1
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Saclier N, Duchemin L, Konecny-Dupré L, Grison P, Eme D, Martin C, Callou C, Lefébure T, François C, Issartel C, Lewis JJ, Stoch F, Sket B, Gottstein S, Delić T, Zagmajster M, Grabowski M, Weber D, Reboleira ASPS, Palatov D, Paragamian K, Knight LRFD, Michel G, Lefebvre F, Hosseini MJM, Camacho AI, De Bikuña BG, Taleb A, Belaidi N, Tuekam Kayo RP, Galassi DMP, Moldovan OT, Douady CJ, Malard F. A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database. Mol Ecol Resour 2024; 24:e13882. [PMID: 37864541 DOI: 10.1111/1755-0998.13882] [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: 04/19/2023] [Revised: 09/09/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023]
Abstract
Transition to novel environments, such as groundwater colonization by surface organisms, provides an excellent research ground to study phenotypic evolution. However, interspecific comparative studies on evolution to groundwater life are few because of the challenge in assembling large ecological and molecular resources for species-rich taxa comprised of surface and subterranean species. Here, we make available to the scientific community an operational set of working tools and resources for the Asellidae, a family of freshwater isopods containing hundreds of surface and subterranean species. First, we release the World Asellidae database (WAD) and its web application, a sustainable and FAIR solution to producing and sharing data and biological material. WAD provides access to thousands of species occurrences, specimens, DNA extracts and DNA sequences with rich metadata ensuring full scientific traceability. Second, we perform a large-scale dated phylogenetic reconstruction of Asellidae to support phylogenetic comparative analyses. Of 424 terminal branches, we identify 34 pairs of surface and subterranean species representing independent replicates of the transition from surface water to groundwater. Third, we exemplify the usefulness of WAD for documenting phenotypic shifts associated with colonization of subterranean habitats. We provide the first phylogenetically controlled evidence that body size of males decreases relative to that of females upon groundwater colonization, suggesting competition for rare receptive females selects for smaller, more agile males in groundwater. By making these tools and resources widely accessible, we open up new opportunities for exploring how phenotypic traits evolve in response to changes in selective pressures and trade-offs during groundwater colonization.
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Affiliation(s)
- Nathanaelle Saclier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
- ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France
| | - Louis Duchemin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Lara Konecny-Dupré
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Philippe Grison
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - David Eme
- INRAE, UR-RiverLY, Centre Lyon-Grenoble Auvergne-Rhône-Alpes, Villeurbanne, France
| | - Chloé Martin
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Cécile Callou
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Tristan Lefébure
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Clémentine François
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Colin Issartel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Julian J Lewis
- Virginia Museum of Natural History, Martinsville, Virginia, USA
- Lewis and Associates, Cave, Karst and Groundwater Biological Consulting, Borden, Indiana, USA
| | - Fabio Stoch
- Evolutionary Biology & Ecology, Université libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Boris Sket
- Department of Biology, SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sanja Gottstein
- Faculty of Science, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Teo Delić
- Department of Biology, SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Zagmajster
