1
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Chang JT, Chao CT, Nakamura K, Liu HL, Luo MX, Liao PC. Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data. FRONTIERS IN PLANT SCIENCE 2022; 13:824158. [PMID: 35615129 PMCID: PMC9125193 DOI: 10.3389/fpls.2022.824158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The divergence process of incipient species is fascinating but elusive by incomplete lineage sorting or gene flow. Species delimitation is also challenging among those morphologically similar allopatric species, especially when lacking comprehensive data. Cycas sect. Asiorientales, comprised of C. taitungensis and C. revoluta in the Ryukyu Archipelago and Taiwan, diverged recently with continuous gene flow, resulting in a reciprocal paraphyletic relationship. Their previous evolutionary inferences are questioned from few genetic markers, incomplete sampling, and incomprehensive morphological comparison by a long-term taxonomic misconception. By whole range sampling, this study tests the geographic mode of speciation in the two species of Asiorientales by approximate Bayesian computation (ABC) using genome-wide single nucleotide polymorphisms (SNPs). The individual tree was reconstructed to delimit the species and track the gene-flow trajectory. With the comparison of diagnostic morphological traits and genetic data, the allopatric speciation was rejected. Alternatively, continuous but spatially heterogeneous gene flow driven by transoceanic vegetative dispersal and pollen flow with contrasting population sizes blurred their species boundary. On the basis of morphological, genetic, and evolutionary evidence, we synonymized these two Cycas species. This study highlights not only the importance of the Kuroshio Current to species evolution but also the disadvantage of using species with geographically structured genealogies as conservation units.
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Affiliation(s)
- Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Hsiao-Lei Liu
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
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2
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Avendaño JE, Cadena CD. Territorial males do not discriminate between local and novel plumage phenotypes in a tropical songbird species complex: implications for the role of social selection in trait evolution. Behav Ecol Sociobiol 2021. [DOI: 10.1007/s00265-021-02976-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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3
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Márquez R, Linderoth TP, Mejía-Vargas D, Nielsen R, Amézquita A, Kronforst MR. Divergence, gene flow, and the origin of leapfrog geographic distributions: The history of colour pattern variation in Phyllobates poison-dart frogs. Mol Ecol 2020; 29:3702-3719. [PMID: 32814358 PMCID: PMC8164878 DOI: 10.1111/mec.15598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 11/26/2022]
Abstract
The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. These geographic patterns have mostly been studied from phylogenetic perspectives to understand how common ancestry and divergent evolution drive their formation. Other processes, such as gene flow between populations, have not received as much attention. Here, we investigate the roles of divergence and gene flow between populations in the origin and maintenance of a leapfrog distribution in Phyllobates poison frogs. We found evidence for high levels of gene flow between neighbouring populations but not over long distances, indicating that gene flow between populations exhibiting the central phenotype may have a homogenizing effect that maintains their similarity, and that introgression between 'leapfroging' taxa has not played a prominent role as a driver of phenotypic diversity in Phyllobates. Although phylogenetic analyses suggest that the leapfrog distribution was formed through independent evolution of the peripheral (i.e. leapfrogging) populations, the elevated levels of gene flow between geographically close populations poise alternative scenarios, such as the history of phenotypic change becoming decoupled from genome-averaged patterns of divergence, which we cannot rule out. These results highlight the importance of incorporating gene flow between populations into the study of geographic variation in phenotypes, both as a driver of phenotypic diversity and as a confounding factor of phylogeographic inferences.
