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Searle PC, Shiozawa DK, Evans RP, Hill JT, Suli A, Stark MR, Belk MC. Heterochronic shift in gene expression leads to ontogenetic morphological divergence between two closely related polyploid species. iScience 2024; 27:109566. [PMID: 38632992 PMCID: PMC11022054 DOI: 10.1016/j.isci.2024.109566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 11/04/2023] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Heterochrony-alteration to the rate or timing of development-is an important mechanism of trait differentiation associated with speciation. Heterochrony may explain the morphological divergence between two polyploid species, June sucker (Chasmistes liorus) and Utah sucker (Catostomus ardens). The larvae of both species have terminal mouths; however, as adults, June sucker and Utah sucker develop subterminal and ventral mouths, respectively. We document a difference in the timing of shape development and a corresponding change in the timing of gene expression, suggesting the distinctive mouth morphology in June suckers may result from paedomorphosis. Specifically, adult June suckers exhibit an intermediate mouth morphology between the larval (terminal) and ancestral (ventral) states. Endemic and sympatric Chasmistes/Catostomus pairs in two other lakes also are morphologically divergent, but genetically similar. These species pairs could have resulted from the differential expression of genes and corresponding divergence in trait development. Paedomorphosis may lead to adaptive diversification in Catostomids.
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Affiliation(s)
- Peter C. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - R. Paul Evans
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jonathon T. Hill
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Arminda Suli
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Michael R. Stark
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Mark C. Belk
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
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2
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Dziedzic E, Sidlauskas B, Cronn R, Anthony J, Cornwell T, Friesen TA, Konstantinidis P, Penaluna BE, Stein S, Levi T. Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA. Mol Ecol Resour 2023; 23:1880-1904. [PMID: 37602732 DOI: 10.1111/1755-0998.13855] [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: 03/23/2022] [Revised: 07/11/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023]
Abstract
Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.
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Affiliation(s)
- Emily Dziedzic
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brian Sidlauskas
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Richard Cronn
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - James Anthony
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Trevan Cornwell
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Thomas A Friesen
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Peter Konstantinidis
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brooke E Penaluna
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - Staci Stein
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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3
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Calixto-Rojas M, Lira-Noriega A, Rubio-Godoy M, Pérez-Ponce de León G, Pinacho-Pinacho CD. Delimitation and species discovery in the Profundulidae fish family: Using genetic, environmental and morphologic data to address taxonomic uncertainty. Mol Phylogenet Evol 2023:107856. [PMID: 37327830 DOI: 10.1016/j.ympev.2023.107856] [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: 12/10/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
The family Profundulidae includes some one of the most enigmatic freshwater fishes of Mesoamerica: despite many attempts, a robust phylogenetic framework to delimit species is lacking, mainly due to limited morphological variation within the group. The accumulation of molecular data of profundulid fishes has led to advances in the description of new taxa, but relatively less progress has been made estimating evolutionary and phylogenetic relationships for this fish family. Here, we adopt an integrative taxonomy approach including the use of nuclear and mitochondrial DNA sequences, morphometric and ecological data, to test species boundaries in profundulid fishes in the westernmost area of their known distribution range in the states of Guerrero and Oaxaca, Mexico. Using a combination of methods for species discovery and validation based on Bayesian gene tree topologies, our analyses support the delimitation of 15 valid species of profundulid fishes - a combination of previously described species validated by this study, the synonymy of unsupported taxa, and the description of two new species. Using species delimitation methods, examination of phenotypic variation, and ecological niche characterization, we also identify five potentially new lineages which require further evidence to be erected as new species. We demonstrate that the use of an integrative taxonomy approach provides a robust methodology to delimit species in a taxonomically complex group like Profundulidae. Accurate taxonomic and ecological information is crucial for the conservation of these microendemic fishes, as several species are endangered.