- Department of Biology, SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michal Grabowski
- Department of Invertebrate Zoology & Hydrobiology, Faculty of Biology & Environmental Protection, University of Lodz, Lodz, Poland
| | - Dieter Weber
- Musée National d'Histoire Naturelle de Luxembourg, Luxembourg City, Luxembourg
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Ana Sofia P S Reboleira
- Departamento de Biologia Animal, and Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Dmitry Palatov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | | | | | - Georges Michel
- CWEPSS, Commission Wallonne d'Etude et de Protection des Sites Souterrains, Bruxelles, Belgium
| | | | - Mohammad-Javad Malek Hosseini
- Jovan Hadži Institute of Biology, Research Centre of the Slovenian Academy of Sciences and Arts (ZRC-SAZU), Ljubljana, Slovenia
- Department of Organisms and Ecosystems Research, National Institute of Biology (NIB), Ljubljana, Slovenia
| | - Ana I Camacho
- Museo Nacional de Ciencias Naturales (CSIC). Dpto. Biodiversidad y Biología Evolutiva, Madrid, Spain
| | - Begoña Gartzia De Bikuña
- Anbiotek, Investigación científica y técnica del medio ambiente, Erandio, Bizkaia, Spain
- Anbiolab, BIC Bizkaia Astondo bidea, Derio, Spain
| | - Amina Taleb
- Laboratoire d'Écologie et Gestion des Ecosystèmes Naturels, University of Tlemcen, Tlemcen, Algeria
| | - Nouria Belaidi
- Laboratoire d'Écologie et Gestion des Ecosystèmes Naturels, University of Tlemcen, Tlemcen, Algeria
| | - Raoul P Tuekam Kayo
- Faculty of Science, Department of Zoology, University of Bamenda, Bambili, Cameroon
| | | | - Oana Teodora Moldovan
- Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
- Centro Nacional de Investigación sobre la Evolución Humana, Burgos, Spain
| | - Christophe J Douady
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| | - Florian Malard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
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Garduño-Sánchez M, Hernández-Lozano J, Moran RL, Miranda-Gamboa R, Gross JB, Rohner N, Elliott WR, Miller J, Lozano-Vilano L, McGaugh SE, Ornelas-García CP. Phylogeographic relationships and morphological evolution between cave and surface Astyanax mexicanus populations (De Filippi 1853) (Actinopterygii, Characidae). Mol Ecol 2023; 32:5626-5644. [PMID: 37712324 DOI: 10.1111/mec.17128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 08/14/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023]
Abstract
The Astyanax mexicanus complex includes two different morphs, a surface- and a cave-adapted ecotype, found at three mountain ranges in Northeastern Mexico: Sierra de El Abra, Sierra de Guatemala and Sierra de la Colmena (Micos). Since their discovery, multiple studies have attempted to characterize the timing and the number of events that gave rise to the evolution of these cave-adapted ecotypes. Here, using RADseq and genome-wide sequencing, we assessed the phylogenetic relationships, genetic structure and gene flow events between the cave and surface Astyanax mexicanus populations, to estimate the tempo and mode of evolution of the cave-adapted ecotypes. We also evaluated the body shape evolution across different cave lineages using geometric morphometrics to examine the role of phylogenetic signal versus environmental pressures. We found strong evidence of parallel evolution of cave-adapted ecotypes derived from two separate lineages of surface fish and hypothesize that there may be up to four independent invasions of caves from surface fish. Moreover, a strong congruence between the genetic structure and geographic distribution was observed across the cave populations, with the Sierra de Guatemala the region exhibiting most genetic drift among the cave populations analysed. Interestingly, we found no evidence of phylogenetic signal in body shape evolution, but we found support for parallel evolution in body shape across independent cave lineages, with cavefish from the Sierra de El Abra reflecting the most divergent morphology relative to surface and other cavefish populations.
