1
|
Lyman RA, Edwards CE. Revisiting the comparative phylogeography of unglaciated eastern North America: 15 years of patterns and progress. Ecol Evol 2022; 12:e8827. [PMID: 35475178 PMCID: PMC9019306 DOI: 10.1002/ece3.8827] [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: 12/13/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022] Open
Abstract
In a landmark comparative phylogeographic study, “Comparative phylogeography of unglaciated eastern North America,” Soltis et al. (Molecular Ecology, 2006, 15, 4261) identified geographic discontinuities in genetic variation shared across taxa occupying unglaciated eastern North America and proposed several common biogeographical discontinuities related to past climate fluctuations and geographic barriers. Since 2006, researchers have published many phylogeographical studies and achieved many advances in genotyping and analytical techniques; however, it is unknown how this work has changed our understanding of the factors shaping the phylogeography of eastern North American taxa. We analyzed 184 phylogeographical studies of eastern North American taxa published between 2007 and 2019 to evaluate: (1) the taxonomic focus of studies and whether a previously detected taxonomic bias towards studies focused on vertebrates has changed over time, (2) the extent to which studies have adopted genotyping technologies that improve the resolution of genetic groups (i.e., NGS DNA sequencing) and analytical approaches that facilitate hypothesis‐testing (i.e., divergence time estimation and niche modeling), and (3) whether new studies support the hypothesized biogeographic discontinuities proposed by Soltis et al. (Molecular Ecology, 2006, 15, 4261) or instead support new, previously undetected discontinuities. We observed little change in taxonomic focus over time, with studies still biased toward vertebrates. Although many technological and analytical advances became available during the period, uptake was slow and they were employed in only a small proportion of studies. We found variable support for previously identified discontinuities and identified one new recurrent discontinuity. However, the limited resolution and taxonomic breadth of many studies hindered our ability to clarify the most important climatological or geographical factors affecting taxa in the region. Broadening the taxonomic focus to include more non‐vertebrate taxa, employing technologies that improve genetic resolution, and using analytical approaches that improve hypothesis testing are necessary to strengthen our inference of the forces shaping the phylogeography of eastern North America.
Collapse
Affiliation(s)
- Rachel Ann Lyman
- Ecology, Evolution, and Population Biology Program Washington University in St. Louis St. Louis Missouri USA
- Center for Conservation and Sustainable Development Missouri Botanical Garden St. Louis Missouri USA
| | - Christine E. Edwards
- Center for Conservation and Sustainable Development Missouri Botanical Garden St. Louis Missouri USA
| |
Collapse
|
2
|
Burbrink FT, Gehara M, McKelvy AD, Myers EA. Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex). Evolution 2021; 75:260-277. [PMID: 33346918 DOI: 10.1111/evo.14141] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 01/04/2023]
Abstract
Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the "gray zone" of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates of gene flow often ignore spatial information, for example when considering the location and width of hybrid zones with respect to changes in the environment between lineages. Using population genomic data from the North American ratsnake complex (Pantherophis obsoletus), we connected phylogeographic estimates of lineage structure, migration, historical demography, and timing of divergence with hybrid zone dynamics. We examined the spatial context of diversification by linking migration and timing of divergence to the location and widths of hybrid zones. Artificial neural network approaches were applied to understand how landscape features and past climate have influenced population genetic structure among these lineages. We found that rates of migration between lineages were associated with the overall width of hybrid zones. Timing of divergence was not related to migration rate or hybrid zone width across species pairs but may be related to the number of alleles weakly introgressing through hybrid zones. This research underscores how incomplete reproductive isolation can be better understood by considering differential allelic introgression and the effects of historical and contemporary landscape features on the formation of lineages as well as overall genomic estimates of migration rates through time.
