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Nishikaku K, Yonezawa T, Nishibori M, Harada M, Kawaguchi F, Sasazaki S, Torii Y, Imakawa K, Kawai K, Liu J, Mannen H, Kobayashi T. Phylogenomics and Spatiotemporal Dynamics of Bovine Leukemia Virus Focusing on Asian Native Cattle: Insights Into the Early Origin and Global Dissemination. Front Microbiol 2022; 13:917324. [PMID: 35814709 PMCID: PMC9263593 DOI: 10.3389/fmicb.2022.917324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Bovine leukemia virus (BLV), the causative agent of enzootic bovine leukosis, is currently one of the most important pathogens affecting the cattle industry worldwide. Determining where and in which host it originated, and how it dispersed across continents will provide valuable insights into its historical emergence as the cattle pathogen. Various species in the Bos genus were domesticated in Asia, where they also diversified. As native cattle (taurine cattle, zebu cattle, yak, and water buffalo) are indigenous and adapted to local environments, we hypothesized that Asian native cattle could have harbored BLV and, therefore, that they were important for virus emergence, maintenance, and spread. In this study, phylogeographic and ancestral trait analyses—including sequences obtained from Asian native cattle—were used to reconstruct the evolutionary history of BLV. It was shown that, since its probable emergence in Asia, the virus spread to South America and Europe via international trade of live cattle. It was inferred that zebu cattle were the hosts for the early origin of BLV, while taurine cattle played the significant role in the transmission worldwide. In addition, the results of positive selection analysis indicate that yak had a substantially minor role in the transmission of this virus. In this study, endogenous deltaretrovirus sequences in bats, collected in Asian countries, were also analyzed on whether these sequences were present in the bat genome. Endogenous deltaretrovirus sequences were detected from bat species endemic to specific regions and geographically isolated for a long time. Endogenous deltaretrovirus sequences from these geographically isolated species represent ancient exogenous deltaretroviruses distributions. The phylogenetic analysis revealed that these newly obtained endogenous deltaretrovirus sequences were closely related to those of BLV from Asian native cattle, indicating that BLV-related ancient deltaretroviruses circulated in Asia long before the emergence of BLV. Together, our analyses provide evidence for origin and spatiotemporal dynamics of BLV.
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Affiliation(s)
- Kohei Nishikaku
- Laboratory of Animal Health, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
| | - Takahiro Yonezawa
- Laboratory of Animal Genetics, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Masashi Harada
- Laboratory Animal Center, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yasushi Torii
- Laboratory of Animal Health, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
| | - Kazuhiko Imakawa
- Laboratory of Molecular Reproduction, Research Institute of Agriculture, Tokai University, Kumamoto, Japan
| | - Kuniko Kawai
- Department of Biology, School of Biological Science, Tokai University, Sapporo, Japan
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry and Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Tomoko Kobayashi
- Laboratory of Animal Health, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
- *Correspondence: Tomoko Kobayashi,
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Kyriazis CC, Alam B, Wjodyla M, Hackett S, Hosner P, Mays HL, Heaney LR, Reddy S. Colonization and diversification of the white-browed shortwing (Aves: Muscicapidae: Brachypteryx montana) in the Philippines. Mol Phylogenet Evol 2018; 121:121-131. [PMID: 29305243 DOI: 10.1016/j.ympev.2017.12.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 12/01/2017] [Accepted: 12/24/2017] [Indexed: 10/18/2022]
Abstract
Molecular phylogenetic approaches have greatly improved our knowledge of the pattern and process of biological diversification across the globe; however, many regions remain poorly documented, even for well-studied vertebrate taxa. The Philippine archipelago, one of the least-studied 'biodiversity hotspots', is an ideal natural laboratory for investigating the factors driving diversification in an insular and geologically dynamic setting. We investigated the history and geography of diversification of the Philippine populations of a widespread montane bird, the White-browed Shortwing (Brachypteryx montana). Leveraging dense archipelago-wide sampling, we generated a multi-locus genetic dataset (one nuclear and two mtDNA markers), which we analyzed using phylogenetic, population genetic, and coalescent-based methods. Our results demonstrate that Philippine shortwings (1) likely colonized the Philippines from the Sunda Shelf to Mindanao in the late Miocene or Pliocene, (2) diversified across inter-island barriers into three divergent lineages during the Pliocene and early Pleistocene, (3) have not diversified within the largest island, Luzon, contrary to patterns observed in other montane taxa, and (4) colonized Palawan from the oceanic Philippines rather than from Borneo, challenging the assumption of Palawan functioning exclusively as a biogeographic extension of the Sunda Shelf. Additionally, our finding that divergent (c. 4.0 mya) lineages are coexisting in secondary sympatry on Mindanao without apparent gene flow suggests that the speciation process is likely complete for these shortwing lineages. Overall, these investigations provide insight into how topography and island boundaries influence diversification within remote oceanic archipelagos and echo the results of many other studies in demonstrating that taxonomic diversity continues to be underestimated in the Philippines.
