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Ho ALFC, Pruett CL, Lin J. Phylogeny and biogeography of Poecilia (Cyprinodontiformes: Poeciliinae) across Central and South America based on mitochondrial and nuclear DNA markers. Mol Phylogenet Evol 2016; 101:32-45. [PMID: 27129899 DOI: 10.1016/j.ympev.2016.04.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 04/16/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
Abstract
Poeciliids are a diverse group of small Neotropical fishes, and despite considerable research attention as models in ecology and evolutionary biology, our understanding of their biogeographic and phylogenetic relationships is still limited. We investigated the phylogenetic relationships of South and Central American Poecilia, by examining 2395 base pairs of mitochondrial DNA (ATPase 8/6, COI) and nuclear DNA (S7) for 18 species across six subgenera. Fifty-eight novel sequences were acquired from newly collected specimens and 20 sequences were obtained from previously published material. Analyses of concatenated and partitioned mitochondrial DNA and nuclear DNA sets resulted in a well-supported phylogeny that resolved several monophyletic groups corresponding to previously hypothesized subgenera and species complexes. A divergence-dating analysis supported the hypothesis of the genus Poecilia dispersing into Central America in the early Pliocene (ancestors of Psychropoecilia+Allopoecilia+Mollienesia: 7.3-2.0Mya) from predominantly South America. Subsequently, one lineage (subgenus Allopoecilia: 5.1-1.3Mya) expanded deeper into South America from Lower-Central America, and one lineage expanded from Nuclear-Central America into South America (subgenus Mollienesia: 0.71-0.14Mya). The subgenus Mollienesia diverged into three monophyletic groups that can be identified by nuptial male dorsal fin morphology and inner jaw dentition. A subclade of the unicuspid short-fins (subgenus Mollienesia) was the lineage that expanded into South America during the middle Pleistocene. Species in this subclade are now distributed across northern South America, where they are partially sympatric with Allopoecilia. However the P. (A.) caucana complex was not monophyletic, with P. (A.) wandae clustering in the Mollienesia subclade that expanded into South America. It is apparent that characters (body size, scale count, pigmentation, and gonopodium morphology) used to define the P. (A.) caucana complex are homoplastic and suggestive of rapid convergence in northern South America. Our improved taxon sampling and divergence-time calibration allowed for insights into the timing and direction of dispersals, and provides an improved understanding of the biogeographic history of an enigmatic group of fishes. Furthermore, we provided strong evidence for the monophyly of the subgenus Mollienesia and further substantiated its species complexes; therefore, we advise a taxonomic re-evaluation for the P. (A.) caucana complex to maintain monophyly of both Mollienesia and Allopoecilia.
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Affiliation(s)
- Adeljean L F C Ho
- Department of Biological Sciences, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA.
| | - Christin L Pruett
- Department of Biological Sciences, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
| | - Junda Lin
- Department of Biological Sciences, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901, USA
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Kartzinel TR, Campbell DA, Trapnell DW. Spatial Patterns of Haplotype Variation in the Epiphytic BromeliadCatopsis nutans. Biotropica 2015. [DOI: 10.1111/btp.12272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tyler R. Kartzinel
- Odum School of Ecology; The University of Georgia; 140 East Green Street Athens GA 30602 U.S.A
| | - Dakotah A. Campbell
- Department of Plant Biology; The University of Georgia; Athens GA 30602 U.S.A
| | - Dorset W. Trapnell
- Department of Plant Biology; The University of Georgia; Athens GA 30602 U.S.A
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53
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Guerrero J, Gallo-Reynoso JP, Biek R. Mitochondrial DNA diversity, genetic structure, and demographic history of the Neotropical otter (Lontra longicaudis) in Mexico. J Mammal 2015. [DOI: 10.1093/jmammal/gyv124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Phillips JG, Deitloff J, Guyer C, Huetteman S, Nicholson KE. Biogeography and evolution of a widespread Central American lizard species complex: Norops humilis, (Squamata: Dactyloidae). BMC Evol Biol 2015; 15:143. [PMID: 26187158 PMCID: PMC4506609 DOI: 10.1186/s12862-015-0391-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/26/2015] [Indexed: 11/15/2022] Open
Abstract
