1
|
Segovia‐Ramírez MG, Ramírez‐Sánchez O, Decena Segarra LP, Rios‐Carlos H, Rovito SM. Determinants of genetic diversity in Neotropical salamanders (Plethodontidae: Bolitoglossini). Ecol Evol 2023; 13:e10707. [PMID: 38020701 PMCID: PMC10654480 DOI: 10.1002/ece3.10707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/09/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Genetic diversity is the raw material of evolution, yet the reasons why it varies among species remain poorly understood. While studies at deeper phylogenetic scales point to the influence of life history traits on genetic diversity, it appears to be more affected by population size but less predictable at shallower scales. We used proxies for population size, mutation rate, direct selection, and linked selection to test factors affecting genetic diversity within a diverse assemblage of Neotropical salamanders, which vary widely for these traits. We estimated genetic diversity of noncoding loci using ddRADseq and coding loci using RNAseq for an assemblage of Neotropical salamanders distributed from northern Mexico to Costa Rica. Using ddRADseq loci, we found no significant association with genetic diversity, while for RNAseq data we found that environmental heterogeneity and proxies of population size predict a substantial portion of the variance in genetic diversity across species. Our results indicate that diversity of coding loci may be more predictable than that of noncoding loci, which appears to be mostly unpredictable at shallower phylogenetic scales. Our results suggest that coding loci may be more appropriate for genetic diversity estimates used in conservation planning because of the lack of any association between the variables we used and genetic diversity of noncoding loci.
Collapse
Affiliation(s)
| | - Obed Ramírez‐Sánchez
- Unidad de Genómica AvanzadaCentro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuatoMexico
| | - Louis Paul Decena Segarra
- Unidad de Genómica AvanzadaCentro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuatoMexico
| | - Hairo Rios‐Carlos
- Unidad de Genómica AvanzadaCentro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuatoMexico
| | - Sean M. Rovito
- Unidad de Genómica AvanzadaCentro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuatoMexico
| |
Collapse
|
2
|
Pyron RA, Beamer DA. A systematic revision of the Shovel-nosed Salamander (Plethodontidae: Desmognathus marmoratus), with re-description of the related D. aureatus and D. intermedius. Zootaxa 2023; 5270:262-280. [PMID: 37518165 DOI: 10.11646/zootaxa.5270.2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 08/01/2023]
Abstract
Shovel-nosed Salamanders, Desmognathus marmoratus (Moore, 1899), were long thought to represent a single species from the southern Appalachian Mountains of the eastern United States, ranging from northeastern Georgia to extreme southwestern Virginia. These populations have a highly derived ecomorphology, being fully aquatic with a specialized flattened and elongated phenotype adapted to rocky riffle zones in fast-flowing, high-gradient mountain streams. Because of this, they were originally described in a separate genus, Leurognathus Moore, 1899. Four additional species or subspecies were described from 1928-1956 based on regional geographic variation in phenotype before being synonymized with L. marmoratus in 1962, which was reassigned to Desmognathus in 1996. Molecular analyses subsequently revealed four distinct candidate lineages in two distantly related clades, which were recently re-delimited into three species. These are D. aureatus (Martof, 1956) from northeastern Georgia, D. intermedius (Pope, 1928) from western North Carolina, and D. marmoratus from northwestern North Carolina. We provide a systematic revision of these taxa, which do not represent a natural group but instead exhibit convergent phenotypes across multiple species, potentially driven by ancient episodes of adaptive introgression between ancestral lineages. Our recent fieldwork revealed an astonishingly disjunct and morphologically distinct population of D. marmoratus in the New River Gorge of West Virginia, which were previously confused with D. kanawha Pyron and Beamer, 2022. This locality is ~120 airline km away from the nearest populations of D. marmoratus in Virginia. No Shovel-nosed Salamanders have ever been found in the New River drainage during our extensive previous explorations or credibly reported in museum specimens or the literature. Additional cryptic populations of these taxa may remain.
Collapse
Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences; The George Washington University; 2023 G St. NW; Washington; DC 20052; Department of Vertebrate Zoology; National Museum of Natural History; Smithsonian Institution; Washington; DC 20560-0162.
| | - David A Beamer
- Office of Research; Economic Development and Engagement; East Carolina University; 209 E 5th St.; Greenville; NC 27858.
| |
Collapse
|
3
|
Anderson SAS, López-Fernández H, Weir JT. Ecology and the origin of non-ephemeral species. Am Nat 2022; 201:619-638. [PMID: 37130236 DOI: 10.1086/723763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractResearch over the past three decades has shown that ecology-based extrinsic reproductive barriers can rapidly arise to generate incipient species-but such barriers can also rapidly dissolve when environments change, resulting in incipient species collapse. Understanding the evolution of unconditional, "intrinsic" reproductive barriers is therefore important for understanding the longer-term buildup of biodiversity. In this article, we consider ecology's role in the evolution of intrinsic reproductive isolation. We suggest that this topic has fallen into a gap between disciplines: while evolutionary ecologists have traditionally focused on the rapid evolution of extrinsic isolation between co-occurring ecotypes, speciation geneticists studying intrinsic isolation in other taxa have devoted little attention to the ecological context in which it evolves. We argue that for evolutionary ecology to close this gap, the field will have to expand its focus beyond rapid adaptation and its traditional model systems. Synthesizing data from several subfields, we present circumstantial evidence for and against different forms of ecological adaptation as promoters of intrinsic isolation and discuss alternative forces that may be significant. We conclude by outlining complementary approaches that can better address the role of ecology in the evolution of nonephemeral reproductive barriers and, by extension, less ephemeral species.