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Affiliation(s)
- Christopher C Kyriazis
- Biology Department, Loyola University Chicago, 1050 W. Sheridan Road, Chicago, IL 60660, USA
| | - Bushra Alam
- Biology Department, Loyola University Chicago, 1050 W. Sheridan Road, Chicago, IL 60660, USA
| | - Mark Wjodyla
- Biology Department, Loyola University Chicago, 1050 W. Sheridan Road, Chicago, IL 60660, USA
| | - Shannon Hackett
- Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Peter Hosner
- Department of Biology, University of Florida, Gainesville, FL 32607, USA
| | - Herman L Mays
- Department of Biological Sciences, Marshall University, Huntington, WV 25755, USA; Cincinnati Museum Center, Cincinnati, OH 45203, USA
| | - Lawrence R Heaney
- Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Sushma Reddy
- Biology Department, Loyola University Chicago, 1050 W. Sheridan Road, Chicago, IL 60660, USA.
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Françoso E, Zuntini AR, Carnaval AC, Arias MC. Comparative phylogeography in the Atlantic forest and Brazilian savannas: pleistocene fluctuations and dispersal shape spatial patterns in two bumblebees. BMC Evol Biol 2016; 16:267. [PMID: 27927169 PMCID: PMC5142330 DOI: 10.1186/s12862-016-0803-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 10/14/2016] [Indexed: 01/23/2023] Open
Abstract
Background Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages. Results Results suggest that Pleistocene climatic oscillations directly influenced the population structure of both species. Correlative species distribution models predict that the warmer conditions of the Last Interglacial contributed to population contraction, while demographic expansion happened during the Last Glacial Maximum. These results are consistent with physiological data suggesting that bumblebees are well adapted to colder conditions. Intra-specific mitochondrial genealogies are not congruent between the two species, which may be explained by their documented differences in dispersal ability. Conclusions While populations of the high-dispersal B. morio are morphologically and genetically homogeneous across the species range, B. pauloensis encompasses multiple (three) mitochondrial lineages, and show clear genetic, geographic, and morphological differences. Because the lineages of B. pauloensis are currently exposed to distinct climatic conditions (and elevations), parapatric diversification may occur within this taxon. The eastern portion of the state of São Paulo, the most urbanized area in Brazil, represents the center of genetic diversity for B. pauloensis. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0803-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elaine Françoso
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, sala 320, 05508-090, São Paulo, SP, Brazil.
| | - Alexandre Rizzo Zuntini
- Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, 13083-970, Campinas, SP, Brazil
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York, New York, USA.,The Graduate Center, City University of New York, New York, NY, USA
| | - Maria Cristina Arias
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, sala 320, 05508-090, São Paulo, SP, Brazil
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Sánchez-González LA, Hosner PA, Moyle RG. Genetic Differentiation in Insular Lowland Rainforests: Insights from Historical Demographic Patterns in Philippine Birds. PLoS One 2015; 10:e0134284. [PMID: 26312748 PMCID: PMC4552387 DOI: 10.1371/journal.pone.0134284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 07/07/2015] [Indexed: 11/25/2022] Open
Abstract
Phylogeographic studies of Philippine birds support that deep genetic structure occurs across continuous lowland forests within islands, despite the lack of obvious contemporary isolation mechanisms. To examine the pattern and tempo of diversification within Philippine island forests, and test if common mechanisms are responsible for observed differentiation, we focused on three co-distributed lowland bird taxa endemic to Greater Luzon and Greater Negros-Panay: Blue-headed Fantail (Rhipidura cyaniceps), White-browed Shama (Copsychus luzoniensis), and Lemon-throated Leaf-Warbler (Phylloscopus cebuensis). Each species has two described subspecies within Greater Luzon, and a single described subspecies on Greater Negros/Panay. Each of the three focal species showed a common geographic pattern of two monophyletic groups in Greater Luzon sister to a third monophyletic group found in Greater Negros-Panay, suggesting that common or similar biogeographic processes may have produced similar distributions. However, studied species displayed variable levels of mitochondrial DNA differentiation between clades, and genetic differentiation within Luzon was not necessarily concordant with described subspecies boundaries. Population genetic parameters for the three species suggested both rapid population growth from small numbers and geographic expansion across Luzon Island. Estimates of the timing of population expansion further supported that these events occurred asynchronously throughout the Pleistocene in the focal species, demanding particular explanations for differentiation, and support that co-distribution may be secondarily congruent.
