Abstract
The “mountain” dusky is a charismatic ecomorph of Dusky Salamander (Desmognathus): smaller (~20–50mm SVL), more terrestrial and montane woodland species, typically with round tails and extremely variable, often colorful patterns. Originally considered a single species (D. ochrophaeus), populations across the Appalachians are now divided into D. abditus, D. carolinensis, D. ochrophaeus, D. ocoee, and D. orestes, which do not form a clade but are instead scattered across the phylogeny of Desmognathus. A Coastal Plain species with a mountain dusky phenotype (D. apalachicolae) is also nested within a lineage related to D. ocoee. Within the current concept of D. ocoee, there are up to 8 genetically distinct geographic lineages which display significantly different but substantially overlapping morphologies. Recent studies have suggested that as many as six species could reasonably be delimited based on genetic data. We evaluate the strength of that evidence here and find support for five species in the D. apalachicolae + D. ocoee group. The first is D. apalachicolae in essentially its originally described form from the Coastal Plain. The second and third are D. adatsihi sp. nov. and D. balsameus sp. nov., endemic to the Great Smoky/Plott Balsam and Great Balsam Mountains, respectively. The fourth corresponds to the resurrected D. perlapsus for populations from the Alarka and Cowee Mountains in North Carolina, through the Chattahoochee River drainage to the Fall Line in the Piedmont of Georgia and Alabama. The fifth is D. ocoee, here restricted to populations in the Nantahala and Unicoi Mountains and southernmost Blue Ridge escarpment, along with previously recognized populations from the Cumberland Escarpment and Cumberland Plateau of south-central Tennessee and northeastern Alabama. This taxon concept of D. ocoee includes three deeply divergent geographic genetic segments that hybridize across two contact zones, while D. apalachicolae may be nested within some southern Blue Ridge populations of D. ocoee. The resurrected form of D. perlapsus also exhibits some admixture with the newly restricted D. ocoee. While this taxonomic arrangement is robust and stably derived from mitochondrial, morphological, and nuclear data, more sophisticated future analyses sampling additional populations and loci to estimate relationships may reach more subtle conclusions regarding the identity of some lineages within D. ocoee.
References
Anderson, J.A. & Tilley, S.G. (2003) Systematics of the Desmognathus ochrophaeus complex in the Cumberland Plateau of Tennessee. Herpetological Monographs, 17, 75–110. https://doi.org/10.1655/0733-1347(2003)017[0075:SOTDOC]2.0.CO;2
Beamer, D.A. & Lamb, T. (2008) Dusky salamanders (Desmognathus, Plethodontidae) from the Coastal Plain: multiple independent lineages and their bearing on the molecular phylogeny of the genus. Molecular Phylogenetics and Evolution, 47, 143–153. https://doi.org/10.1016/j.ympev.2008.01.015
Beamer, D.A. & Lamb, T. (2020) Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): an ecoregion-drainage sampling grid reveals additional cryptic clades. Zootaxa, 4734 (1), 1–61. https://doi.org/10.11646/zootaxa.4734.1.1
Binks, R.M. & Byrne, M. (2022) Species delimitation, hybridization and possible apomixis in a rapid radiation of Western Australian Leptospermum (Myrtaceae). Botanical Journal of the Linnean Society, 2022, boac022. https://doi.org/10.1093/botlinnean/boac022
Blaustein, A.R., Han, B.A., Relyea, R.A., Johnson, P.T.J., Buck, J.C., Gervasi, S.S. & Kats, L.B. (2011) The complexity of amphibian population declines: understanding the role of cofactors in driving amphibian losses. Annals of the New York Academy of Sciences, 1223, 108–119. https://doi.org/10.1111/j.1749-6632.2010.05909.x
Brimley, C.S. (1928) Yellow-cheeked Desmognathus from Macon County, N.C. Copeia, 166, 21–23. https://doi.org/10.2307/1436056
Burbrink, F.T., Pyron, R.A., Gehara, M.C., McKelvy, A.D. & Myers, E.A. (2021) The corrected taxonomic history of the North American ratsnakes (Pantherophis obsoletus complex). Herpetological Review, 53, 537–547.
