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Paraphyletic species no more - genomic data resolve a Pleistocene radiation and validate morphological species of the Melanoplus scudderi complex (Insecta: Orthoptera)

dc.contributor.authorHuang, Jen‐pan
dc.contributor.authorHill, JoVonn G.
dc.contributor.authorOrtego, Joaquín
dc.contributor.authorKnowles, L. Lacey
dc.date.accessioned2020-07-02T20:34:21Z
dc.date.availableWITHHELD_13_MONTHS
dc.date.available2020-07-02T20:34:21Z
dc.date.issued2020-07
dc.identifier.citationHuang, Jen‐pan ; Hill, JoVonn G.; Ortego, Joaquín ; Knowles, L. Lacey (2020). "Paraphyletic species no more - genomic data resolve a Pleistocene radiation and validate morphological species of the Melanoplus scudderi complex (Insecta: Orthoptera)." Systematic Entomology 45(3): 594-605.
dc.identifier.issn0307-6970
dc.identifier.issn1365-3113
dc.identifier.urihttps://hdl.handle.net/2027.42/155980
dc.description.abstractRapid speciation events, with taxa generated over a short time period, are among the most investigated biological phenomena. However, molecular systematics often reveals contradictory results compared with morphological/phenotypical diagnoses of species under scenarios of recent and rapid diversification. In this study, we used molecular data from an average of over 29- 000 loci per sample from RADseq to reconstruct the diversification history and delimit the species boundary in a short- winged grasshopper species complex (Melanoplus scudderi group), where Pleistocene diversification has been hypothesized to generate more than 20 putative species with distinct male genitalic shapes. We found that, based on a maximum likelihood molecular phylogeny, each morphological species indeed forms a monophyletic group, contrary to the result from a previous mitochondrial DNA sequence study. By dating the diversification events, the species complex is estimated to have diversified during the Late Pleistocene, supporting the recent radiation hypothesis. Furthermore, coalescent- based species delimitation analyses provide quantitative support for independent genetic lineages, which corresponds to the morphologically defined species. Our results also showed that male genitalic shape may not be predicted by evolutionary distance among species, not only indicating that this trait is labile, but also implying that selection may play a role in character divergence. Additionally, our findings suggest that the rapid speciation events in this flightless grasshopper complex might be primarily associated with the fragmentation of their grassland habitats during the Late Pleistocene. Collectively, our study highlights the importance of integrating multiple sources of information to delineate species, especially for a species complex that diversified rapidly, and whose divergence may be linked to ecological processes that create geographic isolation (i.e. fragmented habitats), as well as selection acting on characters with direct consequences for reproductive isolation (i.e. genitalic divergence).Genomic data validate morphological species designations in Melanoplus grasshoppers from the southeastern U.S.A.The difference in male genitalic shape, which is evolutionarily labile, can be a good diagnostic character to distinguish species of recent and rapid diversification origin.Fragmentation of grassland habitats in the Late Pleistocene might have facilitated rapid speciation events in the flightless Melanoplus grasshoppers.
dc.publisherWiley Periodicals, Inc.
dc.publisherBlackwell Publishing Ltd
dc.titleParaphyletic species no more - genomic data resolve a Pleistocene radiation and validate morphological species of the Melanoplus scudderi complex (Insecta: Orthoptera)
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelBiology
dc.subject.hlbtoplevelScience
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/155980/1/syen12415-sup-0001-SupInfo.pdf
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/155980/2/syen12415_am.pdf
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/155980/3/syen12415.pdf
dc.identifier.doi10.1111/syen.12415
dc.identifier.sourceSystematic Entomology
dc.identifier.citedreferenceParadis, E. & Schliep, K. ( 2019 ) ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35, 526 - 528.
dc.identifier.citedreferenceOneal, E. & Knowles, L.L. ( 2015 ) Paternity analyses in wild- caught and laboratory- reared Caribbean cricket females reveal the influence of mating environment on post- copulatory sexual selection. Journal of Evolutionary Biology, 28, 2300 - 2307.
dc.identifier.citedreferencePeterson, B.K., Weber, J.N., Kay, E.H., Fisher, H.S. & Hoekstra, H.E. ( 2012 ) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non- model species. PLoS One, 7, e37135.
dc.identifier.citedreferenceRevell, L.J. ( 2012 ) phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3, 217 - 223.
dc.identifier.citedreferenceRussel, D.A., Rich, F.J., Schneider, V. & Lynch- Stieglitz, J. ( 2009 ) A warm thermal enclave in thelate Pleistocene of the south- eastern United States. Biological Reviews, 84, 173 - 202.
