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Li Y, Moritz C, Brennan IG, Zwick A, Nicholls J, Grealy A, Slipinski A. Evolution across the adaptive landscape in a hyperdiverse beetle radiation. Curr Biol 2024; 34:3685-3697.e6. [PMID: 39067451 DOI: 10.1016/j.cub.2024.06.080] [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: 04/02/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
The extraordinary diversification of beetles on Earth is a textbook example of adaptive evolution. Yet, the tempo and drivers of this super-radiation remain largely unclear. Here, we address this problem by investigating macroevolutionary dynamics in darkling beetles (Coleoptera: Tenebrionidae), one of the most ecomorphologically diverse beetle families (with over 30,000 species). Using multiple genomic datasets and analytical approaches, we resolve the long-standing inconsistency over deep relationships in the family. In conjunction with a landmark-based dataset of body shape morphology, we show that the evolutionary history of darkling beetles is marked by ancient rapid radiations, frequent ecological transitions, and rapid bursts of morphological diversification. On a global scale, our analyses uncovered a significant pulse of phenotypic diversification proximal to the Cretaceous-Palaeogene (K/Pg) mass extinction and convergence of body shape associated with recurrent ecological specializations. On a regional scale, two major Australasian radiations, the Adeliini and the Heleine clade, exhibited contrasting patterns of ecomorphological diversification, representing phylogenetic niche conservatism versus adaptive radiation. Our findings align with the Simpsonian model of adaptive evolution across the macroevolutionary landscape and highlight a significant role of ecological opportunity in driving the immense ecomorphological diversity in a hyperdiverse beetle group.
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Affiliation(s)
- Yun Li
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia.
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - James Nicholls
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - Alicia Grealy
- Australian National Herbarium, CSIRO, Canberra, ACT 2601, Australia
| | - Adam Slipinski
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
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2
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Burns MD, Knouft JH, Dillman CB. The role of abiotic and biotic factors in the unequal body shape diversification of a Gondwanan fish radiation (Otophysi: Characiformes). Evolution 2024; 78:253-266. [PMID: 37952199 DOI: 10.1093/evolut/qpad203] [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: 05/26/2023] [Revised: 10/25/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
Understanding why some clades diversify greatly while others do not is a major goal of evolutionary biology. Both abiotic and biotic factors are important in driving unequal morphological diversity across the tree of life. However, few studies have quantified how abiotic habitat and community composition differences influence unequal morphological diversification in spatiotemporally diffuse radiations. We use geometric morphometrics, abiotic habitat data generated by Geographic Information Systems (GIS) analyses, evolutionary simulations, and phylogenetic comparative methods to determine whether random evolution, habitat variation, competition for niches, or a combination of factors influenced the unequal body shape diversity of a Gondwanan freshwater fish radiation. We find that Neotropical characiform lineages, which exhibit substantially more body shape diversity than their African counterparts, occupy significantly more slope and elevation habitats than African lineages. Differences in habitat occupation between the continental radiations occur through a combination of likely competition with cypriniform fishes in Africa restricting access to higher slope and elevation habitats and significantly more low-elevation and slope habitats available in the Neotropics. Our findings suggest that spatiotemporally widespread radiations, like Characiformes, do not diversify across homogenized habitats and biotic assemblages, with differences in community structure and physical habitat playing an important role in driving unequal morphological diversification.
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Affiliation(s)
- Michael D Burns
- Cornell Lab of Ornithology, Cornell University Museum of Vertebrates, Ithaca, NY, United States
- Department of Evolution and Ecology, University of California, Davis, CA, United States
| | - Jason H Knouft
- Department of Biology, Saint Louis University, St. Louis, MO, United States
- National Great Rivers Research and Education Center, East Alton, IL, United States
| | - Casey B Dillman
- Department of Ecology and Evolutionary Biology, Cornell University Museum of Vertebrates, Cornell University, Ithaca, NY, United States
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3
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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.
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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
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Patané JSL, Martins J, Setubal JC. A Guide to Phylogenomic Inference. Methods Mol Biol 2024; 2802:267-345. [PMID: 38819564 DOI: 10.1007/978-1-0716-3838-5_11] [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] [Indexed: 06/01/2024]
Abstract
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. Phylogenomics has significant applications in fields such as evolutionary biology, systematics, comparative genomics, and conservation genetics, providing valuable insights into the origins and relationships of species and contributing to our understanding of biological diversity and evolution. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.
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Affiliation(s)
- José S L Patané
- Laboratório de Genética e Cardiologia Molecular, Instituto do Coração/Heart Institute Hospital das Clínicas - Faculdade de Medicina da Universidade de São Paulo São Paulo, São Paulo, SP, Brazil
| | - Joaquim Martins
- Integrative Omics group, Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - João Carlos Setubal
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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5
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Steenwyk JL, Li Y, Zhou X, Shen XX, Rokas A. Incongruence in the phylogenomics era. Nat Rev Genet 2023; 24:834-850. [PMID: 37369847 DOI: 10.1038/s41576-023-00620-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 06/29/2023]
Abstract
Genome-scale data and the development of novel statistical phylogenetic approaches have greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its branches. However, incongruence - the inference of conflicting evolutionary histories - remains pervasive in phylogenomic data, hampering our ability to reconstruct and interpret the tree of life. Biological factors, such as incomplete lineage sorting, horizontal gene transfer, hybridization, introgression, recombination and convergent molecular evolution, can lead to gene phylogenies that differ from the species tree. In addition, analytical factors, including stochastic, systematic and treatment errors, can drive incongruence. Here, we review these factors, discuss methodological advances to identify and handle incongruence, and highlight avenues for future research.
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Affiliation(s)
- Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
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Roberts WR, Ruck EC, Downey KM, Pinseel E, Alverson AJ. Resolving Marine-Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance. Syst Biol 2023; 72:984-997. [PMID: 37335140 DOI: 10.1093/sysbio/syad038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 06/02/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023] Open
Abstract
Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic data set of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms.
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Affiliation(s)
- Wade R Roberts
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Kala M Downey
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Eveline Pinseel
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
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Bagley JC, Johnson CC, McGregor SW, Breitman MF, Armbruster JW, Harris PM, Oneil PE. Marine and freshwater fishes of Alabama: a revised checklist and discussion of taxonomic issues. Zootaxa 2023; 5357:301-341. [PMID: 38220642 DOI: 10.11646/zootaxa.5357.3.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Indexed: 01/16/2024]
Abstract
Checklists are fundamental and important tools for organizing information about biodiversity that provide a basis for conservation and additional scientific research. While Alabama is recognized as an aquatic biodiversity hotspot with the highest native freshwater fish diversity in the contiguous United States, we currently lack an up-to-date list of the states fishes. In particular, much has changed over the past ~20 years regarding our knowledge of fishes from Alabama and the Mobile River Basin, rendering past comprehensive treatments by Mettee et al. (1996) and Boschung and Mayden (2004) out of date. Here, we provide a revised checklist of marine and freshwater fishes known from the coastal and inland waters of Alabama that includes 463 species (335 primarily freshwater fishes, and 128 marine or diadromous fishes) in 35 orders, 78 families, and 176 genera. Extant, extirpated, and extinct species are included, as are putative candidate species. The checklist is based on prior work, searches of the literature and online sources, as well as parsing a large compilation of >140,000 fish records for Alabama and the Mobile River Basin from 37 data providers in the global Fishnet2 database (www.fishnet2.net) and >4000 marine survey records from the SEAMAP database (https://www.gsmfc.org/seamap.php). After editing and quality control checks, the final combined database contained 144,215 collection records, ~95% of which were georeferenced. We discuss the species descriptions, nomenclatural changes, and updates to marine species that account for changes to the state list, and we close with a discussion of ~13 candidate species forms that remain undescribed, which represent outstanding taxonomic issues in need of further research attention.
