The Pleurobemini (Bivalvia : Unionida) revisited: molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species
Kentaro Inoue A I , David M. Hayes B , John L. Harris C , Nathan A. Johnson D , Cheryl L. Morrison E , Michael S. Eackles E , Tim L. King E , Jess W. Jones F G , Eric M. Hallerman F , Alan D. Christian C H and Charles R. Randklev A
+ Author Affiliations
- Author Affiliations
A Natural Resources Institute, Texas A&M University, Dallas, TX 75252, USA.
B Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475, USA.
C Department of Biological Sciences, Arkansas State University, Jonesboro, AR 72467, USA.
D US Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL 32653, USA.
E US Geological Survey, Leetown Science Center, Kearneysville, WV 25430, USA.
F Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24061, USA.
G US Fish and Wildlife Service, Blacksburg, VA 24061, USA.
H School for the Environment, University of Massachusetts, Boston, MA 02125, USA.
I Corresponding author. Email: kentaro.inoue@ag.tamu.edu
Invertebrate Systematics 32(3) 689-702 https://doi.org/10.1071/IS17059
Submitted: 1 July 2017 Accepted: 25 October 2017 Published: 1 June 2018
Abstract
The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognised taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g. morphology, life history, ecology) are necessary before any taxonomic changes are formalised.
Additional keywords: DNA barcode, freshwater mussels, generalised mixed Yule-coalescent, molecular systematics, phylogenetics, species delimitation.
References
Berendzen, P. B., Simons, A. M., and Wood, R. M. (2003). Phylogeography of the northern hogsucker, Hypentelium nigricans (Teleostei: Cypriniformes): genetic evidence for the existence of the ancient Teays River. Journal of Biogeography 30, 1139–1152.| Phylogeography of the northern hogsucker, Hypentelium nigricans (Teleostei: Cypriniformes): genetic evidence for the existence of the ancient Teays River.Crossref | GoogleScholarGoogle Scholar |
Bergsten, J., Bilton, D. T., Fujisawa, T., Elliott, M., Monaghan, M. T., Balke, M., Hendrich, L., Geijer, J., Herrmann, J., Foster, G. N., Ribera, I., Nilsson, A. N., Barraclough, T. G., and Vogler, A. P. (2012). The effect of geographical scale of sampling on DNA barcoding. Systematic Biology 61, 851–869.
| The effect of geographical scale of sampling on DNA barcoding.Crossref | GoogleScholarGoogle Scholar |
Bickford, D., Lohman, D. J., Sodhi, N. S., Ng, P. K. L., Meier, R., Winker, K., Ingram, K. K., and Das, I. (2006). Cryptic species as a window on diversity and conservation. Trends in Ecology & Evolution 22, 148–155.
| Cryptic species as a window on diversity and conservation.Crossref | GoogleScholarGoogle Scholar |
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., and Drummond, A. J. (2014). BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10, e1003537.
| BEAST 2: a software platform for Bayesian evolutionary analysis.Crossref | GoogleScholarGoogle Scholar |
Burdick, R. C., and White, M. M. (2007). Phylogeography of the Wabash pigtoe, Fusconaia flava (Rafinesque, 1820) (Bivalvia: Unionidae). The Journal of Molluscan Studies 73, 367–375.
| Phylogeography of the Wabash pigtoe, Fusconaia flava (Rafinesque, 1820) (Bivalvia: Unionidae).Crossref | GoogleScholarGoogle Scholar |
Burlakova, L. E., Campbell, D. C., Karatayev, A. Y., and Barclay, D. (2012). Distribution, genetic analysis and conservation priorities for rare Texas freshwater molluscs in the genera Fusconaia and Pleurobema (Bivalvia: Unionidae). Aquatic Biosystems 8, 12.
| Distribution, genetic analysis and conservation priorities for rare Texas freshwater molluscs in the genera Fusconaia and Pleurobema (Bivalvia: Unionidae).Crossref | GoogleScholarGoogle Scholar |
Campbell, D. C., and Lydeard, C. (2012a). The genera of Pleurobemini (Bivalvia: Unionidae: Ambleminae). American Malacological Bulletin 30, 19–38.