dc.identifier.citedreferenceRundell, R. & Price, T.D. ( 2009 ) Adaptive radiation, nonadaptive radiation, ecological speciation and nonecological speciation. Trends in Ecology and Evolution, 24, 394 - 399.
dc.identifier.citedreferenceSatler, J.D. & Carstens, B.C. ( 2016 ) Phylogeographic concordance factors quantify phylogeographic congruence among co- distributed species in the Sarracenia alata pitcher plant system. Evolution, 70, 1105 - 1119.
dc.identifier.citedreferenceSherpa, S., Rioux, D., Goindin, D., Fouque, F., François, O. & Després, L. ( 2018 ) At the origin of a worldwide invasion: unraveling the genetic makeup of the Caribbean bridgehead populations of the dengue vector Aedes aegypti. Genome Biology and Evolution, 10, 56 - 71.
dc.identifier.citedreferenceSilva, G.S.C., Roxo, F.F., Lujan, N.K., Tagliacollo, V.A., Zawadzki, C.H. & Oliveira, C. ( 2016 ) Transcontinental dispersal, ecological opportunity and origins of an adaptive radiation in the Neotropical catfish genus Hypostomus (Siluriformes: Loricariidae). Molecular Ecology, 25, 1511 - 1529.
dc.identifier.citedreferenceSmith, B.T., Ribas, C.C., Whitney, B.M., Hernández- Baños, B.E. & Klicka, J. ( 2013 ) Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus. Molecular Ecology, 22, 483 - 494.
dc.identifier.citedreferenceSolis- Lemus, C., Knowles, L.L. & Ané, C. ( 2014 ) Bayesian species delimitation combining multiple genes and traits in a unified framework. Evolution, 69, 492 - 507.
dc.identifier.citedreferenceStamatakis, A. ( 2014 ) RAxML version 8: a tool for phylogenetic analysis and post- analysis of large phylogenies. Bioinformatics, 30, 1312 - 1313.
dc.identifier.citedreferenceSukumaran, J. & Knowles, L.L. ( 2017 ) Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences, USA, 114, 1607 - 1612.
dc.identifier.citedreferenceSwofford D. L. ( 2002 ) PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods), Version 4.0 Beta 10. Sinauer Association, Sunderland, MA.
dc.identifier.citedreferenceWagner, C.E., Keller, I., Wittwer, S. et al. ( 2013 ) Genome- wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology, 22, 787 - 798.
dc.identifier.citedreferenceWalker, M.J., Stockman, A.K., Marek, P.E. & Bond, J.E. ( 2009 ) Pleistocene glacial refugia across the Appalachian Mountains and coastal plain in the millipede genus Narceus: evidence from population genetic, phylogeography, and paleoclimatic data. BMC Evolutionary Biology, 9, 25.
dc.identifier.citedreferenceYang, Z. & Rannala, B. ( 2014 ) Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution, 31, 3125 - 3135.
dc.identifier.citedreferenceGoolsby, E.W., Bruggeman, J. & Ané, C. ( 2017 ) Rphylopars: fast multivariate phylogenetic comparative methods for missing data and within- species variation. Methods in Ecology and Evolution, 8, 22 - 27.
dc.identifier.citedreferenceHarmon L. ( 2019 ) Phylogenetic Comparative Methods: Learning From Tree. https://doi.org/10.32942/osf.io/e3xnr
dc.identifier.citedreferenceAndrews, K.R., Good, J.M., Miller, M.R., Luikart, G. & Hohenlohe, P.A. ( 2016 ) Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics, 17, 81 - 92.
dc.identifier.citedreferenceBentley, S.J. Sr, Blum, M.D., Maloney, J., Pond, L. & Paulsell, R. ( 2016 ) The Mississippi River source- to- sink system: perspectives on tectonic, climatic, and anthropogenic influences, Miocene to Anthropocene. Earth- Science Reviews, 153, 139 - 174.
dc.identifier.citedreferenceBickford, D., Lohman, D.J., Sodhi, N.S. et al. ( 2007 ) Cryptic species as a window on diversity and conservation. Trends in Ecology and Evolution, 22, 148 - 155.
dc.identifier.citedreferenceBonhemme, V., Picq, S., Gaucherel, C. & Claude, J. ( 2014 ) Momocs: outline analysis using R. Journal of Statistical Software, 56, 1 - 24.
