1
|
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.
Collapse
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
| |
Collapse
|
2
|
Smith CH, Mejia-Trujillo R, Breton S, Pinto BJ, Kirkpatrick M, Havird JC. Mitonuclear Sex Determination? Empirical Evidence from Bivalves. Mol Biol Evol 2023; 40:msad240. [PMID: 37935058 PMCID: PMC10653589 DOI: 10.1093/molbev/msad240] [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: 06/28/2023] [Revised: 10/04/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In certain bivalve lineages that possess doubly uniparental inheritance (DUI), mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination. In these cases, females transmit a female mtDNA to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short noncoding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA sheds a sncRNA partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system.
Collapse
Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, USA
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
3
|
Gomes-dos-Santos A, Lopes-Lima M, Machado AM, Forest T, Achaz G, Teixeira A, Prié V, C. Castro LF, Froufe E. The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758). GIGABYTE 2023; 2023:gigabyte81. [PMID: 37207176 PMCID: PMC10189783 DOI: 10.46471/gigabyte.81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/10/2023] [Indexed: 05/21/2023] Open
Abstract
Contiguous assemblies are fundamental to deciphering the composition of extant genomes. In molluscs, this is considerably challenging owing to the large size of their genomes, heterozygosity, and widespread repetitive content. Consequently, long-read sequencing technologies are fundamental for high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, was recently generated. However, the resulting genome is highly fragmented since the assembly relied on short-read approaches. Here, an improved reference genome assembly was generated using a combination of PacBio CLR long reads and Illumina paired-end short reads. This genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4 Mbp. The ab initio gene prediction resulted in 48,314 protein-coding genes. Our new assembly is a substantial improvement and an essential resource for studying this species' unique biological and evolutionary features, helping promote its conservation.
Collapse
Affiliation(s)
- André Gomes-dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Faculty of Sciences, University of Porto, , Porto, Portugal
- Corresponding authors. E-mail: ;
| | - Manuel Lopes-Lima
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- IUCN SSC Mollusc Specialist Group, c/o IUCN, David Attenborough Building, Pembroke St., Cambridge, England
| | - André M. Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Thomas Forest
- Éco-anthropologie, Muséum National d’Histoire Naturelle, CNRS UMR 7206, Paris, France
- SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, Paris, France
- Institut de Systématique Evolution Biodiversité, CNRS MNHN SU EPHE, CP 51, 55 rue Buffon, 75005, Paris, France
| | - Guillaume Achaz
- Éco-anthropologie, Muséum National d’Histoire Naturelle, CNRS UMR 7206, Paris, France
- SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, Paris, France
| | - Amílcar Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Vincent Prié
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- IUCN SSC Mollusc Specialist Group, c/o IUCN, David Attenborough Building, Pembroke St., Cambridge, England
| | - L. Filipe C. Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Faculty of Sciences, University of Porto, , Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Corresponding authors. E-mail: ;
| |
Collapse
|
4
|
Diversity and Phylogenetics of Freshwater Mussels (Unionidae) from Southern Thailand with the Description of One New Genus and Five New Species-Group Taxa. DIVERSITY 2022. [DOI: 10.3390/d15010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Southern Thailand represents a region of unique freshwater biodiversity with many endemic taxa, including a number of freshwater mussel species (Bivalvia: Unionidae). In this study, we recognize 13 taxa in the tribes Contradentini, Rectidentini, Pseudodontini (subfamily Gonideinae), and Indochinellini (subfamily Parreysiinae) that inhabit different localities in the Songkhla Lake, Tapi River, and Tha Taphao River basins. Based on the results of morphological and phylogenetic analyses, we discovered among these mussels six taxa new to science, including one genus, three species, and two subspecies. New taxonomic names are introduced here as follows: Songkhlanaiagen. nov.; S. tamodienicagen. & sp. nov.; Sundadontina plugpomenicasp. nov.; Monodontina vondembuschiana tapienicassp. nov.; M. vondembuschiana thasaenicassp. nov. (Pseudodontini); and Trapezoideus thachiadensissp. nov. (Contradentini). These new taxa confirm the high conservation priority of the Southern Thai freshwater mussel fauna.