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Affiliation(s)
- Justin C Bagley
- Department of Biology and Environmental Science; Auburn University at Montgomery; 301 Goodwyn Hall; Montgomery; AL 36124; USA; Department of Biology; Virginia Commonwealth University; 1000 W Cary St.; Suite 126; Richmond; VA 23284; USA; Field Operations Division; Alabama Department of Environmental Management; P.O. Box 301463; Montgomery; AL 36130; USA.
| | - Cal C Johnson
- Decatur Field Office; Alabama Department of Environmental Management; 2715 Sandlin Rd SW; Decatur; AL 35603; USA.
| | - Stuart W McGregor
- Geological Survey of Alabama; Walter B. Jones Hall; 420 Hackberry Lane; Tuscaloosa; AL 35487; USA.
| | - Maria F Breitman
- Department of Biology and Environmental Science; Auburn University at Montgomery; 301 Goodwyn Hall; Montgomery; AL 36124; USA.
| | - Jonathan W Armbruster
- Department of Biological Sciences; Auburn University; 120 W Samford Ave; Auburn; AL 36849; USA.
| | - Phillip M Harris
- Department of Biological Sciences, The University of Alabama, 1325 Hackberry Ln, Tuscaloosa, AL 35401, USA.
| | - Patrick E Oneil
- Geological Survey of Alabama, Walter B. Jones Hall, 420 Hackberry Lane, Tuscaloosa, AL 35487, USA.
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8
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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.
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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
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Knyshov A, Gordon ERL, Masonick PK, Castillo S, Forero D, Hoey-Chamberlain R, Hwang WS, Johnson KP, Lemmon AR, Moriarty Lemmon E, Standring S, Zhang J, Weirauch C. Chromosome-Aware Phylogenomics of Assassin Bugs (Hemiptera: Reduvioidea) Elucidates Ancient Gene Conflict. Mol Biol Evol 2023; 40:msad168. [PMID: 37494292 PMCID: PMC10411492 DOI: 10.1093/molbev/msad168] [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: 03/28/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Though the phylogenetic signal of loci on sex chromosomes can differ from those on autosomes, chromosomal-level genome assemblies for nonvertebrates are still relatively scarce and conservation of chromosomal gene content across deep phylogenetic scales has therefore remained largely unexplored. We here assemble a uniquely large and diverse set of samples (17 anchored hybrid enrichment, 24 RNA-seq, and 70 whole-genome sequencing samples of variable depth) for the medically important assassin bugs (Reduvioidea). We assess the performance of genes based on multiple features (e.g., nucleotide vs. amino acid, nuclear vs. mitochondrial, and autosomal vs. X chromosomal) and employ different methods (concatenation and coalescence analyses) to reconstruct the unresolved phylogeny of this diverse (∼7,000 spp.) and old (>180 Ma) group. Our results show that genes on the X chromosome are more likely to have discordant phylogenies than those on autosomes. We find that the X chromosome conflict is driven by high gene substitution rates that impact the accuracy of phylogenetic inference. However, gene tree clustering showed strong conflict even after discounting variable third codon positions. Alternative topologies were not particularly enriched for sex chromosome loci, but spread across the genome. We conclude that binning genes to autosomal or sex chromosomes may result in a more accurate picture of the complex evolutionary history of a clade.
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Affiliation(s)
- Alexander Knyshov
- Department of Entomology, University of California, Riverside, CA, USA
| | - Eric R L Gordon
- Ecology and Evolutionary Biology Department, University of Connecticut, Storrs, CT, USA
| | - Paul K Masonick
- Department of Entomology, University of California, Riverside, CA, USA
| | | | - Dimitri Forero
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogota, Colombia
| | | | - Wei Song Hwang
- Lee Kong Chian Natural History Museum, National University of Singapore, Queenstown, Singapore
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | | | | | - Junxia Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, China
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Mongiardino Koch N, Tilic E, Miller AK, Stiller J, Rouse GW. Confusion will be my epitaph: genome-scale discordance stifles phylogenetic resolution of Holothuroidea. Proc Biol Sci 2023; 290:20230988. [PMID: 37434530 PMCID: PMC10336381 DOI: 10.1098/rspb.2023.0988] [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: 05/02/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023] Open
Abstract
Sea cucumbers (Holothuroidea) are a diverse clade of echinoderms found from intertidal waters to the bottom of the deepest oceanic trenches. Their reduced skeletons and limited number of phylogenetically informative traits have long obfuscated morphological classifications. Sanger-sequenced molecular datasets have also failed to constrain the position of major lineages. Noteworthy, topological uncertainty has hindered a resolution for Neoholothuriida, a highly diverse clade of Permo-Triassic age. We perform the first phylogenomic analysis of Holothuroidea, combining existing datasets with 13 novel transcriptomes. Using a highly curated dataset of 1100 orthologues, our efforts recapitulate previous results, struggling to resolve interrelationships among neoholothuriid clades. Three approaches to phylogenetic reconstruction (concatenation under both site-homogeneous and site-heterogeneous models, and coalescent-aware inference) result in alternative resolutions, all of which are recovered with strong support and across a range of datasets filtered for phylogenetic usefulness. We explore this intriguing result using gene-wise log-likelihood scores and attempt to correlate these with a large set of gene properties. While presenting novel ways of exploring and visualizing support for alternative trees, we are unable to discover significant predictors of topological preference, and our efforts fail to favour one topology. Neoholothuriid genomes seem to retain an amalgam of signals derived from multiple phylogenetic histories.
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Affiliation(s)
| | - Ekin Tilic
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Marine Zoology, Senckenberg Research Institute and Museum, Frankfurt, Germany
| | - Allison K. Miller
- Anatomy Department, University of Otago, Dunedin, Otago, New Zealand
| | - Josefin Stiller
- Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Greg W. Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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11
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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.
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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.
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Zhao M, Kurtis SM, White ND, Moncrieff AE, Leite RN, Brumfield RT, Braun EL, Kimball RT. Exploring Conflicts in Whole Genome Phylogenetics: A Case Study Within Manakins (Aves: Pipridae). Syst Biol 2023; 72:161-178. [PMID: 36130303 PMCID: PMC10452962 DOI: 10.1093/sysbio/syac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Some phylogenetic problems remain unresolved even when large amounts of sequence data are analyzed and methods that accommodate processes such as incomplete lineage sorting are employed. In addition to investigating biological sources of phylogenetic incongruence, it is also important to reduce noise in the phylogenomic dataset by using appropriate filtering approach that addresses gene tree estimation errors. We present the results of a case study in manakins, focusing on the very difficult clade comprising the genera Antilophia and Chiroxiphia. Previous studies suggest that Antilophia is nested within Chiroxiphia, though relationships among Antilophia+Chiroxiphia species have been highly unstable. We extracted more than 11,000 loci (ultra-conserved elements and introns) from whole genomes and conducted analyses using concatenation and multispecies coalescent methods. Topologies resulting from analyses using all loci differed depending on the data type and analytical method, with 2 clades (Antilophia+Chiroxiphia and Manacus+Pipra+Machaeopterus) in the manakin tree showing incongruent results. We hypothesized that gene trees that conflicted with a long coalescent branch (e.g., the branch uniting Antilophia+Chiroxiphia) might be enriched for cases of gene tree estimation error, so we conducted analyses that either constrained those gene trees to include monophyly of Antilophia+Chiroxiphia or excluded these loci. While constraining trees reduced some incongruence, excluding the trees led to completely congruent species trees, regardless of the data type or model of sequence evolution used. We found that a suite of gene metrics (most importantly the number of informative sites and likelihood of intralocus recombination) collectively explained the loci that resulted in non-monophyly of Antilophia+Chiroxiphia. We also found evidence for introgression that may have contributed to the discordant topologies we observe in Antilophia+Chiroxiphia and led to deviations from expectations given the multispecies coalescent model. Our study highlights the importance of identifying factors that can obscure phylogenetic signal when dealing with recalcitrant phylogenetic problems, such as gene tree estimation error, incomplete lineage sorting, and reticulation events. [Birds; c-gene; data type; gene estimation error; model fit; multispecies coalescent; phylogenomics; reticulation].
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Affiliation(s)
- Min Zhao
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Sarah M Kurtis
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Noor D White
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, Bethesda, MD 20892, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Andre E Moncrieff
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USAand
| | - Rafael N Leite
- Graduate Program in Ecology, National Institute of Amazonian Research, Manaus, AM, Brazil
| | - Robb T Brumfield
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USAand
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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13
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DeSalle R, Narechania A, Tessler M. Multiple Outgroups Can Cause Random Rooting in Phylogenomics. Mol Phylogenet Evol 2023; 184:107806. [PMID: 37172862 DOI: 10.1016/j.ympev.2023.107806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/06/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Outgroup selection has been a major challenge since the rise of phylogenetics, and it has remained so in the phylogenomic era. Our goal here is to use large phylogenomic animal datasets to examine the impact of outgroup selection on the final topology. The results of our analyses further solidify the fact that distant outgroups can cause random rooting, and that this holds for concatenated and coalescent-based methods. The results also indicate that the standard practice of using multiple outgroups often causes random rooting. Most researchers go out of their way to get multiple outgroups, as this has been standard practice for decades. Based on our findings, this practice should stop. Instead, our results suggest that a single (most closely) related relative should be selected as the outgroup, unless all outgroups are roughly equally closely related to the ingroup.
