimated from the Late Cretaceous to the Middle Paleogene, with the mean age in the Paleocene, while the origin of most hemiodontid genera except Bivibranchia occurred in the Miocene. Unordered parsimony and likelihood reconstruction indicates that Argonectes and Bivibranchia developed their protractile upper jaw independently.
Collapse
Affiliation(s)
- Acácio F Nogueira
- Programa de Pós-Graduação em Zoologia, Instituto de Ciências Biológicas, Universidade Federal do Pará and Museu Paraense Emílio Goeldi, Rua Augusto Corrêa, 01, 66075-110, Belém, PA, Brazil; Laboratório de Biologia e Genética de Peixes, Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Rua Prof. Dr. Antonio C. W. Zanin, 250, 18618-689, Botucatu, SP, Brazil; Laboratório de Ictiologia, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, 91501-970, Porto Alegre, RS, Brazil.
| | - Claudio Oliveira
- Laboratório de Biologia e Genética de Peixes, Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Rua Prof. Dr. Antonio C. W. Zanin, 250, 18618-689, Botucatu, SP, Brazil.
| | - Francisco Langeani
- Departamento de Ciências Biológicas, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265, 15054-000, São José do Rio Preto, SP, Brazil.
| | - André L Netto-Ferreira
- Laboratório de Ictiologia, Departamento de Zoologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, 91501-970, Porto Alegre, RS, Brazil.
| |
Collapse
|
5
|
Pardo-De la Hoz CJ, Magain N, Piatkowski B, Cornet L, Dal Forno M, Carbone I, Miadlikowska J, Lutzoni F. Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria. Syst Biol 2023; 72:694-712. [PMID: 36827095 DOI: 10.1093/sysbio/syad008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 02/12/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. We demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies. [Anomaly zone; bacteria; horizontal gene transfer; incomplete lineage sorting; Nostocales; phylogenomic conflict; rapid radiation; Rhizonema.].
Collapse
Affiliation(s)
| | - Nicolas Magain
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Luc Cornet
- Evolution and Conservation Biology, InBioS Research Center, Université de Liège, Liège 4000, Belgium
- BCCM/IHEM, Mycology and Aerobiology, Sciensano, Brussels, Belgium
| | | | - Ignazio Carbone
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
| | | | | |
Collapse
|
6
|
Elías DJ, McMahan CD, Alda F, García-Alzate C, Hart PB, Chakrabarty P. Phylogenomics of trans-Andean tetras of the genus Hyphessobrycon Durbin 1908 (Stethaprioninae: Characidae) and colonization patterns of Middle America. PLoS One 2023; 18:e0279924. [PMID: 36662755 PMCID: PMC9858358 DOI: 10.1371/journal.pone.0279924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/16/2022] [Indexed: 01/21/2023] Open
Abstract
Hyphessobrycon is one of the most species rich and widely distributed genera in the family Characidae, with more than 160 species ranging from Veracruz, Mexico to Mar Chiquita Lagoon in Buenos Aires, Argentina. The majority of Hyphessobrycon diversity shows a cis-Andean distribution; only nine species are trans-Andean including H. compressus (Meek 1908). It is well established that Hyphessobrycon is not monophyletic but it has been suggested that natural groups can be identified within the larger Hyphessobrycon species group. In this study, we tested the monophyly of trans-Andean species of Hyphessobrycon and investigated the placement of H. compressus. We inferred the first phylogenomic hypothesis of trans-Andean Hyphessobrycon that includes nearly complete taxonomic sampling (eight of nine valid species) using ultraconserved elements (UCEs). We analyzed 75% (1682 UCEs), 90% (1258 UCEs), and 95% (838 UCEs) complete data matrices, and inferred phylogenomic hypotheses under concatenation and coalescent approaches. In all cases, we recovered the monophyly of trans-Andean Hyphessobrycon inclusive of H. compressus, strong support for three species groups, and evidence of cryptic diversity within the widespread H. compressus and H. condotensis. We used our phylogenomic hypothesis to investigate the biogeographic history of Hyphessobrycon in Middle America. Our ancestral range estimation analysis suggests a single event of cis- to trans-Andean colonization followed by stepwise colonization from the Pacific slope of northwestern South America (Chocó block) to northern Middle America (Maya block). Our work supports the recognition of the trans-Andean species as Hyphessobrycon sensu stricto and provides an evolutionary template to examine morphological characters that will allow us to better understand the diversity of Hyphessobrycon in Middle America.
Collapse
Affiliation(s)
- Diego J. Elías
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Caleb D. McMahan
- Field Museum of Natural History, Chicago, Illinois, United States of America
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
- SimCenter: Center for Excellence in Applied Computational Science and Engineering, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
| | - Carlos García-Alzate
- Grupo de Investigación Estudios en Sistemática y Conservación, Universidad del Atlántico-Corporación Universitaria Autónoma del Cauca, Popayán, Colombia
| | - Pamela B. Hart
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, United States of America
| | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| |
Collapse
|
7
|
Alaei Kakhki N, Schweizer M, Lutgen D, Bowie RCK, Shirihai H, Suh A, Schielzeth H, Burri R. A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats. Mol Biol Evol 2023; 40:6964684. [PMID: 36578177 PMCID: PMC10161543 DOI: 10.1093/molbev/msac278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/01/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
Insights into the processes underpinning convergent evolution advance our understanding of the contributions of ancestral, introgressed, and novel genetic variation to phenotypic evolution. Phylogenomic analyses characterizing genome-wide gene tree heterogeneity can provide first clues about the extent of ILS and of introgression and thereby into the potential of these processes or (in their absence) the need to invoke novel mutations to underpin convergent evolution. Here, we were interested in understanding the processes involved in convergent evolution in open-habitat chats (wheatears of the genus Oenanthe and their relatives). To this end, based on whole-genome resequencing data from 50 taxa of 44 species, we established the species tree, characterized gene tree heterogeneity, and investigated the footprints of ILS and introgression within the latter. The species tree corroborates the pattern of abundant convergent evolution, especially in wheatears. The high levels of gene tree heterogeneity in wheatears are explained by ILS alone only for 30% of internal branches. For multiple branches with high gene tree heterogeneity, D-statistics and phylogenetic networks identified footprints of introgression. Finally, long branches without extensive ILS between clades sporting similar phenotypes provide suggestive evidence for the role of novel mutations in the evolution of these phenotypes. Together, our results suggest that convergent evolution in open-habitat chats involved diverse processes and highlight that phenotypic diversification is often complex and best depicted as a network of interacting lineages.
Collapse
Affiliation(s)
- Niloofar Alaei Kakhki
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany
| | - Manuel Schweizer
- Natural History Museum Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Dave Lutgen
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Ornithological Institute, Sempach, Switzerland
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA.,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom.,Department of Organismal Biology - Systematic Biology (EBC), Science for Life Laboratory, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Holger Schielzeth
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Reto Burri
- Department of Population Ecology, Institute of Ecology and Evolution, Friedrich-Schiller-University Jena, Jena, Germany.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Ornithological Institute, Sempach, Switzerland
| |
Collapse
|
8
|
Melo BF, de Pinna MCC, Rapp Py-Daniel LH, Zuanon J, Conde-Saldaña CC, Roxo FF, Oliveira C. Paleogene emergence and evolutionary history of the Amazonian fossorial fish genus Tarumania (Teleostei: Tarumaniidae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.924860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tarumania walkerae is a rare fossorial freshwater fish species from the lower Rio Negro, Central Amazonia, composing the monotypic and recently described family Tarumaniidae. The family has been proposed as the sister group of Erythrinidae by both morphological and molecular studies despite distinct arrangements of the superfamily Erythrinoidea within Characiformes. Recent phylogenomic studies and time-calibrated analyses of characoid fishes have not included specimens of Tarumania in their analyses. We obtained genomic data for T. walkerae and constructed a phylogeny based on 1795 nuclear loci with 488,434 characters of ultraconserved elements (UCEs) for 108 terminals including specimens of all 22 characiform families. The phylogeny confirms the placement of Tarumaniidae as sister to Erythrinidae but differs from the morphological hypothesis in the placement of the two latter families as sister to the clade with Hemiodontidae, Cynodontidae, Serrasalmidae, Parodontidae, Anostomidae, Prochilodontidae, Chilodontidae, and Curimatidae. The phylogeny calibrated with five characoid fossils indicates that Erythrinoidea diverged from their relatives during the Late Cretaceous circa 90 Ma (108–72 Ma), and that Tarumania diverged from the most recent common ancestor of Erythrinidae during the Paleogene circa 48 Ma (66–32 Ma). The occurrence of the erythrinoid-like †Tiupampichthys in the Late Cretaceous–Paleogene formations of the El Molino Basin of Bolivia supports our hypothesis for the emergence of the modern Erythrinidae and Tarumaniidae during the Paleogene.