Collapse
|
5
|
Klunzinger MW, Whisson C, Zieritz A, Benson JA, Stewart BA, Kirkendale L. Integrated taxonomy reveals new threatened freshwater mussels (Bivalvia: Hyriidae: Westralunio) from southwestern Australia. Sci Rep 2022; 12:20385. [PMID: 36437370 PMCID: PMC9701689 DOI: 10.1038/s41598-022-24767-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
The freshwater mussel Westralunio carteri (Iredale, 1934) has long been considered the sole Westralunio species in Australia, limited to the Southwest and listed as vulnerable on the IUCN Red List and under Australian legislation. Here, we used species delimitation models based on COI mtDNA sequences to confirm existence of three evolutionarily significant units (ESUs) within this taxon and conducted morphometric analyses to investigate whether shell shape differed significantly among these ESUs. "W. carteri" I was found to be significantly larger and more elongated than "W. carteri" II and "W. carteri" II + III combined, but not different from "W. carteri" III alone. We recognise and redescribe "W. carteri" I as Westralunio carteri (Iredale, 1934) from western coastal drainages and describe "W. carteri" II and "W. carteri" III as Westralunio inbisi sp. nov. from southern and lower southwestern drainages. Two subspecies are further delineated: "W. carteri" II is formally described as Westralunio inbisi inbisi subsp. nov. from southern coastal drainages, and "W. carteri" III as Westralunio inbisi meridiemus subsp. nov. from the southwestern corner. Because this study profoundly compresses the range of Westralunio carteri northward and introduces additional southern and southwestern taxa with restricted distributions, new threatened species nominations are necessary.
Collapse
Affiliation(s)
- Michael W Klunzinger
- Australian Rivers Institute, Griffith University, Nathan, QLD, 6111, Australia.
- Mollusc Section, Department of Aquatic Zoology, Western Australian Museum, Welshpool, WA, 6163, Australia.
| | - Corey Whisson
- Mollusc Section, Department of Aquatic Zoology, Western Australian Museum, Welshpool, WA, 6163, Australia
| | - Alexandra Zieritz
- School of Geography, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Justin A Benson
- Centre for Natural Resource Management, UWA School of Agriculture and the Environment, The University of Western Australia, Albany, WA, 6330, Australia
| | - Barbara A Stewart
- Centre for Natural Resource Management, UWA School of Agriculture and the Environment, The University of Western Australia, Albany, WA, 6330, Australia
| | - Lisa Kirkendale
- Mollusc Section, Department of Aquatic Zoology, Western Australian Museum, Welshpool, WA, 6163, Australia
| |
Collapse
|
6
|
Mejia-Trujillo R, Smith CH. The male-type mitochondrial genome of the freshwater mussel Potamilus streckersoni Smith, Johnson, Inoue, Doyle, & Randklev, 2019 (Bivalvia: Unionidae). Mitochondrial DNA B Resour 2022; 7:1854-1858. [PMID: 36325280 PMCID: PMC9621207 DOI: 10.1080/23802359.2022.2134750] [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] [Indexed: 11/06/2022] Open
Abstract
The global decline of freshwater mussels emphasizes the need to establish genetic resources to better understand their biology, including a unique mitochondrial biology known as doubly uniparental inheritance. In this study, we present the complete male-type (M-type) mitochondrial genome of the freshwater mussel, Potamilus streckersoni Smith, Johnson, Inoue, Doyle, & Randklev, 2019. The M-type mtDNA is approximately 16 kilobases and contains 22 tRNAs, two rRNAs, and 14 protein-coding genes, including a male-specific open reading frame. Read coverage revealed that M-type mtDNA was more abundant than female-type mtDNA in male gonadal tissue, with respect to a non-spawning male individual. Novel mitogenomes were resolved within previously described sex-specific monophyletic clades across the subfamily Ambleminae. The availability of high-quality nuclear and mitochondrial genomic data for P. streckersoni makes it a model for future research into the potential role of mtDNA in sex determination or sexual development in freshwater mussels.