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Affiliation(s)
- Rob DeSalle
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Apurva Narechania
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Michael Tessler
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA; St. Francis College, Department of Biology, Brooklyn, NY 11201, USA
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14
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Nie ZL, Hodel R, Ma ZY, Johnson G, Ren C, Meng Y, Ickert-Bond SM, Liu XQ, Zimmer E, Wen J. Climate-influenced boreotropical survival and rampant introgressions explain the thriving of New World grapes in the north temperate zone. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1183-1203. [PMID: 36772845 DOI: 10.1111/jipb.13466] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 02/08/2023] [Indexed: 05/13/2023]
Abstract
The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.
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Affiliation(s)
- Ze-Long Nie
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Richard Hodel
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Ying Meng
- College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China
| | - Stefanie M Ickert-Bond
- Herbarium (ALA), University of Alaska Museum of the North, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Elizabeth Zimmer
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA
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15
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Yu J, Niu Y, You Y, Cox CJ, Barrett RL, Trias-Blasi A, Guo J, Wen J, Lu L, Chen Z. Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan-Hengduan Mountains. THE NEW PHYTOLOGIST 2023; 238:888-903. [PMID: 36305244 DOI: 10.1111/nph.18580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan-Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence. We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data. We focused on reticulations in the trifoliolate lineage in the HHM region using a population-level genome resequencing dataset, incorporating evidence from morphology, distribution, and elevation. Comprehensive analyses confirmed multiple introgressions within Parthenocissus in a robust temporal-spatial framework. Around the HHM region, at least three hybridization hot spots were identified, one of which showed evidence of ongoing speciation reversal. We present a solid case study using an integrative methodological approach to investigate reticulate evolutionary history and its underlying mechanisms in plants. It demonstrates an example of speciation reversal through frequent hybridizations in the HHM region, which provides new perspectives on speciation dynamics in mountainous areas with strong topographic and environmental heterogeneity.
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Affiliation(s)
- Jinren Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanting Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yichen You
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Gambelas, Faro, 8005-319, Portugal
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, 2567, NSW, Australia
| | | | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Limin Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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16
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Feng C, Wang K, Xu W, Yang L, Wanghe K, Sun N, Wu B, Wu F, Yang L, Qiu Q, Gan X, Chen Y, He S. Monsoon boosted radiation of the endemic East Asian carps. SCIENCE CHINA. LIFE SCIENCES 2023; 66:563-578. [PMID: 36166180 DOI: 10.1007/s11427-022-2141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/21/2022] [Indexed: 10/14/2022]
Abstract
Major historical events often trigger the rapid flourishing of a few lineages, which in turn shape established biodiversity patterns. How did this process occur and develop? This study provides a window into this issue. The endemic East Asian carps (EEAC) dominated the ichthyofauna of East Asia and exhibited a high degree of adaptation to monsoonal river-lake ecosystems. A series of evidence, including ecogeography, phylogenetics, and macroevolution, suggests that the EEAC is a lineage that arose with the East Asian monsoon and thrived intimately with subsequent monsoon activities. We further deduce the evolution of the EEAC and find that a range of historical events in the monsoon setting (e.g., marine transgression and regression and glacial-interglacial cycle) have further reshaped the distribution patterns of EEAC's members. Comparative genomics analyses reveal that introgressions during the initial period of EEAC radiation and innovations in the regulation of the brain and nervous system may have aided their adaptation to river-lake ecosystems in a monsoon setting, which boosted radiation. Overall, this study strengthens knowledge of the evolutionary patterns of freshwater fishes in East Asia and provides a model case for understanding the impact of major historical events on the evolution of biota.
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Affiliation(s)
- Chenguang Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kunyuan Wanghe
- Key Laboratory of Adaptation and Evolution of Plateau Biota of Chinese Academy of Sciences, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Feixiang Wu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yiyu Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Natural Science Foundation of China, Beijing, 100085, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
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17
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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.
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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
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18
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Parmentier L, Vila R, Lukhtanov V. Integrative analysis reveals cryptic speciation linked to habitat differentiation within Albanian populations of the anomalous blues (Lepidoptera, Lycaenidae, Polyommatus Latreille, 1804). COMPARATIVE CYTOGENETICS 2022; 16:211-242. [PMID: 36760486 PMCID: PMC9836409 DOI: 10.3897/compcytogen.v16.i4.90558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/19/2022] [Indexed: 06/18/2023]
Abstract
The Balkan Peninsula is one of the greatest hotspots for biodiversity in Europe. While the region has been investigated thoroughly, some parts remain understudied and may still harbour undiscovered diversity, even in well-studied organisms such as Lepidoptera. Here we investigated the group of the so-called anomalous blue butterflies, also known as 'brown complex' of the subgenus Agrodiaetus Hübner, 1822 including the taxa of the entire Polyommatusaroaniensis (Brown, 1976) species complex. This species complex is distributed in the southern part of the Balkan Peninsula and known to be represented by three closely related allopatric species, differentiated by their chromosome numbers (n) and mitochondrial (mt) DNA. These are P.aroaniensis sensu stricto (Southern Greece, Peloponnese, n=47-48; mt haplogroup aroa1), P.timfristos Lukhtanov, Vishnevskaya et Shapoval, 2016 (Central Greece, Attika, n=38, aroa2) and P.orphicus Kolev, 2005 (North-Eastern Greece, Southern Bulgaria, n=41-42, orph1). Based on an analysis of chromosomal, molecular and morphological markers, we demonstrate that a fourth taxon of this species complex exists in Albania. This taxon possesses the mt haplogroup aroa3, which is the most differentiated within the entire P.aroaniensis species complex, and the karyotype (n=42-43), which differs by one fixed chromosome fission from P.orphicus. The Albanian taxon seems to be ecologically specialised (habitat on dark-coloured, ophiolitic substrate soils) and differs in colouration (wing reflectance) from the others taxa of the P.aroaniensis species group. Based on the evidence here presented and following the current view of the taxonomy of the group, we propose considering the Albanian taxon as a new species, here described as Polyommatuslurae sp. nov. At the contact zone between the new species and P.orphicus, in addition to typical ones, we detected specimens with haplogroup orph2, karyotype n=43 and intermediate morphology, which seem to represent P.lurae × P.orphicus hybrids.
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Affiliation(s)
- Laurian Parmentier
- Department of Plants & Crops, Lab Agrozoology, Ghent University, Coupure Links 653, 9000, Ghent, BelgiumGhent UniversityGhentBelgium
- Flemish Entomological Society, Workgroup Butterflies, Moerbeekstraat 29, 9870, Zulte, BelgiumFlemish Entomological Society, Workgroup ButterfliesZulteBelgium
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, SpainCSIC-Universitat Pompeu FabraBarcelonaSpain
| | - Vladimir Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, RussiaZoological Institute of Russian Academy of SciencesSaint PetersburgRussia
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19
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Gong G, Xiong Y, Xiao S, Li XY, Huang P, Liao Q, Han Q, Lin Q, Dan C, Zhou L, Ren F, Zhou Q, Gui JF, Mei J. Origin and chromatin remodeling of young X/Y sex chromosomes in catfish with sexual plasticity. Natl Sci Rev 2022; 10:nwac239. [PMID: 36846302 PMCID: PMC9945428 DOI: 10.1093/nsr/nwac239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/22/2022] [Accepted: 10/21/2022] [Indexed: 11/15/2022] Open
Abstract
Assembly of a complete Y chromosome is a significant challenge in animals with an XX/XY sex-determination system. Recently, we created YY-supermale yellow catfish by crossing XY males with sex-reversed XY females, providing a valuable model for Y-chromosome assembly and evolution. Here, we assembled highly homomorphic Y and X chromosomes by sequencing genomes of the YY supermale and XX female in yellow catfish, revealing their nucleotide divergences with only less than 1% and with the same gene compositions. The sex-determining region (SDR) was identified to locate within a physical distance of 0.3 Mb by FST scanning. Strikingly, the incipient sex chromosomes were revealed to originate via autosome-autosome fusion and were characterized by a highly rearranged region with an SDR downstream of the fusion site. We found that the Y chromosome was at a very early stage of differentiation, as no clear evidence of evolutionary strata and classical structure features of recombination suppression for a rather late stage of Y-chromosome evolution were observed. Significantly, a number of sex-antagonistic mutations and the accumulation of repetitive elements were discovered in the SDR, which might be the main driver of the initial establishment of recombination suppression between young X and Y chromosomes. Moreover, distinct three-dimensional chromatin organizations of the Y and X chromosomes were identified in the YY supermales and XX females, as the X chromosome exhibited denser chromatin structure than the Y chromosome, while they respectively have significantly spatial interactions with female- and male-related genes compared with other autosomes. The chromatin configuration of the sex chromosomes as well as the nucleus spatial organization of the XX neomale were remodeled after sex reversal and similar to those in YY supermales, and a male-specific loop containing the SDR was found in the open chromatin region. Our results elucidate the origin of young sex chromosomes and the chromatin remodeling configuration in the catfish sexual plasticity.