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Affiliation(s)
- Miguel Calixto-Rojas
- Doctorado en Ciencias, Instituto de Ecología, A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico.
| | - Andrés Lira-Noriega
- CONACyT Research Fellow, Instituto de Ecología A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - Miguel Rubio-Godoy
- Instituto de Ecología, A.C., Red de Biología Evolutiva, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - Gerardo Pérez-Ponce de León
- Escuela Nacional de Estudios Superiores unidad Mérida, Universidad Nacional Autónoma de México, Km 4.5 Carretera Mérida-Tetiz, Municipio de Ucú, Yucatán 97357, Mexico
| | - Carlos D Pinacho-Pinacho
- CONACyT Research Fellow, Instituto de Ecología A.C., Red de Estudios Moleculares Avanzados, Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
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4
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Peng Y, Derks MFL, Groenen MAM, Zhao Y, Bosse M. Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds. Front Genet 2023; 13:1070783. [PMID: 36712875 PMCID: PMC9880450 DOI: 10.3389/fgene.2022.1070783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/19/2022] [Indexed: 01/15/2023] Open
Abstract
Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68-98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds.
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Affiliation(s)
- Yebo Peng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Martijn FL Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands,Topigs Norsvin Research Center, Beuningen, Netherlands
| | - Martien AM Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands,Amsterdam Insitute of Life and Environment (A-Life), VU University Amsterdam, Amsterdam, Netherlands,*Correspondence: Mirte Bosse,
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5
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Nedoluzhko A, Sharko F, Tsygankova S, Boulygina E, Slobodova N, Teslyuk A, Galindo-Villegas J, Rastorguev S. Intergeneric hybridization of two stickleback species leads to introgression of membrane-associated genes and invasive TE expansion. Front Genet 2022; 13:863547. [PMID: 36092944 PMCID: PMC9452749 DOI: 10.3389/fgene.2022.863547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/20/2022] [Indexed: 12/03/2022] Open
Abstract
Interspecific hybridization has occurred relatively frequently during the evolution of vertebrates. This process usually abolishes reproductive isolation between the parental species. Moreover, it results in the exchange of genetic material and can lead to hybridogenic speciation. Hybridization between species has predominately been observed at the interspecific level, whereas intergeneric hybridization is rarer. Here, using whole-genome sequencing analysis, we describe clear and reliable signals of intergeneric introgression between the three-spined stickleback (Gasterosteus aculeatus) and its distant mostly freshwater relative the nine-spined stickleback (Pungitius pungitius) that inhabit northwestern Russia. Through comparative analysis, we demonstrate that such introgression phenomena apparently take place in the moderate-salinity White Sea basin, although it is not detected in Japanese sea stickleback populations. Bioinformatical analysis of the sites influenced by introgression showed that they are located near transposable elements, whereas those in protein-coding sequences are mostly found in membrane-associated and alternative splicing-related genes.
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Affiliation(s)
- Artem Nedoluzhko
- Paleogenomics Laboratory, European University at Saint Petersburg, Saint Petersburg, Russia
- Limited Liability Company ELGENE, Moscow, Russia
| | - Fedor Sharko
- Limited Liability Company ELGENE, Moscow, Russia
- Laboratory of Vertebrate Genomics and Epigenomics, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Laboratory of Bioinformatics and Big Data Analysis, Kurchatov Center for Genomic Research, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Svetlana Tsygankova
- Laboratory of Eukaryotic Genomics, Kurchatov Center for Genomic Research, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Eugenia Boulygina
- Laboratory of Eukaryotic Genomics, Kurchatov Center for Genomic Research, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Natalia Slobodova
- Laboratory of Eukaryotic Genomics, Kurchatov Center for Genomic Research, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Anton Teslyuk
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Jorge Galindo-Villegas
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- *Correspondence: Jorge Galindo-Villegas, ; Sergey Rastorguev,
| | - Sergey Rastorguev
- Limited Liability Company ELGENE, Moscow, Russia
- Laboratory of Bioinformatics and Big Data Analysis, Kurchatov Center for Genomic Research, National Research Center “Kurchatov Institute”, Moscow, Russia
- *Correspondence: Jorge Galindo-Villegas, ; Sergey Rastorguev,
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6
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Gregorio Martínez J, David Rangel-Medrano J, Johanna Yepes-Acevedo A, Restrepo-Escobar N, Judith Márquez E. Species limits and introgression in Pimelodus from the Magdalena-Cauca River basin. Mol Phylogenet Evol 2022; 173:107517. [DOI: 10.1016/j.ympev.2022.107517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 03/20/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022]
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Buck R, Flores-Rentería L. The Syngameon Enigma. PLANTS (BASEL, SWITZERLAND) 2022; 11:895. [PMID: 35406874 PMCID: PMC9002738 DOI: 10.3390/plants11070895] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 05/17/2023]
Abstract
Despite their evolutionary relevance, multispecies networks or syngameons are rarely reported in the literature. Discovering how syngameons form and how they are maintained can give insight into processes such as adaptive radiations, island colonizations, and the creation of new hybrid lineages. Understanding these complex hybridization networks is even more pressing with anthropogenic climate change, as syngameons may have unique synergistic properties that will allow participating species to persist. The formation of a syngameon is not insurmountable, as several ways for a syngameon to form have been proposed, depending mostly on the magnitude and frequency of gene flow events, as well as the relatedness of its participants. Episodic hybridization with small amounts of introgression may keep syngameons stable and protect their participants from any detrimental effects of gene flow. As genomic sequencing becomes cheaper and more species are included in studies, the number of known syngameons is expected to increase. Syngameons must be considered in conservation efforts as the extinction of one participating species may have detrimental effects on the survival of all other species in the network.