Collapse
Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024
| | - Marcelo Gehara
- Department of Biological Sciences, Rutgers University Newark, 195 University Ave, Newark, New Jersey, 07102
| | - Alexander D McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, New York, 10016
| | - Edward A Myers
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC
| |
Collapse
|
3
|
Arroyo-Lambaer D, Chapman H, Hale M, Blackburn D. Conservation genetics of two threatened frogs from the Mambilla highlands, Nigeria. PLoS One 2018; 13:e0202010. [PMID: 30110399 PMCID: PMC6093670 DOI: 10.1371/journal.pone.0202010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/26/2018] [Indexed: 11/23/2022] Open
Abstract
Amphibians are the vertebrate group with the highest number of species threatened with extinction, and habitat loss and fragmentation are considered to be among the leading causes of their declines and extinctions. Little is known of the population biology of amphibian species inhabiting montane forests in Central and West Africa, where anthropogenic activities such as farming and cattle raising are major threats to native biodiversity. We used Amplified Fragment Length Polymorphisms (AFLPs) to assess the population genetic structure of two poorly known species, Cardioglossa schioetzi and Leptodactylodon bicolor (both in the Arthroleptidae), in and around Ngel Nyaki Forest Reserve on the Mambilla Plateau in eastern Nigeria. The landscape comprises continuous forest on steep slopes and small riparian forest fragments in a grassland matrix. While increased fragmentation is well documented for these and other forests in the mountains of Cameroon and Nigeria over the past century, there are no previous assessments of the impact of forest fragmentation on montane amphibian populations in this region. Our estimates of genetic diversity are similar across populations within each species with levels of heterozygosity values consistent with local population declines. Except for a pair of populations (C. schioetzi) we did not observe genetic differentiation between forest and riparian forest fragment populations, nor across sites within continuous forest (L. bicolor). Our results demonstrate recent gene flow between forest fragments and the adjacent protected forests and suggest that small forest corridors connecting these may lessen the genetic consequences of at least 30 years of intense and severe fragmentation in Ngel Nyaki.
Collapse
Affiliation(s)
- Denise Arroyo-Lambaer
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Hazel Chapman
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- * E-mail:
| | - Marie Hale
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - David Blackburn
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| |
Collapse
|
4
|
Langone JA, Camargo A, de Sá RO. High genetic diversity but low population structure in the frog Pseudopaludicola falcipes (Hensel, 1867) (Amphibia, Anura) from the Pampas of South America. Mol Phylogenet Evol 2015; 95:137-51. [PMID: 26639101 DOI: 10.1016/j.ympev.2015.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 11/03/2015] [Accepted: 11/07/2015] [Indexed: 11/16/2022]
Abstract
Relative to South America's ecoregions, the temperate grasslands of the Pampas have been poorly studied from a phylogeographic perspective. Based on an intermediate biogeographic setting between subtropical forest (Atlantic Forest) and arid ecosystems (Chaco and Patagonia), Pampean species are expected to show unstable demographic histories due to the Quaternary climatic oscillations. Herein, we investigate the phylogenetic relatedness and phylogeographic history of Pseudopaludicola falcipes, a small and common frog that is widely distributed across the Pampean grasslands. First, we use molecular data to assess if P. falcipes represents a single or multiple, separately evolving cryptic lineages. Because P. falcipes is a small-size species (<20mm) with extensive coloration and morphological variation, we suspected that it might represent a complex of cryptic species. In addition, we expected strong genetic and geographic structuring within Pseudopaludicola falcipes due to its large geographic distribution, potentially short dispersal distances, and multiple riverine barriers. We found that P. falcipes is a single evolutionary lineage with poor geographic structuring. Furthermore, current populations of P. falcipes have a large effective population size, maintain ancestral polymorphisms, and have a complex network of gene flow. We conclude that the demographic history of P. falcipes, combined with its ecological attributes and the landscape features of the Pampas, favored a unique combination among anurans of small body size, large population size, high genetic variability, but high cohesiveness of populations over a wide geographic distribution.