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Affiliation(s)
- Gaorui Gong
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Xiong
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Shijun Xiao
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing 314000, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Peipei Huang
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China,School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qian Liao
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingqing Han
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaohong Lin
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China,State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Cheng Dan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Fan Ren
- Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | | | - Jie Mei
- Corresponding author. E-mail:
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20
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Stout C, Schonhuth S, Mayden R, Garrison NL, Armbruster JW. Phylogenomics and classification of Notropis and related shiners (Cypriniformes: Leuciscidae) and the utility of exon capture on lower taxonomic groups. PeerJ 2022; 10:e14072. [PMID: 36248715 PMCID: PMC9558623 DOI: 10.7717/peerj.14072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/27/2022] [Indexed: 01/20/2023] Open
Abstract
North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis, which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis, such as Cyprinella, Luxilus, Lythrurus, and Pteronotropis, the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius, Luxilus, and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae. Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis, elevation of the subgenus Hydrophlox, expansion of species included in Miniellus, movement of Hudsonius cummingsae to Pteronotropis, and resurrection of the genera Coccotis and Paranotropis. We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala, and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucleotides respectively).
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Affiliation(s)
- Carla Stout
- Department of Biological Sciences, California State Polytechnic University, Pomona, Pomona, CA, United States of America
| | - Susana Schonhuth
- Department of Biology, Saint Louis University, St. Louis, MO, United States of America
| | - Richard Mayden
- Department of Biology, Saint Louis University, St. Louis, MO, United States of America
| | - Nicole L. Garrison
- Department of Biology, West Liberty University, West Liberty, WV, United States of America
| | - Jonathan W. Armbruster
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
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21
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Alexandre EAA, Yamada FH. Diversity and ecology of parasitic fauna of the endemic Serrasalmus brandtii Lütken, 1875 from the Caatinga Domain, Brazil. J NAT HIST 2022. [DOI: 10.1080/00222933.2022.2121233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
| | - Fabio Hideki Yamada
- Laboratório de Ecologia Parasitária (LABEP), Universidade Regional do Cariri (URCA), Crato, Brazil
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22
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Lozano-Fernandez J. A Practical Guide to Design and Assess a Phylogenomic Study. Genome Biol Evol 2022; 14:evac129. [PMID: 35946263 PMCID: PMC9452790 DOI: 10.1093/gbe/evac129] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of "big data" molecular phylogenetics provided a battery of new tools for biologists but simultaneously brought new methodological challenges. The increase in analytical complexity comes at the price of highly specific training in computational biology and molecular phylogenetics, resulting very often in a polarized accumulation of knowledge (technical on one side and biological on the other). Interpreting the robustness of genome-scale phylogenetic studies is not straightforward, particularly as new methodological developments have consistently shown that the general belief of "more genes, more robustness" often does not apply, and because there is a range of systematic errors that plague phylogenomic investigations. This is particularly problematic because phylogenomic studies are highly heterogeneous in their methodology, and best practices are often not clearly defined. The main aim of this article is to present what I consider as the ten most important points to take into consideration when planning a well-thought-out phylogenomic study and while evaluating the quality of published papers. The goal is to provide a practical step-by-step guide that can be easily followed by nonexperts and phylogenomic novices in order to assess the technical robustness of phylogenomic studies or improve the experimental design of a project.
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Affiliation(s)
- Jesus Lozano-Fernandez
- Department of Genetics, Microbiology and Statistics, Biodiversity Research Institute (IRBio), University of Barcelona, Avd. Diagonal 643, 08028 Barcelona, Spain
- Institute of Evolutionary Biology (CSIC – Universitat Pompeu Fabra), Passeig marítim de la Barcelona 37-49, 08003 Barcelona, Spain
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23
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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.
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24
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Smith BT, Merwin J, Provost KL, Thom G, Brumfield RT, Ferreira M, Mauck Iii WM, Moyle RG, Wright T, Joseph L. Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance. Syst Biol 2022; 72:228-241. [PMID: 35916751 DOI: 10.1093/sysbio/syac055] [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: 04/26/2021] [Revised: 02/22/2022] [Accepted: 07/22/2022] [Indexed: 11/14/2022] Open
Abstract
Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within datasets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade's species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower quality samples. Most instances of topological conflict and non-monophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many datasets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Jon Merwin
- Department of Ornithology, Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA.,Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, PA 19103, USA
| | - Kaiya L Provost
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Gregory Thom
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mateus Ferreira
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Av. Cap. Ene Garcez, 2413, Boa Vista, RR, Brazil
| | - William M Mauck Iii
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Robert G Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045, USA
| | - Timothy Wright
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
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25
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Simanovsky SA, Medvedev DA, Tefera F, Golubtsov AS. First cytogenetic data on Afrotropical lutefishes (Citharinidae) in the light of karyotype evolution in Characiformes. COMPARATIVE CYTOGENETICS 2022; 16:143-150. [PMID: 36761810 PMCID: PMC9849050 DOI: 10.3897/compcytogen.v16.i2.79133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/17/2022] [Indexed: 06/18/2023]
Abstract
The Afrotropical lutefish family Citharinidae (Citharinoidei, Characiformes) comprises three genera with eight species in total. Although Citharinidae have been studied in terms of taxonomy and systematics, no cytogenetic information was available for any representative of the family. Furthermore, only one species out of 116 in Citharinoidei (Distichodusaffinis Günther, 1873) has been studied cytogenetically. Here, we report the karyotypes of Citharinuscitharus (Geoffroy St. Hilaire, 1809) from West Africa and Citharinuslatus Müller et Troschel, 1844 from Northeast Africa. The former has the diploid chromosome number 2n = 40 and the fundamental number FN = 80, while the latter has 2n = 44 and FN = 88. Hence, these karyotypes consist exclusively of bi-armed chromosomes. Such karyotypes were previously found in D.affinis and in many lineages of Neotropical species of another suborder of Characiformes, Characoidei. In contrast, the karyotypes dominated by uni-armed elements are typical for a number of phylogenetically basal lineages of Afrotropical and Neotropical Characoidei. We discuss the importance of our data on Citharinidae for the understanding of the karyotype evolution within the order Characiformes.
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Affiliation(s)
- Sergey A. Simanovsky
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninskij prosp., 119071 Moscow, RussiaSevertsov Institute of Ecology and Evolution, Russian Academy of SciencesMoscowRussia
| | - Dmitry A. Medvedev
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninskij prosp., 119071 Moscow, RussiaSevertsov Institute of Ecology and Evolution, Russian Academy of SciencesMoscowRussia
| | - Fekadu Tefera
- National Fishery and Aquatic Life Research Center, Ethiopian Institute of Agricultural Research, P.O. Box 64, Sebeta, EthiopiaNational Fishery and Aquatic Life Research Center, Ethiopian Institute of Agricultural ResearchSebetaEthiopia
| | - Alexander S. Golubtsov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninskij prosp., 119071 Moscow, RussiaSevertsov Institute of Ecology and Evolution, Russian Academy of SciencesMoscowRussia
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26
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LaPotin S, Swartz ME, Luecke DM, Constantinou SJ, Gallant JR, Eberhart JK, Zakon HH. Divergent cis-regulatory evolution underlies the convergent loss of sodium channel expression in electric fish. SCIENCE ADVANCES 2022; 8:eabm2970. [PMID: 35648851 PMCID: PMC9159570 DOI: 10.1126/sciadv.abm2970] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
South American and African weakly electric fish independently evolved electric organs from muscle. In both groups, a voltage-gated sodium channel gene independently lost expression from muscle and gained it in the electric organ, allowing the channel to become specialized for generating electric signals. It is unknown how this voltage-gated sodium channel gene is targeted to muscle in any vertebrate. We describe an enhancer that selectively targets sodium channel expression to muscle. Next, we demonstrate how the loss of this enhancer, but not trans-activating factors, drove the loss of sodium channel gene expression from muscle in South American electric fish. While this enhancer is also altered in African electric fish, key transcription factor binding sites and enhancer activity are retained, suggesting that the convergent loss of sodium channel expression from muscle in these two electric fish lineages occurred via different processes.