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Affiliation(s)
- Luis Antonio Sánchez-González
- Natural History Museum and Biodiversity Institute, Dyche Hall, University of Kansas, 1345 Jayhawk Blvd., Lawrence, Kansas 66045-7561, United States of America
- * E-mail:
| | - Peter A. Hosner
- Natural History Museum and Biodiversity Institute, Dyche Hall, University of Kansas, 1345 Jayhawk Blvd., Lawrence, Kansas 66045-7561, United States of America
| | - Robert G. Moyle
- Natural History Museum and Biodiversity Institute, Dyche Hall, University of Kansas, 1345 Jayhawk Blvd., Lawrence, Kansas 66045-7561, United States of America
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Archipelago colonization by ecologically dissimilar amphibians: evaluating the expectation of common evolutionary history of geographical diffusion in co-distributed rainforest tree frogs in islands of Southeast Asia. Mol Phylogenet Evol 2014; 72:35-41. [PMID: 24389467 DOI: 10.1016/j.ympev.2013.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 12/19/2013] [Accepted: 12/21/2013] [Indexed: 11/24/2022]
Abstract
Widespread, co-distributed species with limited relative dispersal abilities represent compelling focal taxa for comparative phylogeography. Forest vertebrates in island archipelagos often exhibit pronounced population structure resulting from limited dispersal abilities or capacity to overcome marine barriers to dispersal. The exceptionally diverse Old World tree frogs of the family Rhacophoridae have colonized the forested island archipelagos of Southeast Asia on multiple occasions, entering the islands of Indonesia and the Philippines via a "stepping stone" mode of dispersal along elongate island chains, separated by a series of marine channels. Here we evaluate the prediction that two tightly co-distributed Philippine rhacophorids colonized the archipelago during concomitant timescales and in the same, linear, "island-hopping" progression. We use a new multilocus dataset, utilize dense genetic sampling from the eastern arc of the Philippines, and we take a model-based phylogeographic approach to examining the two species for similar topological patterns of diversification, genetic structure, and timescales of diversification. Our results support some common mechanistic predictions (a general south-to-north polarity of colonization) but not others (timescale for colonization and manner and degree of lineage diversification), suggesting differing biogeographic scenarios of geographical diffusion through the archipelago and unique and idiosyncratic ecological capacities and evolutionary histories of each species.
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Brown RM, Siler CD, Oliveros CH, Esselstyn JA, Diesmos AC, Hosner PA, Linkem CW, Barley AJ, Oaks JR, Sanguila MB, Welton LJ, Blackburn DC, Moyle RG, Townsend Peterson A, Alcala AC. Evolutionary Processes of Diversification in a Model Island Archipelago. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110411-160323] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rafe M. Brown
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Cameron D. Siler
- Sam Noble Museum and Department of Biology, University of Oklahoma, Norman, Oklahoma 73073-7029;
| | - Carl H. Oliveros
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803;
| | - Arvin C. Diesmos
- Herpetology Section, Zoology Division, National Museum of the Philippines, Manila, Philippines;
| | - Peter A. Hosner
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Charles W. Linkem
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
- Current address: Department of Biology, University of Washington, Seattle, Washington 98195;
| | - Anthony J. Barley
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Jamie R. Oaks
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | | | - Luke J. Welton
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
- Department of Biology, Brigham Young University, Provo, Utah 84602;
| | - David C. Blackburn
- Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, California 94118;
| | - Robert G. Moyle
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - A. Townsend Peterson
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Angel C. Alcala
- Silliman University-Angelo King Center for Research and Environmental Management (SUAKCREM), SU-Marine Laboratory, 6200 Dumaguete City, Philippines;
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Sargis EJ, Campbell KK, Olson LE. Taxonomic Boundaries and Craniometric Variation in the Treeshrews (Scandentia, Tupaiidae) from the Palawan Faunal Region. J MAMM EVOL 2013. [DOI: 10.1007/s10914-013-9229-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Nesi N, Kadjo B, Pourrut X, Leroy E, Pongombo Shongo C, Cruaud C, Hassanin A. Molecular systematics and phylogeography of the tribe Myonycterini (Mammalia, Pteropodidae) inferred from mitochondrial and nuclear markers. Mol Phylogenet Evol 2013; 66:126-37. [DOI: 10.1016/j.ympev.2012.09.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 09/14/2012] [Accepted: 09/15/2012] [Indexed: 10/27/2022]
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Oaks JR, Sukumaran J, Esselstyn JA, Linkem CW, Siler CD, Holder MT, Brown RM. Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events. Evolution 2012; 67:991-1010. [PMID: 23550751 DOI: 10.1111/j.1558-5646.2012.01840.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co-distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea-level oscillations during the Pleistocene caused diversification across the islands. To guide interpretation of our results, we perform a suite of simulation-based power analyses. Our empirical results strongly support a recent simultaneous divergence event for all 22 taxon pairs, consistent with the prediction of the Pleistocene-driven diversification hypothesis. However, our empirical estimates are sensitive to changes in prior distributions, and our simulations reveal low power of the method to detect random variation in divergence times and bias toward supporting clustered divergences. Our results demonstrate that analyses exploring power and prior sensitivity should accompany ABC model selection inferences. The problems we identify are potentially mitigable with uniform priors over divergence models (rather than classes of models) and more flexible prior distributions on demographic and divergence-time parameters.