Collapse
Affiliation(s)
| | - Chase H. Smith
- Department of Integrative Biology, University of Texas, Austin, TX, USA,CONTACT Chase H. Smith Department of Integrative Biology, University of Texas, Austin, TX, USA
| |
Collapse
|
7
|
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]
|
8
|
Wu R, Liu X, Guo L, Zhou C, Ouyang S, Wu X. DNA barcoding, multilocus phylogeny, and morphometry reveal phenotypic plasticity in the Chinese freshwater mussel Lamprotula caveata (Bivalvia: Unionidae). Ecol Evol 2022; 12:e9035. [PMID: 35845369 PMCID: PMC9277607 DOI: 10.1002/ece3.9035] [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: 01/11/2022] [Revised: 05/16/2022] [Accepted: 05/30/2022] [Indexed: 11/11/2022] Open
Abstract
Accurate species identification is crucial for developing conservation strategies for freshwater mussels, one of the most imperiled faunas in the world. Traditionally, mussel species description primarily relied on conchological characters. However, shell morphology has great variability, which leads to the complexity of species delimitation. As endemic species to China, Lamprotula caveata was originally described by Heude (1877). Lamprotula quadrangulosus and Lamprotula contritus were considered for synonymization of L. caveata based on shell variants in the early 20th century, which has been long debated due to lack of rigorous molecular analysis. Moreover, great morphological variation caused doubt whether there are cryptic species. In this study, we used a combined phylogenetic and morphometric approach to verify the validity of the synonymization of L. caveata. The results of molecular species delimitation showed that two molecular operational taxonomic units (MOTUs) were identified in Lamprotula spp., including the L. leaii lineage and the complex lineage (L. quadrangulosa, L. cornuumlunae, L. contritus, and L. caveata). Phylogenetic analyses revealed that L. cornuumlunae formed a basal monophyletic clade, whose divergence time was relatively recent (4.26 Ma [95% HPD = 1.91–7.22 Ma]), and L. contritus, L. caveata, and L. quadrangulosa formed a large polytomy group with very shallow branches. In the previous study, we have demonstrated the validity of L. cornuumlunae. The molecular evidences supported that the complex (L. quadrangulosa + L. contritus + L. caveata) was a valid species; L. quadrangulosa and L. contritus were synonyms of L. caveata. In addition, three morphospecies (L. quadrangulosa, L. contritus, and L. caveata) were aggregated without clear differentiation based on shell morphometric analysis. We confirmed multiple phenotypes in L. caveata for species identification and presumed that the phenotypic plasticity was a response to specific habitats. This study clarified the diversity and phylogeny of the Lamprotula group, which is a crucial step for developing new conservation and management strategies for this imperiled group.
Collapse
Affiliation(s)
- Ruiwen Wu
- School of Life Science Shanxi Normal University Taiyuan China
| | - Xiongjun Liu
- School of Life Science Jiaying University Meizhou China
| | - Liang Guo
- Fuzhou Wilds of Insects Cultural Creativity Co., Ltd. Fuzhou China
| | - Chunhua Zhou
- School of Life Sciences Nanchang University Nanchang China
| | - Shan Ouyang
- School of Life Sciences Nanchang University Nanchang China
| | - Xiaoping Wu
- School of Life Sciences Nanchang University Nanchang China
| |
Collapse
|
9
|
Moulpied M, Smith CH, Robertson CR, Johnson NA, Lopez R, Randklev CR. Biogeography of freshwater mussels (Bivalvia: Unionida) in Texas and implications on conservation biology. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Michael Moulpied
- Texas A&M Natural Resources Institute Texas A&M AgriLife Research Center at Dallas Dallas Texas USA
| | - Chase H. Smith
- Department of Integrative Biology University of Texas at Austin Austin Texas USA
| | - Clinton R. Robertson
- Inland Fisheries – Management and Conservation Branch Texas Parks & Wildlife Department San Marcos Texas USA
| | - Nathan A. Johnson
- U.S. Geological Survey Wetland and Aquatic Research Center Florida USA
| | - Roel Lopez
- Texas A&M Natural Resources Institute Texas A&M AgriLife Research Center at Dallas Dallas Texas USA
| | - Charles R. Randklev
- Texas A&M Natural Resources Institute Texas A&M AgriLife Research Center at Dallas Dallas Texas USA
| |
Collapse
|
10
|
Saito T, Fujimoto K, Uchida S, Yamazaki D, Hirano T, Sano I, Ye B, Kagawa O, Shariar Shovon M, Tu Do V, Morii Y, Prozorova L, Chiba S. Uncovering overlooked diversity using molecular phylogenetic approach: a case of Japanese sphaeriid clams (Sphaeriidae: Bivalvia). Mol Phylogenet Evol 2022; 173:107508. [DOI: 10.1016/j.ympev.2022.107508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022]
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Wu R, Liu X, Kondo T, Ouyang S, Wu X. New species of the genus Inversidens Haas, 1911 (Unionoida, Unionidae, Gonideinae) from Jiangxi Province, China. Zookeys 2021; 1054:85-93. [PMID: 34393564 PMCID: PMC8354993 DOI: 10.3897/zookeys.1054.69075] [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: 05/24/2021] [Accepted: 07/09/2021] [Indexed: 11/12/2022] Open
Abstract
We diagnose and describe a new freshwater mussel species of the genus Inversidens, I.rentianensis sp. nov. from Jiangxi Province, China based on morphological characters and molecular data. This paper includes a morphological description and photograph of the holotype, and partial sequences of mitochondrial COI as DNA barcode data.