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Affiliation(s)
- Ryan Buck
- Department of Biology, San Diego State University, San Diego, CA 92182, USA;
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8
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Moyer GR, Shaw R, Wertz T. Mitochondrial DNA Barcoding Reveals First Documented Evidence of Golden Redhorse (Moxostoma erythrurum) in the Susquehanna River, Pennsylvania. Northeast Nat (Steuben) 2021. [DOI: 10.1656/045.028.0204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Gregory R Moyer
- Department of Natural Resources, Mansfield University, Mansfield, PA 16933
| | - Ryan Shaw
- Department of Natural Resources, Mansfield University, Mansfield, PA 16933
| | - Timothy Wertz
- Pennsylvania Department of Environmental Protection, Harrisburg, PA 17101
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9
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Kinziger AP, White JL, Nakamoto RJ, Harvey BC. Recent, small beginnings: genetic analysis suggests Catostomus rimiculus (Klamath smallscale sucker) in the Smith River, California, are introduced. JOURNAL OF FISH BIOLOGY 2021; 98:1321-1328. [PMID: 33389757 DOI: 10.1111/jfb.14664] [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: 08/27/2020] [Revised: 11/07/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Identification of introduced species can be important to understanding ecological systems and meeting conservation and management goals, but the process can be surprisingly challenging. The Klamath smallscale sucker Catostomus rimiculus seems likely to be native to the Smith River because the drainage separates two basins believed to be within the fish's native range, the Rogue and Klamath rivers. Further, C. rimiculus is broadly distributed in the Smith River, and the indigenous Dee-ni' People of the Smith River have a unique word for sucker. Nonetheless, a historical survey of fishes that described C. rimiculus from the Rogue and Klamath rivers did not include C. rimiculus among the fishes of the Smith River. To determine whether the genetic structure of the Smith River C. rimiculus reflects expectations for a native sucker population, the authors of this study examined variation in microsatellite and mitochondrial genetic markers from the Smith River and surrounding drainages. The genetic analyses revealed a pattern consistent with extreme founder effects in Smith River C. rimiculus, as would be expected from a single introduction of six or fewer effective individuals. The sharing of a high-frequency haplotype between the Smith River and Klamath River that is not detected in the Rogue River suggests the Klamath River as the likely source for the introduction. The findings highlight that local-scale introductions can be easily overlooked because the newly established populations can appear to be parts of contiguous natural distributions.
