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Macpherson ESB, Hauser FE, Van Nynatten A, Chang BSW, Lovejoy NR. Evolution of rhodopsin in flatfishes (Pleuronectiformes) is associated with depth and migratory behavior. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38859571 DOI: 10.1111/jfb.15828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/06/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024]
Abstract
Visual signals are involved in many fitness-related tasks and are therefore essential for survival in many species. Aquatic organisms are ideal systems to study visual evolution, as the high diversity of spectral properties in aquatic environments generates great potential for adaptation to different light conditions. Flatfishes are an economically important group, with over 800 described species distributed globally, including halibut, flounder, sole, and turbot. The diversity of flatfish species and wide array of environments they occupy provides an excellent opportunity to understand how this variation translates to molecular adaptation of vision genes. Using models of molecular evolution, we investigated how the light environments inhabited by different flatfish lineages have shaped evolution in the rhodopsin gene, which is responsible for mediating dim-light visual transduction. We found strong evidence for positive selection in rhodopsin, and this was correlated with both migratory behavior and several fundamental aspects of habitat, including depth and freshwater/marine evolutionary transitions. We also identified several mutations that likely affect the wavelength of peak absorbance of rhodopsin, and outline how these shifts in absorbance correlate with the response to the light spectrum present in different habitats. This is the first study of rhodopsin evolution in flatfishes that considers their extensive diversity, and our results highlight how ecologically-driven molecular adaptation has occurred across this group in response to transitions to novel light environments.
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Affiliation(s)
- Esme S B Macpherson
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Alexander Van Nynatten
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nathan R Lovejoy
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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Presti P, Pastana MNL, Johnson GD, Datovo A. The gustatory stalk of the Remo flounder exemplifies how complex evolutionary novelties may arise. Sci Rep 2024; 14:11667. [PMID: 38778033 PMCID: PMC11111803 DOI: 10.1038/s41598-024-55958-x] [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: 11/22/2023] [Accepted: 02/29/2024] [Indexed: 05/25/2024] Open
Abstract
The appearance of evolutionary novelties is a central issue in biology. Since Darwin's theory, difficulties in explaining how novel intricate body parts arose have often been used by creationists and other deniers to challenge evolution. Here, we describe the gustatory stalk of the Remo flounder (Oncopterus darwinii), an anatomically and functionally complex organ presumably used as a chemoreceptor probe to detect prey buried in the substrate. We demonstrate that the gustatory stalk is derived from the first dorsal-fin ray, which acquired remarkable modifications in its external morphology, integument, skeleton, muscles, and nerves. Such structural innovations are echoed in both functional and ecological specializations. We reveal that the gustatory stalk arose through the gradual accumulation of changes that evolved at different levels of the phylogenetic tree of ray-finned fishes. At least five preconditions arose in nodes preceding Oncopterus darwinii. This finding constitutes an interesting example of how evolution can deeply remodel body parts to perform entirely new functions. In this case, a trivial support structure primitively used for swimming became a sophisticated sensory tool to uncover hidden prey.
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Affiliation(s)
- Paulo Presti
- Instituto de Biociências da Universidade de São Paulo, São Paulo, SP, Brazil.
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil.