Collapse
Affiliation(s)
- Ruiwen Wu
- School of Life Science, Shanxi Normal University, Linfen 041000, ChinaShanxi Normal UniversityLinfenChina
| | - Xiongjun Liu
- School of Life Science, Jiaying University, Meizhou 514015, ChinaJiaying UniversityMeizhouChina
| | - Takaki Kondo
- Division of Natural Science, Osaka Kyoiku University, Osaka 582-8582, JapanOsaka Kyoiku UniversityOsakaJapan
| | - Shan Ouyang
- School of Life Sciences, Nanchang University, Nanchang 330031, ChinaNanchang UniversityNanchangChina
| | - Xiaoping Wu
- School of Life Sciences, Nanchang University, Nanchang 330031, ChinaNanchang UniversityNanchangChina
| |
Collapse
|
13
|
Smith CH, Johnson NA, Robertson CR, Doyle RD, Randklev CR. Establishing conservation units to promote recovery of two threatened freshwater mussel species (Bivalvia: Unionida: Potamilus). Ecol Evol 2021; 11:11102-11122. [PMID: 34429906 PMCID: PMC8366875 DOI: 10.1002/ece3.7897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 05/11/2021] [Accepted: 06/28/2021] [Indexed: 11/09/2022] Open
Abstract
Population genomics has significantly increased our ability to make inferences about microevolutionary processes and demographic histories, which have the potential to improve protection and recovery of imperiled species. Freshwater mussels (Bivalvia: Unionida) represent one of the most imperiled groups of organisms globally. Despite systemic decline of mussel abundance and diversity, studies evaluating spatiotemporal changes in distribution, demographic histories, and ecological factors that threaten long-term persistence of imperiled species remain lacking. In this study, we use genotype-by-sequencing (GBS) and mitochondrial sequence data (mtDNA) to define conservation units (CUs) for two highly imperiled freshwater mussel species, Potamilus amphichaenus and Potamilus streckersoni. We then synthesize our molecular findings with details from field collections spanning from 1901 to 2019 to further elucidate distributional trends, contemporary status, and other factors that may be contributing to population declines for our focal species. We collected GBS and mtDNA data for individuals of P. amphichaenus and P. streckersoni from freshwater mussel collections in the Brazos, Neches, Sabine, and Trinity drainages ranging from 2012 to 2019. Molecular analyses resolved disputing number of genetic clusters within P. amphichaenus and P. streckersoni; however, we find defensible support for four CUs, each corresponding to an independent river basin. Evaluations of historical and recent occurrence data illuminated a generally increasing trend of occurrence in each of the four CUs, which were correlated with recent increases in sampling effort. Taken together, these findings suggest that P. amphichaenus and P. streckersoni are likely rare throughout their respective ranges. Because of this, the establishment of CUs will facilitate evidence-based recovery planning and ensure potential captive propagation and translocation efforts are beneficial. Our synthesis represents a case study for conservation genomic assessments in freshwater mussels and provides a model for future studies aimed at recovery planning for these highly imperiled organisms.