Collapse
|
9
|
Piller KR, Parker E, Lemmon AR, Moriarty Lemmon E. Investigating the utility of Anchored Hybrid Enrichment data to investigate the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes. Mol Phylogenet Evol 2022; 173:107482. [PMID: 35452841 DOI: 10.1016/j.ympev.2022.107482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 10/18/2022]
Abstract
The Killifishes (Cyprinodontiformes) are a diverse and well-known group of fishes that contains sixteen families inclusive of Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae, Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae, Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae, and Valenciidae and more than 1,200 species that are globally distributed in tropical and temperate, freshwater and estuarine habitats. The evolutionary relationships among the families within the group, based on different molecular and morphological data sets, have remained uncertain. Therefore, the objective of this study was to use a targeted approach, anchored hybrid enrichment, to investigate the phylogenetic relationships among the families within the Cyprindontiformes. This study included more than 100 individuals, representing all sixteen families within the Cyprinodontiformes, including many recently diagnosed families. We recovered an average of 244 loci per individual. These data were submitted to phylogenetic analyses (RaxML and ASTRAL) and although we recovered many of the same relationships as in previous studies of the group, several novel sets of relationships for other families also were recovered. In addition, two well-established clades (Suborders Cyprinodontoidei and Aplocheilodei) were recovered as monophyletic and are in agreement with most previous studies. We also assessed the degree of gene tree discordance in our dataset to evaluate support for alternative topological hypotheses for interfamilial relationships within the Cyprinodontiformes using a variety of different analyses. The results from this study will provide a robust, historical framework needed to investigate a plethora of biogeographic, taxonomic, ecological, and physiological questions for this group of fishes.
Collapse
Affiliation(s)
- Kyle R Piller
- Department of Biological Science, Southeastern Louisiana University, Hammond, LA 70402, USA.
| | - Elyse Parker
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, FL, 32306-4295, USA
| |
Collapse
|
10
|
Hutter CR, Cobb KA, Portik DM, Travers SL, Wood PL, Brown RM. FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales. Mol Ecol Resour 2022; 22:1100-1119. [PMID: 34569723 DOI: 10.1111/1755-0998.13517] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 12/01/2022]
Abstract
Despite the prevalence of high-throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publicly available FrogCap suite of genomic resources, which is a large collection of ~15,000 markers that unifies previous genetic sequencing efforts. FrogCap is designed to be modular, such that subsets of markers and SNPs can be selected based on the desired phylogenetic scale. FrogCap uses a variety of marker types that include exons and introns, ultraconserved elements, and previously sequenced Sanger markers, which span up to 10,000 bp in alignment lengths; in addition, we demonstrate potential for SNP-based analyses. We tested FrogCap using 121 samples distributed across five phylogenetic scales, comparing probes designed using a consensus- or exemplar genome-based approach. Using the consensus design is more resilient to issues with sensitivity, specificity, and missing data than picking an exemplar genome sequence. We also tested the impact of different bait kit sizes (20,020 vs. 40,040) on depth of coverage and found triple the depth for the 20,020 bait kit. We observed sequence capture success (i.e., missing data, sequenced markers/bases, marker length, and informative sites) across phylogenetic scales. The incorporation of different marker types is effective for deep phylogenetic relationships and shallow population genetics studies. Having demonstrated FrogCap's utility and modularity, we conclude that these new resources are efficacious for high-throughput sequencing projects across variable timescales.
Collapse
Affiliation(s)
- Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Kerry A Cobb
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Daniel M Portik
- California Academy of Sciences, San Francisco, California, USA
| | - Scott L Travers
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Department of Biological Sciences, Rutgers University-Newark, Newark, New Jersey, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| |
Collapse
|
11
|
Vera-Alcaraz HS, Rojas BL. FISHES (Actinopteri, Characiformes) FROM THE TAPYTA RESERVE WITH THREE NEW ADDITIONS TO THE PARAGUAYAN ICHTHYOFAUNA. ACTA BIOLÓGICA COLOMBIANA 2022. [DOI: 10.15446/abc.v27n3.90585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The Characiform fish species from the Tapyta Reserve and surrounding area, Caazapa, Paraguay, were inventoried during a year with electrofishing, netting, and trapping. A total of 20 species were registered, being Characidae the richest family. We also report three species as new records to the Paraguayan ichthyofauna and discuss the update of the inventory of fishes from Paraguay.
Collapse
|
12
|
Hart PB, Arnold RJ, Alda F, Kenaley CP, Pietsch TW, Hutchinson D, Chakrabarty P. Evolutionary Relationships Of Anglerfishes (Lophiiformes) Reconstructed Using Ultraconserved Elements. Mol Phylogenet Evol 2022; 171:107459. [DOI: 10.1016/j.ympev.2022.107459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 11/25/2022]
|
13
|
Souza CS, Melo BF, M. T. Mattox G, Oliveira C. Phylogenomic analysis of the Neotropical fish subfamily Characinae using ultraconserved elements (Teleostei: Characidae). Mol Phylogenet Evol 2022; 171:107462. [DOI: 10.1016/j.ympev.2022.107462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 03/10/2022] [Accepted: 03/13/2022] [Indexed: 11/16/2022]
|
14
|
Dornburg A, Near TJ. The Emerging Phylogenetic Perspective on the Evolution of Actinopterygian Fishes. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-122120-122554] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emergence of a new phylogeny of ray-finned fishes at the turn of the twenty-first century marked a paradigm shift in understanding the evolutionary history of half of living vertebrates. We review how the new ray-finned fish phylogeny radically departs from classical expectations based on morphology. We focus on evolutionary relationships that span the backbone of ray-finned fish phylogeny, from the earliest divergences among teleosts and nonteleosts to the resolution of major lineages of Percomorpha. Throughout, we feature advances gained by the new phylogeny toward a broader understanding of ray-finned fish evolutionary history and the implications for topics that span from the genetics of human health to reconsidering the concept of living fossils. Additionally, we discuss conceptual challenges that involve reconciling taxonomic classification with phylogenetic relationships and propose an alternate higher-level classification for Percomorpha. Our review highlights remaining areas of phylogenetic uncertainty and opportunities for comparative investigations empowered by this new phylogenetic perspective on ray-finned fishes.