Background Caribbean anole lizards (Dactyloidae) have frequently been used as models to study questions regarding biogeography and adaptive radiations, but the evolutionary history of Central American anoles (particularly those of the genus Norops) has not been well studied. Previous work has hypothesized a north-to-south dispersal pattern of Central American Norops, but no studies have examined dispersal within any Norops lineages. Here we test two major hypotheses for the dispersal of the N. humilis/quaggulus complex (defined herein, forming a subset within Savage and Guyer’s N. humilis group). Results Specimens of the N. humilis group were collected in Central America, from eastern Mexico to the Canal Zone of Panama. Major nodes were dated for comparison to the geologic history of Central America, and ancestral ranges were estimated for the N. humilis/quaggulus complex to test hypothesized dispersal patterns. These lineages displayed a northward dispersal pattern. We also demonstrate that the N. humilis/quaggulus complex consists of a series of highly differentiated mitochondrial lineages, with more conserved nuclear evolution. The paraphyly of the N. humilis species group is confirmed. A spatial analysis of molecular variance suggests that current populations are genetically distinct from one another, with limited mitochondrial gene flow occurring among sites. Conclusions The observed south-to-north colonization route within the Norops humilis/quaggulus complex represents the first evidence of a Norops lineage colonizing in a south-to-north pattern, (opposite to the previously held hypothesis for mainland Norops). One previously described taxon (N. quaggulus) was nested within N. humilis, demonstrating the paraphyly of this species; while our analyses also reject the monophyly of the Norops humilis species group (sensu Savage and Guyer), with N. tropidonotus, N. uniformis, and N. marsupialis being distantly related to/highly divergent from the N. humilis/quaggulus complex. Our work sheds light on mainland anole biogeography and past dispersal events, providing a pattern to test against other groups of mainland anoles. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0391-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John G Phillips
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, 48859, USA. .,Present address: Department of Biological Sciences, University of Tulsa, Tulsa, OK, 74104, USA.
| | - Jennifer Deitloff
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA.,Present address: Department of Biological Sciences, Lock Haven University, Lock Haven, PA, 17745, USA
| | - Craig Guyer
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sara Huetteman
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, 48859, USA
| | - Kirsten E Nicholson
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, 48859, USA
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Moraes-Barros N, Arteaga MC. Genetic diversity in Xenarthra and its relevance to patterns of neotropical biodiversity. J Mammal 2015. [DOI: 10.1093/jmammal/gyv077] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ingley SJ, Reina RG, Bermingham E, Johnson JB. Phylogenetic analyses provide insights into the historical biogeography and evolution of Brachyrhaphis fishes. Mol Phylogenet Evol 2015; 89:104-14. [PMID: 25916190 DOI: 10.1016/j.ympev.2015.04.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 04/10/2015] [Accepted: 04/17/2015] [Indexed: 12/01/2022]
Abstract
The livebearing fish genus Brachyrhaphis (Poeciliidae) has become an increasingly important model in evolution and ecology research, yet the phylogeny of this group is not well understood, nor has it been examined thoroughly using modern phylogenetic methods. Here, we present the first comprehensive phylogenetic analysis of Brachyrhaphis by using four molecular markers (3mtDNA, 1nucDNA) to infer relationships among species in this genus. We tested the validity of this genus as a monophyletic group using extensive outgroup sampling based on recent phylogenetic hypotheses of Poeciliidae. We also tested the validity of recently described species of Brachyrhaphis that are part of the B. episcopi complex in Panama. Finally, we examined the impact of historical events on diversification of Brachyrhaphis, and made predictions regarding the role of different ecological environments on evolutionary diversification where known historical events apparently fail to explain speciation. Based on our results, we reject the monophyly of Brachyrhaphis, and question the validity of two recently described species (B. hessfeldi and B. roswithae). Historical biogeography of Brachyrhaphis generally agrees with patterns found in other freshwater taxa in Lower Central America, which show that geological barriers frequently predict speciation. Specifically, we find evidence in support of an 'island' model of Lower Central American formation, which posits that the nascent isthmus was partitioned by several marine connections before linking North and South America. In some cases where historic events (e.g., vicariance) fail to explain allopatric species breaks in Brachyrhaphis, ecological processes (e.g., divergent predation environments) offer additional insight into our understanding of phylogenetic diversification in this group.
