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Hu J, Li H, Sakai H, Mukai T, Young Suk H, Li C. Molecular phylogenetics of the fresh water sleepers Odontobutis (Gobiiformes: Odontobutidae) and its implications on biogeography of freshwater ichthyofauna of East Asia. Mol Phylogenet Evol 2023; 186:107871. [PMID: 37422179 DOI: 10.1016/j.ympev.2023.107871] [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: 12/17/2022] [Revised: 06/10/2023] [Accepted: 07/03/2023] [Indexed: 07/10/2023]
Abstract
The genus Odontobutis is a group of freshwater fishes endemic to East Asia. Phylogenetic relationships among the Odontobutis species have never been fully tested due to incomplete taxon sampling and that molecular data have not been collected in many Odontobutis species. In the present study, we sampled 51 specimens from all known eight Odontobutis species with two outgroups (Perccottus glenii and Neodontobutis hainanensis). We collected sequence data of 4434 single-copy nuclear coding loci using gene capture and Illumina sequencing. A robust phylogeny of the Odontobutis with many individuals for each species was built, supporting the current taxonomy that all extant Odontobutis species are valid. The two species from Japan (O. hikimius + O. obscurus) formed an independent clade sister to the "continental odontobutids", whereas the species from southern China (O. sinensis + O. haifengensis) separated from the rest species of the genus. Surprisingly species from the lower reaches of the Yangtze River (O. potamophilus) was more closely related to species from the Korean Peninsula and northeastern China than to the middle reaches of the Yangtze River, such that their relationship was ((O. sinensis + O. haifengensis)(O. platycephala + (O. yaluensis + (O. potamophilus + O. interruptus)))). Divergence time among the Odontobutis was estimated using 100 most clock-like loci and three fossil calibration points. The crown group of the Odontobutis was estimated at 9.0 Ma during the late Miocene (5.6-12.7 Ma, 95% HPDs). Ancestral range of the genus was reconstructed using Reconstruct Ancestral States in Phylogenies (RASP) and BioGeoBEARS. The result suggested that the common ancestor of modern Odontobutis probably was distributed in Japan, southern China or the Korean Peninsula. A series of geographical events in East Asia since the late Miocene, such as the opening of the Japan/East Sea, rapid uplift of the Tibetan Plateau and climate change in the northern region of the Yellow River might account for diversification and current distribution pattern of the Odontobutis.
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Affiliation(s)
- Jiantao Hu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China; Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China.
| | - Hongjie Li
- Genoxor Medical & Science Technology Inc.
| | - Harumi Sakai
- National Fisheries University, Yamaguchi 759-6595, Japan.
| | - Takahiko Mukai
- Faculty of Regional Studies, Gifu University, Gifu, 501-1193, Japan.
| | - Ho Young Suk
- Department of Life Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China; Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China.
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Bartoš O, Bohlen J, Šlechtová VB, Kočí J, Röslein J, Janko K. Sequence capture: Obsolete or irreplaceable? A thorough validation across phylogenetic distances and its applicability to hybrids and allopolyploids. Mol Ecol Resour 2023. [PMID: 37122140 DOI: 10.1111/1755-0998.13806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 05/02/2023]
Abstract
As whole-genome sequencing has become pervasive, some have suggested that reduced genomic representation approaches, for example, sequence capture, are becoming obsolete. In the present study, we argue that these techniques still provide excellent tools in terms of price and quality of data as well as in their ability to provide markers with specific features, as required, for example, in phylogenomics. A potential drawback of the wide-scale application of reduced representation approaches could be their drop in efficiency with increasing phylogenetic distance from the reference species. While some studies have focused on the degree and performance of reduced representation techniques in such situations, to our knowledge, none of them evaluated their applicability to inter-specific hybrids and polyploids. This highlights a significant gap in current knowledge since there is increasing evidence for the frequent occurrence of natural hybrids and polyploids, as well as for the major importance of both phenomena in evolution. The main aim of the present study was to carry out a thorough validation of SEQcap applicability to (1) a set of non-model taxa with a wide range of phylogenetic relatedness and (2) inter-specific hybrids of various ploidies and genomic compositions. Considering the latter point, we especially focused on mechanisms causing allelic bias and consequent allelic dropout, as these could have confounding effects with respect to the evolutionary genomic dynamics of hybrids, especially in asexuals, which virtually reproduce as a frozen F1 generation.