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Affiliation(s)
- Jamie R Oaks
- Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.
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Life in a mosaic landscape: anthropogenic habitat fragmentation affects genetic population structure in a frugivorous bat species. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0434-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Moussy C, Hosken D, Mathews F, Smith G, Aegerter J, Bearhop S. Migration and dispersal patterns of bats and their influence on genetic structure. Mamm Rev 2012. [DOI: 10.1111/j.1365-2907.2012.00218.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caroline Moussy
- Centre for Ecology and Conservation; University of Exeter; Tremough Campus, Penryn; Cornwall; TR10 9EZ; UK
| | - D.J. Hosken
- Centre for Ecology and Conservation; University of Exeter; Tremough Campus, Penryn; Cornwall; TR10 9EZ; UK
| | - F. Mathews
- University of Exeter, Hatherly Laboratories; Prince of Wales Road; Exeter; EX4 4PS; UK
| | - G.C. Smith
- The Food and Environment Research Agency; Sand Hutton; York; YO41 1LZ; UK
| | - J.N. Aegerter
- The Food and Environment Research Agency; Sand Hutton; York; YO41 1LZ; UK
| | - S. Bearhop
- Centre for Ecology and Conservation; University of Exeter; Tremough Campus, Penryn; Cornwall; TR10 9EZ; UK
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Hagen IJ, Donnellan SC, Bull CM. Phylogeography of the prehensile-tailed skink Corucia zebrata on the Solomon Archipelago. Ecol Evol 2012; 2:1220-34. [PMID: 22833796 PMCID: PMC3402196 DOI: 10.1002/ece3.84] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/29/2011] [Accepted: 10/31/2011] [Indexed: 11/11/2022] Open
Abstract
The biogeography of islands is often strongly influenced by prior geological events. Corucia zebrata (Squamata: Scincidae) is endemic to the geologically complex Solomon Archipelago in Northern Melanesia. We examined the level of divergence for different island populations of C. zebrata and discussed these patterns in light of Pleistocene land bridges, island isolation, and island age. Corucia zebrata was sampled from 14 locations across the Solomon Archipelago and sequenced at two mitochondrial genes (ND2 and ND4; 1697 bp in total) and four nuclear loci (rhodopsin, an unknown intron, AKAP9, and PTPN12). Measures of genetic divergence, analyses of genetic variation, and Bayesian phylogenetic inference were used and the data assessed in light of geological information. Populations of C. zebrata on separate islands were found to be genetically different from each other, with reciprocal monophyly on mitochondrial DNA. Populations on islands previously connected by Pleistocene land bridges were marginally less divergent from each other than from populations on other nearby but isolated islands. There are indications that C. zebrata has radiated across the eastern islands of the archipelago within the last 1–4 million years. Nuclear loci were not sufficiently informative to yield further information about the phylogeography of C. zebrata on the Solomon Archipelago. Analyses of the mitochondrial data suggest that dispersal between islands has been very limited and that there are barriers to gene flow within the major islands. Islands that have been isolated during the Pleistocene glacial cycles are somewhat divergent in their mitochondrial genotypes, however, isolation by distance (IBD) and recent colonization of isolated but geologically younger islands appear to have had stronger effects on the phylogeography of C. zebrata than the Pleistocene glacial cycles. This contrasts with patterns reported for avian taxa, and highlights the fact that biogeographic regions for island species cannot be directly extrapolated among taxa of differing dispersal ability.