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Affiliation(s)
- Sarah LaPotin
- Department of Neuroscience, The University of Texas, Austin, TX 78712, USA
| | - Mary E. Swartz
- Department of Molecular Biosciences, The University of Texas, Austin, TX 78712, USA
| | - David M. Luecke
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Savvas J. Constantinou
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Jason R. Gallant
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Johann K. Eberhart
- Department of Molecular Biosciences, The University of Texas, Austin, TX 78712, USA
| | - Harold H. Zakon
- Department of Neuroscience, The University of Texas, Austin, TX 78712, USA
- Department of Integrative Biology, The University of Texas, Austin, TX 78712, USA
- Corresponding author.
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27
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Schedel FDB, Chakona A, Sidlauskas BL, Popoola MO, Usimesa Wingi N, Neumann D, Vreven EJWMN, Schliewen UK. New phylogenetic insights into the African catfish families Mochokidae and Austroglanididae. JOURNAL OF FISH BIOLOGY 2022; 100:1171-1186. [PMID: 35184288 PMCID: PMC9310817 DOI: 10.1111/jfb.15014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/20/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Several hundred catfish species (order: Siluriformes) belonging to 11 families inhabit Africa, of which at least six families are endemic to the continent. Although four of those families are well-known to belong to the 'Big-Africa clade', no previous study has addressed the phylogenetic placement of the endemic African catfish family Austroglanididae in a comprehensive framework with molecular data. Furthermore, interrelationships within the 'Big-Africa clade', including the most diverse family Mochokidae, remain unclear. This study was therefore designed to help reconstruct inter- and intrarelationships of all currently valid mochokid genera, to infer their position within the 'Big Africa clade' and to establish a first molecular phylogenetic hypothesis of the relationships of the enigmatic Austroglanididae within the Siluriformes. We assembled a comprehensive mitogenomic dataset comprising all protein coding genes and representing almost all recognized catfish families (N = 33 of 39) with carefully selected species (N = 239). We recovered the monophyly of the previously identified multifamily clades 'Big Asia' and 'Big Africa' and determined Austroglanididae to be closely related to Pangasiidae, Ictaluroidea and Ariidae. Mochokidae was recovered as the sister group to a clade encompassing Auchenoglanididae, Claroteidae, Malapteruridae and the African Schilbeidae, albeit with low statistical support. The two mochokid subfamilies Mochokinae and Chiloglanidinae as well as the chiloglanid tribe Atopochilini were recovered as reciprocally monophyletic. The genus Acanthocleithron forms the sister group of all remaining Mochokinae, although with low support. The genus Atopodontus is the sister group of all remaining Atopochilini. In contrast to morphological reconstructions, the monophyly of the genus Chiloglanis was strongly supported in our analysis, with Chiloglanis macropterus nested within a Chiloglanis sublineage encompassing only other taxa from the Congo drainage. This is an important result because the phylogenetic relationships of C. macropterus have been controversial in the past, and because we and other researchers assumed that this species would be resolved as sister to most or all other members of Chiloglanis. The apparent paraphyly of Synodontis with respect to Microsynodontis provided an additional surprise, with Synodontis punu turning out to be the sister group of the latter genus.
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Affiliation(s)
- Frederic D. B. Schedel
- Zoological InstituteUniversity of BaselBaselSwitzerland
- Department of IchthyologySNSB‐Bavarian State Collection of ZoologyMunichGermany
- Faculty of BiologyLMU MunichMunichGermany
| | | | - Brian L. Sidlauskas
- Department of Fisheries, Wildlife and Conservation SciencesOregon State UniversityCorvallisOregonUSA
| | | | | | - Dirk Neumann
- Department of IchthyologySNSB‐Bavarian State Collection of ZoologyMunichGermany
| | - Emmanuel J. W. M. N. Vreven
- Vertebrate Section, Royal Museum for Central AfricaTervurenBelgium
- KU Leuven, Laboratory of Biodiversity and Evolutionary GenomicsLeuvenBelgium
| | - Ulrich K. Schliewen
- Department of IchthyologySNSB‐Bavarian State Collection of ZoologyMunichGermany
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Matschiner M, Barth JMI, Tørresen OK, Star B, Baalsrud HT, Brieuc MSO, Pampoulie C, Bradbury I, Jakobsen KS, Jentoft S. Supergene origin and maintenance in Atlantic cod. Nat Ecol Evol 2022; 6:469-481. [PMID: 35177802 PMCID: PMC8986531 DOI: 10.1038/s41559-022-01661-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022]
Abstract
Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation. Atlantic cod carries four supergenes linked to migratory lifestyle and environmental adaptations. Using whole-genome sequencing, the authors show that the genome inversions that underlie the supergenes originated at different times and show gene flux between supergene haplotypes.
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Affiliation(s)
- Michael Matschiner
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway. .,Department of Palaeontology and Museum, University of Zurich, Zurich, Switzerland. .,Natural History Museum, University of Oslo, Oslo, Norway.
| | - Julia Maria Isis Barth
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Ole Kristian Tørresen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Helle Tessand Baalsrud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marine Servane Ono Brieuc
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Ian Bradbury
- Fisheries and Oceans Canada, St John's, Newfoundland and Labrador, Canada
| | - Kjetill Sigurd Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
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29
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Leite PPDM, Sassi FDMC, Marinho MMF, Nirchio M, Moraes RLRD, Toma GA, Bertollo LAC, Cioffi MDB. Tracking the evolutionary pathways among Brazilian Lebiasina species (Teleostei: Lebiasinidae): a chromosomal and genomic comparative investigation. NEOTROPICAL ICHTHYOLOGY 2022. [DOI: 10.1590/1982-0224-2021-0153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Despite several difficulties in chromosomal analyses of small-sized fishes, the cytogenetics of the Lebiasinidae was largely improved in the last years, showing differential patterns in the chromosomal evolution inside the family. In this context, it has been shown that genus Lebiasina preserves its karyotypic macrostructure, composed of 2n = 36 chromosomes, whereas the other genera generally present higher 2n. This study focused on the comparative cytogenetics of three Lebiasina species, one of them analyzed here for the first time, using conventional and molecular procedures. The results reinforced the differentiated evolutionary path of the genus Lebiasina while, at the same time, highlighted the genomic particularities that have accompanied the evolution of each species. In this sense, the repetitive components of the genome played a significant role in the differentiation of each species. It is also notable that L. minuta and L. melanoguttata, the two species that occur exclusively in the Brazilian territory, show greater chromosomal similarities to each other than to the trans-Andean sister species, L. bimaculata.
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30
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Thomson RC, Brown JM. OUP accepted manuscript. Syst Biol 2022; 71:917-920. [PMID: 35088868 PMCID: PMC9203063 DOI: 10.1093/sysbio/syac002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 11/29/2022] Open
Abstract
The scale of data sets used to infer phylogenies has grown dramatically in the last decades, providing researchers with an enormous amount of information with which to draw inferences about evolutionary history. However, standard approaches to assessing confidence in those inferences (e.g., nonparametric bootstrap proportions [BP] and Bayesian posterior probabilities [PPs]) are still deeply influenced by statistical procedures and frameworks that were developed when information was much more limited. These approaches largely quantify uncertainty caused by limited amounts of data, which is often vanishingly small with modern, genome-scale sequence data sets. As a consequence, today’s phylogenomic studies routinely report near-complete confidence in their inferences, even when different studies reach strongly conflicting conclusions and the sites and loci in a single data set contain much more heterogeneity than our methods assume or can accommodate. Therefore, we argue that BPs and marginal PPs of bipartitions have outlived their utility as the primary means of measuring phylogenetic support for modern phylogenomic data sets with large numbers of sites relative to the number of taxa. Continuing to rely on these measures will hinder progress towards understanding remaining sources of uncertainty in the most challenging portions of the Tree of Life. Instead, we encourage researchers to examine the ideas and methods presented in this special issue of Systematic Biology and to explore the area further in their own work. The papers in this special issue outline strategies for assessing confidence and uncertainty in phylogenomic data sets that move beyond stochastic error due to limited data and offer promise for more productive dialogue about the challenges that we face in reaching our shared goal of understanding the history of life on Earth.[Big data; gene tree variation; genomic era; statistical bias.]