Collapse
|
4
|
Camp CD, Felix ZI, Wooten JA. Evidence of morphological homoplasy among large, semi-aquatic species of Desmognathus. AMPHIBIA-REPTILIA 2022. [DOI: 10.1163/15685381-bja10087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The salamander family Plethodontidae is replete with instances of repeated homoplasy. We tested for morphological homoplasy in distantly related species of the plethodontid genus Desmognathus that share similar ecologies. Specifically, we compared species that are large and nearly aquatic. Using morphometric analyses, we compared the respective morphologies of four large, nearly aquatic forms, specifically the Black Mountain Salamander (Desmognathus welteri), the Dwarf Black-bellied Salamander (D. folkertsi), and two phylogenetically divergent lineages of the Black-bellied Salamander (D. quadramaculatus). Morphometric analysis uncovered distinct differences among them. However, all of the large-bodied lineages exhibited the same extent of tail-fin development in spite of D. welteri’s closer phylogenetic relationship to smaller, more-terrestrial species than to the other large, nearly aquatic forms we tested. We hypothesize that large body size is also a consequence of aquatic adaptation. These morphological consequences of a nearly aquatic ecology represent another case of homoplasy within this salamander family.
Collapse
Affiliation(s)
- Carlos D. Camp
- Department of Biology, Piedmont University, 1021 Central Avenue, Demorest, GA 30535, USA
| | - Zachary I. Felix
- Biology Program, Reinhardt University, 7300 Reinhardt Circle, Waleska, GA 30182, USA
| | - Jessica A. Wooten
- Department of Biology, Piedmont University, 1021 Central Avenue, Demorest, GA 30535, USA
| |
Collapse
|
5
|
Pyron RA, O’Connell KA, Lemmon EM, Lemmon AR, Beamer DA. Candidate‐species delimitation in
Desmognathus
salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones. Ecol Evol 2022; 12:e8574. [PMID: 35222955 PMCID: PMC8848459 DOI: 10.1002/ece3.8574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 12/19/2022] Open
Abstract
Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering‐based species delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding (i) species‐level diversity, (ii) hybridization and admixture, and (iii) misleading phylogenetic inference. Using phylogenetic and population‐clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early‐diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation.
Collapse
Affiliation(s)
- Robert Alexander Pyron
- Department of Biological Sciences The George Washington University Washington District of Columbia USA
- Division of Amphibians and Reptiles Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
| | - Kyle A. O’Connell
- Department of Biological Sciences The George Washington University Washington District of Columbia USA
- Division of Amphibians and Reptiles Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
- Global Genome Initiative National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
- Biomedical Data Science Lab Deloitte Consulting LLP Arlington Virginia USA
| | | | - Alan R. Lemmon
- Department of Scientific Computing Florida State University Tallahassee Florida USA
| | - David A. Beamer
- Department of Natural Sciences Nash Community College Rocky Mount North Carolina USA
| |
Collapse
|
6
|
Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
| |
Collapse
|
7
|
Bell RC, Mulcahy DG, Gotte SW, Maley AJ, Mendoza C, Steffensen G, Barron II JC, Hyman O, Flint W, Wynn A, Mcdiarmid RW, Mcleod DS. The Type Locality Project: collecting genomic-quality, topotypic vouchers and training the next generation of specimen-based researchers. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1769224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Rayna C. Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Daniel G. Mulcahy
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Steve W. Gotte
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- U. S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, Museum Support Center, Suitland, MD 20746, USA
| | - Abigail J. Maley
- Biology Department, Eastern Mennonite University, Harrisonburg, VA 22802, USA
- Division of Integrated Sciences, Wilson College, Chambersburg, PA 17201, USA
| | - Cerrie Mendoza
- Biology Department, Eastern Mennonite University, Harrisonburg, VA 22802, USA
| | - Gregory Steffensen
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Joseph C. Barron II
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24060, USA
| | - Oliver Hyman
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - William Flint
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Addison Wynn
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Roy W. Mcdiarmid
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- U. S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, Museum Support Center, Suitland, MD 20746, USA
| | - David S. Mcleod
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| |
Collapse
|
8
|
Pyron RA, O'Connell KA, Lemmon EM, Lemmon AR, Beamer DA. Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus). Mol Phylogenet Evol 2020; 146:106751. [DOI: 10.1016/j.ympev.2020.106751] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 01/02/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
|
9
|
Tonzo V, Papadopoulou A, Ortego J. Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex. Mol Ecol 2019; 28:3869-3886. [DOI: 10.1111/mec.15189] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/14/2019] [Accepted: 07/15/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Vanina Tonzo
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Anna Papadopoulou
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| |
Collapse
|
10
|