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Affiliation(s)
- Roberto Márquez
- Department of Ecology and Evolution, University of Chicago. Chicago, IL. 60637, USA
- Department of Biological Sciences, Universidad de los Andes. A.A. 4976, Bogotá, D.C., Colombia
| | - Tyler P. Linderoth
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley. Berkeley, CA. 94720, USA
| | - Daniel Mejía-Vargas
- Department of Biological Sciences, Universidad de los Andes. A.A. 4976, Bogotá, D.C., Colombia
| | - Rasmus Nielsen
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley. Berkeley, CA. 94720, USA
- Department of Statistics, University of California, Berkeley. Berkeley, CA. 94720, USA
- Center for GeoGenetics, University of Copenhagen, Copenhagen 1350, Denmark
| | - Adolfo Amézquita
- Department of Biological Sciences, Universidad de los Andes. A.A. 4976, Bogotá, D.C., Colombia
| | - Marcus R. Kronforst
- Department of Ecology and Evolution, University of Chicago. Chicago, IL. 60637, USA
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4
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Moreira LR, Hernandez-Baños BE, Smith BT. Spatial predictors of genomic and phenotypic variation differ in a lowland Middle American bird (Icterus gularis). Mol Ecol 2020; 29:3085-3102. [PMID: 32621770 DOI: 10.1111/mec.15536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 06/08/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Spatial patterns of intraspecific variation are shaped by geographical distance among populations, historical changes in gene flow and interactions with local environments. Although these factors are not mutually exclusive and operate on both genomic and phenotypic variation, it is unclear how they affect these two axes of variation. We address this question by exploring the predictors of genomic and phenotypic divergence in Icterus gularis, a broadly distributed Middle American bird that exhibits marked geographical variation in body size across its range. We combined a comprehensive single nucleotide polymorphism and phenotypic data set to test whether genome-wide genetic and phenotypic differentiation are best explained by (i) isolation by distance, (ii) isolation by history or (iii) isolation by environment. We find that the pronounced genetic and phenotypic variation in I. gularis are only partially correlated and differ regarding spatial predictors. Whereas genomic variation is largely explained by historical barriers to gene flow, phenotypic diversity can be best predicted by contemporary environmental heterogeneity. Our genomic analyses reveal strong phylogeographical structure coinciding with the Chivela Pass at the Isthmus of Tehuantepec that was formed during the Pleistocene, when populations were isolated in north-south refugia. In contrast, we found a strong association between body size and environmental variables, such as temperature and precipitation. The relationship between body size and local climate is consistent with a pattern produced by either natural selection or environmental plasticity. Overall, these results provide empirical evidence for why phenotypic and genomic data are often in conflict in taxonomic and phylogeographical studies.
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Affiliation(s)
- Lucas R Moreira
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | | | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
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5
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Picq S, Sperling J, Cheng CJ, Carlson BA, Gallant JR. Genetic drift does not sufficiently explain patterns of electric signal variation among populations of the mormyrid electric fish Paramormyrops kingsleyae. Evolution 2020; 74:911-935. [PMID: 32187650 PMCID: PMC7816287 DOI: 10.1111/evo.13953] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 02/13/2020] [Accepted: 02/20/2020] [Indexed: 11/28/2022]
Abstract
Communication signals serve crucial survival and reproductive functions. In Gabon, the widely distributed mormyrid fish Paramormyrops kingsleyae emits an electric organ discharge (EOD) signal with a dual role in communication and electrolocation that exhibits remarkable variation: populations of P. kingsleyae have either biphasic or triphasic EODs, a feature that characterizes interspecific signal diversity among the Paramormyrops genus. We quantified variation in EODs of 327 P. kingsleyae from nine populations and compared it to genetic variation estimated from microsatellite loci. We found no correlation between electric signal and genetic distances, suggesting that EOD divergence cannot be explained by drift alone. An alternative hypothesis is that EOD differences are used for mate discrimination, which would require P. kingsleyae be capable of differentiating between divergent EOD waveforms. Using a habituation-dishabituation assay, we found that P. kingsleyae can discriminate between biphasic and triphasic EOD types. Nonetheless, patterns of genetic and electric organ morphology divergence provide evidence for hybridization between these signal types. Although reproductive isolation with respect to signal type is incomplete, our results suggest that EOD variation in P. kingsleyae could be a cue for assortative mating.