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Affiliation(s)
- Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
| | - Vendula Bohlen Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
| | - Jan Kočí
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Röslein
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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3
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Han X, Jin S, Han Z, Gao T. The Phylogenetic Relationships of the Family Sciaenidae Based on Genome-Wide Data Analysis. Animals (Basel) 2022; 12:ani12233386. [PMID: 36496907 PMCID: PMC9741161 DOI: 10.3390/ani12233386] [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] [Received: 10/06/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Uncertainty and controversy exist in the phylogenetic status of the Sciaenidae family because of the limited genetic data availability. In this study, a data set of 69,098 bp, covering 309 shared orthologous genes, was extracted from 18 genomes and 5 transcriptomes of 12 species belonging to the Sciaenidae family and used for phylogenetic analysis. The maximum likelihood (ML) and Bayesian approach (BA) methods were used to reconstruct the phylogenetic trees. The resolved ML and BA trees showed similar topology, thus revealing two major evolutionary lineages within the Sciaenidae family, namely, Western Atlantic (WA) and Eastern Atlantic−Indo−West Pacific (EIP). The WA group included four species belonging to four genera: Cynoscion nebulosus, Equetus punctatus, Sciaenops ocellatus, and Micropogonias undulatus. Meanwhile, the EIP group formed one monophyletic clade, harboring eight species (Argyrosomus regius, A. japonicus, Pennahia anea, Nibea albiflora, Miichthys miiuy, Collichthys lucidus, Larimichthys polyactis, and L. crocea) from six genera. Our results indicated that the Western Atlantic (WA) group was more ancient in the studied species, while the Eastern Atlantic−Indo−West Pacific (EIP) group was a younger group. Within the studied species, the genera Collichthys and Larmichthys were the youngest lineages, and we do not suggest that Collichthys and Larmichthys should be considered as one genus. However, the origin of the Sciaenidae family and problems concerning the basal genus were not resolved because of the lack of genomes. Therefore, further sampling and sequencing efforts are needed.
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Astudillo-Clavijo V, Stiassny MLJ, Ilves KL, Musilova Z, Salzburger W, López-Fernández H. Exon-based phylogenomics and the relationships of African cichlid fishes: tackling the challenges of reconstructing phylogenies with repeated rapid radiations. Syst Biol 2022; 72:134-149. [PMID: 35880863 DOI: 10.1093/sysbio/syac051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system.
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Affiliation(s)
- Viviana Astudillo-Clavijo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, 10024-5102, USA
| | - Katriina L Ilves
- Research & Collections, Zoology, Canadian Museum of Nature, Ottawa, K1P 6P4, Canada
| | - Zuzana Musilova
- Department of Zoology, Charles University in Prague, Vinicna 7, Prague, CZ-128 44, Czech Republic
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
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Wang Q, Purrafee Dizaj L, Huang J, Kumar Sarker K, Kevrekidis C, Reichenbacher B, Reza Esmaeili H, Straube N, Moritz T, Li C. Molecular phylogenetics of the Clupeiformes based on exon-capture data and a new classification of the order. Mol Phylogenet Evol 2022; 175:107590. [PMID: 35850406 DOI: 10.1016/j.ympev.2022.107590] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/21/2022] [Accepted: 07/12/2022] [Indexed: 10/17/2022]
Abstract
The Clupeiformes, including among others herrings, anchovies, shads and menhadens are ecologically and commercially important, yet their phylogenetic relationships are still controversial. Previous classification of Clupeiformes were based on morphological characters or lack of synapomorphic characters. More recent studies based on molecular data as well as new morphological evidence are keeping challenging their phylogenetic relations and there is still no consensus on many interrelationships within the Clupeiformes. In this study, we collected nuclear sequence data from 4,434 single-copy protein coding loci using a gene-capture method. We obtained a robust phylogeny based on 1,165 filtered loci with less than 30 % missing data. Our major findings include: 1) reconfirmation of monophyly of the Clupeiformes, that is, Denticipitidae is sister to all other clupeiforms; 2) the polyphyletic nature of dussumieriids and early branching of Spratelloididae from all other clupeoids were confirmed using datasets curated for less missing data and more balanced base composition in the respective taxa. The next branching clade is the monophyletic Engraulidae. Pristigasteridae also is monophyletic, but it was nested in the previously defined "Clupeidae". Within Pristigasteridae there is no support for monophyletic Pelloninae. Chirocentrus is close to Dussumieria and not to engraulids. The miniaturized Sundasalanx is placed close to the ehiravine Clupeonella, however, with a relatively deep split. The genus Clupea, is not part of the diverse "Clupeidae", but part of a clade containing additionally Sprattus and Etrumeus. Within the crown group clades, Alosidae and Dorosomatidae are retrieved as sister clades. Based on new fossil calibration points, we found that major lineages of the clupeiforms diverged in the late Cretaceous and early Paleogene. The extinction event at the end of the Cretaceous may have created ecological niches, which could have fueled the diversification of clupeiform fishes. Based on the strong evidence of the present study, we propose an updated classification of Clupeiformes consisting of ten families: Denticipitidae; Spratelloididae; Engraulidae (Engraulinae + Coiliinae); Clupeidae; Chirocentridae; Dussumieriidae; Pristigasteridae; Ehiravidae; Alosidae, Dorosomatidae.
