1
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Mathur S, Mason AJ, Bradburd GS, Gibbs HL. Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake. Proc Natl Acad Sci U S A 2023; 120:e2303043120. [PMID: 37844221 PMCID: PMC10614936 DOI: 10.1073/pnas.2303043120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/19/2023] [Indexed: 10/18/2023] Open
Abstract
Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation, yet this widely used approach has recently been questioned in the genomics era. Here, we leverage a chromosome-level genome assembly of an endangered rattlesnake (Sistrurus catenatus) combined with whole genome resequencing data (N = 110 individuals) to evaluate the relationship between levels of genome-wide neutral and functional diversity over historical and future timescales. As predicted, we found positive correlations between genome-wide estimates of neutral genetic diversity (π) and inferred levels of adaptive variation and an estimate of inbreeding mutation load, and a negative relationship between neutral diversity and an estimate of drift mutation load. However, these correlations were half as strong for projected future levels of neutral diversity based on contemporary effective population sizes. Broadly, our results confirm that estimates of neutral genetic diversity provide an accurate measure of genetic erosion in populations of a threatened vertebrate. They also provide nuance to the neutral-functional diversity controversy by suggesting that while these correlations exist, anthropogenetic impacts may have weakened these associations in the recent past and into the future.
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Affiliation(s)
- Samarth Mathur
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH48824
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH43210
| | - Andrew J. Mason
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH48824
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH43210
| | - Gideon S. Bradburd
- Evolution and Behavior Program, Department of Integrative Biology, Ecology, Michigan State University, East Lansing, MI48824
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI48109
| | - H. Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH48824
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, OH43210
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2
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Sheridan NE, Seyoum S, Sharp WC, Titus BM, Daly M, Richards CL, Schrey AW. Conservation genomics of an exploited, popular aquarium trade species: the giant Caribbean sea anemone Condylactis gigantea (Anthozoa: Actiniidae). CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01511-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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3
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Martin SA, Peterman WE, Lipps GJ, Gibbs HL. Inferring population connectivity in eastern massasauga rattlesnakes (Sistrurus catenatus) using landscape genetics. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2793. [PMID: 36482809 DOI: 10.1002/eap.2793] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Assessing the environmental factors that influence the ability of a threatened species to move through a landscape can be used to identify conservation actions that connect isolated populations. However, direct observations of species' movement are often limited, making the development of alternate approaches necessary. Here we use landscape genetic analyses to assess the impact of landscape features on the movement of individuals between local populations of a threatened snake, the eastern massasauga rattlesnake (Sistrurus catenatus). We linked connectivity data with habitat information from two landscapes of similar size: a large region of unfragmented habitat and a previously studied fragmented landscape consisting of isolated patches of habitat. We used this analysis to identify features of the landscape where modification or acquisition would enhance population connectivity in the fragmented region. We found evidence that current connectivity was impacted by both contemporary land-cover features, especially roads, and inherent landscape features such as elevation. Next, we derived estimates of expected movement ability using a recently developed pedigree-based approach and least-cost paths through the unfragmented landscape. We then used our pedigree and resistance map to estimate resistance polygons of the potential extent for S. catenatus movement in the fragmented landscape. These polygons identify possible sites for future corridors connecting currently isolated populations in this landscape by linking the impact of future habitat modification or land acquisition to dispersal ability in this species. Overall, our study shows how modeling landscape resistance across differently fragmented landscapes can identify habitat features that affect contemporary movement in threatened species in fragmented landscapes and how this information can be used to guide mitigation actions whose goal is to connect isolated populations.