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Affiliation(s)
- Sophie Picq
- Michigan State University Department of Integrative Biology, East Lansing MI 48824 USA
| | - Joshua Sperling
- Cornell University Department of Neurobiology and Behavior, Ithaca NY 14853 USA
| | - Catherine J. Cheng
- Cornell University Department of Neurobiology and Behavior, Ithaca NY 14853 USA
| | - Bruce A. Carlson
- Washington University in St. Louis Department of Biology, St. Louis, MO 63130 USA
| | - Jason R. Gallant
- Michigan State University Department of Integrative Biology, East Lansing MI 48824 USA
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6
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Gutiérrez‐Pinto N, McCracken KG, Tubaro P, Kopuchian C, Astie A, Cadena CD. Molecular and morphological differentiation among Torrent Duck (
Merganetta armata
) populations in the Andes. ZOOL SCR 2019. [DOI: 10.1111/zsc.12367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Natalia Gutiérrez‐Pinto
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
- School of Biological Sciences University of Nebraska Lincoln Nebraska
| | - Kevin G. McCracken
- Department of Biology University of Miami Coral Gables Florida
- Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Sciences Miami Florida
- Institute of Arctic Biology University of Alaska Museum Fairbanks Alaska
- Department of Biology and Wildlife University of Alaska Fairbanks Fairbanks Alaska
| | - Pablo Tubaro
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN ‐ CONICET) Buenos Aires Argentina
| | - Cecilia Kopuchian
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN ‐ CONICET) Buenos Aires Argentina
- Centro de Ecología Aplicada del Litoral (CECOAL‐CONICET) Corrientes Argentina
| | - Andrea Astie
- Instituto Argentino de Investigaciones de las Zonas Áridas (CONICET‐CCT Mendoza) Mendoza Argentina
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
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7
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Cadena CD, Pérez-emán JL, Cuervo AM, Céspedes LN, Epperly KL, Klicka JT. Extreme genetic structure and dynamic range evolution in a montane passerine bird: implications for tropical diversification. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly207] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Jorge L Pérez-emán
- Instituto de Zoología y Ecología Tropical, Universidad Central de Venezuela, Caracas, Venezuela
- Colección Ornitológica Phelps, Caracas, Venezuela
| | - Andrés M Cuervo
- Louisiana State University Museum of Natural Science, Baton Rouge, LA, USA
- Instituto de Investigación en Recursos Biológicos Alexander von Humboldt, Bogotá, Colombia
| | - Laura N Céspedes
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Kevin L Epperly
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - John T Klicka
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
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8
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Rocha-Méndez A, Sánchez-González LA, Arbeláez-Cortés E, Navarro-Sigüenza AG. Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetesalbinucha (Aves, Passerellidae). Zookeys 2019:125-148. [PMID: 30598618 PMCID: PMC6306474 DOI: 10.3897/zookeys.809.28743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/19/2018] [Indexed: 11/12/2022] Open
Abstract
The White-naped Brushfinch (Atlapetesalbinucha) comprises up to eight allopatric subspecies mainly identified by the color of the underparts (gray vs. yellow belly). Yellow and gray bellied forms were long considered two different species (A.albinucha and A.gutturalis), but they are presently considered as one polytypic species. Previous studies in the genus Atlapetes have shown that the phylogeny, based on molecular data, is not congruent with characters such as coloration, ecology, or distributional patterns. The phylogeography of A.albinucha was analyzed using two mitochondrial DNA regions from samples including 24 different localities throughout montane areas from eastern Mexico to Colombia. Phylogeographic analyses using Bayesian inference, maximum likelihood and haplotype network revealed incomplete geographic structure. The genetic diversity pattern is congruent with a recent process of expansion, which is also supported by Ecological Niche Models (ENM) constructed for the species and projected into three past scenarios. Overall, the results revealed an incomplete genetic divergence among populations of A.albinucha in spite of the species’ ample range, which contrasts with previous results of phylogeographic patterns in other Neotropical montane forest bird species, suggesting idiosyncratic evolutionary histories for different taxa throughout the region.