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Affiliation(s)
- Robert C Thomson
- School of Life Sciences, University of Hawai‘i, 2538 McCarthy Mall, Edmondson Hall 216, Honolulu, HI 96822, USA
- Correspondence to be sent to: School of Life Sciences, University of Hawai‘i, 2538 McCarthy Mall, Edmondson Hall 216, Honolulu, HI 96822, USA; E-mail:
| | - Jeremy M Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
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31
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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32
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OUP accepted manuscript. Syst Biol 2022; 71:973-985. [DOI: 10.1093/sysbio/syac014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 11/12/2022] Open
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33
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Gales SM, Ready JS, Sabaj MH, Bernt MJ, Silva DJF, Oliveira C, Oliveira G, Sales JBL. Molecular diversity and historical phylogeography of the widespread genus Mastiglanis (Siluriformes: Heptapteridae) based on palaeogeographical events in South America. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
The catfish family Heptapteridae, endemic in the Neotropical region, is composed of small- to medium-sized species. The genus Mastiglanis was monotypic until very recently and is often misidentified as Imparfinis because of similarities in diagnostic characters, including the length of maxillary barbels and limited pigmentation. We provide the first molecular inference of diversity for samples identified as Mastiglanis. Partial 16S and COI sequences were produced for 84 samples identified morphologically as Mastiglanis from the Amazon, Orinoco and Essequibo river basins. Species delimitation and phylogenetic methods recovered the genus as monophyletic, but samples assigned to the species Mastiglanis asopos yielded 21 distinct operational taxonomic units, often in sympatry. The first cladogenesis event, at ~12 Mya, was associated with marine incursions and/or vicariance events between the northward-flowing systems in the west and the rivers that drain to the east. Subsequent diversification during the Miocene and Pliocene was inferred to have resulted from environmental changes associated with Andean orogeny, whereas recent diversification in the late Pliocene and Pleistocene was inferred to result from environmental changes during glacial cycles. Despite the many probable cryptic species found across the large geographical distribution of the genus, further sampling is expected to increase taxonomic richness in this genus.
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Affiliation(s)
- Suellen M Gales
- Grupo de Investigação Biológica Integrada, Centro de Estudos Avançados da Biodiversidade (CEABIO), Universidade Federal do Pará, Av. Perimetral da Ciência 01, PCT-Guamá, Lote 11. 66075-750, Belém, PA, Brazil
| | - Jonathan Stuart Ready
- Grupo de Investigação Biológica Integrada, Centro de Estudos Avançados da Biodiversidade (CEABIO), Universidade Federal do Pará, Av. Perimetral da Ciência 01, PCT-Guamá, Lote 11. 66075-750, Belém, PA, Brazil
| | - Mark H Sabaj
- The Academy of Natural Sciences of Philadelphia, Philadelphia, PA, USA
| | - Maxwell J Bernt
- Department of Ichthyology, American Museum of Natural History, NY, USA
| | - Derlan José Ferreira Silva
- Grupo de Investigação Biológica Integrada, Centro de Estudos Avançados da Biodiversidade (CEABIO), Universidade Federal do Pará, Av. Perimetral da Ciência 01, PCT-Guamá, Lote 11. 66075-750, Belém, PA, Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, 250, Botucatu, SP. CEP: 18618-689, Brazil
| | - Guilherme Oliveira
- Instituto Tecnológico Vale, Rua Boa Ventura da Silva, 955, Umarizal, Belém, PA, CEP: 66055-090, Brazil
| | - João Bráullio L Sales
- Grupo de Investigação Biológica Integrada, Centro de Estudos Avançados da Biodiversidade (CEABIO), Universidade Federal do Pará, Av. Perimetral da Ciência 01, PCT-Guamá, Lote 11. 66075-750, Belém, PA, Brazil
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Van Damme K, Cornetti L, Fields PD, Ebert D. Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution. Syst Biol 2021; 71:777-787. [PMID: 34850935 PMCID: PMC9203061 DOI: 10.1093/sysbio/syab094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/04/2021] [Accepted: 11/15/2021] [Indexed: 11/28/2022] Open
Abstract
Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the “Gymnomera”). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.]
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Affiliation(s)
- Kay Van Damme
- Centre for Academic Heritage and Archives & Ghent University Botanical Garden, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.,Tvärminne Zoological Station (TZS), University of Helsinki, J.A. Palménin tie 260, Hanko, Finland
| | - Luca Cornetti
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Peter D Fields
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
| | - Dieter Ebert
- University of Basel, Department of Environmental Sciences, Zoology, Vesalgasse 1, 4051 Basel, Switzerland
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35
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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.
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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
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de Moraes RLR, Sassi FDMC, Bertollo LAC, Marinho MMF, Viana PF, Feldberg E, Oliveira VCS, Deon GA, Al-Rikabi ABH, Liehr T, Cioffi MDB. Tracking the Evolutionary Trends Among Small-Size Fishes of the Genus Pyrrhulina (Characiforme, Lebiasinidae): New Insights From a Molecular Cytogenetic Perspective. Front Genet 2021; 12:769984. [PMID: 34691160 PMCID: PMC8526856 DOI: 10.3389/fgene.2021.769984] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
Miniature fishes have always been a challenge for cytogenetic studies due to the difficulty in obtaining chromosomal preparations, making them virtually unexplored. An example of this scenario relies on members of the family Lebiasinidae which include miniature to medium-sized, poorly known species, until very recently. The present study is part of undergoing major cytogenetic advances seeking to elucidate the evolutionary history of lebiasinids. Aiming to examine the karyotype diversification more deeply in Pyrrhulina, here we combined classical and molecular cytogenetic analyses, including Giemsa staining, C-banding, repetitive DNA mapping, comparative genomic hybridization (CGH), and whole chromosome painting (WCP) to perform the first analyses in five Pyrrhulina species (Pyrrhulina aff. marilynae, Pyrrhulina sp., P. obermulleri, P. marilynae and Pyrrhulina cf. laeta). The diploid number (2n) ranged from 40 to 42 chromosomes among all analyzed species, but P. marilynae is strikingly differentiated by having 2n = 32 chromosomes and a karyotype composed of large meta/submetacentric chromosomes, whose plesiomorphic status is discussed. The distribution of microsatellites does not markedly differ among species, but the number and position of the rDNA sites underwent significant changes among them. Interspecific comparative genome hybridization (CGH) found a moderate divergence in the repetitive DNA content among the species’ genomes. Noteworthy, the WCP reinforced our previous hypothesis on the origin of the X1X2Y multiple sex chromosome system in P. semifasciata. In summary, our data suggest that the karyotype differentiation in Pyrrhulina has been driven by major structural rearrangements, accompanied by high dynamics of repetitive DNAs.