| The genera of Pleurobemini (Bivalvia: Unionidae: Ambleminae).Crossref | GoogleScholarGoogle Scholar |
Campbell, D. C., and Lydeard, C. (2012b). Molecular systematics of Fusconaia (Bivalvia: Unionidae: Ambleminae). American Malacological Bulletin 30, 1–17.
| Molecular systematics of Fusconaia (Bivalvia: Unionidae: Ambleminae).Crossref | GoogleScholarGoogle Scholar |
Campbell, D. C., Serb, J. M., Buhay, J. E., Roe, K. J., Minton, R. L., and Lydeard, C. (2005). Phylogeny of North American amblemines (Bivalvia: Unionoida): prodigious polyphyly proves pervasive across genera. Invertebrate Biology 124, 131–164.
| Phylogeny of North American amblemines (Bivalvia: Unionoida): prodigious polyphyly proves pervasive across genera.Crossref | GoogleScholarGoogle Scholar |
Campbell, D. C., Johnson, P. D., Williams, J. D., Rindsberg, A. K., Serb, J. M., Small, K. K., and Lydeard, C. (2008). Identification of ‘extinct’ freshwater mussel species using DNA barcoding. Molecular Ecology Resources 8, 711–724.
| Identification of ‘extinct’ freshwater mussel species using DNA barcoding.Crossref | GoogleScholarGoogle Scholar |
Crandall, K. A., and Templeton, A. R. (1999). The zoogeography and centers of origin of the crayfish subgenus Procericambarus (Decapoda: Cambaridae). Evolution 53, 123–134.
| The zoogeography and centers of origin of the crayfish subgenus Procericambarus (Decapoda: Cambaridae).Crossref | GoogleScholarGoogle Scholar |
Ezard, T., Fujisawa, T., and Barraclough, T. (2013). SPLITS: SPecies’ LImits by Threshold Statistics. Version 1.0. R Package. Available at: http://r-forge.r-project.org/projects/splits/.
Fontaneto, D., Flot, J.-F., and Tang, C. Q. (2015). Guidelines for DNA taxonomy, with a focus on the meiofauna. Marine Biodiversity 45, 433–451.
| Guidelines for DNA taxonomy, with a focus on the meiofauna.Crossref | GoogleScholarGoogle Scholar |
Fujisawa, T., and Barraclough, T. G. (2013). Delimiting species using single-locus data and the generalized mixed Yule coalescent approach: a revised method and evaluation on simulated data sets. Systematic Biology 62, 707–724.
| Delimiting species using single-locus data and the generalized mixed Yule coalescent approach: a revised method and evaluation on simulated data sets.Crossref | GoogleScholarGoogle Scholar |
Fujita, M. K., Leaché, A. D., Burbrink, F. T., McGuire, J. A., and Moritz, C. (2012). Coalescent-based species delimitation in an integrative taxonomy. Trends in Ecology & Evolution 27, 480–488.
| Coalescent-based species delimitation in an integrative taxonomy.Crossref | GoogleScholarGoogle Scholar |
Gangloff, M. M., Williams, J. D., and Feminella, J. W. (2006). A new species of freshwater mussel (Bivalvia: Unionidae), Pleurobema athearni, from the Coosa River drainage of Alabama, USA. Zootaxa 1118, 43–56.
Graf, D. L., and Cummings, K. S. (2007). Review of the systematics and global diversity of freshwater mussel species (Bivalvia: Unionoida). The Journal of Molluscan Studies 73, 291–314.
| Review of the systematics and global diversity of freshwater mussel species (Bivalvia: Unionoida).Crossref | GoogleScholarGoogle Scholar |
Haag, W. R. (2012). ‘North American Freshwater Mussels: Natural History, Ecology, and Conservation.’ (Cambridge University Press: Cambridge.)
Haag, W. R., and Williams, J. D. (2014). Biodiversity on the brink: an assessment of conservation strategies for North American freshwater mussels. Hydrobiologia 735, 45–60.
| Biodiversity on the brink: an assessment of conservation strategies for North American freshwater mussels.Crossref | GoogleScholarGoogle Scholar |
Hannibal, H. (1912). A synopsis of the recent and tertiary freshwater Mollusca of the Californian Province, based upon an ontogenetic classification. Proceedings of the Malacological Society of London 10, 112–211.