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Affiliation(s)
- Scott A Martin
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - William E Peterman
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
- School of Environmental and Natural Resources, The Ohio State University, Columbus, Ohio, USA
| | - Gregory J Lipps
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
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4
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Limited gene flow and pronounced population genetic structure of Eastern Massasauga (Sistrurus catenatus) in a Midwestern prairie remnant. PLoS One 2022; 17:e0265666. [PMID: 35324968 PMCID: PMC8947261 DOI: 10.1371/journal.pone.0265666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/04/2022] [Indexed: 11/19/2022] Open
Abstract
As anthropogenic changes continue to ecologically stress wildlife, obtaining measures of gene flow and genetic diversity are crucial for evaluating population trends and considering management and conservation strategies for small, imperiled populations. In our study, we conducted a molecular assessment to expand on previous work to elucidate patterns of diversity and connectivity in the remaining disjunct Eastern Massasauga Rattlesnake (Sistrurus catenatus) hibernacula in Illinois. We assayed genetic data for 327 samples collected during 1999–2015 from the Carlyle Lake study area across 21 microsatellite loci. We found hibernacula formed distinct genetic clusters corresponding to the three main study areas (Dam Recreation Areas, Eldon Hazlet State Park, and South Shore State Park). Genetic structuring and low estimates of dispersal indicated that connectivity among these study areas is limited and each is demographically independent. Hibernacula exhibited moderate levels of heterozygosity (0.60–0.73), but estimates of effective population size (5.2–41.0) were low and track census sizes generated via long-term mark-recapture data. Hibernacula at Carlyle Lake, which represent the only Eastern Massasauga remaining in Illinois, are vulnerable to future loss of genetic diversity through lack of gene flow as well as demographic and environmental stochastic processes. Our work highlights the need to include population-level genetic data in recovery planning and suggests that recovery efforts should focus on managing the three major study areas as separate conservation units in order to preserve and maintain long-term adaptive potential of these populations. Specific management goals should include improving connectivity among hibernacula, maintaining existing wet grassland habitat, and minimizing anthropogenic sources of mortality caused by habitat management (e.g., mowing, prescribed fire) and recreational activities. Our molecular study provides additional details about demographic parameters and connectivity at Carlyle Lake that can be used to guide recovery of Eastern Massasauga in Illinois and throughout its range.
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5
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Tao Y, Chen B, Kang M, Liu Y, Wang J. Genome-Wide Evidence for Complex Hybridization and Demographic History in a Group of Cycas From China. Front Genet 2021; 12:717200. [PMID: 34527022 PMCID: PMC8435751 DOI: 10.3389/fgene.2021.717200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/10/2021] [Indexed: 11/24/2022] Open
Abstract
Cycads represent one of the most ancestral living seed plants as well as one of the most threatened plant groups in the world. South China is a major center and potential origin of Cycas, the most rapidly diversified lineage of cycads. However, genomic-wide diversity of Cycas remains poorly understood due to the challenge of generating genomic markers associated with their inherent large genomes. Here, we perform a comprehensive conservation genomic study based on restriction-site associated DNA sequencing (RADseq) data in six representative species of Cycas in South China. Consistently low genetic diversity and strong genetic differentiation were detected across species. Both phylogenetic inference and genetic structure analysis via several methods revealed generally congruent groups among the six Cycas species. The analysis with ADMIXTURE showed low mixing of genetic composition among species, while individuals of C. dolichophylla exhibited substantial genetic admixture with C. bifida, C. changjiangensis, and C. balansae. Furthermore, the results from Treemix, f4-statistic, and ABBA-BABA test were generally consistent and revealed the complex patterns of interspecific gene flow. Relatively strong signals of hybridization were detected between C. dolichophylla and C. szechuanensis, and the ancestor of C. taiwaniana and C. changjiangensis. Distinct patterns of demographic history were inferred for these species by Stairway Plot, and our results suggested that both climate fluctuation and frequent geological activities during the late Pleistocene exerted deep impacts on the population dynamics of these species in South China. Finally, we explore the practical implications of our findings for the development of conservation strategies in Cycas. The present study demonstrates the efficiency of RADseq for conservation genomic studies on non-model species with large and complex genomes. Given the great significance of cycads as a radical transition in the evolution of plant biodiversity, our study provides important insights into the mechanisms of diversification in such recently radiated living fossil taxa.
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Affiliation(s)
- Yueqi Tao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bin Chen
- Shanghai Chenshan Botanical Garden, Shanghai, China.,Eastern China Conservation Center for Wild Endangered Plant Resources, Shanghai, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Yongbo Liu
- State Environment Protection Key Laboratory of Regional Ecological Process and Functional Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
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6
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Ochoa A, Gibbs HL. Genomic signatures of inbreeding and mutation load in a threatened rattlesnake. Mol Ecol 2021; 30:5454-5469. [PMID: 34448259 DOI: 10.1111/mec.16147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/04/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022]
Abstract
Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their genetic load, but recent work suggests that the impact of load may be minimized by purging resulting from long-term population bottlenecks. Empirical studies that examine this idea using genome-wide estimates of inbreeding and genetic load in threatened species are limited. Here we use individual genome resequencing data to compare levels of inbreeding, levels of genetic load (estimated as mutation load) and population history in threatened Eastern massasauga rattlesnakes (Sistrurus catenatus), which exist in small isolated populations, and closely related yet outbred Western massasauga rattlesnakes (Sistrurus tergeminus). In terms of inbreeding, S. catenatus genomes had a greater number of runs of homozygosity of varying sizes, indicating sustained inbreeding through repeated bottlenecks when compared to S. tergeminus. At the species level, outbred S. tergeminus had higher genome-wide levels of mutation load in the form of greater numbers of derived deleterious mutations compared to S. catenatus, presumably due to long-term purging of deleterious mutations in S. catenatus. In contrast, mutations that escaped species-level drift effects within S. catenatus populations were in general more frequent and more often found in homozygous genotypes than in S. tergeminus, suggesting a reduced efficiency of purifying selection in smaller S. catenatus populations for most mutations. Our results support an emerging idea that the historical demography of a threatened species has a significant impact on the type of genetic load present, which impacts implementation of conservation actions such as genetic rescue.
