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Kimble SJA, Unger SD, Williams RN. Genetically derived effective population size estimates of herpetofaunal species should be used with caution. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | - Shem D. Unger
- Department of Biology Wingate University Wingate NC 28174 USA
| | - Rod N. Williams
- Department of Forestry and Natural Resources Purdue University West Lafayette IN 47907 USA
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Bohling J, Small M, Von Bargen J, Louden A, DeHaan P. Comparing inferences derived from microsatellite and RADseq datasets: a case study involving threatened bull trout. CONSERV GENET 2019. [DOI: 10.1007/s10592-018-1134-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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McCallen EB, Kraus BT, Burgmeier NG, Fei S, Williams RN. Movement and Habitat Use of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis) Following Population Augmentation. HERPETOLOGICA 2018. [DOI: 10.1655/0018-0831.283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Emily B. McCallen
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
| | - Bart T. Kraus
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
| | - Nick G. Burgmeier
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
| | - Songlin Fei
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
| | - Rod N. Williams
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
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McCallen EB, Kraus BT, Burgmeier NG, Fei S, Williams RN. Movement and Habitat Use of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis) Following Population Augmentation. HERPETOLOGICA 2018. [DOI: 10.1655/herpetologica-d-17-00044.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Emily B. McCallen
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
| | - Bart T. Kraus
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
| | - Nick G. Burgmeier
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
| | - Songlin Fei
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
| | - Rod N. Williams
- Department of Forestry and Natural Resources, Purdue University, 195 Marsteller Street, West Lafayette, IN 47907, USA
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Unger SD, Williams RN. Genetic confirmation of filial cannibalism in North America’s giant salamander, the Eastern hellbender Cryptobranchus alleganiensis alleganiensis. ETHOL ECOL EVOL 2018. [DOI: 10.1080/03949370.2017.1342696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Shem D. Unger
- Biology Department, Wingate University, Wingate, NC 28174, USA (E-mail: )
| | - Rod N. Williams
- Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN 47907, USA
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Conservation genetics of eastern hellbenders Cryptobranchus alleganiensis alleganiensis in the Tennessee Valley. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1033-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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O'Connell KA, Streicher JW, Smith EN, Fujita MK. Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes. Mol Ecol 2017; 26:5729-5751. [PMID: 28802078 DOI: 10.1111/mec.14295] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 01/08/2023]
Abstract
Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.
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Affiliation(s)
- Kyle A O'Connell
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | | | - Eric N Smith
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
| | - Matthew K Fujita
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA.,The Amphibian and Reptile Diversity Research Center, University of Texas at Arlington, Arlington, TX, USA
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Hernández-Gómez O, Hoverman JT, Williams RN. Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders ( Cryptobranchus alleganiensis alleganiensis). Front Microbiol 2017; 8:1379. [PMID: 28785252 PMCID: PMC5519570 DOI: 10.3389/fmicb.2017.01379] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/07/2017] [Indexed: 12/29/2022] Open
Abstract
Multicellular hosts maintain complex associations with microbial communities. While microbial communities often serve important functional roles for their hosts, our understanding of the local and regional processes that structure these communities remains limited. Metacommunity analyses provide a promising tool for investigating mechanisms shaping microbiome heterogeneity, which is essential for predicting functional variation between hosts. Using a metacommunity framework, we examined heterogeneity in the skin microbiome of the eastern hellbender (Cryptobranchus alleganiensis alleganiensis). Hellbenders are broadly distributed throughout river systems in the eastern United States, but are present in specific environmental locations throughout their range. The large range of the species and history of population fragmentation suggest that local and regional processes contribute to the distribution of cutaneous symbiont diversity. Therefore, we characterized the skin and environmental bacterial communities at eight rivers throughout the range of the species. We observed variation among hellbender populations in skin microbial community diversity and proportion of shared operational taxonomic units (OTUs) between animal and river water communities. Among populations sampled, we noted significant clumped OTU turnover (i.e., Clementsian structure) resulting in unique cutaneous communities. In addition, we observed a significant positive correlation between skin community divergence and hellbender population genetic divergence. Host-population skin community dissimilarity did not correlate strongly with distance between sampling locations, indicating a weak spatial effect on the distribution of symbionts. These results suggest that species sorting mechanisms (i.e., local processes) structure local skin microbial communities in hellbenders. The variation in skin community composition observed among host populations foreshadows a similar pattern in important functional characteristics (e.g., resistance to dysbiosis). Future work should focus on investigating forces shaping microbiome structure in eastern hellbenders, examining functional variation among populations, and evaluating effectiveness of microbiome management recommendations.
