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Krejca JK, McHenry DJ, McDermid KM, Adcock ZC, Forstner MRJ. Genetic characterization and habitat use of Eurycea pterophila salamanders from Jacob's Well, Hays County, Texas. SOUTHWEST NAT 2017. [DOI: 10.1894/0038-4909-62.1.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Jean K. Krejca
- Zara Environmental LLC, 1707 West Farm to Market 1626, Manchaca, TX 78652 (JKK, KMM)
| | - Diana J. McHenry
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX 78666 (DJM, ZCA, MJRF)
| | - Krista M. McDermid
- Zara Environmental LLC, 1707 West Farm to Market 1626, Manchaca, TX 78652 (JKK, KMM)
| | - Zachary C. Adcock
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX 78666 (DJM, ZCA, MJRF)
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Paz-Vinas I, Loot G, Stevens VM, Blanchet S. Evolutionary processes driving spatial patterns of intraspecific genetic diversity in river ecosystems. Mol Ecol 2015; 24:4586-604. [PMID: 26284462 DOI: 10.1111/mec.13345] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 07/30/2015] [Accepted: 08/13/2015] [Indexed: 01/17/2023]
Abstract
Describing, understanding and predicting the spatial distribution of genetic diversity is a central issue in biological sciences. In river landscapes, it is generally predicted that neutral genetic diversity should increase downstream, but there have been few attempts to test and validate this assumption across taxonomic groups. Moreover, it is still unclear what are the evolutionary processes that may generate this apparent spatial pattern of diversity. Here, we quantitatively synthesized published results from diverse taxa living in river ecosystems, and we performed a meta-analysis to show that a downstream increase in intraspecific genetic diversity (DIGD) actually constitutes a general spatial pattern of biodiversity that is repeatable across taxa. We further demonstrated that DIGD was stronger for strictly waterborne dispersing than for overland dispersing species. However, for a restricted data set focusing on fishes, there was no evidence that DIGD was related to particular species traits. We then searched for general processes underlying DIGD by simulating genetic data in dendritic-like river systems. Simulations revealed that the three processes we considered (downstream-biased dispersal, increase in habitat availability downstream and upstream-directed colonization) might generate DIGD. Using random forest models, we identified from simulations a set of highly informative summary statistics allowing discriminating among the processes causing DIGD. Finally, combining these discriminant statistics and approximate Bayesian computations on a set of twelve empirical case studies, we hypothesized that DIGD were most likely due to the interaction of two of these three processes and that contrary to expectation, they were not solely caused by downstream-biased dispersal.
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Affiliation(s)
- I Paz-Vinas
- Centre National de la Recherche Scientifique (CNRS), École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Paul Sabatier, 118 route de Narbonne, 31062, Toulouse Cedex 4, France.,UPS, UMR 5174 (EDB), Université de Toulouse, 118 route de Narbonne, 31062, Toulouse Cedex 4, France.,UMR 7263 - IMBE, Équipe EGE, Centre Saint-Charles, Aix-Marseille Université, CNRS, IRD, Université d'Avignon et des Pays de Vaucluse, Case 36, 3 place Victor Hugo, 13331, Marseille Cedex 3, France
| | - G Loot
- UPS, UMR 5174 (EDB), Université de Toulouse, 118 route de Narbonne, 31062, Toulouse Cedex 4, France.,Station d'Écologie Expérimentale du CNRS à Moulis, USR 2936, Centre National de la Recherche Scientifique (CNRS), 2 route du CNRS, 09200, Moulis, France
| | - V M Stevens
- Station d'Écologie Expérimentale du CNRS à Moulis, USR 2936, Centre National de la Recherche Scientifique (CNRS), 2 route du CNRS, 09200, Moulis, France
| | - S Blanchet
- Centre National de la Recherche Scientifique (CNRS), École Nationale de Formation Agronomique (ENFA), UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Paul Sabatier, 118 route de Narbonne, 31062, Toulouse Cedex 4, France.,Station d'Écologie Expérimentale du CNRS à Moulis, USR 2936, Centre National de la Recherche Scientifique (CNRS), 2 route du CNRS, 09200, Moulis, France
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3
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Cohen AE, Dugan LE, Hendrickson DA, Martin FD, Huynh J, Labay BJ, Casarez MJ. Population of variable platyfish (Xiphophorus variatus) established in Waller Creek, Travis County, Texas. SOUTHWEST NAT 2015. [DOI: 10.1894/mp-10.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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4