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Affiliation(s)
- Alexander Ochoa
- Department of Evolution, Ecology, and Organismal Biology, Ohio Biodiversity Conservation Partnership, Ohio State University, Columbus, Ohio, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, Ohio Biodiversity Conservation Partnership, Ohio State University, Columbus, Ohio, USA
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7
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Forsdick NJ, Martini D, Brown L, Cross HB, Maloney RF, Steeves TE, Knapp M. Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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8
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Holding ML, Sovic MG, Colston TJ, Gibbs HL. The scales of coevolution: comparative phylogeography and genetic demography of a locally adapted venomous predator and its prey. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Abstract
Coevolutionary theory predicts that differences in the genetic demography of interacting species can influence patterns of local adaptation by affecting the potential of local populations to respond to selection. We conducted a comparative phylogeographical study of venomous rattlesnakes and their venom-resistant ground squirrel prey across California, and assessed how effective population size (Ne) estimates correspond with a previously documented pattern of rattlesnake local adaptation. Using RAD sequencing markers, we detected lineage relationships among both the rattlesnakes (Crotalus oreganus ssp.) and ground squirrels (Otospermophilus sp.) that are incongruent with previous phylogenetic hypotheses. Both rattlesnakes and squirrels share a deep divergence at the Sacramento–San Joaquin River Delta. At this broad phylogeographical scale, we found that the locally adapted rattlesnakes had higher Ne than squirrels. At the population scale, snakes also had larger Ne accompanied by larger values of several metrics of population genetic diversity. However, the specific magnitude of local adaptation of venom activity to ground squirrel venom resistance was not significantly correlated with local differences in Ne or other diversity statistics between predator and prey populations, suggesting that other factors in the geographic mosaic of coevolution contribute to the specific local-scale outcomes of this interaction. These results suggest an evolutionary mechanism that may explain some (but clearly not all) of rattlesnake local adaptation in this coevolutionary interaction – larger population sizes raise the adaptive potential of rattlesnakes compared to ground squirrels.
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Affiliation(s)
- Matthew L Holding
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Michael G Sovic
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
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9
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Castelli MA, Georges A, Cherryh C, Rosauer DF, Sarre SD, Contador‐Kelsall I, Holleley CE. Evolving thermal thresholds explain the distribution of temperature sex reversal in an Australian dragon lizard. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13203] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Meghan A. Castelli
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory Australia
- Australian National Wildlife CollectionCSIRO National Research Collections Australia Canberra Australian Capital Territory Australia
| | - Arthur Georges
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory Australia
| | - Caitlin Cherryh
- Australian National Wildlife CollectionCSIRO National Research Collections Australia Canberra Australian Capital Territory Australia
- Department of Ecology and Evolution Research School of Biology Australian National University Canberra Australian Capital Territory Australia
| | - Dan F. Rosauer
- Department of Ecology and Evolution Research School of Biology Australian National University Canberra Australian Capital Territory Australia
| | - Stephen D. Sarre
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory Australia
| | - Isabella Contador‐Kelsall
- School of Earth, Atmospheric and Life Sciences University of Wollongong Wollongong New South Wales Australia
| | - Clare E. Holleley
- Institute for Applied Ecology University of Canberra Canberra Australian Capital Territory Australia
- Australian National Wildlife CollectionCSIRO National Research Collections Australia Canberra Australian Capital Territory Australia
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10
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Martin BT, Douglas MR, Chafin TK, Placyk JS, Birkhead RD, Phillips CA, Douglas ME. Contrasting signatures of introgression in North American box turtle (
Terrapene
spp.) contact zones. Mol Ecol 2020; 29:4186-4202. [DOI: 10.1111/mec.15622] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Bradley T. Martin
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - Marlis R. Douglas
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - Tyler K. Chafin
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
| | - John S. Placyk
- Department of Biology University of Texas Tyler TX USA
- Science Division Trinity Valley Community College Athens TX USA
| | | | - Christopher A. Phillips
- Illinois Natural History Survey Prairie Research Institute University of Illinois Champaign IL USA
| | - Michael E. Douglas
- Department of Biological Sciences University of Arkansas Fayetteville AR USA
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11
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Ochoa A, Broe M, Moriarty Lemmon E, Lemmon AR, Rokyta DR, Gibbs HL. Drift, selection and adaptive variation in small populations of a threatened rattlesnake. Mol Ecol 2020; 29:2612-2625. [PMID: 32557885 DOI: 10.1111/mec.15517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/09/2020] [Accepted: 05/21/2020] [Indexed: 01/22/2023]
Abstract
An important goal of conservation genetics is to determine if the viability of small populations is reduced by a loss of adaptive variation due to genetic drift. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the eastern massasauga rattlesnake (Sistrurus catenatus), a threatened reptile that exists in small isolated populations. We estimated levels of individual polymorphism in 46 toxin loci and 1,467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation of S. catenatus and its closest relative, the western massasauga (S. tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long- and short-term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that pre-date the effects of recent drift, and that functional variation in these loci persists despite small short-term effective sizes. This suggests that much of the adaptive variation present in populations may represent an example of "drift debt," a nonequilibrium state where present-day levels of variation overestimate the amount of functional genetic diversity present in future populations.