Collapse
Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina 28223, USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06511, USA
| |
Collapse
|
15
|
Echevarría LY, De la Riva I, Venegas PJ, Rojas-Runjaic FJM, R Dias I, Castroviejo-Fisher S. Total evidence and sensitivity phylogenetic analyses of egg-brooding frogs (Anura: Hemiphractidae). Cladistics 2021; 37:375-401. [PMID: 34478194 DOI: 10.1111/cla.12447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2020] [Indexed: 01/06/2023] Open
Abstract
We study the phylogenetic relationships of egg-brooding frogs, a group of 118 neotropical species, unique among anurans by having embryos with large bell-shaped gills and females carrying their eggs on the dorsum, exposed or inside a pouch. We assembled a total evidence dataset of published and newly generated data containing 51 phenotypic characters and DNA sequences of 20 loci for 143 hemiphractids and 127 outgroup terminals. We performed six analytical strategies combining different optimality criteria (parsimony and maximum likelihood), alignment methods (tree- and similarity-alignment), and three different indel coding schemes (fifth character state, unknown nucleotide, and presence/absence characters matrix). Furthermore, we analyzed a subset of the total evidence dataset to evaluate the impact of phenotypic characters on hemiphractid phylogenetic relationships. Our main results include: (i) monophyly of Hemiphractidae and its six genera for all our analyses, novel relationships among hemiphractid genera, and non-monophyly of Hemiphractinae according to our preferred phylogenetic hypothesis; (ii) non-monophyly of current supraspecific taxonomies of Gastrotheca, an updated taxonomy is provided; (iii) previous differences among studies were mainly caused by differences in analytical factors, not by differences in character/taxon sampling; (iv) optimality criteria, alignment method, and indel coding caused differences among optimal topologies, in that order of degree; (v) in most cases, parsimony analyses are more sensitive to the addition of phenotypic data than maximum likelihood analyses; (vi) adding phenotypic data resulted in an increase of shared clades for most analyses.
Collapse
Affiliation(s)
- Lourdes Y Echevarría
- Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, Porto Alegre, RS, 90619-900, Brazil.,División de Herpetología-Centro de Ornitología y Biodiversidad (CORBIDI), Urb. Huertos de San Antonio, Santa Rita No. 105 Of. 202, Surco, Lima, Perú
| | - Ignacio De la Riva
- Museo Nacional de Ciencias Naturales-CSIC, C/José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Pablo J Venegas
- División de Herpetología-Centro de Ornitología y Biodiversidad (CORBIDI), Urb. Huertos de San Antonio, Santa Rita No. 105 Of. 202, Surco, Lima, Perú
| | | | - Iuri R Dias
- Graduate Program in Zoology, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, Ilhéus, Bahia, 45662-900, Brazil
| | - Santiago Castroviejo-Fisher
- Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Av. Ipiranga 6681, Porto Alegre, RS, 90619-900, Brazil.,Department of Herpetology, American Museum of Natural History, New York, NY, 10024, USA
| |
Collapse
|
16
|
Alda F, Ludt WB, Elías DJ, McMahan CD, Chakrabarty P. Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree. Genome Biol Evol 2021; 13:evab161. [PMID: 34272856 PMCID: PMC8369075 DOI: 10.1093/gbe/evab161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here, we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different data sets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel data set of ultraconserved elements (UCEs) and a recently published exon data set of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of colonization and diversification in Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent data sets disagreed in areas with low phylogenetic signal that were overwhelmed by incomplete lineage sorting and nonphylogenetic signals. For UCEs, high levels of incomplete lineage sorting were found to be the major cause of gene tree discordance, whereas, for exons, nonphylogenetic signal is most likely caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.
Collapse
Affiliation(s)
- Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Tennessee, USA
| | - William B Ludt
- Department of Ichthyology, Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Diego J Elías
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | | | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| |
Collapse
|
17
|
Smith BT, Mauck WM, Benz BW, Andersen MJ. Uneven Missing Data Skew Phylogenomic Relationships within the Lories and Lorikeets. Genome Biol Evol 2021; 12:1131-1147. [PMID: 32470111 PMCID: PMC7486955 DOI: 10.1093/gbe/evaa113] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2020] [Indexed: 01/21/2023] Open
Abstract
The resolution of the Tree of Life has accelerated with advances in DNA sequencing technology. To achieve dense taxon sampling, it is often necessary to obtain DNA from historical museum specimens to supplement modern genetic samples. However, DNA from historical material is generally degraded, which presents various challenges. In this study, we evaluated how the coverage at variant sites and missing data among historical and modern samples impacts phylogenomic inference. We explored these patterns in the brush-tongued parrots (lories and lorikeets) of Australasia by sampling ultraconserved elements in 105 taxa. Trees estimated with low coverage characters had several clades where relationships appeared to be influenced by whether the sample came from historical or modern specimens, which were not observed when more stringent filtering was applied. To assess if the topologies were affected by missing data, we performed an outlier analysis of sites and loci, and a data reduction approach where we excluded sites based on data completeness. Depending on the outlier test, 0.15% of total sites or 38% of loci were driving the topological differences among trees, and at these sites, historical samples had 10.9× more missing data than modern ones. In contrast, 70% data completeness was necessary to avoid spurious relationships. Predictive modeling found that outlier analysis scores were correlated with parsimony informative sites in the clades whose topologies changed the most by filtering. After accounting for biased loci and understanding the stability of relationships, we inferred a more robust phylogenetic hypothesis for lories and lorikeets.
Collapse
Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, New York
| | - William M Mauck
- Department of Ornithology, American Museum of Natural History, New York, New York.,New York Genome Center, New York, New York
| | - Brett W Benz
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico
| |
Collapse
|
18
|
Duchen P, Salamin N. A Cautionary Note on the Use of Genotype Callers in Phylogenomics. Syst Biol 2021; 70:844-854. [PMID: 33084875 PMCID: PMC8208803 DOI: 10.1093/sysbio/syaa081] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Next-generation-sequencing genotype callers are commonly used in studies to call variants from newly sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are optimized for variant calling at the population level. However, when these callers are used at the phylogenetic level, the consequences for downstream analyses can be substantial. Here, we performed simulations to compare the performance between the genotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show that the genotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also found that the accuracy of heterozygote calls declines with increasing distance to the reference genome. We quantified this decline and found that it is very sharp in GATK, while ATLAS maintains high accuracy even at moderately divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies. [ATLAS; efficiency of SNP calling; GATK; heterozygote calling; next-generation sequencing; reference genome; variant calling.].
Collapse
Affiliation(s)
- Pablo Duchen
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Quartier Sorge, 1015 Lausanne, Switzerland
| |
Collapse
|
19
|
Sidlauskas BL, Assega FM, Melo BF, Oliveira C, Birindelli JLO. Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The nearly 150 species of Anostomidae comprise one of the most diverse and taxonomically dynamic families of Neotropical freshwater fishes. A recent revision of the enigmatic and poorly diagnosed genus Anostomoides demonstrated that it contains two valid species, each with complicated taxonomic histories; however, that study did not address their phylogenetic placement. Herein, we integrate molecular and morphological data to demonstrate their distant evolutionary relationship, and thus the polyphyly of Anostomoides. While we reconstruct one of the species in a previously hypothesized placement within a clade also containing Laemolyta, Rhytiodus and Schizodon, the other represents a morphologically and genetically distinctive lineage that diverged early in the history of the family. We describe and illustrate the osteology of this remarkable species, discuss the evolutionary implications of its unique suite of features, and use those characteristics to diagnose a new genus that evolved independently of all other known members of the family for approximately 37 Myr.
Collapse
Affiliation(s)
- Brian L Sidlauskas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Fernando M Assega
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Estadual de Londrina, Centro de Ciencias Biologicas, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, Londrina, PR, Brazil
| | - Bruno F Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antonio C. W. Zanin, Rubião Jr, Botucatu, SP, Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antonio C. W. Zanin, Rubião Jr, Botucatu, SP, Brazil
| | - José L O Birindelli
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Estadual de Londrina, Centro de Ciencias Biologicas, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, Londrina, PR, Brazil
| |
Collapse
|
20
|
Melo BF, Sidlauskas BL, Near TJ, Roxo FF, Ghezelayagh A, Ochoa LE, Stiassny MLJ, Arroyave J, Chang J, Faircloth BC, MacGuigan DJ, Harrington RC, Benine RC, Burns MD, Hoekzema K, Sanches NC, Maldonado-Ocampo JA, Castro RMC, Foresti F, Alfaro ME, Oliveira C. Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes. Syst Biol 2021; 71:78-92. [PMID: 34097063 DOI: 10.1093/sysbio/syab040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1,288 ultraconserved element loci (UCE) spanning 293 species, 211 genera and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 million years ago (Ma) during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2,150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity.