Collapse
Affiliation(s)
- José A Langone
- Sección Herpetología, Museo Nacional de Historia Natural, Casilla de Correo 399, Código Postal 11.000, Montevideo, Uruguay.
| | - Arley Camargo
- Programa de Desarrollo Universitario, Centro Universitario de Rivera, Universidad de la República. Ituzaingó 667, Código Postal 40.000, Rivera, Uruguay.
| | - Rafael O de Sá
- Sección Herpetología, Museo Nacional de Historia Natural, Casilla de Correo 399, Código Postal 11.000, Montevideo, Uruguay; Department of Biology, University of Richmond, Richmond, VA 23173, USA.
| |
Collapse
|
5
|
Phylogeography of the arid-adapted Malagasy bullfrog, Laliostoma labrosum, influenced by past connectivity and habitat stability. Mol Phylogenet Evol 2015; 92:11-24. [DOI: 10.1016/j.ympev.2015.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 12/21/2022]
|
6
|
Moseley MA, Cox CL, Streicher JW, Roelke CE, Chippindale PT. Phylogeography and lineage-specific patterns of genetic diversity and molecular evolution in a group of North American skinks. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Matthew A. Moseley
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Christian L. Cox
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
- Department of Biology; The University of Virginia; Charlottesville VA 22903 USA
- Department of Biology; Georgia Southern University; Statesboro GA USA
| | - Jeffrey W. Streicher
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
- Department of Life Sciences; The Natural History Museum; London SW7 5BD UK
| | - Corey E. Roelke
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| | - Paul T. Chippindale
- Department of Biology; The University of Texas at Arlington; Arlington TX 76010 USA
| |
Collapse
|
7
|
Rodríguez A, Börner M, Pabijan M, Gehara M, Haddad CFB, Vences M. Genetic divergence in tropical anurans: deeper phylogeographic structure in forest specialists and in topographically complex regions. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9774-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
8
|
Strickland JL, Parkinson CL, McCoy JK, Ammerman LK. Phylogeography ofAgkistrodon piscivoruswith Emphasis on the Western Limit of Its Range. COPEIA 2014. [DOI: 10.1643/cg-13-123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
9
|
Deep phylogeographic break among Octopus variabilis populations in China: Evidence from mitochondrial and nuclear DNA analyses. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
10
|
Cryptic genetic diversity and complex phylogeography of the boreal North American scorpion, Paruroctonus boreus (Vaejovidae). Mol Phylogenet Evol 2013; 71:298-307. [PMID: 24269314 DOI: 10.1016/j.ympev.2013.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 10/25/2013] [Accepted: 11/10/2013] [Indexed: 11/22/2022]
Abstract
Diverse studies in western North America have revealed the role of topography for dynamically shaping genetic diversity within species though vicariance, dispersal and range expansion. We examined patterns of phylogeographical diversity in the widespread but poorly studied North American vaejovid scorpion, Paruroctonus boreus Girard 1854. We used mitochondrial sequence data and parsimony, likelihood, and Bayesian inference to reconstruct phylogenetic relationships across the distributional range of P. boreus, focusing on intermontane western North America. Additionally, we developed a species distribution model to predict its present and historical distributions during the Last Glacial Maximum and the Last Interglacial Maximum. Our results documented complex phylogeographic relationships within P. boreus, with multiple, well-supported crown clades that are either geographically-circumscribed or widespread and separated by short, poorly supported internodes. We also observed subtle variation in predicted habitat suitability, especially at the northern, eastern and southern edges of the predicted distributional range under past climatic conditions. The complex phylogenetic relationships of P. boreus suggests that historical isolation and expansion of populations may have occurred. Variation in the predicted distributional range over time may implicate past climatic fluctuations in generating the patterns of genetic diversity observed in P. boreus. These findings highlight both the potential for cryptic biodiversity in widespread North American scorpion species and the importance of phylogeographical studies for understanding the factors responsible for generating the biodiversity of western North America.
