1
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Johnson NA, Henderson AR, Jones JW, Beaver CE, Ahlstedt SA, Dinkins GR, Eckert NL, Endries MJ, Garner JT, Harris JL, Hartfield PD, Hubbs DW, Lane TW, McGregor MA, Moles KR, Morrison CL, Wagner MD, Williams JD, Smith CH. Glacial vicariance and secondary contact shape demographic histories in a freshwater mussel species complex. J Hered 2024; 115:72-85. [PMID: 38015800 DOI: 10.1093/jhered/esad075] [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: 06/20/2023] [Revised: 10/16/2023] [Accepted: 11/27/2023] [Indexed: 11/30/2023] Open
Abstract
Characterizing the mechanisms influencing the distribution of genetic variation in aquatic species can be difficult due to the dynamic nature of hydrological landscapes. In North America's Central Highlands, a complex history of glacial dynamics, long-term isolation, and secondary contact have shaped genetic variation in aquatic species. Although the effects of glacial history have been demonstrated in many taxa, responses are often lineage- or species-specific and driven by organismal ecology. In this study, we reconstruct the evolutionary history of a freshwater mussel species complex using a suite of mitochondrial and nuclear loci to resolve taxonomic and demographic uncertainties. Our findings do not support Pleurobema rubrum as a valid species, which is proposed for listing as threatened under the U.S. Endangered Species Act. We synonymize P. rubrum under Pleurobema sintoxia-a common and widespread species found throughout the Mississippi River Basin. Further investigation of patterns of genetic variation in P. sintoxia identified a complex demographic history, including ancestral vicariance and secondary contact, within the Eastern Highlands. We hypothesize these patterns were shaped by ancestral vicariance driven by the formation of Lake Green and subsequent secondary contact after the last glacial maximum. Our inference aligns with demographic histories observed in other aquatic taxa in the region and mirrors patterns of genetic variation of a freshwater fish species (Erimystax dissimilis) confirmed to serve as a parasitic larval host for P. sintoxia. Our findings directly link species ecology to observed patterns of genetic variation and may have significant implications for future conservation and recovery actions of freshwater mussels.
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Affiliation(s)
- Nathan A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, United States
| | - Andrew R Henderson
- U.S. Fish and Wildlife Service, Ecological Services, Asheville, NC, United States
| | - Jess W Jones
- U.S. Fish and Wildlife Service, Virginia Tech University, Blacksburg, VA, United States
| | - Caitlin E Beaver
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, United States
| | - Steven A Ahlstedt
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN, United States
| | - Gerald R Dinkins
- McClung Museum of Natural History and Culture, University of Tennessee, Knoxville, TN, United States
| | - Nathan L Eckert
- U.S. Fish and Wildlife Service, Neosho National Fish Hatchery, Neosho, MO, United States
| | - Mark J Endries
- U.S. Fish and Wildlife Service, Ecological Services, Asheville, NC, United States
| | - Jeffrey T Garner
- Alabama Division of Wildlife and Freshwater Fisheries, Florence, AL, United States
| | - John L Harris
- Arkansas State University Museum of Zoology, Jonesboro, AR, United States
| | - Paul D Hartfield
- U.S. Fish and Wildlife Service, Ecological Services, Jackson, MS, United States
| | - Don W Hubbs
- DJH Environmental Services, Camden, TN, United States
| | - Timothy W Lane
- Virginia Department of Wildlife Resources, Marion, VA, United States
| | - Monte A McGregor
- Kentucky Department of Fish and Wildlife Resources, Frankfort, KY, United States
| | - Kendall R Moles
- Arkansas Game and Fish Commission, Benton, AR, United States
| | - Cheryl L Morrison
- U.S. Geological Survey, Eastern Ecological Science Center, Kearneysville, WV, United States
| | - Matthew D Wagner
- U.S. Fish and Wildlife Service, Ecological Services, Jackson, MS, United States
| | - James D Williams
- Florida Museum, University of Florida, Gainesville, FL, United States
| | - Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
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2
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Olivera‐Hyde M, Jones JW, Hallerman EM. Phylogenetic assessment of endangered and look-alike Pigtoe species in a freshwater mussel diversity hotspot. Ecol Evol 2023; 13:e9717. [PMID: 36713491 PMCID: PMC9873586 DOI: 10.1002/ece3.9717] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 01/26/2023] Open
Abstract