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Dantas HL, dos Santos Neto MA, Oliveira KKC, Severi W, Diniz FM, Coimbra MRM. Genetic Diversity of Captive and Wild Threatened CatfishPseudoplatystoma corruscansin the São Francisco River. ACTA ACUST UNITED AC 2013. [DOI: 10.1080/10641262.2013.800787] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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5
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Shipham A, Schmidt DJ, Hughes JM. Indirect Estimates of Natal Dispersal Distance from Genetic Data in a Stream-Dwelling Fish (Mogurnda adspersa). J Hered 2013; 104:779-90. [DOI: 10.1093/jhered/est055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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6
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Jackson ND, Austin CC. Testing the role of meander cutoff in promoting gene flow across a riverine barrier in ground skinks (Scincella lateralis). PLoS One 2013; 8:e62812. [PMID: 23658778 PMCID: PMC3642178 DOI: 10.1371/journal.pone.0062812] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/26/2013] [Indexed: 11/18/2022] Open
Abstract
Despite considerable attention, the long-term impact of rivers on species diversification remains uncertain. Meander loop cutoff (MLC) is one river phenomenon that may compromise a river's diversifying effects by passively transferring organisms from one side of the river to the other. However, the ability of MLC to promote gene flow across rivers has not been demonstrated empirically. Here, we test several predictions of MLC-mediated gene flow in populations of North American ground skinks (Scincella lateralis) separated by a well-established riverine barrier, the Mississippi River: 1) individuals collected from within meander cutoffs should be more closely related to individuals across the river than on the same side, 2) individuals within meander cutoffs should contain more immigrants than individuals away from meander cutoffs, 3) immigration rates estimated across the river should be highest in the direction of the cutoff event, and 4) the distribution of alleles native to one side of the river should be better predicted by the historical rather than current path of the river. To test these predictions we sampled 13 microsatellite loci and mitochondrial DNA from ground skinks collected near three ancient meander loops. These predictions were generally supported by genetic data, although support was stronger for mtDNA than for microsatellite data. Partial support for genetic divergence of samples within ancient meander loops also provides evidence for the MLC hypothesis. Although a role for MLC-mediated gene flow was supported here for ground skinks, the transient nature of river channels and morphologies may limit the long-term importance of MLC in stemming population divergence across major rivers.
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Affiliation(s)
- Nathan D Jackson
- Department of Biological Sciences, Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America.
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Harris LN, Taylor EB, Tallman RF, Reist JD. Gene flow and effective population size in two life-history types of broad whitefish Coregonus nasus from the Canadian Arctic. JOURNAL OF FISH BIOLOGY 2012; 81:288-307. [PMID: 22747819 DOI: 10.1111/j.1095-8649.2012.03339.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this study, the magnitude and direction of gene flow and estimates of effective population sizes (N(e) ) were quantified among two life-history types (lacustrine and anadromous) of broad whitefish Coregonus nasus in the lower Mackenzie River system. The data suggest that dispersal and subsequent gene flow occurs between these groups, with the former appearing to be asymmetrical. Gene flow may potentially be directionally biased as well, a result attributed to source-sink population dynamics and the ongoing process of post-glacial colonization and contemporary range expansion. Additionally, average N(e) estimates were consistently lower for lacustrine populations of C. nasus although confidence intervals for both contemporary and historical estimates broadly overlapped. The lower average estimates of N(e) for lacustrine populations was suggested to be the result of more recent founding events following post-glacial dispersal. This study provides one of the first assessments of gene flow and N(e) in an Arctic coregonine, results that may be relevant to other freshwater and anadromous Arctic species persisting in systems near the periphery of their range.
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Affiliation(s)
- L N Harris
- Fisheries and Oceans Canada, Arctic Aquatic Research Division, 501 University Crescent, Winnipeg, MB, R3T 2N6 Canada.