Collapse
|
11
|
Orozco-terWengel P, Andreone F, Louis E, Vences M. Mitochondrial introgressive hybridization following a demographic expansion in the tomato frogs of Madagascar, genusDyscophus. Mol Ecol 2013; 22:6074-90. [DOI: 10.1111/mec.12558] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 10/06/2013] [Accepted: 10/07/2013] [Indexed: 01/01/2023]
Affiliation(s)
| | - Franco Andreone
- Museo Regionale di Scienze Naturali; Via Giolitti 36 10123 Torino Italy
| | - Edward Louis
- Omaha's Henry Doorly Zoo; 3701 S 10th Street Omaha NE 68107 USA
| | - Miguel Vences
- Division of Evolutionary Biology, Zoological Institute; Technical University of Braunschweig; Mendelssohnstr. 4 38106 Braunschweig Germany
| |
Collapse
|
12
|
Vásquez D, Correa C, Pastenes L, Palma RE, Méndez MA. Low phylogeographic structure of Rhinella arunco (Anura: Bufonidae), an endemic amphibian from the Chilean Mediterranean hotspot. Zool Stud 2013. [DOI: 10.1186/1810-522x-52-35] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
The Mediterranean zone of central Chile (30° to 38°S) is one of the 25 diversity hotspots in the world. However, there are few phylogeographic studies which identify the factors that have influenced population diversification in the fauna of this area. In this study, we investigated the phylogeographic structure of Rhinella arunco, an anuran endemic to Mediterranean Chile, using 160 individuals from 23 localities representative of its entire distribution (32° to 38°S).
Results
The haplotype network revealed four haplogroups, three of which overlap geographically and only one of which has an exclusive geographic distribution. An analysis of molecular variance indicated that neither watershed limits nor the main rivers in the current distribution of this species have been important geographic barriers against the dispersion of individuals. Finally, the Geneland analysis showed three population units, one of which concurs with one of the haplogroups found in the haplotype network. Together, these analyses indicated a low level of phylogeographic structure for this species. On the other hand, the highest levels of intrapopulational genetic variation were concentrated in the central part of the distribution (33° to 34°S), which may indicate an effect of Pleistocene glaciations on the genetic diversity of the populations in the extreme south of its range.
Conclusions
The low phylogeographic structure observed in R. arunco is a rarely documented pattern for amphibians and contrasts with the phylogeographic studies of other vertebrates which inhabit the same zone. This result may be attributed to a series of attributes of bufonids, related mainly to water retention and their reproductive biology, which have allowed them to disperse and colonize an enormous variety of environments.
Collapse
|
13
|
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.
Collapse
Affiliation(s)
- Nathan D Jackson
- Department of Biological Sciences, Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America.
| | | |
Collapse
|
14
|
Vences M, Hauswaldt JS, Steinfartz S, Rupp O, Goesmann A, Künzel S, Orozco-terWengel P, Vieites DR, Nieto-Roman S, Haas S, Laugsch C, Gehara M, Bruchmann S, Pabijan M, Ludewig AK, Rudert D, Angelini C, Borkin LJ, Crochet PA, Crottini A, Dubois A, Ficetola GF, Galán P, Geniez P, Hachtel M, Jovanovic O, Litvinchuk SN, Lymberakis P, Ohler A, Smirnov NA. Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana. Mol Phylogenet Evol 2013; 68:657-70. [PMID: 23632031 DOI: 10.1016/j.ympev.2013.04.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 04/10/2013] [Accepted: 04/16/2013] [Indexed: 11/26/2022]
Abstract
We reconstruct range-wide phylogeographies of two widespread and largely co-occurring Western Palearctic frogs, Rana temporaria and R. dalmatina. Based on tissue or saliva samples of over 1000 individuals, we compare a variety of genetic marker systems, including mitochondrial DNA, single-copy protein-coding nuclear genes, microsatellite loci, and single nucleotide polymorphisms (SNPs) of transcriptomes of both species. The two focal species differ radically in their phylogeographic structure, with R. temporaria being strongly variable among and within populations, and R. dalmatina homogeneous across Europe with a single strongly differentiated population in southern Italy. These differences were observed across the various markers studied, including microsatellites and SNP density, but especially in protein-coding nuclear genes where R. dalmatina had extremely low heterozygosity values across its range, including potential refugial areas. On the contrary, R. temporaria had comparably high range-wide values, including many areas of probable postglacial colonization. A phylogeny of R. temporaria based on various concatenated mtDNA genes revealed that two haplotype clades endemic to Iberia form a paraphyletic group at the base of the cladogram, and all other haplotypes form a monophyletic group, in agreement with an Iberian origin of the species. Demographic analysis suggests that R. temporaria and R. dalmatina have genealogies of roughly the same time to coalescence (TMRCA ~3.5 mya for both species), but R. temporaria might have been characterized by larger ancestral and current effective population sizes than R. dalmatina. The high genetic variation in R. temporaria can therefore be explained by its early range expansion out of Iberia, with subsequent cycles of differentiation in cryptic glacial refugial areas followed by admixture, while the range expansion of R. dalmatina into central Europe is a probably more recent event.