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Affiliation(s)
- Alexander Ochoa
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Michael Broe
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - H Lisle Gibbs
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
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12
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Cros E, Chattopadhyay B, Garg KM, Ng NSR, Tomassi S, Benedick S, Edwards DP, Rheindt FE. Quaternary land bridges have not been universal conduits of gene flow. Mol Ecol 2020; 29:2692-2706. [PMID: 32542783 DOI: 10.1111/mec.15509] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 01/05/2023]
Abstract
Quaternary climate oscillations are a well-known driver of animal diversification, but their effects are most well studied in areas where glaciations lead to habitat fragmentation. In large areas of the planet, however, glaciations have had the opposite effect, but here their impacts are much less well understood. This is especially true in Southeast Asia, where cyclical changes in land distribution have generated enormous land expansions during glacial periods. In this study, we selected a panel of five songbird species complexes covering a range of ecological specificities to investigate the effects Quaternary land bridges have had on the connectivity of Southeast Asian forest biota. Specifically, we combined morphological and bioacoustic analysis with an arsenal of population genomic and modelling approaches applied to thousands of genome-wide DNA markers across a total of more than 100 individuals. Our analyses show that species dependent on forest understorey exhibit deep differentiation between Borneo and western Sundaland, with no evidence of gene flow during the land bridges accompanying the last 1-2 ice ages. In contrast, dispersive canopy species and habitat generalists have experienced more recent gene flow. Our results argue that there remains much cryptic species-level diversity to be discovered in Southeast Asia even in well-known animal groups such as birds, especially in nondispersive forest understorey inhabitants. We also demonstrate that Quaternary land bridges have not been equally suitable conduits of gene flow for all species complexes and that life history is a major factor in predicting relative population divergence time across Quaternary climate fluctuations.
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Affiliation(s)
- Emilie Cros
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Nathaniel S R Ng
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Suzanne Tomassi
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Suzan Benedick
- Sustainable Agriculture School, Universiti Malaysia Sabah, Sabah, Malaysia
| | - David P Edwards
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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13
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Titus BM, Blischak PD, Daly M. Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria). Mol Ecol 2019; 28:3572-3586. [PMID: 31233641 DOI: 10.1111/mec.15157] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 05/21/2019] [Accepted: 06/04/2019] [Indexed: 12/23/2022]
Abstract
Sympatric diversification is recognized to have played an important role in the evolution of biodiversity. However, an in situ sympatric origin for codistributed taxa is difficult to demonstrate because different evolutionary processes can lead to similar biogeographic outcomes, especially in ecosystems that can readily facilitate secondary contact due to a lack of hard barriers to dispersal. Here we use a genomic (ddRADseq), model-based approach to delimit a species complex of tropical sea anemones that are codistributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 and ordinary differential equations in Moments to test competing diversification scenarios that span the allopatric-sympatric continuum. Our results suggest that the corkscrew sea anemone Bartholomea annulata is a cryptic species complex whose members are codistributed throughout their range. Simulation and model selection analyses from both approaches suggest these lineages experienced historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model receives appreciable model support in fastsimcoal2. Leveraging the genome of the closely related Exaiptasia diaphana, we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan and the first range-wide molecular study of a tropical sea anemone, underscoring that anemone diversity is under-described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.