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Willis PM, Rosenthal GG, Ryan MJ. An indirect cue of predation risk counteracts female preference for conspecifics in a naturally hybridizing fish Xiphophorus birchmanni. PLoS One 2012; 7:e34802. [PMID: 22529936 PMCID: PMC3329528 DOI: 10.1371/journal.pone.0034802] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 03/08/2012] [Indexed: 11/18/2022] Open
Abstract
Mate choice is context dependent, but the importance of current context to interspecific mating and hybridization is largely unexplored. An important influence on mate choice is predation risk. We investigated how variation in an indirect cue of predation risk, distance to shelter, influences mate choice in the swordtail Xiphophorus birchmanni, a species which sometimes hybridizes with X. malinche in the wild. We conducted mate choice experiments to determine whether females attend to the distance to shelter and whether this cue of predation risk can counteract female preference for conspecifics. Females were sensitive to shelter distance independent of male presence. When conspecific and heterospecific X. malinche males were in equally risky habitats (i.e., equally distant from shelter), females associated primarily with conspecifics, suggesting an innate preference for conspecifics. However, when heterospecific males were in less risky habitat (i.e., closer to shelter) than conspecific males, females no longer exhibited a preference, suggesting that females calibrate their mate choices in response to predation risk. Our findings illustrate the potential for hybridization to arise, not necessarily through reproductive “mistakes”, but as one of many potential outcomes of a context-dependent mate choice strategy.
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Affiliation(s)
- Pamela M Willis
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America.
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Jones JC, Perez-Sato JA, Meyer A. A phylogeographic investigation of the hybrid origin of a species of swordtail fish from Mexico. Mol Ecol 2012; 21:2692-712. [PMID: 22494472 DOI: 10.1111/j.1365-294x.2012.05571.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hybrid speciation may contribute significantly to generating biodiversity, but only a few well-documented examples for it exist so far that do not involve polyploidization as a mechanism. The swordtail fish, Xiphophorus clemenciae, shows common hallmarks of a hybrid origin and still overlaps in its current geographic distribution with its putative ancestral species (Xiphophorus hellerii and Xiphophorus maculatus). Xiphophorus clemenciae provides an ideal system for investigating the possible continued genetic interactions between a hybrid and its parental species. Here, we use microsatellite and mitochondrial markers to investigate the population structure of these species of swordtails and search for signs of recent hybridization. Individuals were sampled from 21 localities across the known range of X. clemenciae- the Isthmus of Tehuantepec (IT) Mexico, and several environmental parameters that might represent barriers to dispersal were recorded. The hybridization event that gave rise to X. clemenciae appears to be rather ancient, and a single origin is likely. We find negligible evidence for ongoing hybridization and introgression between the putative ancestral species, because they now occupy distinct ecological niches, and a common haplotype is shared by most populations of X. clemenciae. The population structure within these species shows an isolation-by-distance (IBD) pattern and genetic differentiation between most populations is significant and high. We infer that tectonic evolution in the Isthmus has greatly restricted gene flow between the southern and central IT populations of X. clemenciae and X. helleriii and provide preliminary information to aid in conservation management of this geographically restricted hybrid species, X. clemenciae.
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Affiliation(s)
- Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätstrasse 10, 78457 Konstanz, Germany
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Thaler AD, Zelnio K, Saleu W, Schultz TF, Carlsson J, Cunningham C, Vrijenhoek RC, Van Dover CL. The spatial scale of genetic subdivision in populations of Ifremeria nautilei, a hydrothermal-vent gastropod from the southwest Pacific. BMC Evol Biol 2011; 11:372. [PMID: 22192622 PMCID: PMC3265507 DOI: 10.1186/1471-2148-11-372] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 12/22/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deep-sea hydrothermal vents provide patchy, ephemeral habitats for specialized communities of animals that depend on chemoautotrophic primary production. Unlike eastern Pacific hydrothermal vents, where population structure has been studied at large (thousands of kilometres) and small (hundreds of meters) spatial scales, population structure of western Pacific vents has received limited attention. This study addresses the scale at which genetic differentiation occurs among populations of a western Pacific vent-restricted gastropod, Ifremeria nautilei. RESULTS We used mitochondrial and DNA microsatellite markers to infer patterns of gene flow and population subdivision. A nested sampling strategy was employed to compare genetic diversity in discrete patches of Ifremeria nautilei separated by a few meters within a single vent field to distances as great as several thousand kilometres between back-arc basins that encompass the known range of the species. No genetic subdivisions were detected among patches, mounds, or sites within Manus Basin. Although I. nautilei from Lau and North Fiji Basins (~1000 km apart) also exhibited no evidence for genetic subdivision, these populations were genetically distinct from the Manus Basin population. CONCLUSIONS An unknown process that restricts contemporary gene flow isolates the Manus Basin population of Ifremeria nautilei from widespread populations that occupy the North Fiji and Lau Basins. A robust understanding of the genetic structure of hydrothermal vent populations at multiple spatial scales defines natural conservation units and can help minimize loss of genetic diversity in situations where human activities are proposed and managed.