Burbrink, F.T., Crother, B.I., Murray, C.M., Smith, B.T., Ruane, S., Myers, E.A. & Pyron, R.A. (2022) Empirical and philosophical problems with the subspecies rank. Ecology and Evolution, 12, e9069. https://doi.org/10.22541/au.164847286.69025170/v1
Camp, C., Barbour, M. & Wooten, J. (2014) Morphological differentiation between the larval forms of two cryptic species of dusky salamander (Desmognathus). Amphibia-Reptilia, 35, 117–122. https://doi.org/10.1163/15685381-00002922
Camp, C.D., Seymour, Z.L. & Wooten, J.A. (2013) Morphological variation in the cryptic species Desmognathus quadramaculatus (Black-bellied Salamander) and Desmognathus folkertsi (Dwarf Black-bellied Salamander). Journal of Herpetology, 47, 471–479. https://doi.org/10.1670/11-287
Camp, C.D. & Tilley, S.G. (2005) Desmognathus ocoee Nicholls, 1949: Ocoee Salamander. In: M. J. Lannoo (Ed), Amphibian declines: the conservation status of United States species. University of California Press, Los Angeles, California, pp. 719–721.
Campbell, C.R., Poelstra, J.W. & Yoder, A.D. (2018) What is speciation genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species. Biological Journal of the Linnean Society, 124, 561–583. https://doi.org/10.1093/biolinnean/bly063
Carstens, B.C., Pelletier, T.A., Reid, N.M. & Satler, J.D. (2013) How to fail at species delimitation. Molecular Ecology, 22, 4369–4383. https://doi.org/10.1111/mec.12413
Caruso, N. & Lips, K. (2013) Truly enigmatic declines in terrestrial salamander populations in Great Smoky Mountains National Park. Diversity and Distributions, 19, 38–48. https://doi.org/10.2307/23480722
Casas, L., Saenz‐Agudelo, P., Villegas‐Ríos, D., Irigoien, X. & Saborido‐Rey, F. (2021) Genomic landscape of geographically structured colour polymorphism in a temperate marine fish. Molecular Ecology, 30, 1281–1296. https://doi.org/10.1111/mec.15805
Chan, K.O., Hutter, C.R., Wood, P.L., Grismer, L.L., Das, I. & Brown, R.M. (2020) Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Molecular Ecology, 29, 3970–3987. https://doi.org/10.1111/mec.15603
Cope, E.D. (1859) On the primary divisions of the Salamandridae, with descriptions of two new species. Proceedings of the Academy of Natural Sciences of Philadelphia, 11, 122–128.
Cox, J.L., McKinney, M.L., Fitzpatrick, B.M., Leppanen, C. & Nichols, R.J. (2022) Coniferous conservation supporting a plethora of plethodontids: implications of conserving eastern hemlock (Tsuga canadensis) on southern Appalachian montane salamanders. Forest Ecology and Management, 508, 120010. https://doi.org/10.1016/j.foreco.2022.120010
Crisp, M. & Chandler, G. (1996) Paraphyletic species. Telopea, 6, 813–844. https://doi.org/10.7751/telopea19963037
Dodd, C.K. (2004) The amphibians of Great Smoky Mountains National Park. University of Tennessee Press, Knoxville, 283 pp.
Dolinay, M., Nečas, T., Zimkus, B.M., Schmitz, A., Fokam, E.B., Lemmon, E.M., Lemmon, A.R. & Gvoždík, V. (2021) Gene flow in phylogenomics: sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands. Molecular Phylogenetics and Evolution, 163, 107258. https://doi.org/10.1016/j.ympev.2021.107258
Drukker, S.S., Cecala, K.K., Gould, P.R., McKenzie, B.A. & de Ven, C.V. (2018) The ecology and natural history of the Cumberland Dusky Salamander (Desmognathus abditus): distribution and demographics. Herpetological Conservation and Biology, 13, 33–46.