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Affiliation(s)
- Obed Hernández-Gómez
- Department of Forestry and Natural Resources, Purdue University, West LafayetteIN, United States
| | - Jason T Hoverman
- Department of Forestry and Natural Resources, Purdue University, West LafayetteIN, United States
| | - Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, West LafayetteIN, United States
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Phylogeographical structure and demographic expansion in the endemic alpine stream salamander (Hynobiidae: Batrachuperus) of the Qinling Mountains. Sci Rep 2017; 7:1871. [PMID: 28500336 PMCID: PMC5431969 DOI: 10.1038/s41598-017-01799-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/31/2017] [Indexed: 11/29/2022] Open
Abstract
The Qinling Mountains of China provide an excellent study area for assessing the effect of Pleistocene climatic oscillations and paleogeological events on intraspecific diversification. To assess genetic diversity of an endemic stream salamander, Batrachuperus tibetanus, for its conservation, a phylogeographical survey was performed based on mitochondrial DNA and morphological data. The mitochondrial data revealed three lineages of B. tibetanus in the Qinling Mountains. A lineage present in the northwestern Qinling Mountains groups with the Tibet lineage of B. tibetanus, and the remaining Qinling populations are eastern and western lineages that separated ~3–4 million years ago (Ma). The eastern and western Qinling lineage delineation is supported by three morphological variables (snout length, eye diameter and axilla-groin length). The divergence of the two major lineages was likely caused by orogenesis of the Qinling Mountains during the late Cenozoic, and the two lineages were subsequently affected at different levels by Pleistocene climatic oscillations showing different signals of demographic expansion. A large suitable area of B. tibetanus through the Qinling Mountains since the last glacial maximum (LGM) indicated the adaptation of this species to the climatic changes. However, low genetic diversity within populations indicate the urgency of preserving the vulnerable populations and endemic lineages.
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Hernández-Gómez O, Kimble SJA, Briggler JT, Williams RN. Characterization of the Cutaneous Bacterial Communities of Two Giant Salamander Subspecies. MICROBIAL ECOLOGY 2017; 73:445-454. [PMID: 27677893 DOI: 10.1007/s00248-016-0859-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 09/09/2016] [Indexed: 05/21/2023]
Abstract
Pathogens currently threaten the existence of many amphibian species. In efforts to combat global declines, researchers have characterized the amphibian cutaneous microbiome as a resource for disease management. Characterization of microbial communities has become useful in studying the links between organismal health and the host microbiome. Hellbender salamanders (Cryptobranchus alleganiensis) provide an ideal system to explore the cutaneous microbiome as this species requires extensive conservation management across its range. In addition, the Ozark hellbender subspecies (Cryptobranchus alleganiensis bishopi) exhibits chronic wounds hypothesized to be caused by bacterial infections, whereas the eastern hellbender (Cryptobranchus alleganiensis alleganiensis) does not. We assessed the cutaneous bacterial microbiome of both subspecies at two locations in the state of Missouri, USA. Through 16S rRNA gene-based amplicon sequencing, we detected more than 1000 distinct operational taxonomic units (OTUs) in the cutaneous and environmental bacterial microbiome. Phylogenetic and abundance-based dissimilarity matrices identified differences in the bacterial communities between the two subspecies, but only the abundance-based dissimilarity matrix identified differences between wounds and healthy skin on Ozark hellbenders. The higher abundance of OTUs on Ozark wounds suggests that commensal bacteria present on the skin and environment may be opportunistically colonizing the wounds. This brief exploration of the hellbender cutaneous bacterial microbiome provides foundational support for future studies seeking to understand the hellbender cutaneous bacterial microbiome and the role of the bacterial microbiota on chronic wounds of Ozark hellbenders.