dc.identifier.citedreferenceCadena, C.D., Zapata, F. & Jiménez, I. ( 2018 ) Issues and perspectives in species delimitation using phenotypic data: Atlantean evolution in Darwin’s finches. Systematic Biology, 67, 181 - 194.
dc.identifier.citedreferenceCarstens, B.C. & Knowles, L.L. ( 2007 ) Shifting distributions and speciation: species divergence during rapid climate change. Molecular Ecology, 16, 619 - 627.
dc.identifier.citedreferenceChifman, J. & Kubatko, L. ( 2014 ) Quartet inference from SNP data under the coalescent model. Bioinformatics, 30, 3317 - 3324.
dc.identifier.citedreferenceCohen, B.L. ( 2018 ) Match and mismatch of morphological and molecular phylogenies: causes, implications, and new light on cladistics. Zoological Journal of the Linnean Society, 184, 516 - 527.
dc.identifier.citedreferenceCohn, T.J., Swanson, D.R. & Fontana, P. ( 2013 ) Dichopetala and New Related North American Genera: A Study in Genitalic Similarity in Sympatry and Genitalic Differences in Allopatry (Tettigoniidae: Phaneropterinae: Odonturini). Museum of Zoology. University of Michigan, Miscellaneous Publications. NO. 203, Ann Arbor, Michigan.
dc.identifier.citedreferenceDickson, B.V. & Pierce, S.E. ( 2019 ) Functional performance of turtle humerus shape across an ecological adaptive landscape. Evolution, 73, 1265 - 1277.
dc.identifier.citedreferenceEaton, D.A. ( 2014 ) PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics, 30, 1844 - 1849.
dc.identifier.citedreferenceEaton, D.A. & Ree, R.H. ( 2013 ) Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae). Systematic Biology, 62, 689 - 706.
dc.identifier.citedreferenceEberhard, W.G. ( 1996 ) Female Control: Sexual Selection by Cryptic Female Choice. Princeton University Press, Princeton, NJ, USA.
dc.identifier.citedreferenceFarrington, H.L., Lawson, L.P., Clark, C.M. & Petren, K. ( 2014 ) The evolutionary history of Darwin’s finches: speciation, gene flow, and introgression in a fragmented landscape. Evolution, 68, 2932 - 2944.
dc.identifier.citedreferenceFiduccia, C.M. & Mattheyses, R.M. ( 1982 ) A linear time heuristic for improving network partitions. Proceedings of ACM/IEEE Design Conference, pp. 175 - 181. https://doi.org/10.1109/DAC.1982.1585498
dc.identifier.citedreferenceFlouri, T., Jiao, X., Rannala, B. & Yang, Z. ( 2018 ) Species tree inference with bpp using genomic sequences and the multispecies coalescent. Molecular Biology and Evolution, 35, 2585 - 2593.
dc.identifier.citedreferenceFreudenstein, J.V., Broe, M.B., Folk, R.A. & Sinn, B.T. ( 2017 ) Biodiversity and species concept- lineages are not rnough. Systematic Biology, 66, 644 - 656.
dc.identifier.citedreferenceFujisawa, T., Sasabe, M., Nagata, N., Takami, Y. & Sota, T. ( 2019 ) Genetic basis of species- specific genitalia reveals role in species diversification. Science Advance, 5 eaav9939.
dc.identifier.citedreferenceHickerson, M.J., Meyer, C.P. & Moritz, C. ( 2006 ) DNA barcoding will often fail to discover new animal species over broad parameter space. Systematic Biology, 55, 729 - 739.
dc.identifier.citedreferenceHill, J.G. ( 2015 ) Revision and biogeography of the Melanoplus Scudderi species group with the description of 21 new species and establishment of the Carnegiei and Davisi species groups. Transactions of the American Entomological Society, 141, 252 - 350.
dc.identifier.citedreferenceHillis, D.M. ( 1987 ) Molecular versus morphological approaches to systematics. Annual Review in Ecology and Systematics, 18, 23 - 42.
dc.identifier.citedreferenceHuang, J.- P. ( 2018 ) What have been and what can be delimited as species using molecular data under the multi- species coalescent model? A case study using Hercules beetles. Insect Systematics and Diversity, 2, 3.
dc.identifier.citedreferenceHuang, J.- P. ( 2016 ) Parapatric genetic introgression and phenotypic assimilation: testing conditions for introgression between Hercules beetles (Dynastes, Dynastidae). Molecular Ecology, 25, 5513 - 5526.