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Affiliation(s)
- Benjamin M Titus
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Paul D Blischak
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, USA
| | - Marymegan Daly
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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14
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Sovic M, Fries A, Martin SA, Lisle Gibbs H. Genetic signatures of small effective population sizes and demographic declines in an endangered rattlesnake, Sistrurus catenatus. Evol Appl 2019; 12:664-678. [PMID: 30976301 PMCID: PMC6439488 DOI: 10.1111/eva.12731] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 09/28/2018] [Accepted: 10/01/2018] [Indexed: 12/15/2022] Open
Abstract
Endangered species that exist in small isolated populations are at elevated risk of losing adaptive variation due to genetic drift. Analyses that estimate short-term effective population sizes, characterize historical demographic processes, and project the trajectory of genetic variation into the future are useful for predicting how levels of genetic diversity may change. Here, we use data from two independent types of genetic markers (single nucleotide polymorphisms [SNPs] and microsatellites) to evaluate genetic diversity in 17 populations spanning the geographic range of the endangered eastern massasauga rattlesnake (Sistrurus catenatus). First, we use SNP data to confirm previous reports that these populations exhibit high levels of genetic structure (overall Fst = 0.25). Second, we show that most populations have contemporary Ne estimates <50. Heterozygosity-fitness correlations in these populations provided no evidence for a genetic cost to living in small populations, though these tests may lack power. Third, model-based demographic analyses of individual populations indicate that all have experienced declines, with the onset of many of these declines occurring over timescales consistent with anthropogenic impacts (<200 years). Finally, forward simulations of the expected loss of variation in relatively large (Ne = 50) and small (Ne = 10) populations indicate they will lose a substantial amount of their current standing neutral variation (63% and 99%, respectively) over the next 100 years. Our results argue that drift has a significant and increasing impact on levels of genetic variation in isolated populations of this snake, and efforts to assess and mitigate associated impacts on adaptive variation should be components of the management of this endangered reptile.
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Affiliation(s)
- Michael Sovic
- Department of Evolution, Ecology and Organismal Biology and Ohio Biodiversity Conservation PartnershipThe Ohio State UniversityColumbusOhio
- Present address:
College of PharmacyThe Ohio State UniversityColumbusOhio
| | - Anthony Fries
- Department of Evolution, Ecology and Organismal Biology and Ohio Biodiversity Conservation PartnershipThe Ohio State UniversityColumbusOhio
- United States Air Force School of Aerospace MedicineWright‐Patterson AFBColumbusOhio
| | - Scott A. Martin
- Department of Evolution, Ecology and Organismal Biology and Ohio Biodiversity Conservation PartnershipThe Ohio State UniversityColumbusOhio
| | - H. Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology and Ohio Biodiversity Conservation PartnershipThe Ohio State UniversityColumbusOhio
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15
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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.
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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
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Myers EA, Bryson RW, Hansen RW, Aardema ML, Lazcano D, Burbrink FT. Exploring Chihuahuan Desert diversification in the gray-banded kingsnake, Lampropeltis alterna (Serpentes: Colubridae). Mol Phylogenet Evol 2019; 131:211-218. [DOI: 10.1016/j.ympev.2018.10.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 12/20/2022]
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18
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Holding ML, Margres MJ, Rokyta DR, Gibbs HL. Local prey community composition and genetic distance predict venom divergence among populations of the northern Pacific rattlesnake (
Crotalus oreganus
). J Evol Biol 2018; 31:1513-1528. [DOI: 10.1111/jeb.13347] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 06/23/2018] [Accepted: 06/28/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Matthew L. Holding
- Department of Evolution, Ecology, and Organismal Biology The Ohio State University Columbus OH USA
- Department of Biological Sciences Florida State University Tallahassee FL USA
| | - Mark J. Margres
- Department of Biological Sciences Florida State University Tallahassee FL USA
| | - Darin R. Rokyta
- Department of Biological Sciences Florida State University Tallahassee FL USA
| | - H. Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology The Ohio State University Columbus OH USA
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Gibbs HL, Sovic M, Amazonas D, Chalkidis H, Salazar-Valenzuela D, Moura-Da-Silva AM. Recent lineage diversification in a venomous snake through dispersal across the Amazon River. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx158] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, USA
- Ohio Biodiversity Conservation Partnership, Ohio State University, Columbus, OH, USA
| | - Michael Sovic
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Diana Amazonas
- Laboratório de Imunopatologia, Instituto Butantan, São Paulo, Brazil
| | | | - David Salazar-Valenzuela
- Centro de Investigación de la Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, Quito, Ecuador
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