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Affiliation(s)
- Qian Wang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China.
| | - Leyli Purrafee Dizaj
- Ichthyology and Molecular Systematics Research Laboratory, Zoology Section, Department of Biology, School of Science, Shiraz University, Shiraz, Iran.
| | - Junman Huang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China; Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China.
| | - Kishor Kumar Sarker
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China; Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China.
| | - Charalampos Kevrekidis
- Ludwig-Maximilians-Universität München, Department für Geo- und Umweltwissenschaften, Paläontologie & Geobiologie, Richard-Wagner-Str. 10, 80333 Munich, Germany.
| | - Bettina Reichenbacher
- Ludwig-Maximilians-Universität München, Department für Geo- und Umweltwissenschaften, Paläontologie & Geobiologie, Richard-Wagner-Str. 10, 80333 Munich, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Hamid Reza Esmaeili
- Ichthyology and Molecular Systematics Research Laboratory, Zoology Section, Department of Biology, School of Science, Shiraz University, Shiraz, Iran.
| | - Nicolas Straube
- University Museum, Department of Natural History, University of Bergen, Norway.
| | - Timo Moritz
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany; Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059 Rostock, Germany.
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China; Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China.
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6
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Hu Y, Li H, Xia J, Li C. Population Structure, Genetic Diversity, and Conservation Strategies of a Commercially Important Sleeper Fish, Odontobutis potamophilus (Gobiiformes: Odontobutidae) Based on Gene-Capture Data. Front Genet 2022; 13:843848. [PMID: 35685434 PMCID: PMC9171042 DOI: 10.3389/fgene.2022.843848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Odontobutis potamophilus is a popular food fish in China, distributed mainly in the middle and lower reaches of the Yangtze River, where it is a famous delicacy and a newly focused species for aquaculture. The wild populations of O. potamophilus are facing the problem of overfishing and habitat degradation. Therefore, it is very necessary to investigate and protect the wild populations of O. potamophilus. In this study, 72 fish were sampled from 18 different sites over its distribution range. Nuclear sequence data of 4,267 loci were collected using a gene-capture method. Phylogenetic reconstruction revealed that there were three major clades: Oujiang clade (OJ), Qiantang and lower Yangtze clade (QY), and middle Yangtze clade (MY). The discriminant analysis of principal components (DAPC) and a STRUCTURE analysis confirmed that there are three major groups within O. potamophilus. A fastsimcoal2 analysis corroborated the population history and suggested that there was discernible gene flow among these three groups, especially between QY and MY. Estimated pairwise FST suggested that Linhai (LH) and Shexian (SX) populations were the most divergent pair (FST = 0.7077). Taking the nucleotide diversity, population divergence, and admixture status altogether into consideration, we recommend that the LH, Gaoyou (GY) and Chaohu (CH) populations could be protected as the preferred resource for breeding projects. According to the results of genetic analyses, all populations of O. potamophilus should be protected due to low genetic diversity.
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Affiliation(s)
- Yun Hu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
| | - Hongjie Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
| | - Jianhong Xia
- Shanghai Natural History Museum, Branch of the Shanghai Science and Technology Museum, Shanghai, China
- *Correspondence: Jianhong Xia, ; Chenhong Li,
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- *Correspondence: Jianhong Xia, ; Chenhong Li,
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Cheng T, Yuan X, Yuan S, Zhu J, Tang S, Zhang Y. ITGB5 mutation discovered in a Chinese family with blepharophimosis-ptosis-epicanthus inversus syndrome. Open Life Sci 2021; 16:1268-1277. [PMID: 34966851 PMCID: PMC8665901 DOI: 10.1515/biol-2021-0129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/28/2021] [Accepted: 11/12/2021] [Indexed: 12/16/2022] Open
Abstract
Blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) is a rare autosomal-dominant genetic disorder, and mutations in the forkhead box L2 (FOXL2) gene are one of the major genetic causes. As this study shows, there are many patients with BPES who do not have FOXL2 mutations, as the screening results in all family members were negative. Using whole-exome sequence analysis, we discovered another possible mutational cause of BPES in integrin subunit beta 5 (ITGB5). The ITGB5 mutation (c.608T>C, p.Ile203Thr) appears in the base sequence of all BPES+ patients in this family, and it appears to be a three-generation-inherited mutation. It can cause changes in base sequence and protein function, and there may be cosegregation of disease phenotypes. ITGB5 is located on the long arm of chromosome three (3q21.2) and is close to the known pathogenic gene FOXL2 (3q23). This study is the first to report ITGB5 mutations in BPES, and we speculate that it may be directly involved in the pathogenesis of BPES or indirectly through the regulation of FOXL2.