Collapse
Affiliation(s)
- Chase H. Smith
- Department of Integrative BiologyUniversity of TexasAustinTexasUSA
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at DallasDallasTexasUSA
- Biology DepartmentBaylor UniversityWacoTexasUSA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research CenterGainesvilleFloridaUSA
| | | | | | - Charles R. Randklev
- Texas A&M Natural Resources Institute, Texas A&M AgriLife Research Center at DallasDallasTexasUSA
| |
Collapse
|
14
|
New freshwater mussels from two Southeast Asian genera Bineurus and Thaiconcha (Pseudodontini, Gonideinae, Unionidae). Sci Rep 2021; 11:8244. [PMID: 33972560 PMCID: PMC8110783 DOI: 10.1038/s41598-021-87633-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/31/2021] [Indexed: 11/17/2022] Open
Abstract
The Mekong and Chao Phraya rivers harbor a species-rich freshwater mussel assemblage containing a large radiation of the Pseudodontini species. Members of the genera Bineurus Simpson 1900 and Thaiconcha Bolotov et al., 2020 primarily inhabit small and medium-sized tributaries of these rivers. Here, we present an integrative taxonomic review of these genus-level clades. We show that Bineurus contains four species: B. mouhotii (Lea, 1863), B. exilis (Morelet, 1866) stat. rev., B. anodontinum (Rochebrune, 1882) stat. rev., and B. loeiensis sp. nov. In its turn, Thaiconcha comprises three species: T. callifera (Martens, 1860), T. munelliptica sp. nov., and T. thaiensis sp. nov. Two species, Pseudodon ovalis Morlet, 1889 and P. thomsoni Morlet, 1884, are considered here as questionable taxa. These findings further highlight that Southeast Asia represents a significant evolutionary hotspot of freshwater mussels, which requires further international collaborative research and conservation efforts.
Collapse
|
15
|
Smith CH. A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). Genome Biol Evol 2021; 13:evab029. [PMID: 33570560 PMCID: PMC7937423 DOI: 10.1093/gbe/evab029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
From a genomics perspective, bivalves (Mollusca: Bivalvia) have been poorly explored with the exception for those of high economic value. The bivalve order Unionida, or freshwater mussels, has been of interest in recent genomic studies due to their unique mitochondrial biology and peculiar life cycle. However, genomic studies have been hindered by the lack of a high-quality reference genome. Here, I present a genome assembly of Potamilus streckersoni using Pacific Bioscience single-molecule real-time long reads and 10X Genomics-linked read sequencing. Further, I use RNA sequencing from multiple tissue types and life stages to annotate the reference genome. The final assembly was far superior to any previously published freshwater mussel genome and was represented by 2,368 scaffolds (2,472 contigs) and 1,776,755,624 bp, with a scaffold N50 of 2,051,244 bp. A high proportion of the assembly was comprised of repetitive elements (51.03%), aligning with genomic characteristics of other bivalves. The functional annotation returned 52,407 gene models (41,065 protein, 11,342 tRNAs), which was concordant with the estimated number of genes in other freshwater mussel species. This genetic resource, along with future studies developing high-quality genome assemblies and annotations, will be integral toward unraveling the genomic bases of ecologically and evolutionarily important traits in this hyper-diverse group.
Collapse
Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, Texas, USA
- Biology Department, Baylor University, Waco, Texas, USA
| |
Collapse
|
16
|
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
| |
Collapse
|
17
|
Novel Molecular Resources to Facilitate Future Genetics Research on Freshwater Mussels (Bivalvia: Unionidae). DATA 2020. [DOI: 10.3390/data5030065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Molecular data have been an integral tool in the resolution of the evolutionary relationships and systematics of freshwater mussels, despite the limited number of nuclear markers available for Sanger sequencing. To facilitate future studies, we evaluated the phylogenetic informativeness of loci from the recently published anchored hybrid enrichment (AHE) probe set Unioverse and developed novel Sanger primer sets to amplify two protein-coding nuclear loci with high net phylogenetic informativeness scores: fem-1 homolog C (FEM1) and UbiA prenyltransferase domain-containing protein 1 (UbiA). We report the methods used for marker development, along with the primer sequences and optimized PCR and thermal cycling conditions. To demonstrate the utility of these markers, we provide haplotype networks, DNA alignments, and summary statistics regarding the sequence variation for the two protein-coding nuclear loci (FEM1 and UbiA). Additionally, we compare the DNA sequence variation of FEM1 and UbiA to three loci commonly used in freshwater mussel genetic studies: the mitochondrial genes cytochrome c oxidase subunit 1 (CO1) and NADH dehydrogenase subunit 1 (ND1), and the nuclear internal transcribed spacer 1 (ITS1). All five loci distinguish among the three focal species (Potamilus fragilis, Potamilus inflatus, and Potamilus purpuratus), and the sequence variation was highest for ND1, followed by CO1, ITS1, UbiA, and FEM1, respectively. The newly developed Sanger PCR primers and methodologies for extracting additional loci from AHE probe sets have great potential to facilitate molecular investigations targeting supraspecific relationships in freshwater mussels, but may be of limited utility at shallow taxonomic scales.