dc.identifier.citedreferenceHuang, J.- P. & Knowles, L.L. ( 2016 ) The species versus subspecies conundrum: quantitative delimitation from integrating multiple data types within a single Bayesian approachin Hercules beetles. Systematic Biology, 65, 685 - 699.
dc.identifier.citedreferenceHuang, H. & Knowles, L.L. ( 2016b ) Unforeseen consequences of excluding missing data from next- generation sequences: simulation study of RAD sequences. Systematic Biology, 65, 357 - 365.
dc.identifier.citedreferenceKeightley, P.D., Pinharanda, A., Ness, R.W. et al. ( 2015 ) Estimation of the spontaneous mutation rate in Heliconius melpomene. Molecular Biology and Evolution, 32, 239 - 243.
dc.identifier.citedreferenceKlingenberg, C.P. & Gidaszewski, N.A. ( 2010 ) Testing and quantifying phylogenetic signals and homoplasy in morphometric data. Systematic Biology, 59, 245 - 261.
dc.identifier.citedreferenceKnowles, L.L. ( 2001 ) Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Molecular Ecology, 10, 691 - 701.
dc.identifier.citedreferenceKnowles, L.L. ( 2001b ) Genealogical portraits of speciation in montane grasshoppers (genus Melanoplus ) from the sky islands of the Rocky Mountains. Proceedings of the Royal Society London Series B., 268, 319 - 324.
dc.identifier.citedreferenceKnowles, L.L. & Cohn, T.J. ( 2016 ) Tests of the role of sexual selection in genitalic divergence with multiple hybrid clines. Journal of Orthoptera Research, 25, 75 - 82.
dc.identifier.citedreferenceKnowles, L.L. & Kubatko, L.S., co- editors ( 2010 ) Estimating Species Trees: Practical and Theoretical Aspects. Wiley- Blackwell.
dc.identifier.citedreferenceKnowles, L.L. & Otte, D. ( 2000 ) Phylogenetic analysis of montane grasshoppers from western North America (genus Melanoplus, Acrididae: Melanoplinae). Annals of the Entomological Society of America, 93, 421 - 431.
dc.identifier.citedreferenceKnowles, L.L. & Richards, C. ( 2005 ) Importance of genetic drift during Pleistocene divergence as revealed by analysis of genomic variation. Molecular Ecology, 14, 4023 - 4032.
dc.identifier.citedreferenceKnowles, L.L., Chappell, T.M., Marquez, E.J. & Cohn, T.J. ( 2016 ) Tests of the role of sexual selection in genitalic divergence with multiple hybrid clines. Journal of Orthoptera Research, 25, 75 - 82.
dc.identifier.citedreferenceKuhl, F.P. & Giardina, C.R. ( 1982 ) Elliptic Fourier features of a closed contour. Computer Graphics and Image Processing, 18, 236 - 258.
dc.identifier.citedreferenceLosos, J.B. & De Queiroz, K. ( 1997 ) Evolutionary consequences of ecological release in Caribbean Anolis lizards. Biological Journal of the Linnean Society, 61, 459 - 483.
dc.identifier.citedreferenceMárquez, E.J. & Knowles, L.L. ( 2007 ) Correlated evolution of multivariate traits: detecting co- divergence across multiple dimensions. Journal of Evolutionary Biology, 20, 2334 - 2348.
dc.identifier.citedreferenceSites, J.W. Jr & Marshall, J.C. ( 2004 ) Operational criteria for delimiting species. Annual Review of Ecology, Evolution, and Systematics, 35, 199 - 227.
dc.identifier.citedreferenceMasly, J.P. ( 2012 ) 170- years of - lock- and- key- : genital morphology and reproductive isolation. International Journal of Evolutionary Biology, 2012, 24736.
dc.identifier.citedreferenceMayr, E. ( 1942 ) Systematics and the Origin of Species from the Viewpoint of a Zoologist. Columbia University Press, New York.
dc.identifier.citedreferenceMcCormack, J.E., Hird, S.M., Zellmer, A.J., Carstens, B.C. & Brumfield, R.T. ( 2013 ) Applications of next- generation sequencing to phylogeography and phylogenetics. Molecular Phylogenetics and Evolution, 66, 526 - 538.
dc.identifier.citedreferenceOneal, E. & Knowles, L.L. ( 2013 ) Ecological selection as the cause and sexual differentiation as the consequence of species divergence? Proceedings of the Royal Society B: Biological Sciences, 280, 20122236.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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