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Affiliation(s)
- Alberto Rocha-Méndez
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, México City 04510, México Universidad Nacional Autónoma de México México City Mexico
| | - Luis A Sánchez-González
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, México City 04510, México Universidad Nacional Autónoma de México México City Mexico
| | - Enrique Arbeláez-Cortés
- Grupo de Estudios en Biodiversidad, Escuela de Biología, Facultad de Ciencias, Universidad Industrial de Santander, Carrera 27 Calle 9. Bucaramanga, Santander, Colombia Universidad Industrial de Santander Bucaramanga Colombia
| | - Adolfo G Navarro-Sigüenza
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-399, México City 04510, México Universidad Nacional Autónoma de México México City Mexico
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9
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Uva V, Päckert M, Cibois A, Fumagalli L, Roulin A. Comprehensive molecular phylogeny of barn owls and relatives (Family: Tytonidae), and their six major Pleistocene radiations. Mol Phylogenet Evol 2018. [PMID: 29535030 DOI: 10.1016/j.ympev.2018.03.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The owl family Tytonidae comprises two genera: Phodilus, limited to the forests of central Africa and South-East Asia, and the ubiquitous Tyto. The genus Tyto is majorly represented by the cosmopolitan Common Barn Owl group, with more than 30 subspecies worldwide. Discrete differences in body size and plumage colouration have led to the classification of this family into many species and subspecies, but the taxonomic status and phylogenetic relationships between taxa remain unclear, and in some groups controversial. Although several previous studies attempted to resolve this problem, they have been limited in their taxonomic and geographical coverage, or have relied on restricted molecular evidence and low sample sizes. Based on the most comprehensive sampling to date (16 out of 17 Tyto species, and one out of three Phodilus species), a multi-locus approach using seven mitochondrial and two nuclear markers, and taking advantage of field data and museum collections available worldwide, our main questions in this study were: (1) what are the phylogenetic relationships and classification status of the whole family; (2) when and where did the most important speciation events occur? We confirm that the Common Barn Owl, Tyto alba is divided into three main evolutionary units: the American Barn Owl, T. furcata; the Western Barn Owl, T. alba; and the Eastern Barn Owl, T. javanica, and suggest a Late Miocene (ca. 6 mya) Australasian and African origin of the group. Our results are supported by fossil age information, given that the most recent common ancestor between the Tytonidae genera Phodilus and Tyto was probably from the Oligocene (ca. 28 mya) of Australasia. We finally reveal six major Pleistocene radiations of Tyto, all resulting in wide-range distributions.
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Affiliation(s)
- Vera Uva
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Martin Päckert
- Senckenberg Natural History Collections, Königsbrücker, Landstraße 159, 01109 Dresden, Germany.
| | - Alice Cibois
- Museum of Natural History of Geneva, Route de Managnou 1, 1208 Geneva, Switzerland.
| | - Luca Fumagalli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Rue du Bugnon 21, 1011 Lausanne, Switzerland.
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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10
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On geographic barriers and Pleistocene glaciations: Tracing the diversification of the Russet-crowned Warbler (Myiothlypis coronata) along the Andes. PLoS One 2018. [PMID: 29522515 PMCID: PMC5844518 DOI: 10.1371/journal.pone.0191598] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We studied the phylogeography and plumage variation of the Russet-crowned Warbler (Myiothlypis coronata), from Venezuela to Bolivia, with focus on populations from Ecuador and northern Peru. We analyzed sequences of mitochondrial and nuclear genes, geographic distributions, as well as photographs of specimens deposited at museum collections. Phylogenetic analyses identified three major lineages formed by populations from: Venezuela and Colombia (M. c. regulus), Ecuador and northern Peru (M. elata, M. castaneiceps, M. orientalis, M. c. chapmani), and central Peru and Bolivia (M. c. coronata). We found further population structure within M. c. regulus and M. c. coronata, and population structure and complexity of plumage variation within the Ecuador-northern Peru lineage. Time-calibrated trees estimated that most intraspecific variation originated during the Pleistocene; however, this pattern may not be attributed to an increase in diversification rate during that period. We discuss these results in the context of the importance of geographic-ecological barriers in promoting lineage diversification along the Andes and put forward a preliminary taxonomic proposal for major lineages identified in this study.
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11
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de Abreu FHT, Schietti J, Anciães M. Spatial and environmental correlates of intraspecific morphological variation in three species of passerine birds from the Purus–Madeira interfluvium, Central Amazonia. Evol Ecol 2018. [DOI: 10.1007/s10682-018-9929-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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12
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Picq S, Alda F, Bermingham E, Krahe R. Drift-driven evolution of electric signals in a Neotropical knifefish. Evolution 2016; 70:2134-44. [PMID: 27436179 DOI: 10.1111/evo.13010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 04/12/2016] [Accepted: 07/11/2016] [Indexed: 11/29/2022]
Abstract
Communication signals are highly diverse traits. This diversity is usually assumed to be shaped by selective forces, whereas the null hypothesis of divergence through drift is often not considered. In Panama, the weakly electric fish Brachyhypopomus occidentalis is widely distributed in multiple independent drainage systems, which provide a natural evolutionary laboratory for the study of genetic and signal divergence in separate populations. We quantified geographic variation in the electric signals of 109 fish from five populations, and compared it to the neutral genetic variation estimated from cytochrome oxidase I (COI) sequences of the same individuals, to test whether drift may be driving divergence of their signals. Signal distances were highly correlated with genetic distances, even after controlling for geographic distances, suggesting that drift alone is sufficient to explain geographic variation in electric signals. Significant differences at smaller geographic scales (within drainages) showed, however, that electric signals may evolve at a faster rate than expected under drift, raising the possibility that additional adaptive forces may be contributing to their evolution. Overall, our data point to stochastic forces as main drivers of signal evolution in this species and extend the role of drift in the evolution of communication systems to fish and electrocommunication.