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Affiliation(s)
- Renata Luiza Rosa de Moraes
- Laboratorio de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | | | - Luiz Antonio Carlos Bertollo
- Laboratorio de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Manoela Maria Ferreira Marinho
- Museu de Zoologia da Universidade de São Paulo (MZUSP), São Paulo, Brazil.,Laboratório de Sistemática e Morfologia de Peixes, Departamento de Sistemática e Ecologia (DSE), Universidade Federal da Paraíba (UFPB), João Pessoa, Brazil
| | - Patrik Ferreira Viana
- Laboratório de Gentética Animal, Instituto Nacional de Pesquisa da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Eliana Feldberg
- Laboratório de Gentética Animal, Instituto Nacional de Pesquisa da Amazônia, Coordenação de Biodiversidade, Manaus, Brazil
| | - Vanessa Cristina Sales Oliveira
- Laboratorio de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Geize Aparecida Deon
- Laboratorio de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil.,Laboratório de Biologia Cromossômica, Estrutura e Função, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | | | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Marcelo de Bello Cioffi
- Laboratorio de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
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Nesi N, Tsagkogeorga G, Tsang SM, Nicolas V, Lalis A, Scanlon AT, Riesle-Sbarbaro SA, Wiantoro S, Hitch AT, Juste J, Pinzari CA, Bonaccorso FJ, Todd CM, Lim BK, Simmons NB, McGowen MR, Rossiter SJ. Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae). Syst Biol 2021; 70:1077-1089. [PMID: 33693838 PMCID: PMC8513763 DOI: 10.1093/sysbio/syab013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/27/2021] [Accepted: 03/03/2021] [Indexed: 11/14/2022] Open
Abstract
The family Pteropodidae (Old World fruit bats) comprises $>$200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with $>$50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the main pteropodid lineages is essential if we are to fully understand their evolutionary distinctiveness, and the extent to which these bats have transitioned to nectar-feeding. Here we generated orthologous sequences for $>$1400 nuclear protein-coding genes (2.8 million base pairs) across 114 species from 43 genera of Old World fruit bats (57% and 96% of extant species- and genus-level diversity, respectively), and combined phylogenomic inference with filtering by information content to resolve systematic relationships among the major lineages. Concatenation and coalescent-based methods recovered three distinct backbone topologies that were not able to be reconciled by filtering via phylogenetic information content. Concordance analysis and gene genealogy interrogation show that one topology is consistently the best supported, and that observed phylogenetic conflicts arise from both gene tree error and deep incomplete lineage sorting. In addition to resolving long-standing inconsistencies in the reported relationships among major lineages, we show that Old World fruit bats have likely undergone at least seven independent dietary transitions from frugivory to nectarivory. Finally, we use this phylogeny to identify and describe one new genus. [Chiroptera; coalescence; concordance; incomplete lineage sorting; nectar feeder; species tree; target enrichment.].
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Affiliation(s)
- Nicolas Nesi
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Susan M Tsang
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Zoology Section, National Museum of Natural History, Manila, Philippines
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Aude Lalis
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Annette T Scanlon
- School of Natural and Built Environments, University of South Australia, Mawson Lakes, SA, Australia
| | - Silke A Riesle-Sbarbaro
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Institute of Zoology, Zoological Society of London, London, UK
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Sigit Wiantoro
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Alan T Hitch
- Department of Wildlife, Fish, and Conservation Biology, University of California Davis, CA, USA
| | - Javier Juste
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | | | | | - Christopher M Todd
- The Hawkesbury institute for the Environment, Western Sydney University, Australia
| | - Burton K Lim
- Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
| | - Michael R McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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Favarato RM, Ribeiro LB, Campos A, Porto JIR, Nakayama CM, Ota RP, Feldberg E. Comparative cytogenetics of Serrasalmidae (Teleostei: Characiformes): The relationship between chromosomal evolution and molecular phylogenies. PLoS One 2021; 16:e0258003. [PMID: 34618832 PMCID: PMC8496811 DOI: 10.1371/journal.pone.0258003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022] Open
Abstract
Serrasalmidae has high morphological and chromosomal diversity. Based on molecular hypotheses, the family is currently divided into two subfamilies, Colossomatinae and Serrasalminae, with Serrasalminae composed of two tribes: Myleini (comprising most of pacus species) and Serrasalmini (represented by Metynnis, Catoprion, and remaining piranha’s genera). This study aimed to analyze species of the tribes Myleini (Myloplus asterias, M. lobatus, M. rubripinnis, M. schomburgki, and Tometes camunani) and Serrasalmini (Metynnis cuiaba, M. hypsauchen, and M. longipinnis) using classical and molecular cytogenetic techniques in order to understand the chromosomal evolution of the family. The four species of the genus Myloplus and T. camunani presented 2n = 58 chromosomes, while the species of Metynnis presented 2n = 62 chromosomes. The distribution of heterochromatin occurred predominantly in pericentromeric regions in all species. Tometes camunani and Myloplus spp. presented only one site with 5S rDNA. Multiple markers of 18S rDNA were observed in T. camunani, M. asterias, M. lobatus, M. rubripinnis, and M. schomburgkii. For Metynnis, however, synteny of the 18S and 5S rDNA was observed in the three species, in addition to an additional 5S marker in M. longipinnis. These data, when superimposed on the phylogeny of the family, suggest a tendency to increase the diploid chromosome number from 54 to 62 chromosomes, which occurred in a nonlinear manner and is the result of several chromosomal rearrangements. In addition, the different karyotype formulas and locations of ribosomal sequences can be used as cytotaxonomic markers and assist in the identification of species.
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Affiliation(s)
- Ramon Marin Favarato
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, Manaus, Amazonas, Brazil
- * E-mail:
| | - Leila Braga Ribeiro
- Centro de Ciências da Saúde, Universidade Federal de Roraima, Avenida Capitão Ene Garcêz, Boa Vista, RR, Brazil
| | - Alber Campos
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, Manaus, Amazonas, Brazil
| | - Jorge Ivan Rebelo Porto
- Coordenação de Pesquisas em Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, Manaus, Amazonas, Brazil
| | - Celeste Mutuko Nakayama
- Coordenação de Pesquisas em Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, Manaus, Amazonas, Brazil
| | - Rafaela Priscila Ota
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Botucatu, São Paulo, Brazil
| | - Eliana Feldberg
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, Manaus, Amazonas, Brazil
- Coordenação de Pesquisas em Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Petrópolis, Manaus, Amazonas, Brazil
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Cruaud A, Delvare G, Nidelet S, Sauné L, Ratnasingham S, Chartois M, Blaimer BB, Gates M, Brady SG, Faure S, van Noort S, Rossi JP, Rasplus JY. Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea). Cladistics 2021; 37:1-35. [PMID: 34478176 DOI: 10.1111/cla.12416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2020] [Indexed: 11/30/2022] Open
Abstract
Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, a group of parasitoid wasps, with a representative sampling (144 ingroups and seven outgroups) that covers all described subfamilies and tribes, and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent/divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artifactual results. We highlight a GC content bias for maximum-likelihood approaches, an artifactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data (>85% missing UCEs) on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and ten tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.
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Affiliation(s)
- Astrid Cruaud
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Gérard Delvare
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France.,UMR CBGP, CIRAD, F-34398, Montpellier, France
| | - Sabine Nidelet
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Laure Sauné
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Marguerite Chartois
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Michael Gates
- USDA, ARS, SEL, c/o Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Seán G Brady
- Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Sariana Faure
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Simon van Noort
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, PO Box 61, Cape Town, 8000, South Africa.,Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, 7701, Cape Town, South Africa
| | - Jean-Pierre Rossi
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Jean-Yves Rasplus
- CBGP, CIRAD, INRAe, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
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40
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Mongiardino Koch N. Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci. Mol Biol Evol 2021; 38:4025-4038. [PMID: 33983409 DOI: 10.1101/2021.02.13.431075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.
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41
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Abstract
Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.
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42
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Ferreira KM, Mirande JM, Quagio‐Grassiotto I, Santana JCO, Baicere‐Silva CM, Menezes NA. Testing the phylogenetic hypotheses of Stevardiinae Gill, 1858 in light of new phenotypic data (Teleostei: Characidae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Juan Marcos Mirande
- Fundación Miguel Lillo Unidad Ejecutora Lillo (CONICET‐FML) San Miguel de Tucumán Argentina
| | - Irani Quagio‐Grassiotto
- Depto de Morfologia, Instituto de Biociências Universidade Estadual Paulista Júlio de Mesquita Filho Botucatu Brazil
| | - Júlio C. O. Santana
- Instituto de Biociências Universidade Federal do Mato Grosso do Sul Campo Grande Brazil
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Ferrer Obiol J, James HF, Chesser RT, Bretagnolle V, González-Solís J, Rozas J, Riutort M, Welch AJ. Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds. Syst Biol 2021; 70:976-996. [PMID: 33512506 PMCID: PMC8357341 DOI: 10.1093/sysbio/syaa101] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 11/13/2020] [Accepted: 12/15/2020] [Indexed: 01/01/2023] Open
Abstract
The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic data sets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq data sets for phylogenetics, divergence time estimation, and inference of introgression, and we propose a strategy to optimize RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales. [Aves; incomplete lineage sorting; introgression; PE-ddRAD-Seq; phylogenomics; radiations; shearwaters; UCEs.].