Collapse
Affiliation(s)
- Bruno F Melo
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Brian L Sidlauskas
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Thomas J Near
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Fabio F Roxo
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Ava Ghezelayagh
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Luz E Ochoa
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil.,Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Palmira, Valle del Cauca, 763547, Colombia
| | - Melanie L J Stiassny
- Dept of Ichthyology, American Museum of Natural History, New York, NY, 10024, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Jonathan Chang
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Brant C Faircloth
- Dept of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Daniel J MacGuigan
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Richard C Harrington
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Ricardo C Benine
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Michael D Burns
- Cornell Lab of Ornithology, Cornell University Museum of Vertebrates, Ithaca, NY, 14850, USA
| | - Kendra Hoekzema
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Natalia C Sanches
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Javier A Maldonado-Ocampo
- Dept de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia (in memoriam)
| | - Ricardo M C Castro
- Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Fausto Foresti
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Michael E Alfaro
- Dept of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudio Oliveira
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| |
Collapse
|
21
|
Roussel J, Covain R, Vigouroux R, Allard L, Treguier A, Papa Y, Le Bail P. Fish communities critically depend on forest subsidies in small neotropical streams with high biodiversity value. Biotropica 2021. [DOI: 10.1111/btp.12949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jean‐Marc Roussel
- INRAE Institut Agro, Ecology and Ecosystem Health (UMR ESE) Rennes France
| | - Raphael Covain
- Department of Herpetology and Ichthyology JM Roussel Geneva Switzerland
| | - Regis Vigouroux
- Laboratoire Environnement de Petit Saut Hydreco Guyane Kourou France
| | - Luc Allard
- Laboratoire Environnement de Petit Saut Hydreco Guyane Kourou France
| | - Anne Treguier
- INRAE Institut Agro, Ecology and Ecosystem Health (UMR ESE) Rennes France
| | - Yvan Papa
- Department of Herpetology and Ichthyology JM Roussel Geneva Switzerland
| | | |
Collapse
|
22
|
dos Santos RZ, Calegari RM, Silva DMZDA, Ruiz-Ruano FJ, Melo S, Oliveira C, Foresti F, Uliano-Silva M, Porto-Foresti F, Utsunomia R. A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed. Genome Biol Evol 2021; 13:evab002. [PMID: 33502491 PMCID: PMC8210747 DOI: 10.1093/gbe/evab002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satellite DNAs (satDNAs). These sequences are highly dynamic and tend to be genus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that an satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, ∼140-78 Ma, whereas its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satDNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidium gomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within single-molecule real-time long reads of Astyanax paranae (536 bp-3.1 kb) and A. mexicanus (501 bp-3.9 kb). Such arrays consisted of head-to-tail repeats and could be found interspersed with other sequences, inverted sequences, or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satDNA evolution.
Collapse
Affiliation(s)
- Rodrigo Zeni dos Santos
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Rodrigo Milan Calegari
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | | | - Francisco J Ruiz-Ruano
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology
Centre, Uppsala University, Uppsala, Sweden
| | - Silvana Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | | | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS,
Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janerio,
Brazil
| |
Collapse
|
23
|
Lopes F, Oliveira LR, Kessler A, Beux Y, Crespo E, Cárdenas-Alayza S, Majluf P, Sepúlveda M, Brownell RL, Franco-Trecu V, Páez-Rosas D, Chaves J, Loch C, Robertson BC, Acevedo-Whitehouse K, Elorriaga-Verplancken FR, Kirkman SP, Peart CR, Wolf JBW, Bonatto SL. Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere. Syst Biol 2020; 70:786-802. [PMID: 33367817 DOI: 10.1093/sysbio/syaa099] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 12/25/2022] Open
Abstract
The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here, we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 and 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be nonmonophyletic, with California (Zalophus californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Zalophus wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family. [Hybridization; ILS; phylogenomics; Pleistocene; Pliocene; monophyly.].
Collapse
Affiliation(s)
- Fernando Lopes
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil.,Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil
| | - Larissa R Oliveira
- Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, Brazil.,GEMARS, Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, 95560-000 Torres, RS, Brazil
| | - Amanda Kessler
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
| | - Yago Beux
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
| | - Enrique Crespo
- Centro Nacional Patagónico - CENPAT, CONICET, Puerto Madryn, Argentina
| | - Susana Cárdenas-Alayza
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Patricia Majluf
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maritza Sepúlveda
- Centro de Investigación y Gestión de Recursos Naturales (CIGREN), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Robert L Brownell
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, NOAA, La Jolla, USA
| | - Valentina Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Diego Páez-Rosas
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jaime Chaves
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador.,Department of Biology, San Francisco State University, 1800 Holloway Ave, San Francisco, CA, USA
| | - Carolina Loch
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | | | - Karina Acevedo-Whitehouse
- Unit for Basic and Applied Microbiology, School of Natural Sciences, Universidad Autónoma de Querétaro, Querétaro, Mexico
| | | | - Stephen P Kirkman
- Department of Environmental Affairs, Oceans and Coasts, Cape Town, South Africa
| | - Claire R Peart
- Department Biologie II, Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Jochen B W Wolf
- Department Biologie II, Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Sandro L Bonatto
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, 90619-900 Porto Alegre, RS, Brazil
| |
Collapse
|
24
|
Hughes LC, Ortí G, Saad H, Li C, White WT, Baldwin CC, Crandall KA, Arcila D, Betancur-R R. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Mol Ecol Resour 2020; 21:816-833. [PMID: 33084200 DOI: 10.1111/1755-0998.13287] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022]
Abstract
Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.
Collapse
Affiliation(s)
- Lily C Hughes
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Guillermo Ortí
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Hadeel Saad
- Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Chenhong Li
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - William T White
- CSIRO Australian National Fish Collection, National Research Collections of Australia, Hobart, TAS, Australia
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Keith A Crandall
- Department of Biological Sciences, George Washington University, Washington, DC, USA.,Computational Biology Institute, Milken Institute of Public Health, George Washington University, Washington, DC, USA
| | - Dahiana Arcila
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Sam Noble Oklahoma Museum of Natural History, Norman, OK, USA.,Department of Biology, University of Oklahoma, Norman, OK, USA
| | | |
Collapse
|
25
|
Albert JS, Tagliacollo VA, Dagosta F. Diversification of Neotropical Freshwater Fishes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-011620-031032] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neotropical freshwater fishes (NFFs) constitute the most diverse continental vertebrate fauna on Earth, with more than 6,200 named species compressed into an aquatic footprint <0.5% of the total regional land-surface area and representing the greatest phenotypic disparity and functional diversity of any continental ichthyofauna. Data from the fossil record and time-calibrated molecular phylogenies indicate that most higher taxa (e.g., genera, families) diversified relatively continuously through the Cenozoic, across broad geographic ranges of the South American platform. Biodiversity data for most NFF clades support a model of continental radiation rather than adaptive radiation, in which speciation occurs mainly in allopatry, and speciation and adaptation are largely decoupled. These radiations occurred under the perennial influence of river capture and sea-level oscillations, which episodically fragmented and merged portions of adjacent river networks. The future of the NFF fauna into the Anthropocene is uncertain, facing numerous threats at local, regional, and continental scales.
Collapse
Affiliation(s)
- James S. Albert
- Department of Biology, University of Louisiana at Lafayette, Louisiana 70504, USA
| | | | - Fernando Dagosta
- Faculty of Biological and Environmental Sciences, Universidade Federal da Grande Dourados, Brazil 79825-070
| |
Collapse
|
26
|
Kolmann MA, Hughes LC, Hernandez LP, Arcila D, Betancur-R R, Sabaj MH, López-Fernández H, Ortí G. Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy. Syst Biol 2020; 70:576-592. [PMID: 32785670 DOI: 10.1093/sysbio/syaa065] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023] Open
Abstract
The Amazon and neighboring South American river basins harbor the world's most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of the top riverine predators as well as the primary seed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial. For example, the sister taxon to serrasalmids is contentious, the relationships of major clades within the family are inconsistent across different methodologies, and half of the extant serrasalmid genera are suggested to be non-monophyletic. We analyzed exon capture to reexamine the evolutionary relationships among 63 (of 99) species across all 16 serrasalmid genera and their nearest outgroups, including multiple individuals per species to account for cryptic lineages. To reconstruct the timeline of serrasalmid diversification, we time-calibrated this phylogeny using two different fossil-calibration schemes to account for uncertainty in taxonomy with respect to fossil teeth. Finally, we analyzed diet evolution across the family and comment on associated changes in dentition, highlighting the ecomorphological diversity within serrasalmids. We document widespread non-monophyly of genera within Myleinae, as well as between Serrasalmus and Pristobrycon, and propose that reliance on traits like teeth to distinguish among genera is confounded by ecological homoplasy, especially among herbivorous and omnivorous taxa. We clarify the relationships among all serrasalmid genera, propose new subfamily affiliations, and support hemiodontids as the sister taxon to Serrasalmidae. [Characiformes; exon capture; ichthyochory; molecular time-calibration; piscivory.].