Dufresnes, C., Pribille, M., Alard, B., Gonçalves, H., Amat, F., Crochet, P.A., Dubey, S., Perrin, N., Fumagalli, L., Vences, M. & Martínez-Solano, I. (2020) Integrating hybrid zone analyses in species delimitation: lessons from two anuran radiations of the Western Mediterranean. Heredity, 124, 423–438.
Dufresnes, C., Brelsford, A., Jeffries, D.L., Mazepa, G., Suchan, T., Canestrelli, D., Nicieza, A., Fumagalli, L., Dubey, S., Martínez-Solano, I. & Litvinchuk, S.N. (2021) Mass of genes rather than master genes underlie the genomic architecture of amphibian speciation. Proceedings of the National Academy of Sciences, 118, e2103963118. https://doi.org/10.1073/pnas.2103963118
Dunn, E.R. (1916) Two new salamanders of the genus Desmognathus. Proceedings of the Biological Society of Washington, 29, 73–76.
Dunn, E.R. (1927) A new mountain race of Desmognathus. Copeia, 164, 84–86. https://doi.org/10.2307/1435656
Feldmeier, S., Schmidt, B.R., Zimmermann, N.E., Veith, M., Ficetola, G.F. & Lötters, S. (2020) Shifting aspect or elevation? The climate change response of ectotherms in a complex mountain topography. Diversity and Distributions, 26, 1483–1495. https://doi.org/10.1111/ddi.13146
Friday, B., Holzheuser, C., Lips, K.R. & Longo, A.V. (2020) Preparing for invasion: assessing risk of infection by chytrid fungi in southeastern plethodontid salamanders. Journal of Experimental Zoology Part A: Ecological and Integrative Physiology, 333, 829–840. https://doi.org/10.1002/jez.2427
Gautier, M., Yamaguchi, J., Foucaud, J., Loiseau, A., Ausset, A., Facon, B., Gschloessl, B., Lagnel, J., Loire, E., Parrinello, H., Severac, D., Lopez-Roques, C., Donnadieu, C., Manno, M., Berges, H., Gharbi, K., Lawson-Handley, L., Zang, L.-S., Vogel, H., Estoup, A. & Prud’homme, B. (2018) The genomic basis of color pattern polymorphism in the Harlequin Ladybird. Current Biology, 28, 3296-3302.e7. https://doi.org/10.1016/j.cub.2018.08.023
Gilbert, C.R. (1974) Catalogue of type specimens in the Department of Natural Sciences, Florida State Museum. Bulletin of the Florida State Museum, 18, 101–120.
González-del-Pliego, P., Freckleton, R.P., Edwards, D.P., Koo, M.S., Scheffers, B.R., Pyron, R.A. & Jetz, W. (2019) Phylogenetic and trait-based prediction of extinction risk for data-deficient amphibians. Current Biology, 29, 1557–1563.e3. https://doi.org/10.1016/j.cub.2019.04.005
Higham, T.E., Ferry, L.A., Schmitz, L., Irschick, D.J., Starko, S., Anderson, P.S.L., Bergmann, P.J., Jamniczky, H.A., Monteiro, L.R., Navon, D., Messier, J., Carrington, E., Farina, S.C., Feilich, K.L., Hernandez, L.P., Johnson, M.A., Kawano, S.M., Law, C.J., Longo, S.J., Martin, C.H., Martone, P.T., Rico-Guevara, A., Santana, S.E. & Niklas, K.J. (2021) Linking ecomechanical models and functional traits to understand phenotypic diversity. Trends in Ecology & Evolution, 36, 860–873. https://doi.org/10.1016/j.tree.2021.05.009
Highton, R. (2005) Declines of Eastern North American Woodland Salamanders (Plethodon). In: M. Lannoo (Ed), Amphibian Declines. University of California Press, California, Los Angeles, pp. 34–46.
Huheey, J.E. (1966a) Studies in warning coloration and mimicry. V. Red-cheeked dusky salamanders in North Carolina. Journal of the Elisha Mitchell Scientific Society, 82, 126–131.