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Affiliation(s)
- Marco Garduño-Sánchez
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jorge Hernández-Lozano
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rachel L Moran
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, USA
| | - Ramsés Miranda-Gamboa
- Instituto de Energías Renovables, Universidad Nacional Autónoma de México, Temixco, Mexico
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
- Department of Molecular & Integrative Physiology, KU Medical Center, Kansas City, Kansas, USA
| | - William R Elliott
- Association for Mexican Cave Studies, Austin, Texas, USA
- Missouri Department of Conservation, Georgetown, Texas, USA
| | - Jeff Miller
- Department of Molecular Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Lourdes Lozano-Vilano
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - C Patricia Ornelas-García
- Colección Nacional de Peces, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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3
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Balart-García P, Aristide L, Bradford TM, Beasley-Hall PG, Polak S, Cooper SJB, Fernández R. Parallel and convergent genomic changes underlie independent subterranean colonization across beetles. Nat Commun 2023; 14:3842. [PMID: 37386018 PMCID: PMC10310748 DOI: 10.1038/s41467-023-39603-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/21/2023] [Indexed: 07/01/2023] Open
Abstract
Adaptation to life in caves is often accompanied by dramatically convergent changes across distantly related taxa, epitomized by the loss or reduction of eyes and pigmentation. Nevertheless, the genomic underpinnings underlying cave-related phenotypes are largely unexplored from a macroevolutionary perspective. Here we investigate genome-wide gene evolutionary dynamics in three distantly related beetle tribes with at least six instances of independent colonization of subterranean habitats, inhabiting both aquatic and terrestrial underground systems. Our results indicate that remarkable gene repertoire changes mainly driven by gene family expansions occurred prior to underground colonization in the three tribes, suggesting that genomic exaptation may have facilitated a strict subterranean lifestyle parallelly across beetle lineages. The three tribes experienced both parallel and convergent changes in the evolutionary dynamics of their gene repertoires. These findings pave the way towards a deeper understanding of the evolution of the genomic toolkit in hypogean fauna.
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Affiliation(s)
- Pau Balart-García
- Metazoa Phylogenomics Lab, Biodiversity Program, Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
| | - Leandro Aristide
- Metazoa Phylogenomics Lab, Biodiversity Program, Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Tessa M Bradford
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, and Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Museum, Adelaide, SA, 5000, Australia
| | - Perry G Beasley-Hall
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, and Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Museum, Adelaide, SA, 5000, Australia
| | - Slavko Polak
- Notranjska Museum Postojna, Kolodvorska c. 3, 6230, Postojna, Slovenia
| | - Steven J B Cooper
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, and Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Museum, Adelaide, SA, 5000, Australia
| | - Rosa Fernández
- Metazoa Phylogenomics Lab, Biodiversity Program, Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
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4
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Bastide P, Soneson C, Stern DB, Lespinet O, Gallopin M. A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data. Mol Biol Evol 2023; 40:6889356. [PMID: 36508357 DOI: 10.1093/molbev/msac269] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/14/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Interspecies RNA-Seq datasets are increasingly common, and have the potential to answer new questions about the evolution of gene expression. Single-species differential expression analysis is now a well-studied problem that benefits from sound statistical methods. Extensive reviews on biological or synthetic datasets have provided the community with a clear picture on the relative performances of the available methods in various settings. However, synthetic dataset simulation tools are still missing in the interspecies gene expression context. In this work, we develop and implement a new simulation framework. This tool builds on both the RNA-Seq and the phylogenetic comparative methods literatures to generate realistic count datasets, while taking into account the phylogenetic relationships between the samples. We illustrate the usefulness of this new framework through a targeted simulation study, that reproduces the features of a recently published dataset, containing gene expression data in adult eye tissue across blind and sighted freshwater crayfish species. Using our simulated datasets, we perform a fair comparison of several approaches used for differential expression analysis. This benchmark reveals some of the strengths and weaknesses of both the classical and phylogenetic approaches for interspecies differential expression analysis, and allows for a reanalysis of the crayfish dataset. The tool has been integrated in the R package compcodeR, freely available on Bioconductor.