Collapse
Affiliation(s)
- M A Kolmann
- Dept of Biological Sciences, George Washington University, 2029 G St. NW, Washington, DC 20052, USA.,Dept of Natural History, Royal Ontario Museum, 100 Queens Park, Toronto, ON M5S 2C6, Canada
| | - L C Hughes
- Dept of Biological Sciences, George Washington University, 2029 G St. NW, Washington, DC 20052, USA.,Dept of Ichthyology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| | - L P Hernandez
- Dept of Biological Sciences, George Washington University, 2029 G St. NW, Washington, DC 20052, USA
| | - D Arcila
- Dept of Ichthyology, Sam Noble Museum, 2401 Chautauqua Ave, Norman, OK 73072, USA.,Dept of Biology, University of Oklahoma, 660 Parrington Oval, Norman, OK 73019, USA
| | - R Betancur-R
- Dept of Ichthyology, Sam Noble Museum, 2401 Chautauqua Ave, Norman, OK 73072, USA.,Dept of Biology, University of Oklahoma, 660 Parrington Oval, Norman, OK 73019, USA
| | - M H Sabaj
- Dept of Ichthyology, The Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Pkwy, Philadelphia, PA 19103, USA
| | - H López-Fernández
- Museum of Zoology, University of Michigan, 1105 North University Dr., Ann Arbor, MI 48109, USA
| | - G Ortí
- Dept of Biological Sciences, George Washington University, 2029 G St. NW, Washington, DC 20052, USA.,Dept of Ichthyology, Smithsonian National Museum of Natural History, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| |
Collapse
|
27
|
Escobar-Camacho D, Carleton KL, Narain DW, Pierotti MER. Visual pigment evolution in Characiformes: The dynamic interplay of teleost whole-genome duplication, surviving opsins and spectral tuning. Mol Ecol 2020; 29:2234-2253. [PMID: 32421918 DOI: 10.1111/mec.15474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 01/06/2023]
Abstract
Vision represents an excellent model for studying adaptation, given the genotype-to-phenotype map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light, making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we showcase the visual system evolution of neotropical Characiformes and the spectral tuning mechanisms they exhibit to modulate their visual sensitivities. Such mechanisms include gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A1 /A2 -chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the characiform's entire opsin gene repertoire is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS- and RH1-duplicates originated from a teleost specific whole-genome duplication as well as characiform-specific duplication events. Both LWS-opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS-paralogues has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. Furthermore, characiforms' colour vision is based on the expression of both LWS-paralogues and SWS2. Finally, we found interspecific and intraspecific variation in A1 /A2 -chromophores proportions, correlating with the light environment. These multiple mechanisms may be a result of the diverse visual environments where Characiformes have evolved.
Collapse
Affiliation(s)
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Devika W Narain
- Environmental Sciences, Anton de Kom University of Suriname, Paramaribo, Suriname
| | - Michele E R Pierotti
- Naos Marine Laboratories, Smithsonian Tropical Research Institute, Panama, Republic of Panama
| |
Collapse
|
28
|
Wcisel DJ, Howard JT, Yoder JA, Dornburg A. Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly. BMC Evol Biol 2020; 20:41. [PMID: 32228442 PMCID: PMC7106827 DOI: 10.1186/s12862-020-01603-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/11/2020] [Indexed: 01/05/2023] Open
Abstract
Background Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to efficiently identify orthologous sequences currently hinders effective harnessing of this resource. Results We introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-defined acceptable missing data levels for a given research question. Conclusions TOAST provides a comprehensive set of tools for assembly of sequence alignments of orthologs for comparative transcriptomic and phylogenomic studies. This software empowers easy assembly of public and novel sequences for any target database of candidate orthologs, and fills a critically needed niche for tools that enable quantification and testing of the impact of missing data. As open-source software, TOAST is fully customizable for integration into existing or novel custom informatic pipelines for phylogenomic inference. Software, a detailed manual, and example data files are available through github carolinafishes.github.io
Collapse
Affiliation(s)
- Dustin J Wcisel
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
| | - J Thomas Howard
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA.,Comparative Medicine Institute, NC State University, Raleigh, NC, USA.,Center for Human Health and the Environment, NC State University, Raleigh, NC, USA
| | - Alex Dornburg
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA.
| |
Collapse
|
29
|
Phylogenomic analysis of trichomycterid catfishes (Teleostei: Siluriformes) inferred from ultraconserved elements. Sci Rep 2020; 10:2697. [PMID: 32060350 PMCID: PMC7021825 DOI: 10.1038/s41598-020-59519-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 01/28/2020] [Indexed: 11/22/2022] Open
Abstract
The family Trichomycteridae is one of the most diverse groups of freshwater catfishes in South and Central America with eight subfamilies, 41 genera and more than 300 valid species. Its members are widely distributed throughout South America, reaching Costa Rica in Central America and are recognized by extraordinary anatomical specializations and trophic diversity. In order to assess the phylogenetic relationships of Trichomycteridae, we collected sequence data from ultraconserved elements (UCEs) of the genome from 141 specimens of Trichomycteridae and 12 outgroup species. We used a concatenated matrix to assess the phylogenetic relationships by Bayesian inference (BI) and maximum likelihood (ML) searches and a coalescent analysis of species trees. The results show a highly resolved phylogeny with broad agreement among the three distinct analyses, providing overwhelming support for the monophyletic status of subfamily Trichomycterinae including Ituglanis and Scleronema. Previous relationship hypotheses among subfamilies are strongly corroborated, such as the sister relationship between Copionodontinae and Trichogeninae forming a sister clade to the remaining trichomycterids and the intrafamilial clade TSVSG (Tridentinae-Stegophilinae-Vandelliinae-Sarcoglanidinae-Glanapteryginae). Monophyly of Glanapteryginae and Sarcoglanidinae was not supported and the enigmatic Potamoglanis is placed outside Tridentinae.