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Affiliation(s)
- Obed Hernández-Gómez
- Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, IN, 47907, USA.
| | - Steven J A Kimble
- Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, IN, 47907, USA
| | - Jeffrey T Briggler
- Missouri Department of Conservation, 2901 W. Truman Blvd, Jefferson City, MO, 65109, USA
| | - Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, 715 W. State St., West Lafayette, IN, 47907, USA
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McCartney-Melstad E, Shaffer HB. Amphibian molecular ecology and how it has informed conservation. Mol Ecol 2015; 24:5084-109. [PMID: 26437125 DOI: 10.1111/mec.13391] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems.
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Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, 610 Charles E Young Drive South, Los Angeles, CA, USA
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Miller WL, Snodgrass JW, Gasparich GE. The importance of terrestrial dispersal for connectivity among headwater salamander populations. Ecosphere 2015. [DOI: 10.1890/es15-00302.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Unger SD, Williams RN. Genetic analysis reveals multiple parentage in captive reared eastern hellbender salamanders (Cryptobranchus alleganiensis). Zoo Biol 2015; 34:535-7. [PMID: 26301598 DOI: 10.1002/zoo.21242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 07/28/2015] [Accepted: 08/06/2015] [Indexed: 11/06/2022]
Abstract
Information on the parentage of captive reared clutches is vital for conservation head-starting programs. Molecular methods, such as genotyping individuals with hyper-variable markers, can elucidate the genealogical contribution of captive-reared, reintroduced individuals to native populations. In this study, we used 12 polymorphic microsatellite loci to infer parentage of a clutch of 18 eastern hellbenders collected from a single nest from Buffalo Creek, West Virginia, subsequently reared in captivity, and used for translocations in Indiana. Collectively, these markers successfully detected the presence of multiple parentage for this species of conservation concern presently used in captive management programs in zoos across many states. This study highlights the need for genetic analysis of captive reared clutches used in translocations to minimize the loss of genetic diversity and potential for genetic swamping at release sites.
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Affiliation(s)
- Shem D Unger
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina
| | - Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana
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Within-river gene flow in the hellbender (Cryptobranchus alleganiensis) and implications for restorative release. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0591-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Single nucleotide polymorphisms reveal genetic structuring of the carpathian newt and provide evidence of interspecific gene flow in the nuclear genome. PLoS One 2014; 9:e97431. [PMID: 24820116 PMCID: PMC4018350 DOI: 10.1371/journal.pone.0097431] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/19/2014] [Indexed: 12/25/2022] Open
Abstract
Genetic variation within species is commonly structured in a hierarchical manner which may result from superimposition of processes acting at different spatial and temporal scales. In organisms of limited dispersal ability, signatures of past subdivision are detectable for a long time. Studies of contemporary genetic structure in such taxa inform about the history of isolation, range changes and local admixture resulting from geographically restricted hybridization with related species. Here we use a set of 139 transcriptome-derived, unlinked nuclear single nucleotide polymorphisms (SNP) to assess the genetic structure of the Carpathian newt (Lissotriton montandoni, Lm) and introgression from its congener, the smooth newt (L. vulgaris, Lv). Two substantially differentiated groups of Lm populations likely originated from separate refugia, both located in the Eastern Carpathians. The colonization of the present range in north-western and south-western directions was accompanied by a modest loss of variation; admixture between the two groups has occurred in the middle of the Eastern Carpathians. Local, apparently recent introgression of Lv alleles into several Lm populations was detected, demonstrating increased power for admixture detection in comparison to a previous study based on a limited number of microsatellite markers. The level of introgression was higher in Lm populations classified as admixed than in syntopic populations. We discuss the possible causes and propose further tests to distinguish between alternatives. Several outlier loci were identified in tests of interspecific differentiation, suggesting genomic heterogeneity of gene flow between species.
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