Collapse
|
18
|
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
| |
Collapse
|
19
|
Smith CH, Pfeiffer JM, Johnson NA. Comparative phylogenomics reveal complex evolution of life history strategies in a clade of bivalves with parasitic larvae (Bivalvia: Unionoida: Ambleminae). Cladistics 2020; 36:505-520. [DOI: 10.1111/cla.12423] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2020] [Indexed: 01/27/2023] Open
Affiliation(s)
| | - John M. Pfeiffer
- National Museum of Natural History Smithsonian Institution Washington DC USA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center 7920 NW 71st Street Gainesville FL32653 USA
| |
Collapse
|
20
|
Bolotov IN, Konopleva ES, Vikhrev IV, Gofarov MY, Lopes-Lima M, Bogan AE, Lunn Z, Chan N, Win T, Aksenova OV, Tomilova AA, Tanmuangpak K, Tumpeesuwan S, Kondakov AV. New freshwater mussel taxa discoveries clarify biogeographic division of Southeast Asia. Sci Rep 2020; 10:6616. [PMID: 32313058 PMCID: PMC7171101 DOI: 10.1038/s41598-020-63612-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/31/2020] [Indexed: 01/22/2023] Open
Abstract
While a growing body of modern phylogenetic research reveals that the Western Indochina represents a separate biogeographic subregion having a largely endemic freshwater fauna, the boundaries of this subregion are still unclear. We use freshwater mussels (Unionidae) as a model to reconstruct spatial patterns of freshwater biogeographic divides throughout Asia. Here, we present an updated freshwater biogeographic division of mainland Southeast Asia and describe 12 species and 4 genera of freshwater mussels new to science. We show that the Isthmus of Kra represents a significant southern biogeographic barrier between freshwater mussel faunas of the Western Indochina and Sundaland subregions, while the Indian and Western Indochina subregions are separated by the Naga Hills, Chin Hills, and Rakhine Yoma mountain ranges. Our findings highlight that the freshwater bivalve fauna of Southeast Asia primarily originated within three evolutionary hotspots (Western Indochina, Sundaland, and East Asian) supplemented by ancient immigrants from the Indian Subcontinent.
Collapse
Affiliation(s)
- Ivan N Bolotov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation.
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation.
| | - Ekaterina S Konopleva
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Ilya V Vikhrev
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Mikhail Yu Gofarov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Manuel Lopes-Lima
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, c/o The David Attenborough Building, Pembroke Street, CB2 3QZ, Cambridge, United Kingdom
| | - Arthur E Bogan
- North Carolina Museum of Natural Sciences, 11 West Jones St., Raleigh, NC, 27601, USA
| | - Zau Lunn
- Fauna & Flora International - Myanmar Programme, Yangon, Myanmar
| | - Nyein Chan
- Fauna & Flora International - Myanmar Programme, Yangon, Myanmar
| | - Than Win
- Department of Zoology, Dawei University, Dawei, Tanintharyi Region, Myanmar
| | - Olga V Aksenova
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Alena A Tomilova
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| | - Kitti Tanmuangpak
- Department of Science, Faculty of Science and Technology, Loei Rajabhat University, Loei, Thailand
| | - Sakboworn Tumpeesuwan
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
| | - Alexander V Kondakov
- Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russian Federation
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russian Federation
| |
Collapse
|