| | | | - G David Johnson
- National Museum of Natural History of the Smithsonian Institution, Washington, DC, USA
| | - Aléssio Datovo
- Museu de Zoologia da Universidade de São Paulo, São Paulo, Brazil
- National Museum of Natural History of the Smithsonian Institution, Washington, DC, USA
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Kundu S, Palimirmo FS, Kang HE, Kim AR, Lee SR, Gietbong FZ, Song SH, Kim HW. Insights into the Mitochondrial Genetic Makeup and Miocene Colonization of Primitive Flatfishes (Pleuronectiformes: Psettodidae) in the East Atlantic and Indo-West Pacific Ocean. BIOLOGY 2023; 12:1317. [PMID: 37887027 PMCID: PMC10604034 DOI: 10.3390/biology12101317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]
Abstract
The mitogenomic evolution of the Psettodes flatfishes is still poorly known from their range distribution in eastern Atlantic and Indo-West Pacific Oceans. The study delves into the matrilineal evolutionary pathway of these primitive flatfishes, with a specific focus on the complete mitogenome of the Psettodes belcheri species, as determined through next-generation sequencing. The mitogenome in question spans a length of 16,747 base pairs and comprises a total of 37 genes, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Notably, the mitogenome of P. belcheri exhibits a bias towards AT base pairs, with a composition of 54.15%, mirroring a similar bias observed in its close relative, Psettodes erumei, which showcases percentages of 53.07% and 53.61%. Most of the protein-coding genes commence with an ATG initiation codon, except for Cytochrome c oxidase I (COI), which initiates with a GTG codon. Additionally, four protein-coding genes commence with a TAA termination codon, while seven others exhibit incomplete termination codons. Furthermore, two protein-coding genes, namely NAD1 and NAD6, terminate with AGG and TAG stop codons, respectively. In the mitogenome of P. belcheri, the majority of transfer RNAs demonstrate the classical cloverleaf secondary structures, except for tRNA-serine, which lacks a DHU stem. Comparative analysis of conserved blocks within the control regions of two Psettodidae species unveiled that the CSB-II block extended to a length of 51 base pairs, surpassing the other blocks and encompassing highly variable sites. A comprehensive phylogenetic analysis using mitochondrial genomes (13 concatenated PCGs) categorized various Pleuronectiformes species, highlighting the basal position of the Psettodidae family and showed monophyletic clustering of Psettodes species. The approximate divergence time (35-10 MYA) between P. belcheri and P. erumei was estimated, providing insights into their separation and colonization during the early Miocene. The TimeTree analysis also estimated the divergence of two suborders, Psettodoidei and Pleuronectoidei, during the late Paleocene to early Eocene (56.87 MYA). The distribution patterns of Psettodes flatfishes were influenced by ocean currents and environmental conditions, contributing to their ecological speciation. In the face of climate change and anthropogenic activities, the conservation implications of Psettodes flatfishes are emphasized, underscoring the need for regulated harvesting and adaptive management strategies to ensure their survival in changing marine ecosystems. Overall, this study contributes to understanding the evolutionary history, genetic diversity, and conservation needs of Psettodes flatfishes globally. However, the multifaceted exploration of mitogenome and larger-scale genomic data of Psettodes flatfish will provide invaluable insights into their genetic characterization, evolutionary history, environmental adaptation, and conservation in the eastern Atlantic and Indo-West Pacific Oceans.
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Affiliation(s)
- Shantanu Kundu
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | - Flandrianto Sih Palimirmo
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency, Cibinong 16911, Indonesia
| | - Hye-Eun Kang
- Institute of Marine Life Science, Pukyong National University, Busan 48513, Republic of Korea
| | - Ah Ran Kim
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | - Soo Rin Lee
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Se Hyun Song
- Fisheries Resources Management Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea
| | - Hyun-Woo Kim
- Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
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Bitencourt JA, Affonso PRAM, Ramos RTC, Schneider H, Sampaio I. Phylogenetic relationships and the origin of New World soles (Teleostei: Pleuronectiformes: Achiridae): The role of estuarine habitats. Mol Phylogenet Evol 2023; 178:107631. [PMID: 36162736 DOI: 10.1016/j.ympev.2022.107631] [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: 05/08/2022] [Revised: 09/08/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022]
Abstract
Even though the monophyletic status of Achiridae has been supported by morphological and molecular data, the interrelationships within the representatives of this family are poorly resolved. In the present study, we carried out the most complete molecular phylogenetic analysis of this group, encompassing all genera and employing both nuclear (Rhodopsin, Recombination activator [Rag 1], Mixed - lineage Leukemia [MLL] and Early Growth Response Protein 3 [EGR3]) and mitochondrial (Cytochrome C Oxidase Subunit I [COI], Cytochrome B [CytB], ATPase 6.8, 16S and 12S RNAr) genes. All topologies based on Maximum Likelihood, Bayesian inferences and Bayesian Inference of the Multispecies Coalescent confirmed the monophyletism of Achiridae, in spite of some incongruences in relation to Achirus mucuri, A. lineatus, Apionichthys finis and Trinectes microphthalmus. In fact, Achirus and Trinectes proved to be non-monophyletic genera while Hypoclinemus mentalis was closely related to A. achirus, suggesting this species should be reevaluated. We provided evidence that Achiridae has first arisen in estuaries (about 23.5 million years ago) and some lineages have evolved independently to either marine or freshwater habitats. Furthermore, we propose a diversification scenario of New World soles involving at least two events of marine incursions during Miocene and Pliocene - Pleistocene associated with natural geographic barriers (Victoria-Trindade chain), the width and exposure of continental shelf and headwater capture along the Amazon basin. Finally, the evolutionary dependence of Achirid soles on estuaries, characterized as highly dynamic environments, has probably driven the recent divergence of many species of Achiridae.