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Affiliation(s)
- Paul Bastide
- IMAG, Université de Montpellier, CNRS, Montpellier, France
| | - Charlotte Soneson
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - David B Stern
- Department of Integrative Biology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Olivier Lespinet
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Mélina Gallopin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
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5
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Langille BL, Tierney SM, Bertozzi T, Beasley-Hall PG, Bradford TM, Fagan-Jeffries EP, Hyde J, Leijs R, Richardson M, Saint KM, Stringer DN, Villastrigo A, Humphreys WF, Austin AD, Cooper SJB. Parallel decay of vision genes in subterranean water beetles. Mol Phylogenet Evol 2022; 173:107522. [PMID: 35595008 DOI: 10.1016/j.ympev.2022.107522] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022]
Abstract
In the framework of neutral theory of molecular evolution, genes specific to the development and function of eyes in subterranean animals living in permanent darkness are expected to evolve by relaxed selection, ultimately becoming pseudogenes. However, definitive empirical evidence for the role of neutral processes in the loss of vision over evolutionary time remains controversial. In previous studies, we characterized an assemblage of independently-evolved water beetle (Dytiscidae) species from a subterranean archipelago in Western Australia, where parallel vision and eye loss have occurred. Using a combination of transcriptomics and exon capture, we present evidence of parallel coding sequence decay, resulting from the accumulation of frameshift mutations and premature stop codons, in eight phototransduction genes (arrestins, opsins, ninaC and transient receptor potential channel genes) in 32 subterranean species in contrast to surface species, where these genes have open reading frames. Our results provide strong evidence to support neutral evolutionary processes as a major contributing factor to the loss of phototransduction genes in subterranean animals, with the ultimate fate being the irreversible loss of a light detection system.
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Affiliation(s)
- Barbara L Langille
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia.
| | - Simon M Tierney
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Terry Bertozzi
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Perry G Beasley-Hall
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Tessa M Bradford
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Erinn P Fagan-Jeffries
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Josephine Hyde
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Western Australia Department of Biodiversity Conservation and Attractions, Kensington, WA 6151, Australia
| | - Remko Leijs
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Matthew Richardson
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Kathleen M Saint
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Danielle N Stringer
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Adrián Villastrigo
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia; Institute of Evolutionary Biology, Passeig Marítim de la Barceloneta, 37-49, 08003, Spain
| | - William F Humphreys
- Western Australian Museum, Locked Bag 40, Welshpool DC, WA 6986, Australia; School of Animal Biology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, Department of Ecology and Evolution, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
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6
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Drozdova P, Kizenko A, Saranchina A, Gurkov A, Firulyova M, Govorukhina E, Timofeyev M. The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae). BMC Ecol Evol 2021; 21:81. [PMID: 33971810 PMCID: PMC8108468 DOI: 10.1186/s12862-021-01806-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/20/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Vision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species. RESULTS We evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning. CONCLUSIONS This repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.
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Affiliation(s)
- Polina Drozdova
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | | | | | - Anton Gurkov
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | - Maria Firulyova
- Computer Technologies Department, ITMO University, St. Petersburg, Russia
| | | | - Maxim Timofeyev
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
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7
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Sondhi Y, Ellis EA, Bybee SM, Theobald JC, Kawahara AY. Light environment drives evolution of color vision genes in butterflies and moths. Commun Biol 2021; 4:177. [PMID: 33564115 PMCID: PMC7873203 DOI: 10.1038/s42003-021-01688-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Opsins, combined with a chromophore, are the primary light-sensing molecules in animals and are crucial for color vision. Throughout animal evolution, duplications and losses of opsin proteins are common, but it is unclear what is driving these gains and losses. Light availability is implicated, and dim environments are often associated with low opsin diversity and loss. Correlations between high opsin diversity and bright environments, however, are tenuous. To test if increased light availability is associated with opsin diversification, we examined diel niche and identified opsins using transcriptomes and genomes of 175 butterflies and moths (Lepidoptera). We found 14 independent opsin duplications associated with bright environments. Estimating their rates of evolution revealed that opsins from diurnal taxa evolve faster-at least 13 amino acids were identified with higher dN/dS rates, with a subset close enough to the chromophore to tune the opsin. These results demonstrate that high light availability increases opsin diversity and evolution rate in Lepidoptera.