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Affiliation(s)
- Sophie Picq
- Department of Biology, McGill University, Montreal, Quebec, H3A 1B1, Canada. .,Smithsonian Tropical Research Institute, Apartado 0843-03092 Balboa, Ancón, Republic of Panama. .,Current Address: GEOMAR Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, Kiel, 24105, Germany.
| | - Fernando Alda
- Smithsonian Tropical Research Institute, Apartado 0843-03092 Balboa, Ancón, Republic of Panama.,Current Address: Museum of Natural Science, Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA
| | - Eldredge Bermingham
- Department of Biology, McGill University, Montreal, Quebec, H3A 1B1, Canada.,Smithsonian Tropical Research Institute, Apartado 0843-03092 Balboa, Ancón, Republic of Panama.,Current Address: Patricia and Phillip Frost Museum of Science, 3280 South Miami Avenue, Miami, FL
| | - Rüdiger Krahe
- Department of Biology, McGill University, Montreal, Quebec, H3A 1B1, Canada
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13
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Benham PM, Witt CC. The dual role of Andean topography in primary divergence: functional and neutral variation among populations of the hummingbird, Metallura tyrianthina. BMC Evol Biol 2016; 16:22. [PMID: 26801894 PMCID: PMC4724075 DOI: 10.1186/s12862-016-0595-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/18/2016] [Indexed: 11/10/2022] Open
Abstract
Background The ridges and valleys of the Andes create physical barriers that limit animal dispersal and cause deterministic local variation in rainfall. This has resulted in physical isolation of animal populations and variation in habitats, each of which has likely contributed to the evolution of high species diversity in the region. However, the relative influences of geographic isolation, ecoclimatic conditions, and their potential interactions remain poorly understood. To address this, we compared patterns of genetic and morphological diversity in Peruvian populations of the hummingbird Metallura tyrianthina. Results Phylogenetic and variation partitioning analyses showed that geographic isolation rather than climatic dissimilarity explained the greatest proportion of genetic variance. In contrast, bill length variation was explained by climatic seasonality, but not by genetic divergence. We found that mutation-scaled migration rate (m) between persistently humid and semi-humid environments was nearly 20 times higher when the habitats were contiguous (m = 39.9) than when separated by a barrier, the Cordillera de Vilcanota (m = 2.1). Moreover, the population experiencing more gene flow exhibited a lesser degree of bill length divergence despite similar differences in climate. Conclusions Geographic isolation is necessary for genetic divergence. Ecological differences, represented here by climate characteristics, are necessary for functional divergence. Gene flow appears to hinder the evolution of functional traits toward local adaptive optima. This suggests that functional diversification requires geographic isolation followed or accompanied by a shift in ecological conditions. Andean topography causes both isolation and climatic variation, underscoring its dual role in biotic diversification. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0595-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Phred M Benham
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, 167 Castetter Hall MSC03 2020, 1 University of New Mexico, Albuquerque, NM, 87131, USA. .,Present address: Division of Biological Sciences, University of Montana, 32 Campus Dr. HS104, Missoula, MT, 59812, USA.
| | - Christopher C Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, 167 Castetter Hall MSC03 2020, 1 University of New Mexico, Albuquerque, NM, 87131, USA.