Huheey, J.E. (1966b) The desmognathine salamanders of the Great Smoky Mountains National Park. Journal of the Ohio Herpetological Society, 5, 63–72. https://doi.org/10.2307/1562609
Jackson, N.D. (2005) Phylogenetic history, morphological parallelism, and speciation in a complex of Appalachian salamanders (genus: Desmognathus). Master of Science thesis, Brigham Young University, Provo, Utah, 64 pp.
Jones, K.S. & Weisrock, D.W. (2018) Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders. Evolution, 72, 2378–2393. https://doi.org/10.1111/evo.13606
Kaliontzopoulou, A. (2011) Geometric morphometrics in herpetology: modern tools for enhancing the study of morphological variation in amphibians and reptiles. Basic and Applied Herpetology, 25, 5–32. https://doi.org/10.11160/bah.11016
Karanovic, T., Djurakic, M. & Eberhard, S.M. (2016) Cryptic species or inadequate taxonomy? Implementation of 2D geometric morphometrics based on integumental organs as landmarks for delimitation and description of copepod taxa. Systematic Biology 65, 304–327. https://doi.org/10.1093/sysbio/syv088
Karlin, A.A. & Guttman, S.I. (1986) Systematics and geographic isozyme variation in the plethodontid salamander Desmognathus fuscus (Rafinesque). Herpetologica, 42, 283–301.
Korshunova, T., Picton, B., Furfaro, G., Mariottini, P., Pontes, M., Prkić, J., Fletcher, K., Malmberg, K., Lundin, K. & Martynov, A. (2019) Multilevel fine-scale diversity challenges the “cryptic species” concept. Scientific Reports, 9, 6732. https://doi.org/10.1038/s41598-019-42297-5
Kozak, K.H., Larson, A., Bonett, R.M. & Harmon, L.J. (2005) Phylogenetic analysis of ecomorphological divergence, community structure, and diversification rates in dusky salamanders (Plethodontidae: Desmognathus). Evolution, 59, 2000–2016. https://doi.org/10.1111/j.0014-3820.2005.tb01069.x
Kuchta, S.R. & Wake, D.B. (2016) Wherefore and whither the ring species? Copeia, 104, 189–201. https://doi.org/10.1643/OT-14-176
Labanick, G.M. (1983) Inheritance of the red-leg and red-cheek traits in the salamander Desmognathus ochrophaeus. Herpetologica, 39, 114–120.
Lawson, D.J., van Dorp, L. & Falush, D. (2018) A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. Nature Communications, 9, 3258. https://doi.org/10.1038/s41467-018-05257-7
Maes, D., Isaac, N.J., Harrower, C.A., Collen, B., Van Strien, A.J. & Roy, D.B. (2015) The use of opportunistic data for IUCN Red List assessments. Biological Journal of the Linnean Society, 115, 690–706. https://doi.org/10.1111/bij.12530
Martof, B.S. & Rose, F.L. (1963) Geographic variation in southern populations of Desmognathus ochrophaeus. The American Midland Naturalist, 69, 376–425. https://doi.org/10.2307/2422917
Mead, L.S., Tilley, S.G. & Katz, L.A. (2001) Genetic structure of the Blue Ridge Dusky Salamander (Desmognathus orestes): inferences from allozymes, mitochondrial DNA, and behavior. Evolution, 55, 2287–2302. https://doi.org/10.1111/j.0014-3820.2001.tb00743.x
Means, D.B. (1974) The status of Desmognathus brimleyorum Stejneger and an analysis of the genus Desmognathus (Amphibia, Urodela) in Florida. Bulletin of the Florida State Museum, 18, 1–100.
Means, D.B. (1975) Competitive exclusion along a habitat gradient between two species of salamanders (Desmognathus) in western Florida. Journal of Biogeography, 2, 253–263. https://doi.org/10.2307/3037999
Means, D.B. (2005) Desmognathus apalachicolae Means and Karlin, 1989: Apalachicola Dusky Salamander. In: Lannoo, M. (Ed.), Amphibian Declines: The Conservation Status of United States Species. University of California Press, Berkeley, California, pp. 698–699.
Means, D.B. & Karlin, A.A. (1989) A new species of Desmognathus from the eastern Gulf Coastal Plain. Herpetologica, 37–46.