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Affiliation(s)
- Yash Sondhi
- Department of Biology, Florida International University, Miami, FL, USA.
| | - Emily A Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Jamie C Theobald
- Department of Biology, Florida International University, Miami, FL, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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8
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Audino JA, Serb JM, Marian JEAR. Hard to get, easy to lose: Evolution of mantle photoreceptor organs in bivalves (Bivalvia, Pteriomorphia). Evolution 2020; 74:2105-2120. [PMID: 32716056 DOI: 10.1111/evo.14050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/08/2020] [Accepted: 06/24/2020] [Indexed: 12/25/2022]
Abstract
Morphologically diverse eyes have evolved numerous times, yet little is known about how eye gain and loss is related to photic environment. The pteriomorphian bivalves (e.g., oysters, scallops, and ark clams), with a remarkable range of photoreceptor organs and ecologies, are a suitable system to investigate the association between eye evolution and ecological shifts. The present phylogenetic framework was based on amino acid sequences from transcriptome datasets and nucleotide sequences of five additional genes. In total, 197 species comprising 22 families from all five pteriomorphian orders were examined, representing the greatest taxonomic sampling to date. Morphological data were acquired for 162 species and lifestyles were compiled from the literature for all 197 species. Photoreceptor organs occur in 11 families and have arisen exclusively in epifaunal lineages, that is, living above the substrate, at least five times independently. Models for trait evolution consistently recovered higher rates of loss over gain. Transitions to crevice-dwelling habit appear associated with convergent gains of eyespots in epifaunal lineages. Once photoreceptor organs have arisen, multiple losses occurred in lineages that shift to burrowing lifestyles and deep-sea habitats. The observed patterns suggest that eye evolution in pteriomorphians might have evolved in association with light-guided behaviors, such as phototaxis, body posture, and alarm responses.
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Affiliation(s)
- Jorge Alves Audino
- Department of Zoology, University of São Paulo, São Paulo, 05508-090, Brazil
| | - Jeanne Marie Serb
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011
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9
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Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus. Genes (Basel) 2019; 11:genes11010042. [PMID: 31905778 PMCID: PMC7016750 DOI: 10.3390/genes11010042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 12/18/2022] Open
Abstract
Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms.
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Stern DB, Crandall KA. The Evolution of Gene Expression Underlying Vision Loss in Cave Animals. Mol Biol Evol 2019; 35:2005-2014. [PMID: 29788330 PMCID: PMC6063295 DOI: 10.1093/molbev/msy106] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Dissecting the evolutionary genetic processes underlying eye reduction and vision loss in obligate cave-dwelling organisms has been a long-standing challenge in evolutionary biology. Independent vision loss events in related subterranean organisms can provide critical insight into these processes as well as into the nature of convergent loss of complex traits. Advances in evolutionary developmental biology have illuminated the significant role of heritable gene expression variation in the evolution of new forms. Here, we analyze gene expression variation in adult eye tissue across the freshwater crayfish, representing four independent vision-loss events in caves. Species and individual expression patterns cluster by eye function rather than phylogeny, suggesting convergence in transcriptome evolution in independently blind animals. However, this clustering is not greater than what is observed in surface species with conserved eye function after accounting for phylogenetic expectations. Modeling expression evolution suggests that there is a common increase in evolutionary rates in the blind lineages, consistent with a relaxation of selective constraint maintaining optimal expression levels. This is evidence for a repeated loss of expression constraint in the transcriptomes of blind animals and that convergence occurs via a similar trajectory through genetic drift.
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Affiliation(s)
- David B Stern
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, Computational Biology Institute, The George Washington University, Washington, DC
| | - Keith A Crandall
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, Computational Biology Institute, The George Washington University, Washington, DC
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Porter ML, Sumner-Rooney L. Evolution in the Dark: Unifying our Understanding of Eye Loss. Integr Comp Biol 2018; 58:367-371. [PMID: 30239782 DOI: 10.1093/icb/icy082] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Megan L Porter
- Department of Biology, University of Hawai‘i at Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Lauren Sumner-Rooney
- Oxford University Museum of Natural History, University of Oxford, Parks Road, Oxford OX1 3PW, UK
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