Helaers, R., and Milinkovitch, M. C. (2010). MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics. BMC Bioinformatics 11, 379.
| MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics.Crossref | GoogleScholarGoogle Scholar |
Howells, R. G., Neck, R. W., and Murray, H. D. (1996). ‘Freshwater Mussels of Texas.’ (Texas Park and Wildlife Department: Austin, TX.)
Howells, R. G., Randklev, C. R., and Ford, N. B. (2012). Taxonomic status of pigtoe unionids in Texas. Ellipsaria 14, 11–15.
Huson, D. H., and Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23, 254–267.
| Application of phylogenetic networks in evolutionary studies.Crossref | GoogleScholarGoogle Scholar |
Inoue, K., Hayes, D. M., Harris, J. L., and Christian, A. D. (2013). Phylogenetic and morphometric analyses reveal ecophenotypic plasticity in freshwater mussels Obovaria jacksoniana and Villosa arkansasensis (Bivalvia: Unionidae). Ecology and Evolution 3, 2670–2683.
| Phylogenetic and morphometric analyses reveal ecophenotypic plasticity in freshwater mussels Obovaria jacksoniana and Villosa arkansasensis (Bivalvia: Unionidae).Crossref | GoogleScholarGoogle Scholar |
Inoue, K., McQueen, A. L., Harris, J. L., and Berg, D. J. (2014). Molecular phylogenetics and morphological variation reveal recent speciation in freshwater mussels of the genera Arcidens and Arkansia (Bivalvia: Unionidae). Biological Journal of the Linnean Society. Linnean Society of London 112, 535–545.
| Molecular phylogenetics and morphological variation reveal recent speciation in freshwater mussels of the genera Arcidens and Arkansia (Bivalvia: Unionidae).Crossref | GoogleScholarGoogle Scholar |
Jones, J. W., Neves, R. J., Ahlstedt, S. A., and Hallerman, E. M. (2006). A holistic approach to taxonomic evaluation of two closely related endangered freshwater mussel species, the oyster mussel Epioblasma capsaeformis and tan riffleshell Epioblasma florentina walkeri (Bivalvia: Unionidae). The Journal of Molluscan Studies 72, 267–283.
| A holistic approach to taxonomic evaluation of two closely related endangered freshwater mussel species, the oyster mussel Epioblasma capsaeformis and tan riffleshell Epioblasma florentina walkeri (Bivalvia: Unionidae).Crossref | GoogleScholarGoogle Scholar |
Jones, J. W., Johnson, N. A., Grobler, P. J., Schilling, D. E., Neves, R. J., and Hallerman, E. M. (2015). Endangered rough pigtoe pearlymussel: assessment of phylogenetic status and genetic differentiation of two disjunct populations. Journal of Fish and Wildlife Management 6, 338–349.
| Endangered rough pigtoe pearlymussel: assessment of phylogenetic status and genetic differentiation of two disjunct populations.Crossref | GoogleScholarGoogle Scholar |
Kass, R. E., and Raftery, A. E. (1995). Bayes factors. Journal of the American Statistical Association 90, 773–795.
| Bayes factors.Crossref | GoogleScholarGoogle Scholar |
Katoh, K., and Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30, 772–780.
| MAFFT multiple sequence alignment software version 7: improvements in performance and usability.Crossref | GoogleScholarGoogle Scholar |
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16, 111–120.
| A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.Crossref | GoogleScholarGoogle Scholar |
Labarca, C., and Paigen, K. (1980). A simple, rapid, and sensitive DNA assay procedure. Analytical Biochemistry 102, 344–352.
| A simple, rapid, and sensitive DNA assay procedure.Crossref | GoogleScholarGoogle Scholar |
Lohse, K. (2009). Can mtDNA barcodes be used to delimit species? A response to Pons et al. (2006). Systematic Biology 58, 439–442.