Milanovich, J.R., Peterman, W.E., Nibbelink, N.P. & Maerz, J.C. (2010) Projected loss of a salamander diversity hotspot as a consequence of projected global climate change. PLOS ONE, 5, e12189. https://doi.org/10.1371/journal.pone.0012189
Neill, W.T. (1950) A new species of salamander, genus Desmognathus, from Georgia. Research Division, Ross Allen’s Reptile Institute, Silver Springs, Florida, 6 pp.
Nicholls, J.C. (1949) A new salamander of the genus Desmognathus from east Tennessee. Journal of the Tennessee Academy of Science, 24, 127–129.
Niemiller, M.L., Fitzpatrick, B.M. & Miller, B.T. (2008) Recent divergence with gene flow in Tennessee cave salamanders (Plethodontidae: Gyrinophilus) inferred from gene genealogies. Molecular Ecology, 17, 2258–2275. https://doi.org/10.1111/j.1365-294X.2008.03750.x
Nosil, P. (2008) Speciation with gene flow could be common. Molecular Ecology, 17, 2103–2106. https://doi.org/10.1111/j.1365-294X.2008.03715.x
Omernik, J.M. & Griffith, G.E. (2014) Ecoregions of the conterminous United States—evolution of a hierarchical spatial framework. Environmental Management, 54, 1249–1266. https://doi.org/10.1007/s00267-014-0364-1
Pyron R.A. & Beamer, D.A. (2022) Nomenclatural solutions for diagnosing ‘cryptic’ species using molecular and morphological data facilitate a taxonomic revision of the Black-bellied Salamanders (Urodela: Desmognathus ‘quadramaculatus’) from the southern Appalachian Mountains. Bionomina, 27, 1–43.
Pyron, R.A., Duncan, S.C., Burbrink, F.T., O’Connell, K.A. & Beamer, D.A. (2022a) Speciation hypotheses from phylogeographic delimitation yield an integrative taxonomy for Seal Salamanders (Desmognathus monticola). Systematic Biology. [in press]
Pyron, R.A., O’Connell, K.A., Lamb, J.Y. & Beamer, D.A. (2022b) A new, narrowly endemic species of swamp-dwelling dusky salamander (Plethodontidae: Desmognathus) from the Gulf Coastal Plain of Mississippi and Alabama. Zootaxa, 5133 (1), 53–82. https://doi.org/10.11646/zootaxa.5133.1.3
Pyron, R.A., O’Connell, K.A., Lemmon, E.M., Lemmon, A.R. & Beamer, D.A. (2022c) Candidate‐species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones. Ecology and Evolution, 12, e8574. https://doi.org/10.1002/ece3.8574
Pyron, R.A., O’Connell, K.A., Lemmon, E.M., Lemmon, A.R. & Beamer, D.A. (2020) Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus). Molecular Phylogenetics and Evolution, 146, 106751. https://doi.org/10.1016/j.ympev.2020.106751
Quattrini, A.M., Wu, T., Soong, K., Jeng, M.S., Benayahu, Y. & McFadden, C.S. (2019) A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals. BMC Evolutionary Biology, 19, 116. https://doi.org/10.1186/s12862-019-1427-y
de Queiroz, K. (2007) Species concepts and species delimitation. Systematic Biology, 56, 879–886. https://doi.org/10.1080/10635150701701083
Schluter, D. & Rieseberg, L.H. (2022) Three problems in the genetics of speciation by selection. Proceedings of the National Academy of Sciences, 119, e2122153119. https://doi.org/10.1073/pnas.2122153119
Schmidt, K.P. (1953) A Check List of North American Amphibians and Reptiles. 6th ed. University of Chicago Press, Chicago, Illinois, 280 pp.