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Affiliation(s)
- Jamille A Bitencourt
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Campus Jequié, Av. José Moreira Sobrinho, S/N, Jequiezinho, 45208-190 Jequié, BA, Brazil.
| | - Paulo R A M Affonso
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Campus Jequié, Av. José Moreira Sobrinho, S/N, Jequiezinho, 45208-190 Jequié, BA, Brazil
| | - Robson T C Ramos
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Campus I Lot. Cidade Universitária, 58051-900 João Pessoa, PB, Brazil
| | - Horacio Schneider
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Universitário de Bragança, Alameda Leandro Ribeiro, 68600-000 Bragança, PA, Brazil
| | - Iracilda Sampaio
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Campus Universitário de Bragança, Alameda Leandro Ribeiro, 68600-000 Bragança, PA, Brazil
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Coca‐de‐la‐Iglesia M, Medina NG, Wen J, Valcárcel V. Evaluation of tropical-temperate transitions: An example of climatic characterization in the Asian Palmate group of Araliaceae. AMERICAN JOURNAL OF BOTANY 2022; 109:1488-1507. [PMID: 36039662 PMCID: PMC9826302 DOI: 10.1002/ajb2.16059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
PREMISE There has been a great increase in using climatic data in phylogenetic studies over the past decades. However, compiling the high-quality spatial data needed to perform accurate climatic reconstructions is time-consuming and can result in poor geographical coverage. Therefore, researchers often resort to qualitative approximations. Our aim was to evaluate the climatic characterization of the genera of the Asian Palmate Group (AsPG) of Araliaceae as an exemplar lineage of plants showing tropical-temperate transitions. METHODS We compiled a curated worldwide spatial database of the AsPG genera and created five raster layers representing bioclimatic regionalizations of the world. Then, we crossed the database with the layers to climatically characterize the AsPG genera. RESULTS We found large disagreement in the climatic characterization of genera among regionalizations and little support for the climatic nature of the tropical-temperate distribution of the AsPG. Both results are attributed to the complexity of delimiting tropical, subtropical, and temperate climates in the world and to the distribution of the study group in regions with transitional climatic conditions. CONCLUSIONS The complexity in the climatic classification of this example of the tropical-temperate transitions calls for a general climatic revision of other tropical-temperate lineages. In fact, we argue that, to properly evaluate tropical-temperate transitions across the tree of life, we cannot ignore the complexity of distribution ranges.