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Affiliation(s)
- Joan Ferrer Obiol
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Helen F James
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - R Terry Chesser
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- U.S. Geological Survey, Patuxent Wildlife Research Center, Laurel, MD, USA
| | - Vincent Bretagnolle
- Centre d’Études Biologiques de Chizé, CNRS & La Rochelle Université, 79360, Villiers en Bois, France
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Marta Riutort
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
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44
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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.
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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
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45
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Goloboff PA, Catalano SA, Torres A. Parsimony analysis of phylogenomic datasets (II): evaluation of PAUP*, MEGA and MPBoot. Cladistics 2021; 38:126-146. [DOI: 10.1111/cla.12476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2021] [Indexed: 12/11/2022] Open
Affiliation(s)
- Pablo A. Goloboff
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 San Miguel de Tucumán Tucumán4000Argentina
- American Museum of Natural History 200 Central Park West New York NY10024USA
| | - Santiago A. Catalano
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 San Miguel de Tucumán Tucumán4000Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo Universidad Nacional de Tucumán Miguel Lillo 205 San Miguel de Tucumán Tucumán4000Argentina
| | - Ambrosio Torres
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 San Miguel de Tucumán Tucumán4000Argentina
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46
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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.
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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
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47
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Walker JF, Smith SA, Hodel RGJ, Moyroud E. Concordance-based approaches for the inference of relationships and molecular rates with phylogenomic datasets. Syst Biol 2021; 71:943-958. [PMID: 34240209 DOI: 10.1093/sysbio/syab052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/23/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022] Open
Abstract
Gene tree conflict is common and finding methods to analyze and alleviate the negative effects that conflict has on species tree analysis is a crucial part of phylogenomics. This study aims to expand the discussion of inferring species trees and molecular branch lengths when conflict is present. Conflict is typically examined in two ways: inferring its prevalence, and inferring the influence of the individual genes (how strongly one gene supports any given topology compared to an alternative topology). Here, we examine a procedure for incorporating both conflict and the influence of genes in order to infer evolutionary relationships. All supported relationships in the gene trees are analyzed and the likelihood of the genes constrained to these relationships is summed to provide a likelihood for the relationship. Consensus tree assembly is conducted based on the sum of likelihoods for a given relationship and choosing relationships based on the most likely relationship assuming it does not conflict with a relationship that has a higher likelihood score. If it is not possible for all most likely relationships to be combined into a single bifurcating tree then multiple trees are produced and a consensus tree with a polytomy is created. This procedure allows for more influential genes to have greater influence on an inferred relationship, does not assume conflict has arisen from any one source, and does not force the dataset to produce a single bifurcating tree. Using this approach on three empirical datasets, we examine and discuss the relationship between influence and prevalence of gene tree conflict. We find that in one of the datasets, assembling a bifurcating consensus tree solely composed of the most likely relationships is impossible. To account for conflict in molecular rate analysis we also introduce a concordance-based approach to the summary and estimation of branch lengths suitable for downstream comparative analyses. We demonstrate through simulation that even under high levels of stochastic conflict, the mean and median of the concordant rates recapitulate the true molecular rate better than using a supermatrix approach. Using a large phylogenomic dataset, we examine rate heterogeneity across concordant genes with a focus on the branch subtending crown angiosperms. Notably, we find highly variable rates of evolution along the branch subtending crown angiosperms. The approaches outlined here have several limitations, but they also represent some alternative methods for harnessing the complexity of phylogenomic datasets and enrich our inferences of both species' relationships and evolutionary processes.
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Affiliation(s)
- Joseph F Walker
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607 U.S.A
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Richard G J Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Edwige Moyroud
- The Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, Cambridge CB2 1LR, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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48
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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.
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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
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49
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Ren C, Wang L, Nie ZL, Johnson G, Yang QE, Wen J. Development and phylogenetic utilities of a new set of single-/low-copy nuclear genes in Senecioneae (Asteraceae), with new insights into the tribal position and the relationships within subtribe Tussilagininae. Mol Phylogenet Evol 2021; 162:107202. [PMID: 33992786 DOI: 10.1016/j.ympev.2021.107202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/13/2021] [Accepted: 05/06/2021] [Indexed: 11/26/2022]
Abstract
The tribe Senecioneae is one of the largest tribes in Asteraceae, with a nearly cosmopolitan distribution. Despite great efforts devoted to elucidate the evolution of Senecioneae, many questions still remain concerning the systematics of this group, from the tribal circumscription and position to species relationships in many genera. The hybridization-based target enrichment method of next-generation sequencing has been accepted as a promising approach to resolve phylogenetic problems. We herein develop a set of single-/low-copy genes for Senecioneae, and test their phylogenetic utilities. Our results demonstrate that these genes work highly efficiently for Senecioneae, with a high average gene recovery of 98.8% across the tribe and recovering robust phylogenetic hypotheses at different levels. In particular, the delimitation of the Senecioneae has been confirmed to include Abrotanella and exclude Doronicum, with the former sister to core Senecioneae and the latter shown to be more closely related to Calenduleae. Moreover, Doronicum and Calenduleae are inferred to be the closest relatives of Senecioneae, which is a new hypothesis well supported by statistical topology tests, morphological evidence, and the profile of pyrrolizidine alkaloids, a special kind of chemical characters generally used to define Senecioneae. Furthermore, this study suggests a complex reticulation history in the diversification of Senecioneae, accounting for the prevalence of polyploid groups in the tribe. With subtribe Tussilagininae s.str. as a case study showing a more evident pattern of gene duplication, we further explored reconstructing the phylogeny in the groups with high ploidy levels. Our results also demonstrate that tree topologies based on sorted paralogous copies are stable across different methods of phylogenetic inference, and more congruent with the morphological evidence and the results of previous phylogenetic studies.
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Affiliation(s)
- Chen Ren
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Long Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, Hunan 416000, China
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Qin-Er Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China; Key Laboratory of Digital Botanical Garden of Guangdong Province, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China.
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA.
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50
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Faustino-Fuster DR, Meza-Vargas V, Lovejoy NR, Lujan NK. Multi-locus phylogeny with dense Guiana Shield sampling supports new suprageneric classification of the neotropical three-barbeled catfishes (Siluriformes: Heptapteridae). Mol Phylogenet Evol 2021; 162:107186. [PMID: 33932613 DOI: 10.1016/j.ympev.2021.107186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 04/07/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
The catfish family Heptapteridae is ubiquitous across a range of freshwater habitats from southern Mexico to northern Argentina and contains 23 genera and 228 valid species. After a century of mostly morphology-based systematic analyses of these fishes, we provide the first molecular phylogenetic hypothesis spanning most valid Heptapteridae genera (16 of 23). We examined eight of 14 valid genera in the Nemuroglanis-subclade (Heptapterini), all valid genera in the Brachyglanis-subclade (Brachyglaniini) and most valid Brachyglaniini species (11 of 15). Maximum likelihood and Bayesian analyses of a 4156-base alignment of five gene regions (three mitochondrial: COI, Cyt b, and ND2; two nuclear: RAG2, Glyt) yielded thoroughly resolved and statistically robust phylogenies that were largely congruent with each other and with previous morphology-based hypotheses. We propose a revised phylogenetic classification consisting of two subfamilies (Rhamdiinae, Heptapterinae) each with two tribes. Dense taxonomic sampling of Brachyglaniini, including type species of Brachyglanis, Gladioglanis, Leptorhamdia, and Myoglanis, revealed widespread paraphyly. Newly recovered clades within Brachyglaniini are closely associated with either the upper Orinoco or the Essequibo suggesting repeated dispersals and/or range expansions/contractions across the western Guiana Shield highlands and from there to the upper Amazon and Brazilian Shield. These biogeographical processes appear to have been an important driver of allopatric diversification in the clade.
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Affiliation(s)
- Dario R Faustino-Fuster
- Departamento de Ictiología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Avenida Arenales 1256, Lima 14, Peru; Departamento de Zoologia, Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Campus do Vale, 91509-900 Porto Alegre, RS, Brazil.
| | - Vanessa Meza-Vargas
- Departamento de Ictiología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Avenida Arenales 1256, Lima 14, Peru; Laboratório de Sistemática de Vertebrados, Pontifícia Universidade Católica do Rio Grande do Sul., Av. Ipiranga, 6681, 90619-900 Porto Alegre, RS, Brazil
| | - Nathan R Lovejoy
- Department of Biological Sciences, University of Toronto Scarborough, Toronto M1C 1A4, Canada
| | - Nathan K Lujan
- Department of Ichthyology, American Museum of Natural History, New York, NY 10024, USA
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