Hyseni C, Garrick RC. The role of glacial-interglacial climate change in shaping the genetic structure of eastern subterranean termites in the southern Appalachian Mountains, USA. Ecol Evol 2019; 9:4621-4636. [PMID: 31031931 PMCID: PMC6476779 DOI: 10.1002/ece3.5065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/27/2019] [Accepted: 02/25/2019] [Indexed: 11/30/2022] Open
Abstract
The eastern subterranean termite, Reticulitermes flavipes, currently inhabits previously glaciated regions of the northeastern U.S., as well as the unglaciated southern Appalachian Mountains and surrounding areas. We hypothesized that Pleistocene climatic fluctuations have influenced the distribution of R. flavipes, and thus the evolutionary history of the species. We estimated contemporary and historical geographic distributions of R. flavipes by constructing Species Distribution Models (SDM). We also inferred the evolutionary and demographic history of the species using mitochondrial (cytochrome oxidase I and II) and nuclear (endo-beta-1,4-glucanase) DNA sequence data. To do this, genetic populations were delineated using Bayesian spatial-genetic clustering, competing hypotheses about population divergence were assessed using approximate Bayesian computation (ABC), and changes in population size were estimated using Bayesian skyline plots. SDMs identified areas in the north with suitable habitat during the transition from the Last Interglacial to the Last Glacial Maximum, as well as an expanding distribution from the mid-Holocene to the present. Genetic analyses identified three geographically cohesive populations, corresponding with northern, central, and southern portions of the study region. Based on ABC analyses, divergence between the Northern and Southern populations was the oldest, estimated to have occurred 64.80 thousand years ago (kya), which corresponds with the timing of available habitat in the north. The Central and Northern populations diverged in the mid-Holocene, 8.63 kya, after which the Central population continued to expand. Accordingly, phylogeographic patterns of R. flavipes in the southern Appalachians appear to have been strongly influenced by glacial-interglacial climate change. OPEN RESEARCH BADGES This article has been awarded Open Materials, Open Data Badges. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.5hr7f31.
Collapse
Affiliation(s)
- Chaz Hyseni
- Department of BiologyUniversity of MississippiOxfordMississippi
| | - Ryan C. Garrick
- Department of BiologyUniversity of MississippiOxfordMississippi
| |
Collapse
|
11
|
Folt B, Bauder J, Spear S, Stevenson D, Hoffman M, Oaks JR, Wood PL, Jenkins C, Steen DA, Guyer C. Taxonomic and conservation implications of population genetic admixture, mito-nuclear discordance, and male-biased dispersal of a large endangered snake, Drymarchon couperi. PLoS One 2019; 14:e0214439. [PMID: 30913266 PMCID: PMC6435180 DOI: 10.1371/journal.pone.0214439] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Accurate species delimitation and description are necessary to guide effective conservation of imperiled species, and this synergy is maximized when multiple data sources are used to delimit species. We illustrate this point by examining Drymarchon couperi (Eastern Indigo Snake), a large, federally-protected species in North America that was recently divided into two species based on gene sequence data from three loci and heuristic morphological assessment. Here, we re-evaluate the two-species hypothesis for D. couperi by evaluating both population genetic and gene sequence data. Our analyses of 14 microsatellite markers revealed 6–8 genetic population clusters with significant admixture, particularly across the contact zone between the two hypothesized species. Phylogenetic analyses of gene sequence data with maximum-likelihood methods suggested discordance between mitochondrial and nuclear markers and provided phylogenetic support for one species rather than two. For these reasons, we place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA are driven by high dispersal of males relative to females. We advocate for species delimitation exercises that evaluate admixture and gene flow in addition to phylogenetic analyses, particularly when the latter reveal monophyletic lineages. This is particularly important for taxa, such as squamates, that exhibit strong sex-biased dispersal. Problems associated with over-delimitation of species richness can become particularly acute for threatened and endangered species, because of high costs to conservation when taxonomy demands protection of more individual species than are supported by accumulating data.
Collapse
Affiliation(s)
- Brian Folt
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
- * E-mail:
| | - Javan Bauder
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts, United States of America
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
| | - Stephen Spear
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
- The Wilds, Cumberland, Ohio United States of America
| | - Dirk Stevenson
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
- Altamaha Environmental Consulting, Hinesville, Georgia, United States of America
| | - Michelle Hoffman
- The Orianne Center for Indigo Conservation, Central Florida Zoo and Botanical Gardens, Sanford, Florida, United States of America
| | - Jamie R. Oaks
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
| | - Perry L. Wood
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
| | - Christopher Jenkins
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
| | - David A. Steen
- Georgia Sea Turtle Center, Jekyll Island Authority, Jekyll Island, Georgia, United States of America
| | - Craig Guyer
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
| |
Collapse
|