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Affiliation(s)
- Tianling Cheng
- Institute of Plastic Surgery, Weifang Medical University, Weifang, Shandong, 261000, China
| | - Xiaobin Yuan
- Department of Disease Control and Prevention, Qingdao Hospital of Traditional Chinese Medicine, Qingdao, Shandong, 266000, China
| | - Shaopeng Yuan
- Department of Research and Development, Beijing Shunlei Technology Co., Ltd, Beijing, 100000, China
| | - Jianying Zhu
- Zibo Yimei Plastic Surgery Hospital, Zibo, Shandong, 255000, China
| | - Shengjian Tang
- Institute of Plastic Surgery, Weifang Medical University, Weifang, Shandong, 261000, China
| | - Yujie Zhang
- Institute of Plastic Surgery, Weifang Medical University, Weifang, Shandong, 261000, China
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Atta CJ, Yuan H, Li C, Arcila D, Betancur-R R, Hughes LC, Ortí G, Tornabene L. Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei). Mol Phylogenet Evol 2021; 166:107315. [PMID: 34537325 DOI: 10.1016/j.ympev.2021.107315] [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: 12/19/2020] [Revised: 05/12/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
There is an extensive collection of literature on the taxonomy and phylogenetics of flatfishes (Pleuronectiformes) that extends over two centuries, but consensus on many of their evolutionary relationships remains elusive. Phylogenetic uncertainty stems from highly divergent results derived from morphological and genetic characters, and between various molecular datasets. Deciphering relationships is complicated by rapid diversification early in the Pleuronectiformes tree and an abundance of studies that incompletely and inconsistently sample taxa and genetic markers. We present phylogenies based on a genome-wide dataset (4,434 nuclear markers via exon-capture) and wide taxon sampling (86 species spanning 12 of 16 families) of the largest flatfish suborder (Pleuronectoidei). Nine different subsets of the data and two tree construction approaches (eighteen phylogenies in total) are remarkably consistent with other recent molecular phylogenies, and show strong support for the monophyly of all families included except Pleuronectidae. Analyses resolved a novel phylogenetic hypothesis for the family Rhombosoleidae as being within the Pleuronectoidea rather than the Soleoidea, and failed to support the subfamily Hippoglossinae as a monophyletic group. Our results were corroborated with evidence from previous phylogenetic studies to outline regions of persistent phylogenetic uncertainty and identify groups in need of further phylogenetic inference.
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Affiliation(s)
- Calder J Atta
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, USA; Burke Museum of Natural History and Culture, Seattle, USA.