Semlitsch, R.D., Ryan, T.J., Hamed, K., Chatfield, M., Drehman, B., Pekarek, N., Spath, M. & Watland, A. (2007) Salamander abundance along road edges and within abandoned logging roads in Appalachian forests. Conservation Biology, 21, 159–167. https://doi.org/10.1111/j.1523-1739.2006.00571.x
Tilley, S.G. (1969) Variation in the dorsal pattern of Desmognathus ochrophaeus at Mt. Mitchell, North Carolina, and elsewhere in the southern Appalachian Mountains. Copeia, 1969, 161–175. https://doi.org/10.2307/1441706
Tilley, S.G. (1981) A new species of Desmognathus (Amphibia: Caudata: Plethodontidae) from the southern Appalachian Mountains. Occasional Papers of the Museum of Zoology, University of Michigan, 695, 1–24.
Tilley, S.G. (2000) The systematics of Desmognathus imitator. In: Bruce, R.C., Jaeger, R.G. & Houck, L.D. (Eds.), The Biology of Plethodontid Salamanders. Springer US, Boston, Massachusetts, pp. 121–147.
Tilley, S.G., Bernardo, J., Katz, L.A., López, L., Devon Roll, J., Eriksen, R.L., Kratovil, J., Bittner, N.K.J. & Crandall, K.A. (2013) Failed species, innominate forms, and the vain search for species limits: cryptic diversity in dusky salamanders (Desmognathus) of eastern Tennessee. Ecology and Evolution, 3, 2547–2567. https://doi.org/10.1002/ece3.636
Tilley, S.G. & Mahoney, M.J. (1996) Patterns of genetic differentiation in salamanders of the Desmognathus ochrophaeus complex (Amphibia: Plethodontidae). Herpetological Monographs, 10, 1–42. https://doi.org/10.2307/1466979
Tilley, S.G., Merritt, R.B., Wu, B. & Highton, R. (1978) Genetic differentiation in salamanders of the Desmognathus ochrophaeus complex (Plethodontidae). Evolution, 32, 93–115.
Tilley, S.G., Verrell, P.A. & Arnold, S.J. (1990) Correspondence between sexual isolation and allozyme differentiation: a test in the salamander Desmognathus ochrophaeus. Proceedings of the National Academy of Sciences, 87, 2715–2719. https://doi.org/10.1073/pnas.87.7.2715
Titus, T.A. & Larson, A. (1996) Molecular phylogenetics of desmognathine salamanders (Caudata: Plethodontidae): a reevaluation of evolution in ecology, life history, and morphology. Systematic Biology, 45, 451–472. https://doi.org/10.1093/sysbio/45.4.451
Valentine, B.D. (1961) Variation and distribution of Desmognathus ocoee Nicholls (Amphibia: Plethodontidae). Copeia, 1961, 315–322. https://doi.org/10.2307/1439806
Valentine, B.D. (1964) Desmognathus ocoee. In: Reimer, W.J. (Ed.), Catalogue of American Amphibians and Reptiles. Vol. 7. American Society of Ichthyologists and Herpetologists, Kensington, pp. 1–2.
Van Belleghem, S.M., Papa, R., Ortiz-Zuazaga, H., Hendrickx, F., Jiggins, C.D., Owen McMillan, W. & Counterman, B.A. (2018) patternize: an R package for quantifying colour pattern variation. Methods in Ecology and Evolution, 9, 390–398. https://doi.org/10.1111/2041-210X.12853
Verrell, P.A. (1990) Frequency of interspecific mating in salamanders of the plethodontid genus Desmognathus: different experimental designs may yield different results. Journal of Zoology, 221, 441–451.
Weller, H.I. & Westneat, M.W. (2019) Quantitative color profiling of digital images with earth mover’s distance using the R package colordistance. PeerJ, 7, e6398. https://doi.org/10.7717/peerj.6398
Wolf, J.B. & Ellegren, H. (2017) Making sense of genomic islands of differentiation in light of speciation. Nature Reviews Genetics, 18, 87–100. https://doi.org/10.1038/nrg.2016.133
Zhang, D., Tang, L., Cheng, Y., Hao, Y., Xiong, Y., Song, G., Qu, Y., Rheindt, F.E., Alström, P., Jia, C. & Lei, F. (2019) “Ghost introgression” as a cause of deep mitochondrial divergence in a bird species complex. Molecular Biology and Evolution, 36, 2375–2386. https://doi.org/10.1093/molbev/msz170