The Green River in Kentucky in the eastern United States is a freshwater mussel biodiversity hotspot, with 71 known species. Among them, the endangered Pleurobema plenum coexists with other morphologically similar species in the genera Fusconaia and Pleurobema, known colloquially as "pigtoes." Identification of species in these genera is challenging even for mussel experts familiar with them. In our study, the correct identification of these species by experts ranged from 57% to 83%. We delineated taxonomic boundaries among seven species and tested for cryptic biodiversity among these look-alike mussels utilizing mitochondrial and nuclear DNA sequence variation. Phylogenetic analysis of combined (1215 bp) mitochondrial DNA cytochrome oxidase I (COI) and NADH dehydrogenase 1 (ND1) genes showed five well-diverged groups that included F. flava, F. subrotunda, P. cordatum, and P. plenum as distinct clades, with P. sintoxia and P. rubrum grouped into a single clade. While our mitochondrial DNA analyses did not distinguish P. sintoxia and P. rubrum as phylogenetically distinct species, the typical shell forms of these two nominal taxa are very distinct. Further phylogenetic analysis using nuclear ribosomal transcribed spacer region subunit I (ITS1) DNA sequences also showed that P. sintoxia and P. rubrum were not distinct lineages. No cryptic species were detected in the Fusconaia and Pleurobema samples analyzed from the Green River. The highest haplotype diversity (h), average number of nucleotide differences (k), and nucleotide diversity (π) were observed for F. subrotunda at both the COI (h = 0.896, k = 3.805, π = 0.00808) and ND1 (h = 0.984, k = 6.595, π = 0.00886) markers, with similarly high genetic diversity in the other taxa. Our results give managers confidence that cryptic taxa do not occur within or among these morphologically similar species in the Green River, and populations appear genetically diverse, indicative of large and healthy populations.
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Affiliation(s)
- Miluska Olivera‐Hyde
- Department of Fish and Wildlife ConservationVirginia Polytecnic Institute and State UniversityBlacksburgVirginiaUSA,Present address:
U.S. Geological SurveyEastern Ecological Science Center at the Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Jess W. Jones
- U.S. Fish and Wildlife ServiceBlacksburgVirginiaUSA,Present address:
U.S. Geological SurveyEastern Ecological Science Center at the Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Eric M. Hallerman
- Department of Fish and Wildlife ConservationVirginia Polytecnic Institute and State UniversityBlacksburgVirginiaUSA
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3
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Complete mitochondrial genome of freshwater pearl mussel Lamellidens marginalis (Lamarck, 1819) and its phylogenetic relation within unionidae family. Mol Biol Rep 2022; 49:9593-9603. [DOI: 10.1007/s11033-022-07857-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/11/2022] [Indexed: 10/15/2022]
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4
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Morrison CL, Johnson NA, Jones JW, Eackles MS, Aunins AW, Fitzgerald DB, Hallerman EM, King TL. Genetic and morphological characterization of the freshwater mussel clubshell species complex ( Pleurobema clava and Pleurobema oviforme) to inform conservation planning. Ecol Evol 2021; 11:15325-15350. [PMID: 34765181 PMCID: PMC8571583 DOI: 10.1002/ece3.8219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/14/2021] [Accepted: 08/26/2021] [Indexed: 11/09/2022] Open
Abstract
The shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined to the Tennessee and the upper Cumberland River basins. We used two mitochondrial DNA (mtDNA) genes, 13 novel nuclear DNA microsatellite markers, and shell morphometrics to help resolve this taxonomic confusion. Evidence for a single species was apparent in phylogenetic analyses of each mtDNA gene, revealing monophyletic relationships with minimal differentiation and shared haplotypes. Analyses of microsatellites showed significant genetic structuring, with four main genetic clusters detected, respectively, in the upper Ohio River basin, the lower Ohio River and Great Lakes, and upper Tennessee River basin, and a fourth genetic cluster, which included geographically intermediate populations in the Ohio and Tennessee river basins. While principal components analysis (PCA) of morphometric variables (i.e., length, height, width, and weight) showed significant differences in shell shape, only 3% of the variance in shell shape was explained by nominal species. Using Linear Discriminant and Random Forest (RF) analyses, correct classification rates for the two species' shell forms were 65.5% and 83.2%, respectively. Random Forest classification rates for some populations were higher; for example, for North Fork Holston (HOLS), it was >90%. While nuclear DNA and shell morphology indicate that the HOLS population is strongly differentiated, perhaps indicative of cryptic biodiversity, we consider the presence of a single widespread species the most likely biological scenario for many of the investigated populations based on our mtDNA dataset. However, additional sampling of P. oviforme populations at nuclear loci is needed to corroborate this finding.