| | - Hao Yuan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
| | - Chenhong Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
| | - Dahiana Arcila
- Sam Noble Oklahoma Museum of Natural History, The University of Oklahoma, Norman, OK 73072, USA; Department of Biology, The University of Oklahoma, Norman, OK 73072, USA
| | - Ricardo Betancur-R
- Sam Noble Oklahoma Museum of Natural History, The University of Oklahoma, Norman, OK 73072, USA; Department of Biology, The University of Oklahoma, Norman, OK 73072, USA
| | - Lily C Hughes
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA; National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Guillermo Ortí
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, USA; Burke Museum of Natural History and Culture, Seattle, USA
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9
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Roa-Varón A, Dikow RB, Carnevale G, Tornabene L, Baldwin CC, Li C, Hilton EJ. Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes). Syst Biol 2020; 70:739-755. [PMID: 33346841 PMCID: PMC8561434 DOI: 10.1093/sysbio/syaa095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/27/2020] [Accepted: 12/02/2020] [Indexed: 11/14/2022] Open
Abstract
Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large data sets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or incorrect parameter estimates when reconstructing phylogeny by using the gadiform fishes as a model clade. Gadiformes include some of the most economically important fishes in the world (e.g., Cods, Hakes, and Rattails). Despite many attempts, a robust higher-level phylogenetic framework was lacking due to limited character and taxonomic sampling, particularly from several species-poor families that have been recalcitrant to phylogenetic placement. We compiled the first phylogenomic data set, including 14,208 loci (\documentclass[12pt]{minimal}
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}{}$>$\end{document}2.8 M bp) from 58 species representing all recognized gadiform families, to infer a time-calibrated phylogeny for the group. Data were generated with a gene-capture approach targeting coding DNA sequences from single-copy protein-coding genes. Species-tree and concatenated maximum-likelihood (ML) analyses resolved all family-level relationships within Gadiformes. While there were a few differences between topologies produced by the DNA and the amino acid data sets, most of the historically unresolved relationships among gadiform lineages were consistently well resolved with high support in our analyses regardless of the methodological and biological approaches used. However, at deeper levels, we observed inconsistency in branch support estimates between bootstrap and gene and site coefficient factors (gCF, sCF). Despite numerous short internodes, all relationships received unequivocal bootstrap support while gCF and sCF had very little support, reflecting hidden conflict across loci. Most of the gene-tree and species-tree discordance in our study is a result of short divergence times, and consequent lack of informative characters at deep levels, rather than incomplete lineage sorting. We use this phylogeny to establish a new higher-level classification of Gadiformes as a way of clarifying the evolutionary diversification of the order. We recognize 17 families in five suborders: Bregmacerotoidei, Gadoidei, Ranicipitoidei, Merluccioidei, and Macrouroidei (including two subclades). A time-calibrated analysis using 15 fossil taxa suggests that Gadiformes evolved \documentclass[12pt]{minimal}
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}{}$\sim $\end{document}79.5 Ma in the late Cretaceous, but that most extant lineages diverged after the Cretaceous–Paleogene (K-Pg) mass extinction (66 Ma). Our results reiterate the importance of examining phylogenomic analyses for evidence of systematic error that can emerge as a result of unsuitable modeling of biological factors and/or methodological issues, even when data sets are large and yield high support for phylogenetic relationships. [Branch length heterogeneity; Codfishes; commercial fish species; Cretaceous-Paleogene (K-Pg); heterotachy; systematic error; target enrichment.]
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Affiliation(s)
- Adela Roa-Varón
- National Systematics Laboratory of the National Oceanic Atmospheric Administration Fisheries Service, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA.,Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA 23062, USA
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, 35, 10125 Torino, Italy
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, WA 98105, USA.,Burke Museum of Natural History and Culture, 4300 15th Ave NE, Seattle, WA 98105, USA
| | - Carole C Baldwin
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, DC 20560, USA
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, 999 Hucheng Ring Rd, Pudong, Shanghai, China
| | - Eric J Hilton
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA 23062, USA
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10
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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.
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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
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11
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Carducci F, Barucca M, Canapa A, Carotti E, Biscotti MA. Mobile Elements in Ray-Finned Fish Genomes. Life (Basel) 2020; 10:E221. [PMID: 32992841 PMCID: PMC7599744 DOI: 10.3390/life10100221] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.
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Affiliation(s)
| | | | | | | | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (F.C.); (M.B.); (A.C.); (E.C.)
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12
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Data, time and money: evaluating the best compromise for inferring molecular phylogenies of non-model animal taxa. Mol Phylogenet Evol 2020; 142:106660. [DOI: 10.1016/j.ympev.2019.106660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022]
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13
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Cheng F, Wang Q, Maisano Delser P, Li C. Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River. Ecol Evol 2019; 9:12202-12215. [PMID: 31832154 PMCID: PMC6854117 DOI: 10.1002/ece3.5708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/05/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022] Open
Abstract
Freshwater fish evolved from anadromous ancestors can be found in almost all continents. The roles of paleogeographic events and nature selection in speciation process often are under focus of research. We studied genetic diversity of anadromous and resident tapertail anchovies (Coilia nasus species complex) in the Yangtze River Basin using 4,434 nuclear loci, and tested the history of freshwater invasion of C. nasus. We found that both C. brachygnathus and C. nasus were valid species, but the resident C. nasus taihuensis and the anadromous C. nasus were not different genetically based on Bayes factor species delimitation (BFD*). Maximum likelihood tree, Network, PCA and STRUCTURE analyses all corroborated the results of BFD*. Two independent freshwater invasion events of C. nasus were supported, with the first event occurring around 4.07 Ma and the second happened around 3.2 Ka. The time of the two freshwater invasions is consistent with different paleogeographic events. Estimation showed that gene flow was higher within ecotypes than between different ecotypes. F-DIST analyses identified 120 disruptive outliers by comparing C. brachygnathus to anadromous C. nasus, and 21 disruptive outliers by comparing resident C. nasus to anadromous C. nasus. Nine outliers were found to be common between the two comparisons, indicating that independent freshwater invasion of C. nasus might involve similar molecular pathways. The results of this study suggest that adaptation to landlocked freshwater environment of migratory fish can evolve multiple times independently, and morphology of landlocked ecotypes may cause confusion in their taxonomy.