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Affiliation(s)
- Andrew P Kinziger
- Department of Fisheries Biology, Humboldt State University, Arcata, California, USA
| | - Jason L White
- U.S. Forest Service, Pacific Southwest Research Station, Arcata, California, USA
| | - Rodney J Nakamoto
- U.S. Forest Service, Pacific Southwest Research Station, Arcata, California, USA
| | - Bret C Harvey
- U.S. Forest Service, Pacific Southwest Research Station, Arcata, California, USA
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10
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Nedoluzhko A, Sharko F, Tsygankova S, Boulygina E, Ibragimova A, Teslyuk A, Galindo-Villegas J, Rastorguev S. Genomic evidence supports the introgression between two sympatric stickleback species inhabiting the White Sea basin. Heliyon 2021; 7:e06160. [PMID: 33604473 PMCID: PMC7875830 DOI: 10.1016/j.heliyon.2021.e06160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/16/2020] [Accepted: 01/27/2021] [Indexed: 11/26/2022] Open
Abstract
Interspecies hybridization is driven by a complex interplay of factors where introgression plays an important role. In the present study, the transfer of genetic material, between two quite distant fish species from different genera, through spontaneous hybridization was documented with dedicated molecular and bioinformatics tools. We investigate the genomic landscape of putative stickleback-relative introgression by carefully analyzing the tractable transposable elements (TE) on the admixed genome of some individuals of two sympatric stickleback species inhabiting northwestern Russia, namely the three-spined (Gasterosteus aculeatus) and the nine-spined (Pungitius pungitius) sticklebacks. Our data revealed that unique TE amplification types exist, supporting our proposed hypothesis that infers on the interspecific introgression. By running a restriction site-associated DNA sequencing (RAD-Seq) with eight samples of G. aculeatus and P. pungitius and subjecting further the results to a contrasting analysis by variated bioinformatic tools, we identified the related introgression-linked markers. The admixture nature observed in a single sample of the nine-spined stickleback demonstrated the possible traces of remote introgression between these two species. Our work reveals the potential that introgression has on providing particular variants at a high-frequency speed while linking blocks of sequence with multiple functional mutations. However, even though our results are of significant interest, an increased number of samples displaying the introgression are required to further ascertain our conclusions.
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Affiliation(s)
- Artem Nedoluzhko
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- Corresponding author.
| | - Fedor Sharko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | | | - Eugenia Boulygina
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | - Amina Ibragimova
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | - Anton Teslyuk
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
| | - Jorge Galindo-Villegas
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- Corresponding author.
| | - Sergey Rastorguev
- National Research Center “Kurchatov Institute”, 123182 Moscow, Russia
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11
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Bangs MR, Douglas MR, Brunner PC, Douglas ME. Reticulate evolution as a management challenge: Patterns of admixture with phylogenetic distance in endemic fishes of western North America. Evol Appl 2020; 13:1400-1419. [PMID: 32684966 PMCID: PMC7359839 DOI: 10.1111/eva.13042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
Admixture in natural populations is a long-standing management challenge, with population genomic approaches offering means for adjudication. We now more clearly understand the permeability of species boundaries and the potential of admixture for promoting adaptive evolution. These issues particularly resonate in western North America, where tectonism and aridity have fragmented and reshuffled rivers over millennia, in turn promoting reticulation among endemic fishes, a situation compounded by anthropogenic habitat modifications and non-native introductions. The melding of historic and contemporary admixture has both confused and stymied management. We underscore this situation with a case study that quantifies basin-wide admixture among a group of native and introduced fishes by employing double-digest restriction site-associated DNA (ddRAD) sequencing. Our approach: (a) quantifies the admixed history of 343 suckers (10 species of Catostomidae) across the Colorado River Basin; (b) gauges admixture within the context of phylogenetic distance and "ecological specialization"; and (c) extrapolates potential drivers of introgression across hybrid crosses that involve endemic as well as invasive species. Our study extends across an entire freshwater basin and expands previous studies more limited in scope both geographically and taxonomically. Our results detected admixture involving all 10 species, with habitat alterations not only accelerating the breakdown of reproductive isolation, but also promoting introgression. Hybridization occurred across the genus despite phylogenetic distance, whereas introgression was only detected within subgenera, implicating phylogenetic distance and/or ecological specialization as drivers of reproductive isolation. Understanding the extent of admixture and reproductive isolation across multiple species serves to disentangle their reticulate evolutionary histories and provides a broadscale perspective for basin-wide conservation and management.