Collapse
Affiliation(s)
- Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Lee-Yaw JA, Irwin DE. Large geographic range size reflects a patchwork of divergent lineages in the long-toed salamander (Ambystoma macrodactylum). J Evol Biol 2012; 25:2276-87. [DOI: 10.1111/j.1420-9101.2012.02604.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J. A. Lee-Yaw
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
| | - D. E. Irwin
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
| |
Collapse
|
16
|
Streicher JW, Cox CL, Campbell JA, Smith EN, de Sá RO. Rapid range expansion in the Great Plains narrow-mouthed toad (Gastrophryne olivacea) and a revised taxonomy for North American microhylids. Mol Phylogenet Evol 2012; 64:645-53. [DOI: 10.1016/j.ympev.2012.05.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 05/18/2012] [Accepted: 05/21/2012] [Indexed: 11/29/2022]
|
17
|
Extremely low genetic diversity indicating the endangered status of Ranodon sibiricus (Amphibia: Caudata) and implications for phylogeography. PLoS One 2012; 7:e33378. [PMID: 22428037 PMCID: PMC3299782 DOI: 10.1371/journal.pone.0033378] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 02/08/2012] [Indexed: 10/29/2022] Open
Abstract
BACKGROUND The Siberian salamander (Ranodon sibiricus), distributed in geographically isolated areas of Central Asia, is an ideal alpine species for studies of conservation and phylogeography. However, there are few data regarding the genetic diversity in R. sibiricus populations. METHODOLOGY/PRINCIPAL FINDINGS We used two genetic markers (mtDNA and microsatellites) to survey all six populations of R. sibiricus in China. Both of the markers revealed extreme genetic uniformity among these populations. There were only three haplotypes in the mtDNA, and the overall nucleotide diversity in the mtDNA was 0.00064, ranging from 0.00000 to 0.00091 for the six populations. Although we recovered 70 sequences containing microsatellite repeats, there were only two loci that displayed polymorphism. We used the approximate Bayesian computation (ABC) method to study the demographic history of the populations. This analysis suggested that the extant populations diverged from the ancestral population approximately 120 years ago and that the historical population size was much larger than the present population size; i.e., R. sibiricus has experienced dramatic population declines. CONCLUSION/SIGNIFICANCE Our findings suggest that the genetic diversity in the R. sibiricus populations is the lowest among all investigated amphibians. We conclude that the isolation of R. sibiricus populations occurred recently and was a result of recent human activity and/or climatic changes. The Pleistocene glaciation oscillations may have facilitated intraspecies genetic homogeneity rather than enhanced divergence. A low genomic evolutionary rate and elevated inbreeding frequency may have also contributed to the low genetic variation observed in this species. Our findings indicate the urgency of implementing a protection plan for this endangered species.