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Affiliation(s)
- Fangyuan Cheng
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and EvolutionShanghaiChina
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and BreedingShanghaiChina
- Key Laboratory of Exploration and Utilization of Aquatic Genetic ResourcesMinistry of EducationShanghai Ocean UniversityShanghaiChina
| | - Qian Wang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and EvolutionShanghaiChina
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and BreedingShanghaiChina
- Key Laboratory of Exploration and Utilization of Aquatic Genetic ResourcesMinistry of EducationShanghai Ocean UniversityShanghaiChina
| | - Pierpaolo Maisano Delser
- Department of ZoologyUniversity of CambridgeCambridgeUK
- Smurfit Institute of GeneticsTrinity CollegeUniversity of DublinDublinIreland
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and EvolutionShanghaiChina
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and BreedingShanghaiChina
- Key Laboratory of Exploration and Utilization of Aquatic Genetic ResourcesMinistry of EducationShanghai Ocean UniversityShanghaiChina
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14
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Yuan H, Atta C, Tornabene L, Li C. Assexon: Assembling Exon Using Gene Capture Data. Evol Bioinform Online 2019; 15:1176934319874792. [PMID: 31523128 PMCID: PMC6732846 DOI: 10.1177/1176934319874792] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/30/2022] Open
Abstract
Exon capture across species has been one of the most broadly applied approaches
to acquire multi-locus data in phylogenomic studies of non-model organisms.
Methods for assembling loci from short-read sequences (eg, Illumina platforms)
that rely on mapping reads to a reference genome may not be suitable for studies
comprising species across a wide phylogenetic spectrum; thus, de novo assembling
methods are more generally applied. Current approaches for assembling targeted
exons from short reads are not particularly optimized as they cannot (1)
assemble loci with low read depth, (2) handle large files efficiently, and (3)
reliably address issues with paralogs. Thus, we present Assexon: a streamlined
pipeline that de novo assembles targeted exons and their flanking sequences from
raw reads. We tested our method using reads from Lepisosteus
osseus (4.37 Gb) and Boleophthalmus pectinirostris
(2.43 Gb), which are captured using baits that were designed based on genome
sequence of Lepisosteus oculatus and Oreochromis
niloticus, respectively. We compared performance of Assexon to
PHYLUCE and HybPiper, which are commonly used pipelines to assemble
ultra-conserved element (UCE) and Hyb-seq data. A custom exon capture analysis
pipeline (CP) developed by Yuan et al was compared as well. Assexon accurately
assembled more than 3400 to 3800 (20%-28%) loci than PHYLUCE and more than 1900
to 2300 (8%-14%) loci than HybPiper across different levels of phylogenetic
divergence. Assexon ran at least twice as fast as PHYLUCE and HybPiper. Number
of loci assembled using CP was comparable with Assexon in both tests, while
Assexon ran at least 7 times faster than CP. In addition, some steps of CP
require the user’s interaction and are not fully automated, and this user time
was not counted in our calculation. Both Assexon and CP retrieved no paralogs in
the testing runs, but PHYLUCE and Hybpiper did. In conclusion, Assexon is a tool
for accurate and efficient assembling of large read sets from exon capture
experiments. Furthermore, Assexon includes scripts to filter poorly aligned
coding regions and flanking regions, calculate summary statistics of loci, and
select loci with reliable phylogenetic signal. Assexon is available at https://github.com/yhadevol/Assexon.
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Affiliation(s)
- Hao Yuan
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution (Shanghai Ocean University), Shanghai, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean Universitiy), Ministry of Education, Shanghai, China
| | - Calder Atta
- School of Aquatic and Fishery Sciences and the Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences and the Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - Chenhong Li
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution (Shanghai Ocean University), Shanghai, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean Universitiy), Ministry of Education, Shanghai, China
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