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Affiliation(s)
| | - Nagore G. Medina
- Departamento de BiologíaUniversidad Autónoma de MadridMadrid28049Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadrid28049Spain
| | - Jun Wen
- Department of Botany/MRC 166Smithsonian InstitutionWashington, DCUSA
| | - Virginia Valcárcel
- Departamento de BiologíaUniversidad Autónoma de MadridMadrid28049Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadrid28049Spain
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Atta CJ, Yuan H, Li C, Arcila D, Betancur-R R, Hughes LC, Ortí G, Tornabene L. Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei). Mol Phylogenet Evol 2021; 166:107315. [PMID: 34537325 DOI: 10.1016/j.ympev.2021.107315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/12/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
There is an extensive collection of literature on the taxonomy and phylogenetics of flatfishes (Pleuronectiformes) that extends over two centuries, but consensus on many of their evolutionary relationships remains elusive. Phylogenetic uncertainty stems from highly divergent results derived from morphological and genetic characters, and between various molecular datasets. Deciphering relationships is complicated by rapid diversification early in the Pleuronectiformes tree and an abundance of studies that incompletely and inconsistently sample taxa and genetic markers. We present phylogenies based on a genome-wide dataset (4,434 nuclear markers via exon-capture) and wide taxon sampling (86 species spanning 12 of 16 families) of the largest flatfish suborder (Pleuronectoidei). Nine different subsets of the data and two tree construction approaches (eighteen phylogenies in total) are remarkably consistent with other recent molecular phylogenies, and show strong support for the monophyly of all families included except Pleuronectidae. Analyses resolved a novel phylogenetic hypothesis for the family Rhombosoleidae as being within the Pleuronectoidea rather than the Soleoidea, and failed to support the subfamily Hippoglossinae as a monophyletic group. Our results were corroborated with evidence from previous phylogenetic studies to outline regions of persistent phylogenetic uncertainty and identify groups in need of further phylogenetic inference.
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Affiliation(s)
- Calder J Atta
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, USA; Burke Museum of Natural History and Culture, Seattle, USA.
| | - Hao Yuan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
| | - Chenhong Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China
| | - Dahiana Arcila
- Sam Noble Oklahoma Museum of Natural History, The University of Oklahoma, Norman, OK 73072, USA; Department of Biology, The University of Oklahoma, Norman, OK 73072, USA
| | - Ricardo Betancur-R
- Sam Noble Oklahoma Museum of Natural History, The University of Oklahoma, Norman, OK 73072, USA; Department of Biology, The University of Oklahoma, Norman, OK 73072, USA
| | - Lily C Hughes
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA; National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Guillermo Ortí
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Luke Tornabene
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, USA; Burke Museum of Natural History and Culture, Seattle, USA
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Campbell MA, Tongboonkua P, Chanet B, Chen WJ. The distribution of the recessus orbitalis across flatfishes (order: Pleuronectiformes). JOURNAL OF FISH BIOLOGY 2020; 97:293-297. [PMID: 32333611 DOI: 10.1111/jfb.14356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
The recessus orbitalis is an accessory organ of flatfishes functioning in the protrusion of the eyes. This character, along with cranial asymmetry and a forward insertion of the dorsal fin, have been considered synapomorphies for the Pleuronectiformes. New dissections and examination of images taken in the wild show that the recessus orbitalis is present in all representatives of Pleuronectoidei examined but is absent in the single species of Psettoidei dissected. Psettoidei, the most primitive pleuronectiform lineage, contains three recognized species; thus, the absence of the recessus orbitalis in this whole lineage is unclear without further dissections. Ancestral character estimation at the family level for the recessus orbitalis indicates that the recessus orbitalis was likely absent in the common ancestor of Pleuronectiformes but was most likely present in the common ancestor of the Pleuronectoidei. Given that so few species of flatfishes have been assessed for the recessus orbitalis to date, additional characterization of the distribution of the recessus orbitalis across flatfishes will further inform what states this character may have and if it is a synapomorphy of Pleuronectiformes or simply a derived character state of Pleuronectoidei.
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Affiliation(s)
| | | | - Bruno Chanet
- Équipe Homologies, Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, Paris, France
| | - Wei-Jen Chen
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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Girard MG, Davis MP, Smith WL. The Phylogeny of Carangiform Fishes: Morphological and Genomic Investigations of a New Fish Clade. COPEIA 2020. [DOI: 10.1643/ci-19-320] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Matthew G. Girard
- Biodiversity Institute, 1345 Jayhawk Boulevard, University of Kansas, Lawrence, Kansas 66045; (MGG) . Send reprint requests to MGG
| | - Matthew P. Davis
- Department of Biological Sciences, St. Cloud State University, St. Cloud, Minnesota 56301
| | - W. Leo Smith
- Biodiversity Institute, 1345 Jayhawk Boulevard, University of Kansas, Lawrence, Kansas 66045; (MGG) . Send reprint requests to MGG
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