Collapse
|
18
|
Koroma AP, Jones R, Michalak P. Snapshot of DNA methylation changes associated with hybridization in Xenopus. Physiol Genomics 2011; 43:1276-80. [PMID: 21914783 DOI: 10.1152/physiolgenomics.00110.2011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Hybridization often results in dramatic genome reconfigurations including epigenetic changes that control gene expression. Here we survey methylation patterns of interspecific Xenopus F1 hybrids relative to parental species X. laevis and X. muelleri, using methyl-sensitive amplification polymorphisms (MSAPs). Out of a total of 546 MSAP markers, 364 were effective in elucidating the difference in methylation patterns between the hybrids and the parental species. Principal coordinate analysis of methylated fragments revealed four distinct clusters with the two parental species separate from hybrid males and females. On average, hybrids were characterized by a higher proportion (70.6%) of methylated fragments compared with the parental species (64.5%), and this difference was consistent with previously observed disruptions of hybrid transcriptomes. The proportion of methylated fragments did not correlate with variation in genome size, as measured with flow cytometry. The levels of methylation in sterile hybrid males (73.8%) were higher than in fertile hybrid females (68.6%), but this difference was not statistically significant. A total of 76 methylated fragments (20.9%) were hybrid-unique, presumably originating from methylation alterations in hybrid genomes.
Collapse
|
19
|
Molecular systematics of the Middle American genus Hypopachus (Anura: Microhylidae). Mol Phylogenet Evol 2011; 61:265-77. [PMID: 21798357 DOI: 10.1016/j.ympev.2011.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Revised: 06/11/2011] [Accepted: 07/05/2011] [Indexed: 11/21/2022]
Abstract
We present the first phylogenetic study on the widespread Middle American microhylid frog genus Hypopachus. Partial sequences of mitochondrial (12S and 16S ribosomal RNA) and nuclear (rhodopsin) genes (1275 bp total) were analyzed from 43 samples of Hypopachus, three currently recognized species of Gastrophryne, and seven arthroleptid, brevicipitid and microhylid outgroup taxa. Maximum parsimony (PAUP), maximum likelihood (RAxML) and Bayesian inference (MrBayes) optimality criteria were used for phylogenetic analyses, and BEAST was used to estimate divergence dates of major clades. Population-level analyses were conducted with the programs NETWORK and Arlequin. Results confirm the placement of Hypopachus and Gastrophryne as sister taxa, but the latter genus was strongly supported as paraphyletic. The African phrynomerine genus Phrynomantis was recovered as the sister taxon to a monophyletic Chiasmocleis, rendering our well-supported clade of gastrophrynines paraphyletic. Hypopachus barberi was supported as a disjunctly distributed highland species, and we recovered a basal split in lowland populations of Hypopachus variolosus from the Pacific versant of Mexico and elsewhere in the Mesoamerican lowlands. Dating analyses from BEAST estimate speciation within the genus Hypopachus occurred in the late Miocene/early Pliocene for most clades. Previous studies have not found bioacoustic or morphological differences among these lowland clades, and our molecular data support the continued recognition of two species in the genus Hypopachus.