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Affiliation(s)
- Andrew D Thaler
- Marine Laboratory, Nicholas School of the Environment, Duke University, Beaufort, NC 28516, USA.
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KANNO YOICHIRO, VOKOUN JASONC, LETCHER BENJAMINH. Fine-scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks. Mol Ecol 2011; 20:3711-29. [DOI: 10.1111/j.1365-294x.2011.05210.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Willis PM, Ryan MJ, Rosenthal GG. Encounter rates with conspecific males influence female mate choice in a naturally hybridizing fish. Behav Ecol 2011. [DOI: 10.1093/beheco/arr119] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Phylogeography of the red coral (Corallium rubrum): inferences on the evolutionary history of a temperate gorgonian. Genetica 2011; 139:855-69. [PMID: 21739159 DOI: 10.1007/s10709-011-9589-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 06/08/2011] [Indexed: 12/29/2022]
Abstract
The red coral Corallium rubrum (Cnidaria, Octocorallia) is an exploited, long-lived sessile species from the Mediterranean Sea and the adjacent coastline in the Atlantic Ocean. Surveys of genetic variation using microsatellites have shown that populations of C. rubrum are characterized by strong differentiation at the local scale but a study of the phylogeography of this species was still lacking. Here, we used seven polymorphic microsatellite loci, together with sequence data from an intron of the elongation factor 1 (EF1) gene, to investigate the genetic structure of C. rubrum across its geographical range in the western Mediterranean Sea and in the Adriatic Sea. The EF1 sequences were also used to analyse the consequences of demographic fluctuations linked with past environmental change. Clustering analysis with microsatellite loci highlighted three to seven genetic groups with the distinction of North African and Adriatic populations; this distinction appeared significant with AMOVA and differentiation tests. Microsatellite and EF1 data extended the isolation by distance pattern previously observed for this species at the western Mediterranean scale. EF1 sequences confirmed the genetic differentiation observed between most samples with microsatellites. A statistical parsimony network of EF1 haplotypes provided no evidence of high sequence divergence among regions, suggesting no long-term isolation. Selective neutrality tests on microsatellites and EF1 were not significant but should be interpreted with caution in the case of EF1 because of the low sample sizes for this locus. Our results suggest that recent Quaternary environmental fluctuations had a limited impact on the genetic structure of C. rubrum.
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Marko PB, Hart MW. The complex analytical landscape of gene flow inference. Trends Ecol Evol 2011; 26:448-56. [PMID: 21722987 DOI: 10.1016/j.tree.2011.05.007] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 04/29/2011] [Accepted: 05/17/2011] [Indexed: 11/25/2022]
Abstract
Gene flow estimation is essential for characterizing local adaptation, speciation potential and connectivity among threatened populations. New model-based population genetic methods can resolve complex demographic histories, but many studies in fields such as landscape genetics continue to rely on simple rules of thumb focused on gene flow to explain patterns of spatial differentiation. Here, we show how methods that use gene genealogies can reveal cryptic demographic histories and provide better estimates of gene flow with other parameters that contribute to genetic variation across landscapes and seascapes. We advocate for the expanded use and development of methods that consider spatial differentiation as the product of multiple forces interacting over time, and caution against a routine reliance on post-hoc gene flow interpretations.
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Affiliation(s)
- Peter B Marko
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA.
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Marko PB, Hart MW. Retrospective coalescent methods and the reconstruction of metapopulation histories in the sea. Evol Ecol 2011. [DOI: 10.1007/s10682-011-9467-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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