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14
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Kattan GH, Tello SA, Giraldo M, Cadena CD. Neotropical bird evolution and 100 years of the enduring ideas of Frank M. Chapman. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gustavo H. Kattan
- Departamento de Ciencias Naturales y Matemáticas; Pontificia Universidad Javeriana Seccional Cali; Cali Colombia
| | - Sofía A. Tello
- Asociación para el Estudio y Conservación de las Aves Acuáticas en Colombia - Calidris; Cali Colombia
| | - Manuel Giraldo
- Departamento de Biología; Universidad del Valle; Cali Colombia
| | - C. D. Cadena
- Laboratorio de Biología Evolutiva; Departamento de Ciencias Biológicas; Universidad de Los Andes; Bogotá Colombia
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15
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Winger BM, Hosner PA, Bravo GA, Cuervo AM, Aristizábal N, Cueto LE, Bates JM. Inferring speciation history in the Andes with reduced‐representation sequence data: an example in the bay‐backed antpittas (Aves; Grallariidae;
Grallaria hypoleuca
s. l.). Mol Ecol 2015; 24:6256-77. [DOI: 10.1111/mec.13477] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/06/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Benjamin M. Winger
- Committee on Evolutionary Biology The University of Chicago Chicago IL 60637 USA
- Life Sciences Section Integrative Research Center The Field Museum of Natural History Chicago IL 60605 USA
| | - Peter A. Hosner
- Department of Ecology and Evolutionary Biology and Biodiversity Institute University of Kansas Lawrence KS 66045 USA
- Department of Biology University of Florida Gainesville FL 32603 USA
| | - Gustavo A. Bravo
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
- Secão de Aves Museu de Zoologia Universidade de São Paulo (MZUSP) São Paulo SP 04263‐000 Brasil
| | - Andrés M. Cuervo
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
- Department of Ecology and Evolutionary Biology Tulane University New Orleans LA 70118 USA
| | - Natalia Aristizábal
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
- Departamento de Ecologia Instituto de Biociências Universidade de São Paulo São Paulo SP 05508‐900 Brasil
| | - Luis E. Cueto
- Life Sciences Section Integrative Research Center The Field Museum of Natural History Chicago IL 60605 USA
| | - John M. Bates
- Life Sciences Section Integrative Research Center The Field Museum of Natural History Chicago IL 60605 USA
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Winger BM, Bates JM. The tempo of trait divergence in geographic isolation: Avian speciation across the Marañon Valley of Peru. Evolution 2015; 69:772-87. [DOI: 10.1111/evo.12607] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 01/07/2015] [Indexed: 01/30/2023]
Affiliation(s)
- Benjamin M. Winger
- Committee on Evolutionary Biology; The University of Chicago; Culver Hall 402 Chicago Illinois 60637
- Life Sciences Section, Integrative Research Center; The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago Illinois 60605
| | - John M. Bates
- Committee on Evolutionary Biology; The University of Chicago; Culver Hall 402 Chicago Illinois 60637
- Life Sciences Section, Integrative Research Center; The Field Museum of Natural History; 1400 S. Lake Shore Drive Chicago Illinois 60605
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Sigurðsson S, Cracraft J. Deciphering the diversity and history of New World nightjars (Aves: Caprimulgidae) using molecular phylogenetics. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12109] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Snorri Sigurðsson
- Department of Ornithology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
- The Graduate Center; City University of New York; 365 Fifth Avenue New York NY 10016 USA
| | - Joel Cracraft
- Department of Ornithology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
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18
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Bonaccorso E, Guayasamin JM. On the Origin of Pantepui montane biotas: A Perspective Based on the Phylogeny of Aulacorhynchus toucanets. PLoS One 2013; 8:e67321. [PMID: 23840663 PMCID: PMC3694146 DOI: 10.1371/journal.pone.0067321] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/16/2013] [Indexed: 11/18/2022] Open
Abstract
To understand the origin of Pantepui montane biotas, we studied the biogeography of toucanets in the genus Aulacorhynchus. These birds are ideal for analyzing historical relationships among Neotropical montane regions, given their geographic distribution from Mexico south to Bolivia, including northern Venezuela (Cordillera de la Costa), and the Pantepui. Analyses were based on molecular phylogenies using mitochondrial and nuclear DNA sequences. Topology tests were applied to compare alternative hypotheses that may explain the current distribution of Aulacorhynchus toucanets, in the context of previous hypotheses of the origin of Pantepui montane biotas. Biogeographic reconstructions in RASP and Lagrange were used to estimate the ancestral area of the genus, and an analysis in BEAST was used to estimate a time framework for its diversification. A sister relationship between the Pantepui and Andes+Cordillera de la Costa was significantly more likely than topologies indicating other hypothesis for the origin of Pantepui populations. The Andes was inferred as the ancestral area for Aulacorhynchus, and the group has diversified since the late Miocene. The biogeographic patterns found herein, in which the Andes are the source for biotas of other regions, are consistent with those found for flowerpiercers and tanagers, and do not support the hypothesis of the geologically old Pantepui as a source of Neotropical montain diversity. Based on the high potential for cryptic speciation and isolation of Pantepui populations, we consider that phylogenetic studies of additional taxa are important from a conservation perspective.