Collapse
|
30
|
Faircloth BC, Alda F, Hoekzema K, Burns MD, Oliveira C, Albert JS, Melo BF, Ochoa LE, Roxo FF, Chakrabarty P, Sidlauskas BL, Alfaro ME. A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes. COPEIA 2020. [DOI: 10.1643/cg-18-139] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Brant C. Faircloth
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803; (BCF) ; and (PC) . Send reprint requests to BCF
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403;
| | - Kendra Hoekzema
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Michael D. Burns
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - James S. Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana 70503;
| | - Bruno F. Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - Luz E. Ochoa
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo 18618-689, Brazil; (CO) ; (BFM) ; and (LEO)
| | - Fábio F. Roxo
- Departamento de Zoologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil;
| | - Prosanta Chakrabarty
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803; (BCF) ; and (PC) . Send reprint requests to BCF
| | - Brian L. Sidlauskas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon 97331; (KH) ; and (BLS)
| | - Michael E. Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095;
| |
Collapse
|
31
|
Yang L, Jiang H, Chen J, Lei Y, Sun N, Lv W, Near TJ, He S. Comparative Genomics Reveals Accelerated Evolution of Fright Reaction Genes in Ostariophysan Fishes. Front Genet 2019; 10:1283. [PMID: 31921316 PMCID: PMC6936194 DOI: 10.3389/fgene.2019.01283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/21/2019] [Indexed: 11/13/2022] Open
Abstract
The ostariophysian fishes are the most species-rich clade in freshwaters. This diversification has been suggested to be associated with the fright reaction presented in most ostariophysians. However, the genetic forces that underlie fright reaction remains poorly understood. In the present study, through integrating behavioral, physiological, transcriptomic, and evolutionary genomic analyses, we found that the fright reaction has a broad impact on zebrafish at multiple levels, including changes in swimming behaviors, cortisol levels, and gene expression patterns. In total, 1,555 and 1,599 differentially expressed genes were identified in olfactory mucosae and brain of zebrafish, respectively, with a greater number upregulated after the fright reaction. Functional annotation showed that response to stress and signal transduction were strongly represented, which is directly associated with the fright reaction. These differentially expressed genes were shown to be evolved accelerated under the influence of positive selection, indicating that protein-coding evolution has played a major role in fright reaction. We found the basal vomeronasal type 2 receptors (v2r) gene, v2rl1, displayed significantly decrease expression after fright reaction, which suggests that v2rs may be important to detect the alarm substance and induce the fright reaction. Collectively, based on our transcriptome and evolutionary genomics analyses, we suggest that transcriptional plasticity of gene may play an important role in fright reaction in ostariophysian fishes.
Collapse
Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Juan Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi Lei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning Sun
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT, United States
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
32
|
Cabra-García J, Hormiga G. Exploring the impact of morphology, multiple sequence alignment and choice of optimality criteria in phylogenetic inference: a case study with the Neotropical orb-weaving spider genus Wagneriana (Araneae: Araneidae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Abstract
We present a total evidence phylogenetic analysis of the Neotropical orb-weaving spider genus Wagneriana and discuss the phylogenetic impacts of methodological choices. We analysed 167 phenotypic characters and nine loci scored for 115 Wagneriana and outgroups, including 46 newly sequenced species. We compared total evidence analyses and molecular-only analyses to evaluate the impact of phenotypic evidence, and we performed analyses using the programs POY, TNT, RAxML, GARLI, IQ-TREE and MrBayes to evaluate the effects of multiple sequence alignment and optimality criteria. In all analyses, Wagneriana carimagua and Wagneriana uropygialis were nested in the genera Parawixia and Alpaida, respectively, and the remaining species of Wagneriana fell into three main clades, none of which formed a pair of sister taxa. However, sister-group relationships among the main clades and their internal relationships were strongly influenced by methodological choices. Alignment methods had comparable topological effects to those of optimality criteria in terms of ‘subtree pruning and regrafting’ moves. The inclusion of phenotypic evidence, 2.80–3.05% of the total evidence matrices, increased support irrespective of the optimality criterion used. The monophyly of some groups was recovered only after the addition of morphological characters. A new araneid genus, Popperaneus gen. nov., is erected, and Paraverrucosa is resurrected. Four new synonymies and seven new combinations are proposed.
Collapse
Affiliation(s)
- Jimmy Cabra-García
- Departamento de Biología, Universidad del Valle, Cali, AA, Colombia
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gustavo Hormiga
- The George Washington University, Department of Biological Sciences, Washington, DC, USA
| |
Collapse
|
33
|
Pastana MNL, Bockmann FA, Datovo A. The cephalic lateral-line system of Characiformes (Teleostei: Ostariophysi): anatomy and phylogenetic implications. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz105] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractThe lateral-line system has been traditionally recognized as an important source of phylogenetic information for different groups of fishes. Although extensively studied in Siluriformes and Cypriniformes, the lateral-line system of Characiformes remained underexplored. In the present study, the anatomy of the cephalic lateral-line canals of characiforms is described in detail and a unifying terminology that considers the ontogeny and homologies of the components of this system is offered. Aspects of the arrangement of lateral-line canals, as well as the number, location and size of canal tubules and pores, resulted in the identification of novel putative synapomorphies for Characiformes and several of its subgroups. The study also revised synapomorphies previously proposed for different characiform families and provided comments on their observed distribution across the order based on extensive taxon sampling. Information from the ontogenetic studies of the cephalic lateral-line canal system and a proposal for the proper use of these data to detect truncations in the development of the lateral-line canals across the order is also offered.
Collapse
Affiliation(s)
- Murilo N L Pastana
- Laboratório de Ictiologia, Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
| | - Flávio A Bockmann
- Laboratório de Ictiologia de Ribeirão Preto, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Aléssio Datovo
- Laboratório de Ictiologia, Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
34
|
Abstract
Abstract
The Afrotropics house a diverse freshwater ichthyofauna with > 3000 species, almost all of which are endemic. Recent progress in dated phylogenetics and palaeontology of several groups of Afrotropical freshwater fishes (AFFs) has allowed the testing of palaeoecology- and palaeogeography-based hypotheses explaining their early presence in Africa. Seven hypotheses were tested for 37 most-inclusive monophyletic groups of AFFs. Results indicated that ten lineages originated from direct, but asynchronous, marine-to-freshwater shifts. These lineages contribute < 2% to the current AFF species richness. Eleven lineages colonized the Afrotropics from the Orient after the Afro-Arabian plate collided with Eurasia in the early Oligocene. These lineages contribute ~20% to the total diversity. There are seven sister relationships between Afrotropical and Neotropical taxa. For only three of them (4% of the species diversity), the continental drift vicariance hypothesis was not rejected. Distributions of the other four younger trans-Atlantic lineages are better explained by post-drifting long-distance dispersal. In those cases, I discuss the possibility of dispersal through the Northern Hemisphere as an alternative to direct trans-Atlantic dispersal. The origins of ten AFF lineages, including the most species-rich Pseudocrenilabrinae (> 1100 species), are not yet established with confidence.
Collapse
Affiliation(s)
- Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| |
Collapse
|
35
|
Crampton WGR. Electroreception, electrogenesis and electric signal evolution. JOURNAL OF FISH BIOLOGY 2019; 95:92-134. [PMID: 30729523 DOI: 10.1111/jfb.13922] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 02/05/2019] [Indexed: 05/06/2023]
Abstract
Electroreception, the capacity to detect external underwater electric fields with specialised receptors, is a phylogenetically widespread sensory modality in fishes and amphibians. In passive electroreception, a capacity possessed by c. 16% of fish species, an animal uses low-frequency-tuned ampullary electroreceptors to detect microvolt-range bioelectric fields from prey, without the need to generate its own electric field. In active electroreception (electrolocation), which occurs only in the teleost lineages Mormyroidea and Gymnotiformes, an animal senses its surroundings by generating a weak (< 1 V) electric-organ discharge (EOD) and detecting distortions in the EOD-associated field using high-frequency-tuned tuberous electroreceptors. Tuberous electroreceptors also detect the EODs of neighbouring fishes, facilitating electrocommunication. Several other groups of elasmobranchs and teleosts generate weak (< 10 V) or strong (> 50 V) EODs that facilitate communication or predation, but not electrolocation. Approximately 1.5% of fish species possess electric organs. This review has two aims. First, to synthesise our knowledge of the functional biology and phylogenetic distribution of electroreception and electrogenesis in fishes, with a focus on freshwater taxa and with emphasis on the proximate (morphological, physiological and genetic) bases of EOD and electroreceptor diversity. Second, to describe the diversity, biogeography, ecology and electric signal diversity of the mormyroids and gymnotiforms and to explore the ultimate (evolutionary) bases of signal and receptor diversity in their convergent electrogenic-electrosensory systems. Four sets of potential drivers or moderators of signal diversity are discussed. First, selective forces of an abiotic (environmental) nature for optimal electrolocation and communication performance of the EOD. Second, selective forces of a biotic nature targeting the communication function of the EOD, including sexual selection, reproductive interference from syntopic heterospecifics and selection from eavesdropping predators. Third, non-adaptive drift and, finally, phylogenetic inertia, which may arise from stabilising selection for optimal signal-receptor matching.