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Affiliation(s)
- Max R. Bangs
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
- Department of Biological SciencesFlorida State UniversityTallahasseeFLUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Patrick C. Brunner
- Integrative BiologySwiss Federal Institute of Technology (ETH)ZürichSwitzerland
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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12
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Bangs MR, Douglas MR, Chafin TK, Douglas ME. Gene flow and species delimitation in fishes of Western North America: Flannelmouth ( Catostomus latipinnis) and Bluehead sucker ( C. Pantosteus discobolus). Ecol Evol 2020; 10:6477-6493. [PMID: 32724527 PMCID: PMC7381754 DOI: 10.1002/ece3.6384] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 02/02/2023] Open
Abstract
The delimitation of species boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life histories codistributed in the highly modified Colorado River (i.e., flannelmouth sucker, Catostomus latipinnis; bluehead sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double-digest restriction site-associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in bluehead sucker, supporting elevation of C. (P.) virescens to species status and recognizing C. (P.) discobolus yarrowi (Zuni bluehead sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate flannelmouth sucker lineages as ESUs (evolutionarily significant units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the agreement of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolation versus secondary contact.
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Affiliation(s)
- Max R. Bangs
- Department of Biological SciencesFlorida State UniversityTallahasseeFLUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Tyler K. Chafin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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13
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Peek RA, Bedwell M, O'Rourke SM, Goldberg C, Wengert GM, Miller MR. Hybridization between two parapatric ranid frog species in the northern Sierra Nevada, California, USA. Mol Ecol 2019; 28:4636-4647. [DOI: 10.1111/mec.15236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 08/19/2019] [Accepted: 08/27/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Ryan A. Peek
- Center for Watershed Sciences University of California Davis CA USA
- Department of Animal Science University of California Davis CA USA
| | - Mallory Bedwell
- School of the Environment Washington State University Pullman WA USA
| | - Sean M. O'Rourke
- Department of Animal Science University of California Davis CA USA
| | - Caren Goldberg
- School of the Environment Washington State University Pullman WA USA
| | | | - Michael R. Miller
- Center for Watershed Sciences University of California Davis CA USA
- Department of Animal Science University of California Davis CA USA
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Markle DF. DRAINAGE EVOLUTION AND FRESHWATER FISH ZOOGEOGRAPHY IN COASTAL OREGON AND WASHINGTON. ACTA ACUST UNITED AC 2019. [DOI: 10.1898/nwn-18-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Douglas F Markle
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97331 USA;
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15
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Santos JCMD, Ferreira ES, Oliveira C, Oliveira TB, Costa ASLD, Queiroz AKOD, Schneider H, Sampaio I, Santos S. Phylogeny of the genus Hypophthalmus Cuvier, 1829 (Pimelodidae - Siluriformes), based on a multilocus analysis, indicates diversification and introgression in the Amazon basin. Mol Phylogenet Evol 2019; 137:285-292. [PMID: 31121309 DOI: 10.1016/j.ympev.2019.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 05/14/2019] [Accepted: 05/19/2019] [Indexed: 10/26/2022]
Abstract
The genus Hypophthalmus encompasses four valid South American freshwater catfish species: H. marginatus, H. edentatus, H. fimbriatus, and H. oremaculatus. More recently two new species were proposed Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2. While Hypophthalmus species are a fundamentally important resource for the commercial fisheries that operate in the continental waters of the Amazon basin, their phylogenetic relationships and the true diversity of the genus have yet to be defined conclusively. Given this, the present study analyzed sequences of the mitochondrial COI gene and four nuclear markers (RAG2, Myh6, Plagl2 and Glyt) to evaluate the phylogenetic relationships and the diversity of the species of this genus. All the analyses showed that Hypophthalmus is monophyletic, and the species delimitation tests recovered all the Hypophthalmus taxa as distinct species. The putative new species Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2 presented mean genetic divergence similar to or greater than that observed between valid Hypophthalmus taxa. All the analyses showed that H. oremaculatus is the sister group of H. n. sp. 1, which together group with H. fimbriatus. This clade is the sister group of the clade containing H. edentatus and H. n. sp. 2. One specimen, morphologically identified as H. oremaculatus, presented the nuclear genome of this species and the mitochondrial genome of H. n. sp. 1; while another specimen, morphologically identified as H. n. sp. 2, presented the nuclear Myh6 of H. n. sp. 2 and the mitochondrial and RAG2 genome of H. edentatus. These results indicate that hybridization and introgression has occurred between species in Hypophthalmus. The findings of this study indicate that the diversity of the Hypophthalmus is underestimated, emphasize the need for a taxonomic review of the genus, and a more systematic evaluation of the hybridization patterns found, to understanding the role of hybridization and introgression in the evolution of the genus.