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Affiliation(s)
- Elisa Bonaccorso
- Centro de Investigación en Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, Quito, Pichincha, Ecuador
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Juan M. Guayasamin
- Centro de Investigación en Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, Quito, Pichincha, Ecuador
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Kerr KCR, Dove CJ. Delimiting shades of gray: phylogeography of the Northern Fulmar, Fulmarus glacialis. Ecol Evol 2013; 3:1915-30. [PMID: 23919139 PMCID: PMC3728934 DOI: 10.1002/ece3.597] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 04/12/2013] [Accepted: 04/15/2013] [Indexed: 11/17/2022] Open
Abstract
The Northern Fulmar (Fulmarus glacialis) is a common tube-nosed seabird with a disjunct Holarctic range. Taxonomic divisions within the Northern Fulmar have historically been muddled by geographical variation notably including highly polymorphic plumage. Recent molecular analyses (i.e., DNA barcoding) have suggested that genetic divergence between Atlantic and Pacific populations could be on par with those typically observed between species. We employ a multigene phylogenetic analysis to better explore the level of genetic divergence between these populations and to test an old hypothesis on the origin of the modern distribution of color morphs across their range. Additionally, we test whether mutations in the melanocortin-1 receptor gene (MC1R) are associated with dark plumage in the Northern Fulmar. We confirmed that mitochondrial lineages in the Atlantic and Pacific populations are highly divergent, but nuclear markers revealed incomplete lineage sorting. Genetic divergence between these populations is consistent with that observed between many species of Procellariiformes and we recommend elevating these two forms to separate species. We also find that MC1R variation is not associated with color morph but rather is better explained by geographical divergence.
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Affiliation(s)
- Kevin C R Kerr
- Division of Birds, National Museum of Natural History, Smithsonian Institution Washington, DC, 20560
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Barrera-Guzmán AO, Milá B, Sánchez-González LA, Navarro-Sigüenza AG. Speciation in an avian complex endemic to the mountains of Middle America (Ergaticus, Aves: Parulidae). Mol Phylogenet Evol 2011; 62:907-20. [PMID: 22155712 DOI: 10.1016/j.ympev.2011.11.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 11/20/2011] [Accepted: 11/22/2011] [Indexed: 01/29/2023]
Abstract
The implementation of the phylogeographic approach for the study of biodiversity is critical in poorly sampled regions like the montane systems of Middle America, as complex evolutionary histories often result in the presence of independent lineages not properly considered by traditional taxonomy. Herein we sequenced 2370 bp of mtDNA (ND2, cyt b and ATPase) from 81 individuals of Ergaticus, a complex of birds endemic to the montane forests of Middle America. Although current taxonomy recognizes two species, the results reveal considerable genetic structure with the presence of four mtDNA lineages. Two of these lineages within Ergaticus ruber evidence the need of a revaluation of the species limits for this taxon. The general phylogeographic pattern can be explained as a consequence of relative isolation of the populations in different mountain ranges separated by low elevation barriers. Most population groups did not show signals of demographic expansion with the exception of the one corresponding to clade 1. The divergence time estimates point to the Pleistocene as an important time period for the diversification of this complex.
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Affiliation(s)
- Alfredo O Barrera-Guzmán
- Museo de Zoología Alfonso Herrera, Universidad Nacional Autónoma de México, México DF 04510, Mexico.