Collapse
|
36
|
Yang L, Jiang H, Wang Y, Lei Y, Chen J, Sun N, Lv W, Wang C, Near TJ, He S. Expansion of vomeronasal receptor genes ( OlfC) in the evolution of fright reaction in Ostariophysan fishes. Commun Biol 2019; 2:235. [PMID: 31263779 PMCID: PMC6588630 DOI: 10.1038/s42003-019-0479-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/28/2019] [Indexed: 12/15/2022] Open
Abstract
Ostariophysans are the most diverse group of freshwater fishes and feature a pheromone-elicited fright reaction. However, the genetic basis of fright reaction is unclear. Here, we compared vomeronasal type 2 receptor-like (OlfC) genes from fishes having and lacking fright reaction, to provide insight into evolution of pheromonal olfaction in fishes. We found OlfC genes expanded remarkably in ostariophysans having fright reaction compared with fishes lacking fright reaction. Phylogenetic analysis indicates OlfC subfamily 9 expanded specifically in ostariophysans having fright reaction. Principle component and phylogenetic logistic regression analysis partitioned fishes by ecotype (having or lacking fright reaction) and identified OlfC subfamily 9 as being an important factor for fright reaction. Expression levels of expanded OlfC subfamily genes after fright reaction in zebrafish changed more than did genes that had not expanded. Furthermore, evidence of positive selection was found in the expanded OlfC proteins in ostariophysan fishes having fright reaction. These results provide new insight into the genetic basis of fright reaction in ostariophysan fish and will enable future research into the mechanism of action of OlfC proteins.
Collapse
Affiliation(s)
- Liandong Yang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 People’s Republic of China
| | - Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 People’s Republic of China
- University of Chinese Academy of Sciences, 100049 Beijing, People’s Republic of China
| | - Ying Wang
- School of Life Sciences, Jianghan University, 430056 Wuhan, People’s Republic of China
| | - Yi Lei
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 People’s Republic of China
- University of Chinese Academy of Sciences, 100049 Beijing, People’s Republic of China
| | - Juan Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 People’s Republic of China
- University of Chinese Academy of Sciences, 100049 Beijing, People’s Republic of China
| | - Ning Sun
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 People’s Republic of China
- University of Chinese Academy of Sciences, 100049 Beijing, People’s Republic of China
| | - Wenqi Lv
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 People’s Republic of China
- University of Chinese Academy of Sciences, 100049 Beijing, People’s Republic of China
| | - Cheng Wang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 People’s Republic of China
- University of Chinese Academy of Sciences, 100049 Beijing, People’s Republic of China
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520 USA
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 People’s Republic of China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, People’s Republic of China
| |
Collapse
|
37
|
Roxo FF, Ochoa LE, Sabaj MH, Lujan NK, Covain R, Silva GS, Melo BF, Albert JS, Chang J, Foresti F, Alfaro ME, Oliveira C. Phylogenomic reappraisal of the Neotropical catfish family Loricariidae (Teleostei: Siluriformes) using ultraconserved elements. Mol Phylogenet Evol 2019; 135:148-165. [DOI: 10.1016/j.ympev.2019.02.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/09/2019] [Accepted: 02/18/2019] [Indexed: 12/15/2022]
|
38
|
Parker E, Dornburg A, Domínguez-Domínguez O, Piller KR. Assessing phylogenetic information to reveal uncertainty in historical data: An example using Goodeinae (Teleostei: Cyprinodontiformes: Goodeidae). Mol Phylogenet Evol 2019; 134:282-290. [DOI: 10.1016/j.ympev.2019.01.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/17/2019] [Accepted: 01/30/2019] [Indexed: 01/18/2023]
|
39
|
Jiang J, Yuan H, Zheng X, Wang Q, Kuang T, Li J, Liu J, Song S, Wang W, Cheng F, Li H, Huang J, Li C. Gene markers for exon capture and phylogenomics in ray-finned fishes. Ecol Evol 2019; 9:3973-3983. [PMID: 31015981 PMCID: PMC6468074 DOI: 10.1002/ece3.5026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/30/2022] Open
Abstract
Gene capture coupled with the next-generation sequencing has become one of the preferred methods of subsampling genomes for phylogenomic studies. Many exon markers have been developed in plants, sharks, frogs, reptiles, fishes, and others, but no universal exon markers have been tested in ray-finned fishes. Here, we identified a suite of "single-copy" protein-coding sequence (CDS) markers through comparing eight fish genomes, and tested them empirically in 83 species (33 families and nine orders or higher clades: Acipenseriformes, Lepisosteiformes, Elopomorpha, Osteoglossomorpha, Clupeiformes, Cypriniformes, Gobiaria, Carangaria, and Eupercaria; sensu Betancur et al. 2013). Sorting the markers according to their completeness and phylogenetic decisiveness in taxa tested resulted in a selection of 4,434 markers, which were proven to be useful in reconstructing phylogenies of the ray-finned fishes at different taxonomic levels. We also proposed a strategy of refining baits (probes) design a posteriori based on empirical data. The markers that we have developed may greatly enrich the batteries of exon markers for phylogenomic study in ray-finned fishes.
Collapse
Affiliation(s)
- Jiamei Jiang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Hao Yuan
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Xin Zheng
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Qian Wang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Ting Kuang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Jingyan Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Junning Liu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Shuli Song
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Weicai Wang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Fangyuan Cheng
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Hongjie Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Junman Huang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, ShanghaiNational Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University)ShanghaiChina
| |
Collapse
|
40
|
Montero‐Mendieta S, Dheer A. Digest: Resolving phylogenomic conflicts in characiform fishes†. Evolution 2019; 73:416-418. [DOI: 10.1111/evo.13666] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/12/2018] [Indexed: 11/28/2022]
Affiliation(s)
| | - Arjun Dheer
- Department of Evolutionary EcologyLeibniz Institute for Zoo and Wildlife Research (IZW) Berlin Germany
| |
Collapse
|
41
|
Butt ZD, O'Brien E, Volkoff H. Effects of fasting on the gene expression of appetite regulators in three Characiformes with different feeding habits (Gymnocorymbus ternetzi, Metynnis argenteus and Exodon paradoxus). Comp Biochem Physiol A Mol Integr Physiol 2019; 227:105-115. [DOI: 10.1016/j.cbpa.2018.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
|
42
|
Alda F, Tagliacollo VA, Bernt MJ, Waltz BT, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P. Resolving Deep Nodes in an Ancient Radiation of Neotropical Fishes in the Presence of Conflicting Signals from Incomplete Lineage Sorting. Syst Biol 2018; 68:573-593. [DOI: 10.1093/sysbio/syy085] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Fernando Alda
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA
| | - Victor A Tagliacollo
- Museu de Zoologia da Universidade de São Paulo (MZUSP), Ipirianga, 04263-000, São Paulo, São Paulo, Brazil
| | - Maxwell J Bernt
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - Brandon T Waltz
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - William B Ludt
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Brant C Faircloth
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - James S Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70503, USA
| | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| |
Collapse
|
43
|
Betancur-R R, Arcila D, Vari RP, Hughes LC, Oliveira C, Sabaj MH, Ortí G. Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes. Evolution 2018; 73:329-345. [PMID: 30426469 DOI: 10.1111/evo.13649] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 10/23/2018] [Accepted: 11/05/2018] [Indexed: 11/30/2022]
Abstract
Phylogenomic studies using genome-wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than 1000 exons, 500 ultraconserved element (UCE) loci, and transcriptomic sequences that support incongruent hypotheses. The contentious non-monophyly of the order Characiformes proposed by two studies is shown to be a spurious outcome induced by sample contamination in the transcriptomic dataset and an ambiguous result due to poor taxonomic sampling in the UCE dataset. By exploring the effects of number of taxa and loci used for analysis, we show that the power of GGI to discriminate among competing hypotheses is diminished by limited taxonomic sampling, but not equally sensitive to gene sampling. Taken together, our results reinforce the notion that merely increasing the number of genetic loci for a few representative taxa is not a robust strategy to advance phylogenetic knowledge of recalcitrant groups. We leverage the expanded exon capture dataset generated here for Characiformes (206 species in 23 out of 24 families) to produce a comprehensive phylogeny and a revised classification of the order.