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Affiliation(s)
- Julya Caroline Mesquita Dos Santos
- Laboratório de Microbiologia do Pescado, Universidade Federal do Pará, Instituto de Estudos Costeiros, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, Pará, Brazil.
| | - Edinaldo Silva Ferreira
- Instituto Federal de Educação, Ciência e Tecnologia do Pará (IFPA), Av. dos Bragançanos, s/n - Vila Sinhá, 68600-000 Bragança, Pará, Brazil.
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rua Professor Doutor Antônio Celso Wagner Zanin, s/n, 18618-689 Botucatu, São Paulo, Brazil.
| | - Tamyres Barbosa Oliveira
- Laboratório de Microbiologia do Pescado, Universidade Federal do Pará, Instituto de Estudos Costeiros, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, Pará, Brazil.
| | - Antonia Silvia Lima da Costa
- Laboratório de Microbiologia do Pescado, Universidade Federal do Pará, Instituto de Estudos Costeiros, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, Pará, Brazil.
| | - Anna Karolina Oliveira de Queiroz
- Laboratório de Microbiologia do Pescado, Universidade Federal do Pará, Instituto de Estudos Costeiros, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, Pará, Brazil.
| | - Horacio Schneider
- Laboratório de Genética e Biologia Molecular, Universidade Federal do Pará, Instituto de Estudos Costeiros, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, Pará, Brazil
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Universidade Federal do Pará, Instituto de Estudos Costeiros, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, Pará, Brazil.
| | - Simoni Santos
- Laboratório de Microbiologia do Pescado, Universidade Federal do Pará, Instituto de Estudos Costeiros, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, Pará, Brazil.
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16
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Horn RL, Marques AJD, Manseau M, Golding B, Klütsch CFC, Abraham K, Wilson PJ. Parallel evolution of site-specific changes in divergent caribou lineages. Ecol Evol 2018; 8:6053-6064. [PMID: 29988428 PMCID: PMC6024114 DOI: 10.1002/ece3.4154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 12/15/2022] Open
Abstract
The parallel evolution of phenotypes or traits within or between species provides important insight into the basic mechanisms of evolution. Genetic and genomic advances have allowed investigations into the genetic underpinnings of parallel evolution and the independent evolution of similar traits in sympatric species. Parallel evolution may best be exemplified among species where multiple genetic lineages, descended from a common ancestor, colonized analogous environmental niches, and converged on a genotypic or phenotypic trait. Modern North American caribou (Rangifer tarandus) originated from three ancestral sources separated during the Last Glacial Maximum (LGM): the Beringian-Eurasian lineage (BEL), the North American lineage (NAL), and the High Arctic lineage (HAL). Historical introgression between the NAL and the BEL has been found throughout Ontario and eastern Manitoba. In this study, we first characterized the functional differentiation in the cytochrome-b (cytB) gene by identifying nonsynonymous changes. Second, the caribou lineages were used as a direct means to assess site-specific parallel changes among lineages. There was greater functional diversity within the NAL despite the BEL having greater neutral diversity. The patterns of amino acid substitutions occurring within different lineages supported the parallel evolution of cytB amino acid substitutions suggesting different selective pressures among lineages. This study highlights the independent evolution of identical amino acid substitutions within a wide-ranging mammal species that have diversified from different ancestral haplogroups and where ecological niches can invoke parallel evolution.