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Toon A, Austin JJ, Dolman G, Pedler L, Joseph L. Evolution of arid zone birds in Australia: leapfrog distribution patterns and mesic-arid connections in quail-thrush (Cinclosoma, Cinclosomatidae). Mol Phylogenet Evol 2011; 62:286-95. [PMID: 22040766 DOI: 10.1016/j.ympev.2011.09.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 09/26/2011] [Accepted: 09/30/2011] [Indexed: 11/24/2022]
Abstract
The quail-thrush, Cinclosoma, include between five and seven species distributed broadly across arid and semi-arid inland Australia, mesic forests of south-eastern Australia and New Guinea. It has been suggested that the arid zone species of quail-thrush arose from forest ancestors as Australia changed from a warm wet climate to a cooler drier climate since the late-Miocene. We generated multilocus (mitochondrial ND2 and eight nuclear loci) gene and species trees with complete taxon sampling of Cinclosoma to investigate evolutionary relationships and species status of some taxa. Topologies reconstructed in congruent, highly-resolved gene trees and species trees that supported the recognition of seven species. Ancestral state reconstruction and divergence time estimates suggest that arid-adapted taxa radiated in parallel with a drying climate and changing habitat. A 'leapfrog' distribution in phenotypes of arid zone taxa was likely a result of ancestral retention of inconspicuous (or camouflaged) plumage patterns. A specimen-based report from 1968 of hybridization between non-sister taxa Cinclosoma castanotum and Cinclosoma marginatum was verified using molecular analysis on specimens collected at the same locality 40 years later. We discuss the implications of hybridization to the evolution of this species group.
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Affiliation(s)
- Alicia Toon
- Australian National Wildlife Collection, CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, ACT 2601, Australia.
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González C, Ornelas JF, Gutiérrez-Rodríguez C. Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis). BMC Evol Biol 2011; 11:38. [PMID: 21299905 PMCID: PMC3045325 DOI: 10.1186/1471-2148-11-38] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 02/08/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mesoamerica is one of the most threatened biodiversity hotspots in the world, yet we are far from understanding the geologic history and the processes driving population divergence and speciation for most endemic taxa. In species with highly differentiated populations selective and/or neutral factors can induce rapid changes to traits involved in mate choice, promoting reproductive isolation between allopatric populations that can eventually lead to speciation. We present the results of genetic differentiation, and explore drift and selection effects in promoting acoustic and morphological divergence among populations of Campylopterus curvipennis, a lekking hummingbird with an extraordinary vocal variability across Mesoamerica. RESULTS Analyses of two mitochondrial genes and ten microsatellite loci genotyped for 160 individuals revealed the presence of three lineages with no contemporary gene flow: C. c. curvipennis, C. c. excellens, and C. c. pampa disjunctly distributed in the Sierra Madre Oriental, the Tuxtlas region and the Yucatan Peninsula, respectively. Sequence mtDNA and microsatellite data were congruent with two diversification events: an old vicariance event at the Isthmus of Tehuantepec (c. 1.4 Ma), and a more recent Pleistocene split, isolating populations in the Tuxtlas region. Hummingbirds of the excellens group were larger, and those of the pampa group had shorter bills, and lineages that have been isolated the longest shared fewer syllables and differed in spectral and temporal traits of a shared syllable. Coalescent simulations showed that fixation of song types has occurred faster than expected under neutrality but the null hypothesis that morphological divergence resulted from drift was not rejected. CONCLUSIONS Our phylogeographic analyses uncovered the presence of three Mesoamerican wedge-tailed sabrewing lineages, which diverged at different time scales. These results highlight the importance of the Isthmus of Tehuantepec and more recent Pleistocene climatic events in driving isolation and population divergence. Coalescent analyses of the evolution of phenotypic traits suggest that selection is driving song evolution in wedge-tailed sabrewings but drift could not be rejected as a possibility for morphological divergence.
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Affiliation(s)
- Clementina González
- Departamento de Biología Evolutiva, Instituto de Ecología AC, carretera antigua a Coatepec No. 351, El Haya, Xalapa, Veracruz 91070 México
- Posgrado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), México, D. F., 04510 México
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología AC, carretera antigua a Coatepec No. 351, El Haya, Xalapa, Veracruz 91070 México
| | - Carla Gutiérrez-Rodríguez
- Departamento de Biología Evolutiva, Instituto de Ecología AC, carretera antigua a Coatepec No. 351, El Haya, Xalapa, Veracruz 91070 México
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