Collapse
Affiliation(s)
- Ricardo Betancur-R
- Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico, 00931.,Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013
| | - Dahiana Arcila
- Department of Biology, University of Oklahoma, Norman, Oklahoma, 73019.,Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, Oklahoma, 73019
| | - Richard P Vari
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, Oklahoma, 73019
| | - Lily C Hughes
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Department of Biological Sciences, The George Washington University, Washington, DC, 20052
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Mark H Sabaj
- Department of Ichthyology, The Academy of Natural Sciences of Drexel University, Philadelphia, Pennsylvania, 19103
| | - Guillermo Ortí
- Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20013.,Department of Biological Sciences, The George Washington University, Washington, DC, 20052
| |
Collapse
|
44
|
Straube N, Li C, Mertzen M, Yuan H, Moritz T. A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies. BMC Evol Biol 2018; 18:158. [PMID: 30352561 PMCID: PMC6199709 DOI: 10.1186/s12862-018-1267-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 09/26/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Previous molecular studies on the phylogeny and classification of clupeocephalan fishes revealed numerous new taxonomic entities. For re-analysing these taxa, we perform target gene capturing and subsequent next generation sequencing of putative ortholog exons of major clupeocephalan lineages. Sequence information for the RNA bait design was derived from publicly available genomes of bony fishes. Newly acquired sequence data comprising > 800 exon sequences was subsequently used for phylogenetic reconstructions. RESULTS Our results support monophyletic Otomorpha comprising Alepocephaliformes. Within Ostariophysi, Gonorynchiformes are sister to a clade comprising Cypriniformes, Characiformes, Siluriformes and Gymnotiformes, where the interrelationships of Characiformes, Siluriformes and Gymnotiformes remain enigmatic. Euteleosts comprise four major clades: Lepidogalaxiiformes, Protacanthopterygii, Stomiatii, and Galaxiiformes plus Neoteleostei. The monotypic Lepidogalaxiiformes form the sister-group to all remaining euteleosts. Protacanthopterygii, comprising Argentini-, Esoci- and Salmoniformes, is sister to Stomiatii (Osmeriformes and Stomiatiformes) and Galaxiiformes plus Neoteleostei. CONCLUSIONS Several proposed monophyla defined by morphological apomorphies within the Clupeocephalan phylogeny are confirmed by the phylogenetic estimates presented herein. However, other morphologically described groups cannot be reconciled with molecular phylogenies. Thus, numerous morphological apomoprhies of supposed monophyla are called into question. The interpretation of suggested morphological synapomorphies of otomorph fishes is strongly affected by the inclusion of deep-sea inhabiting, and to that effect morphologically adapted Alepocephaliformes. Our revision of these potential synapomorphies, in the context that Alepocephaliformes are otomorph fishes, reveals that only a single character of the total nine characters proposed as synapomorphic for the group is clearly valid for all otomorphs. Three further characters remain possible apomorphies since their status remains unclear in the deep-sea adapted Alepocephaliformes showing developmental lag and lacking a swim bladder. Further, our analysis places Galaxiiformes as sister group to neoteleosts, which contradicts some previous molecular phylogenetic studies. This needs further investigation from a morphological perspective, as suggested synapomophies for several euteleostean lineages are challenged or still lacking. For the verification of results presented herein, a denser phylogenomic-level taxon sampling should be applied.
Collapse
Affiliation(s)
- Nicolas Straube
- Institut für Zoologie & Evolutionsbiologie, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
- Zoologische Staatssammlung München, Staatliche Naturwissenschaftliche Sammlungen Bayerns, Münchhausenstraße 21, 81247 Munich, Germany
| | - Chenhong Li
- Key Laboratory of Exploration and Utilization of Aquatic, Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306 China
| | - Matthias Mertzen
- Institut für Zoologie & Evolutionsbiologie, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany
| | - Hao Yuan
- Key Laboratory of Exploration and Utilization of Aquatic, Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, 201306 China
| | - Timo Moritz
- Institut für Zoologie & Evolutionsbiologie, Friedrich-Schiller-Universität Jena, Erbertstraße 1, 07743 Jena, Germany
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany
| |
Collapse
|
45
|
Capobianco A, Friedman M. Vicariance and dispersal in southern hemisphere freshwater fish clades: a palaeontological perspective. Biol Rev Camb Philos Soc 2018; 94:662-699. [DOI: 10.1111/brv.12473] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Alessio Capobianco
- Museum of Paleontology and Department of Earth and Environmental Sciences; University of Michigan; 1105 N. University Ave, Ann Arbor MI 48109-1079 U.S.A
| | - Matt Friedman
- Museum of Paleontology and Department of Earth and Environmental Sciences; University of Michigan; 1105 N. University Ave, Ann Arbor MI 48109-1079 U.S.A
| |
Collapse
|
46
|
Arratia G. Otomorphs (= otocephalans or ostarioclupeomorphs) revisited. NEOTROPICAL ICHTHYOLOGY 2018. [DOI: 10.1590/1982-0224-20180079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT A morphological revision is presented here on the cohort Otomorpha, a clade currently interpreted as the most primitive among the large supercohort Clupeocephala. Otomorpha is a morphologically heterogeneous group represented by clupei forms , alepocephaliforms, and ostariophysans (gonorynchiforms, cypriniforms, characiforms, siluriforms, and gymnoti forms) that inhabit various marine and freshwater environments worldwide. Otomorphs have a long (ca. 145 Ma) and diverse fossil record. They are the largest fish teleostean clade worldwide, as well as the largest of the Neotropical Region. While molecular studies strongly confirm the monophyly of Otomorpha, most potential morphological synapomorphies of the group become homoplastic largely due to the peculiar morphological character states (either losses or transformations) present in alepocephaliforms. The fusion of haemal arches with their respective vertebral centra anterior to preural centrum 2 stands as an unambiguous synapomorphy of the clade. The ankylosis or fusion of the extrascapular and parietal bones, and silvery areas associated with the gas bladder are also interpreted as synapomorphies, although they are homoplastic characters mainly due to secondary losses or further transformations of the morphological features in the alepocephaliforms.
Collapse
|
47
|
Malmstrøm M, Britz R, Matschiner M, Tørresen OK, Hadiaty RK, Yaakob N, Tan HH, Jakobsen KS, Salzburger W, Rüber L. The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes. Genome Biol Evol 2018; 10:1088-1103. [PMID: 29684203 PMCID: PMC5906920 DOI: 10.1093/gbe/evy058] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2018] [Indexed: 12/20/2022] Open
Abstract
The world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in Southeast Asia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number of miniaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8 mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris, mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified system closely related to zebrafish, Paedocypris provides novel insights into vertebrate development.
Collapse
Affiliation(s)
- Martin Malmstrøm
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway.,Zoological Institute, University of Basel, Switzerland
| | - Ralf Britz
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Michael Matschiner
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway.,Zoological Institute, University of Basel, Switzerland
| | - Ole K Tørresen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway
| | - Renny Kurnia Hadiaty
- Ichthyology Laboratory, Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Norsham Yaakob
- Forest Research Institute Malaysia (FRIM), Kepong, Selangor Darul Ehsan, Malaysia
| | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Kjetill Sigurd Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway
| | - Walter Salzburger
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Norway.,Zoological Institute, University of Basel, Switzerland
| | - Lukas Rüber
- Naturhistorisches Museum Bern, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Switzerland
| |
Collapse
|
48
|
|
49
|
Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proc Natl Acad Sci U S A 2018; 115:6249-6254. [PMID: 29760103 DOI: 10.1073/pnas.1719358115] [Citation(s) in RCA: 306] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.
Collapse
|
50
|
Advancing Understanding of Amphibian Evolution, Ecology, Behavior, and Conservation with Massively Parallel Sequencing. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_61] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|