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Affiliation(s)
| | | | - Micheline Manseau
- Science and TechnologyEnvironment and Climate Change CanadaOttawaONCanada
- Natural Resources InstituteUniversity of ManitobaWinnipegMBCanada
| | - Brian Golding
- Department of BiologyMcMaster UniversityHamiltonONCanada
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17
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Li X, Shen X, Chen X, Xiang D, Murphy RW, Shen Y. Detection of Potential Problematic Cytb Gene Sequences of Fishes in GenBank. Front Genet 2018; 9:30. [PMID: 29467794 PMCID: PMC5808227 DOI: 10.3389/fgene.2018.00030] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/22/2018] [Indexed: 02/05/2023] Open
Abstract
Fishes are, by far, the most diverse group of vertebrates. Their classification relies heavily on morphology. In practice, the correct morphological identification of species often depends on personal experience because many species vary in their body shape, color and other external characters. Thus, the identification of a species may be prone to errors. Due to the rapid development of molecular biology, the number of sequences of fishes deposited in GenBank has grown explosively. These published data likely contain errors owing to invalid or incorrectly identified species. The erroneous data can lead to downstream problems. Thus, it is critical that such errors get identified and corrected. A strategy based on DNA barcoding can detect potentially erroneous data, especially when intraspecific K2P variation exceeds interspecific K2P divergence. Analyses of the most used DNA marker for fishes (mitochondrial Cytb) discovers that intraspecific differences of fishes are generally less than 1%, while interspecific differences are generally higher than 10%. Based on this ruler, our analyses identify 1,303 potential problematic Cytb sequences of fishes in GenBank and point to taxonomic problems, errors in identification, genetic introgression and other concerns. Care must be taken to avoid the perpetuation of errors when using these available data.
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Affiliation(s)
- Xiaobing Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xuejuan Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Dan Xiang
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, China
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
- *Correspondence: Yongyi Shen
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18
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Zhang QP, Hu WF, Zhou TT, Kong SS, Liu ZF, Zheng RQ. Interspecies introgressive hybridization in spiny frogs Quasipaa (Family Dicroglossidae) revealed by analyses on multiple mitochondrial and nuclear genes. Ecol Evol 2017; 8:1260-1270. [PMID: 29375796 PMCID: PMC5773314 DOI: 10.1002/ece3.3728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 01/08/2023] Open
Abstract
Introgression may lead to discordant patterns of variation among loci and traits. For example, previous phylogeographic studies on the genus Quasipaa detected signs of genetic introgression from genetically and morphologically divergent Quasipaa shini or Quasipaa spinosa. In this study, we used mitochondrial and nuclear DNA sequence data to verify the widespread introgressive hybridization in the closely related species of the genus Quasipaa, evaluate the level of genetic diversity, and reveal the formation mechanism of introgressive hybridization. In Longsheng, Guangxi Province, signs of asymmetrical nuclear introgression were detected between Quasipaa boulengeri and Q. shini. Unidirectional mitochondrial introgression was revealed from Q. spinosa to Q. shini. By contrast, bidirectional mitochondrial gene introgression was detected between Q. spinosa and Q. shini in Lushan, Jiangxi Province. Our study also detected ancient hybridizations between a female Q. spinosa and a male Q. jiulongensis in Zhejiang Province. Analyses on mitochondrial and nuclear genes verified three candidate cryptic species in Q. spinosa, and a cryptic species may also exist in Q. boulengeri. However, no evidence of introgressive hybridization was found between Q. spinosa and Q. boulengeri. Quasipaa exilispinosa from all the sampling localities appeared to be deeply divergent from other communities. Our results suggest widespread introgressive hybridization in closely related species of Quasipaa and provide a fundamental basis for illumination of the forming mechanism of introgressive hybridization, classification of species, and biodiversity assessment in Quasipaa.
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Affiliation(s)
- Qi-Peng Zhang
- Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province Jinhua Zhejiang China.,Institute of Ecology Zhejiang Normal University Jinhua Zhejiang China
| | - Wen-Fang Hu
- Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province Jinhua Zhejiang China.,Institute of Ecology Zhejiang Normal University Jinhua Zhejiang China
| | - Ting-Ting Zhou
- Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province Jinhua Zhejiang China.,Institute of Ecology Zhejiang Normal University Jinhua Zhejiang China
| | - Shen-Shen Kong
- Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province Jinhua Zhejiang China.,Institute of Ecology Zhejiang Normal University Jinhua Zhejiang China
| | - Zhi-Fang Liu
- Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province Jinhua Zhejiang China.,Institute of Ecology Zhejiang Normal University Jinhua Zhejiang China
| | - Rong-Quan Zheng
- Key Lab of Wildlife Biotechnology and Conservation and Utilization of Zhejiang Province Jinhua Zhejiang China.,Institute of Ecology Zhejiang Normal University Jinhua Zhejiang China.,Xingzhi College of Zhejiang Normal University Jinhua Zhejiang China
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