| Can mtDNA barcodes be used to delimit species? A response to Pons et al. (2006).Crossref | GoogleScholarGoogle Scholar |
Lopes-Lima, M., Froufe, E., Do, V. T., Ghamizi, M., Mock, K. E., Kebapci, U., Klishko, O., Kovitvadhi, S., Kovitvadhi, U., Paulo, O. S., Pfeiffer, J. M., Raley, M., Riccardi, N., Sereflisan, H., Sousa, R., Teixeira, A., Varandas, S., Wu, X., Zanatta, D. T., Zieritz, A., and Bogan, A. E. (2017). Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): defining modern subfamilies and tribes. Molecular Phylogenetics and Evolution 106, 174–191.
| Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): defining modern subfamilies and tribes.Crossref | GoogleScholarGoogle Scholar |
Miller, M. A., Pfeiffer, W., and Schwartz, T. (2010). Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In ‘Proceedings of the Gateway Computing Environments Workshop (GCE), 14 Nov. 2010, New Orleans, LA’. (Ed. Institute of Electrical and Electronics Engineers, IEEE.) pp. 1–8. (Curran Associates: New York.)
Morrison, C. L., Lemarié, D. P., Wood, R. M., and King, T. L. (2006). Phylogeographic analyses suggest multiple lineages of Crystallaria asprella (Percidae: Etheostominae). Conservation Genetics 7, 129–147.
| Phylogeographic analyses suggest multiple lineages of Crystallaria asprella (Percidae: Etheostominae).Crossref | GoogleScholarGoogle Scholar |
Nylander, J., Ronquist, F., Huelsenbeck, J., and Nieves-Aldrey, J. (2004). Bayesian phylogenetic analysis of combined data. Systematic Biology 53, 47–67.
| Bayesian phylogenetic analysis of combined data.Crossref | GoogleScholarGoogle Scholar |
Ortmann, A. E. (1920). Correlation of shape and station in fresh-water mussels (Naiades). Proceedings of the American Philosophical Society 59, 268–312.
Ortmann, A. E. (1925). The naiad-fauna of the Tennessee River system below Walden Gorge. American Midland Naturalist 9, 321–372.
| The naiad-fauna of the Tennessee River system below Walden Gorge.Crossref | GoogleScholarGoogle Scholar |
Perkins, M. A., Johnson, N. A., and Gangloff, M. M. (2017). Molecular systematics of the critically-endangered North American spinymussels (Unionidae: Elliptio and Pleurobema) and description of Parvaspina gen. nov. Conservation Genetics 18, 745–757.
| Molecular systematics of the critically-endangered North American spinymussels (Unionidae: Elliptio and Pleurobema) and description of Parvaspina gen. nov.Crossref | GoogleScholarGoogle Scholar |
Pfeiffer, J. M., Johnson, N. A., Randklev, C. R., Howells, R. G., and Williams, J. D. (2016). Generic reclassification and species boundaries in the rediscovered freshwater mussel ‘Quadrula’ mitchelli (Simpson in Dall, 1896). Conservation Genetics 17, 279–292.
| Generic reclassification and species boundaries in the rediscovered freshwater mussel ‘Quadrula’ mitchelli (Simpson in Dall, 1896).Crossref | GoogleScholarGoogle Scholar |
Pons, J., Barraclough, T., Gomez-Zurita, J., Cardoso, A., Duran, D., Hazell, S., Kamoun, S., Sumlin, W., and Vogler, A. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology 55, 595–609.
| Sequence-based species delimitation for the DNA taxonomy of undescribed insects.Crossref | GoogleScholarGoogle Scholar |
Puillandre, N., Strong, E. E., Bouchet, P., Boisselier, M. C., Couloux, A., and Samadi, S. (2009). Identifying gastropod spawn from DNA barcodes: possible but not yet practicable. Molecular Ecology Resources 9, 1311–1321.
| Identifying gastropod spawn from DNA barcodes: possible but not yet practicable.Crossref | GoogleScholarGoogle Scholar |
Puillandre, N., Lambert, A., Brouillet, S., and Achaz, G. (2012). ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology 21, 1864–1877.
| ABGD, Automatic Barcode Gap Discovery for primary species delimitation.Crossref | GoogleScholarGoogle Scholar |
R Core Team (2015). R: a language and environment for statistical computing. Available at: http://www.R-project.org/.