Collapse
|
20
|
Zhang YX, He CZ, Dudgeon D, Zhang ZY, Wang GM. Mountain Ridge and Sea: Geographic-Barrier Effects on Genetic Diversity and Differentiation of the Hong Kong Newt (Paramesotriton hongkongensis) Revealed by AFLP. ANN ZOOL FENN 2011. [DOI: 10.5735/086.048.0204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
21
|
Fontenot BE, Makowsky R, Chippindale PT. Nuclear–mitochondrial discordance and gene flow in a recent radiation of toads. Mol Phylogenet Evol 2011; 59:66-80. [DOI: 10.1016/j.ympev.2010.12.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 12/12/2010] [Accepted: 12/23/2010] [Indexed: 12/01/2022]
|
22
|
Moncrief ND, Lack JB, Van Den Bussche RA. Eastern fox squirrel (Sciurus niger) lacks phylogeographic structure: recent range expansion and phenotypic differentiation. J Mammal 2010. [DOI: 10.1644/09-mamm-a-266.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
23
|
Makowsky R, Marshall JC, McVay J, Chippindale PT, Rissler LJ. Phylogeographic analysis and environmental niche modeling of the plain-bellied watersnake (Nerodia erythrogaster) reveals low levels of genetic and ecological differentiation. Mol Phylogenet Evol 2010; 55:985-95. [PMID: 20302955 DOI: 10.1016/j.ympev.2010.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 02/22/2010] [Accepted: 03/11/2010] [Indexed: 11/25/2022]
Abstract
Species that exhibit geographically defined phenotypic variation traditionally have been divided into subspecies. Subspecies based on phenotypic features may not comprise monophyletic groups due to selection, gene flow, and/or convergent evolution. In many taxonomic groups the number of species once designated as widespread is dwindling rapidly, and many workers reject the concept of subspecies altogether. We tested whether currently recognized subspecies in the plain-bellied watersnake Nerodia erythrogaster are concordant with relationships based on mitochondrial markers, and whether it represents a single widespread species. The range of this taxon spans multiple potential biogeographic barriers (especially the Mississippi and Apalachicola Rivers) that correspond with lineage breaks in many species, including other snakes. We sequenced three mitochondrial genes (NADH-II, Cyt-b, Cox-I) from 156 geo-referenced specimens and developed ecological niche models using Maxent and spatially explicit climate data to examine historical and ecological factors affecting variation in N. erythrogaster across its range. Overall, we found little support for the recognized subspecies as either independent evolutionary lineages or geographically circumscribed units and conclude that although some genetic and niche differentiation has occurred, most populations assigned to N. erythrogaster appear to represent a single, widespread species. However, additional sampling and application of nuclear markers are necessary to clarify the status of the easternmost populations.
Collapse
Affiliation(s)
- Robert Makowsky
- University of Texas at Arlington, Department of Biology, Arlington, TX, USA.
| | | | | | | | | |
Collapse
|
24
|
Milá B, Carranza S, Guillaume O, Clobert J. Marked genetic structuring and extreme dispersal limitation in the Pyrenean brook newt Calotriton asper (Amphibia: Salamandridae) revealed by genome-wide AFLP but not mtDNA. Mol Ecol 2009; 19:108-20. [PMID: 19943891 DOI: 10.1111/j.1365-294x.2009.04441.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Direct estimation of dispersal rates at large geographic scales can be technically and logistically challenging, especially in small animals of low vagility like amphibians. The use of molecular markers to reveal patterns of genetic structure provides an indirect way to infer dispersal rates and patterns of recent and historical gene flow among populations. Here, we use mitochondrial DNA (mtDNA) sequence data and genome-wide amplified fragment length polymorphism markers to examine population structure in the Pyrenean brook newt (Calotriton asper) across four main drainages in the French Pyrenees. mtDNA sequence data (2040 bp) revealed three phylogroups shallowly differentiated and with low genetic diversity. In sharp contrast, variation in 382 amplified fragment length polymorphism loci was high and revealed a clear pattern of isolation by distance consistent with long-term restriction of gene flow at three spatial scales: (i) among all four main drainages, (ii) between sites within drainages, and (iii) even between adjacent populations separated by less than 4 km. The high pairwise F(ST) values between localities across numerous loci, together with the high frequency of fixed alleles in several populations, suggests a combination of marked geographic isolation, small population sizes and very limited dispersal in C. asper. The contrasting lack of variation detected in mtDNA sequence data is intriguing and underscores the importance of multilocus approaches to detect true patterns of gene flow in natural populations of amphibians.
Collapse
Affiliation(s)
- Borja Milá
- Station d'Ecologie Experimentale, Centre National de la Recherche Scientifique, USR 2936, Moulis, 09200 Saint Girons, France.
| | | | | | | |
Collapse
|
25
|
Wooten JA, Camp CD, Rissler LJ. Genetic diversity in a narrowly endemic, recently described dusky salamander, Desmognathus folkertsi, from the southern Appalachian Mountains. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9916-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|