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Affiliation(s)
- Spencer J Ingley
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, 401 WIDB, Provo, UT 84602, USA.
| | - Ruth G Reina
- Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Panama
| | | | - Jerald B Johnson
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, 401 WIDB, Provo, UT 84602, USA; Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT 84602, USA
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Bagley JC, Alda F, Breitman MF, Bermingham E, van den Berghe EP, Johnson JB. Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae). PLoS One 2015; 10:e0121139. [PMID: 25849959 PMCID: PMC4388586 DOI: 10.1371/journal.pone.0121139] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 02/10/2015] [Indexed: 12/20/2022] Open
Abstract
Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of testing for hybridization versus incomplete lineage sorting, which aids inference of not only species limits but also evolutionary processes influencing genetic diversity.
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Affiliation(s)
- Justin C. Bagley
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, Provo, Utah, 84602, United States of America
- * E-mail:
| | - Fernando Alda
- Smithsonian Tropical Research Institute, Balboa, Panamá
| | - M. Florencia Breitman
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, Provo, Utah, 84602, United States of America
- Centro Nacional Patagónico (CENPAT-CONICET), U9120ACD, Puerto Madryn, Chubut, Argentina
| | | | - Eric P. van den Berghe
- Centro Zamorano de Biodiversidad, Departamento de Ambiente y Desarrollo, Zamorano University, Tegucigalpa, Honduras
| | - Jerald B. Johnson
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, Provo, Utah, 84602, United States of America
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, Utah, 84602, United States of America
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Gottscho AD. Zoogeography of the San Andreas Fault system: Great Pacific Fracture Zones correspond with spatially concordant phylogeographic boundaries in western North America. Biol Rev Camb Philos Soc 2014; 91:235-54. [DOI: 10.1111/brv.12167] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 10/28/2014] [Accepted: 11/11/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew D. Gottscho
- Department of Biology; San Diego State University; 5500 Campanile Drive San Diego CA 92182 U.S.A
- Department of Biology; University of California; Riverside CA 92521 U.S.A
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Bagley JC, Johnson JB. Testing for shared biogeographic history in the lower Central American freshwater fish assemblage using comparative phylogeography: concerted, independent, or multiple evolutionary responses? Ecol Evol 2014; 4:1686-705. [PMID: 24967085 PMCID: PMC4063468 DOI: 10.1002/ece3.1058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/13/2014] [Accepted: 03/14/2014] [Indexed: 11/10/2022] Open
Abstract
A central goal of comparative phylogeography is determining whether codistributed species experienced (1) concerted evolutionary responses to past geological and climatic events, indicated by congruent spatial and temporal patterns ("concerted-response hypothesis"); (2) independent responses, indicated by spatial incongruence ("independent-response hypothesis"); or (3) multiple responses ("multiple-response hypothesis"), indicated by spatial congruence but temporal incongruence ("pseudocongruence") or spatial and temporal incongruence ("pseudoincongruence"). We tested these competing hypotheses using DNA sequence data from three livebearing fish species codistributed in the Nicaraguan depression of Central America (Alfaro cultratus, Poecilia gillii, and Xenophallus umbratilis) that we predicted might display congruent responses due to co-occurrence in identical freshwater drainages. Spatial analyses recovered different subdivisions of genetic structure for each species, despite shared finer-scale breaks in northwestern Costa Rica (also supported by phylogenetic results). Isolation-with-migration models estimated incongruent timelines of among-region divergences, with A. cultratus and Xenophallus populations diverging over Miocene-mid-Pleistocene while P. gillii populations diverged over mid-late Pleistocene. Approximate Bayesian computation also lent substantial support to multiple discrete divergences over a model of simultaneous divergence across shared spatial breaks (e.g., Bayes factor [B 10] = 4.303 for Ψ [no. of divergences] > 1 vs. Ψ = 1). Thus, the data support phylogeographic pseudoincongruence consistent with the multiple-response hypothesis. Model comparisons also indicated incongruence in historical demography, for example, support for intraspecific late Pleistocene population growth was unique to P. gillii, despite evidence for finer-scale population expansions in the other taxa. Empirical tests for phylogeographic congruence indicate that multiple evolutionary responses to historical events have shaped the population structure of freshwater species codistributed within the complex landscapes in/around the Nicaraguan depression. Recent community assembly through different routes (i.e., different past distributions or colonization routes), and intrinsic ecological differences among species, has likely contributed to the unique phylogeographical patterns displayed by these Neotropical fishes.
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Affiliation(s)
- Justin C Bagley
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University Provo, Utah, 84602
| | - Jerald B Johnson
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University Provo, Utah, 84602 ; Monte L. Bean Life Science Museum, Brigham Young University Provo, Utah, 84602
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