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Affiliation(s)
- Cheryl L. Morrison
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research CenterGainesvilleFloridaUSA
| | - Jess W. Jones
- U.S. Fish and Wildlife Service, Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Michael S. Eackles
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Aaron W. Aunins
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Daniel B. Fitzgerald
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Eric M. Hallerman
- Department of Fish and Wildlife ConservationVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Tim L. King
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
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5
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Bieler R. Isaac Lea's (1792–1886) Substitutions and Other Modifications of His Own Names of Molluscan Species. MALACOLOGIA 2021. [DOI: 10.4002/040.064.0101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Rüdiger Bieler
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, Illinois 60605-2496, U.S.A.
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6
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Smith CH, Johnson NA, Havlik K, Doyle RD, Randklev CR. Resolving species boundaries in the critically imperiled freshwater mussel species,
Fusconaia mitchelli
(Bivalvia: Unionidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chase H. Smith
- Biology Department Baylor University Waco TX USA
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
- Department of Integrative Biology University of Texas Austin TX USA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center Gainesville FL USA
| | | | | | - Charles R. Randklev
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas TX USA
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7
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Randklev CR, Wolverton S, Johnson NA, Smith CH, DuBose TP, Robertson CR, Conley J. The utility of zooarchaeological data to guide listing efforts for an imperiled mussel species (Bivalvia: Unionidae:
Pleurobema riddellii
). CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Charles R. Randklev
- Texas A&M Natural Resources InstituteTexas A&M AgriLife Research Center at Dallas Dallas Texas USA
| | - Steve Wolverton
- Department of Geography and the Environment & the Advanced Environmental Research InstituteUniversity of North Texas Denton Texas USA
| | - Nathan A. Johnson
- US Geological Survey, Wetland and Aquatic Research Center Gainesville Florida USA
| | - Chase H. Smith
- Department of Integrative BiologyUniversity of Texas Austin Texas USA
| | - Traci P. DuBose
- Oklahoma Biological Survey, Department of Biology, and Ecology and Evolutionary Biology Graduate ProgramUniversity of Oklahoma Norman Oklahoma USA
| | | | - Julian Conley
- Department of GeosciencesEast Tennessee State University Johnson City Tennessee USA
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8
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Inoue K, Harris JL, Robertson CR, Johnson NA, Randklev CR. A comprehensive approach uncovers hidden diversity in freshwater mussels (Bivalvia: Unionidae) with the description of a novel species. Cladistics 2020; 36:88-113. [PMID: 34618970 DOI: 10.1111/cla.12386] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2019] [Indexed: 11/30/2022] Open
Abstract
Major geological processes have shaped biogeographical patterns of riverine biota. The Edwards Plateau of central Texas, USA, exhibits unique aquatic communities and endemism, including several species of freshwater mussels. Lampsilis bracteata (Gould, 1855) is endemic to the Edwards Plateau region; however, its phylogenetic relationship with other species in the Gulf coastal rivers and Mississippi River basin is unknown. We evaluated phylogenetic relationships, shell morphologies and soft anatomy characters of L. bracteata and a closely related congener, Lampsilis hydiana (Lea, 1838) throughout their ranges. Our results showed the presence of an undescribed species: Lampsilis bergmanni sp.n. Lampsilis bracteata and L. bergmanni sp.n. share similar shell morphologies and soft anatomy characters; however, they are genetically distinct. Geological processes, such as faulting and sea-level changes during the Miocene to Pliocene, are likely to have facilitated diversification of Lampsilis species, resulting in isolation of L. bracteata on the Edwards Plateau and diversification between L. bergmanni sp.n. and L. hydiana. We conclude that L. bracteata range is restricted to the Colorado River basin, whereas L. bergmanni sp.n. occurs only in upstream reaches of the Guadalupe River basin. Conservation actions are warranted for both species due to their restricted distributions and potential anthropogenic threats.