Rafinesque, C. S. (1820). Monographie des coquilles bivalves fluvutules de la Riviére Ohio, contenant douze genres et soixante-huit espéces. Annales generales des sciences Physiques, a Bruxelles 5, 287–322.
Rambaut, A., and Drummond, A. J. (2009). Tracer v1.5. Available at: http://tree.bio.ed.ac.uk/software/tracer/.
Reid, N. M., and Carstens, B. C. (2012). Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evolutionary Biology 12, 196.
| Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model.Crossref | GoogleScholarGoogle Scholar |
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., and Huelsenbeck, J. P. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61, 539–542.
| MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.Crossref | GoogleScholarGoogle Scholar |
Saghai-Maroof, M. A., Soliman, K. M., Jorgensen, R. A., and Allard, R. W. (1984). Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences of the United States of America 81, 8014–8018.
| Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics.Crossref | GoogleScholarGoogle Scholar |
Serb, J. M., Buhay, J. E., and Lydeard, C. (2003). Molecular systematics of the North American freshwater bivalve genus Quadrula (Unionidae: Ambleminae) based on mitochondrial ND1 sequences. Molecular Phylogenetics and Evolution 28, 1–11.
| Molecular systematics of the North American freshwater bivalve genus Quadrula (Unionidae: Ambleminae) based on mitochondrial ND1 sequences.Crossref | GoogleScholarGoogle Scholar |
Shea, C. P., Peterson, J. T., Wisniewski, J. M., and Johnson, N. A. (2011). Misidentification of freshwater mussel species (Bivalvia: Unionidae): contributing factors, management implications, and potential solutions. Journal of the North American Benthological Society 30, 446–458.
| Misidentification of freshwater mussel species (Bivalvia: Unionidae): contributing factors, management implications, and potential solutions.Crossref | GoogleScholarGoogle Scholar |
Tanabe, A. S. (2011). Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data. Molecular Ecology Resources 11, 914–921.
| Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data.Crossref | GoogleScholarGoogle Scholar |
Taylor, H. R., and Harris, W. E. (2012). An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Molecular Ecology Resources 12, 377–388.
| An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding.Crossref | GoogleScholarGoogle Scholar |
Turgeon, D. D., Quinn, J. F., Jr, Bogan, A. E., Coan, E. V., Hochberg, F. G., Jr, Lyons, W. G., Mikkelsen, P. M., Neves, R. J., Roper, C. F. E., Rosenberg, G., Roth, B., Scheltema, A., Thompson, F. G., Vecchione, M., and Williams, J. D. (1998). Common and Scientific Names of Aquatic Invertebrates from the United States and Canada: Mollusks.’ 2nd edn. Special Publication No. 26. (American Fisheries Society: Bethesda, MD.)
Via, S., Gomulkiewicz, R., De Jong, G., Scheiner, S. M., Schlichting, C. D., and Tienderen, P. V. (1995). Adaptive phenotypic plasticity: consensus and controversy. Trends in Ecology & Evolution 10, 212–217.
| Adaptive phenotypic plasticity: consensus and controversy.Crossref | GoogleScholarGoogle Scholar |
Vidrine, M. F. (1993). ‘The Historical Distributions of Freshwater Mussels in Louisiana.’ (Gail Q. Vidrine Collectibles: Eunice, LA.)
Watters, G. T. (1994). Form and function of unionoidean shell sculpture and shape (Bivalvia). American Malacological Bulletin 11, 1–20.
Watters, G. T., Hoggarth, M. A., and Stansbery, D. H. (2009). ‘The Freshwater Mussels of Ohio.’ (Ohio State University: Columbus, OH.)
Williams, J. D., Warren, M. L., Cummings, K. S., Harris, J. L., and Neves, R. J. (1993). Conservation status of freshwater mussels of the United States and Canada. Fisheries (Bethesda, Md.) 18, 6–22.
| Conservation status of freshwater mussels of the United States and Canada.Crossref | GoogleScholarGoogle Scholar |
Williams, J. D., Bogan, A. E., and Garner, J. T. (2008). ‘Freshwater Mussels of Alabama and the Mobile Basin in Georgia, Mississippi & Tennessee.’ (The University of Alabama Press: Tuscaloosa, AL.)