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Affiliation(s)
- Kentaro Inoue
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at Dallas, Dallas, TX, 75252, USA.,Daniel P. Haerther Center for Research and Conservation, John G. Shedd Aquarium, 1200 South Lake Shore Drive, Chicago, IL, 60605, USA
| | - John L Harris
- Department of Biological Sciences, Arkansas State University, Jonesboro, AR, 72467, USA
| | - Clinton R Robertson
- River Studies Program, Texas Parks and Wildlife Department, San Marcos, TX, 78667, USA
| | - Nathan A Johnson
- Wetland and Aquatic Research Center, U.S. Geological Survey, Gainesville, FL, 32653, USA
| | - Charles R Randklev
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at Dallas, Dallas, TX, 75252, USA
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9
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Lane TW, Hallerman EM, Jones JW. Population genetic assessment of two critically endangered freshwater mussel species, Tennessee bean Venustaconcha trabalis and Cumberland bean Venustaconcha troostensis. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01171-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Smith CH, Johnson NA, Inoue K, Doyle RD, Randklev CR. Integrative taxonomy reveals a new species of freshwater mussel, Potamilus streckersoni sp. nov. (Bivalvia: Unionidae): implications for conservation and management. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1607615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Chase H. Smith
- Biology Department, Baylor University, Waco, TX, 76798, USA
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Nathan A. Johnson
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL, 32653, USA
| | - Kentaro Inoue
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at Dallas, Dallas, TX, 75252, USA
| | | | - Charles R. Randklev
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at Dallas, Dallas, TX, 75252, USA
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11
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Keogh SM, Simons AM. Molecules and morphology reveal 'new' widespread North American freshwater mussel species (Bivalvia: Unionidae). Mol Phylogenet Evol 2019; 138:182-192. [PMID: 31129350 DOI: 10.1016/j.ympev.2019.05.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 05/10/2019] [Accepted: 05/22/2019] [Indexed: 10/26/2022]
Abstract
In the Family Unionidae, the greatest radiation of freshwater mussels, malacologists have been misled by extreme intraspecific shell variation and conversely interspecific conchological stasis or convergence. We characterized the genetic and morphological diversity of two phenotypes of Lampsilis teres from specimens (n = 108) collected across its distribution using geometric and traditional morphometrics and multilocus molecular phylogenetics to test the hypothesis that phenotypes represent separate species. Results from our morphometric and molecular phylogenetic analyses unanimously indicate that L. teres sensu lato is made up of two divergent, widespread species with overlapping distributions. We describe a new species and provide a revised description of L. teres sensu stricto. We use morphometrics and machine-learning classification algorithms to test if shell morphology alone can be used to discriminate between these species. Classification percentages of 97.02% and 93.86% demonstrate that shell morphology is highly informative for species identification. This study highlights our lack of understanding of species diversity of freshwater mussels and the importance of multiple characters and quantitative approaches to species delimitation.
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Affiliation(s)
- Sean M Keogh
- Conservation Sciences Graduate Program, University of Minnesota, 135B Skok Hall, 2003 Upper Buford Circle, St Paul, MN 55108, USA; Bell Museum of Natural History, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, St. Paul, MN 55108, USA.
| | - Andrew M Simons
- Bell Museum of Natural History, University of Minnesota, 100 Ecology, 1987 Upper Buford Circle, St. Paul, MN 55108, USA; Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, 135B Skok Hall, 2003 Upper Buford Circle, St Paul, MN 55108, USA
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