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Heaney LR. Nyctalus plancyi and Falsistrellus petersi (Chiroptera: Vespertilionidae) from Northern Luzon, Philippines: Ecology, Phylogeny, and Biogeographic Implications. ACTA CHIROPTEROLOGICA 2012. [DOI: 10.3161/150811012x661602] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Lawrence R. Heaney
- Department of Zoology, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
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Linkem CW, Diesmos AC, Brown RM. Molecular systematics of the Philippine forest skinks (Squamata: Scincidae: Sphenomorphus): testing morphological hypotheses of interspecific relationships. Zool J Linn Soc 2011; 163:1217-1243. [PMID: 32336789 PMCID: PMC7165859 DOI: 10.1111/j.1096-3642.2011.00747.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 03/06/2011] [Accepted: 03/08/2011] [Indexed: 11/28/2022]
Abstract
Skinks of the genus Sphenomorphus are the most diverse clade of squamates in the Philippine Archipelago. Morphological examination of these species has defined six phenotypic groups that are commonly used in characterizations of taxonomic hypotheses. We used a molecular phylogeny based on four mitochondrial and two nuclear genes to assess the group's biogeographical history in the archipelago and examine the phylogenetic validity of the currently recognized Philippine species groups. We re‐examined traditional characters used to define species groups and used multivariate statistics to quantitatively evaluate group structure in morphometric space. Clustering analyses of phenotypic similarity indicate that some (but not all) members of previously defined species groups are phenotypically most similar to other members of the same group. However, when species group membership was mapped on our partitioned Bayesian phylogenetic hypothesis, only one species group corresponds to a clade; all other species group arrangements are strongly rejected by our phylogeny. Our results demonstrate that (1) previously recognized species group relationships were misled by phenotypic convergence; (2) Sphenomorphus is widely paraphyletic; and (3) multiple lineages have independently invaded the Philippines. Based on this new perspective on the phylogenetic relationships of Philippine Sphenomorphus, we revise the archipelago's diverse assemblage of species at the generic level, and resurrect and/or expand four previously recognized genera, and describe two new genera to accommodate the diversity of Philippine skinks of the Sphenomorphus group. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163, 1217–1243.
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Affiliation(s)
- Charles W Linkem
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Arvin C Diesmos
- National Museum of the Philippines, Rizal Park, Padre Burgos Ave. Ermita 1000, Manila, Philippines
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA
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Esselstyn JA, Maher SP, Brown RM. Species interactions during diversification and community assembly in an island radiation of shrews. PLoS One 2011; 6:e21885. [PMID: 21760918 PMCID: PMC3131392 DOI: 10.1371/journal.pone.0021885] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Accepted: 06/09/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Closely related, ecologically similar species often have adjacent distributions, suggesting competitive exclusion may contribute to the structure of some natural communities. In systems such as island archipelagos, where speciation is often tightly associated with dispersal over oceanic barriers, competitive exclusion may prevent population establishment following inter-island dispersal and subsequent cladogenesis. METHODOLOGY/PRINCIPAL FINDINGS Using a combination of tools, we test the hypothesis that the distributions of shrew (Crocidura) species in the Philippines are the result of competitive exclusion preventing secondary invasion of occupied islands. We first compare ecological niche models between two widespread, allopatric species and find statistical support for their ecological similarity, implying that competition for habitat between these species is possible. We then examine dispersion patterns among sympatric species and find some signal for overdispersion of body size, but not for phylogenetic branch length. Finally, we simulate the process of inter-island colonization under a stochastic model of dispersal lacking ecological forces. Results are dependent on the geographic scope and colonization probability employed. However, some combinations suggest that the number of inter-island dispersal events necessary to populate the archipelago may be much higher than the minimum number of colonization events necessary to explain current estimates of species richness and phylogenetic relationships. If our model is appropriate, these results imply that alternative factors, such as competitive exclusion, may have influenced the process of inter-island colonization and subsequent cladogenesis. CONCLUSIONS/SIGNIFICANCE We interpret the combined results as providing tenuous evidence that similarity in body size may prevent co-occurrence in Philippine shrews and that competitive exclusion among ecologically similar species, rather than an inability to disperse among islands, may have limited diversification in this group, and, possibly other clades endemic to island archipelagos.
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Exploring demographic, physical, and historical explanations for the genetic structure of two lineages of Greater Antillean bats. PLoS One 2011; 6:e17704. [PMID: 21445291 PMCID: PMC3061861 DOI: 10.1371/journal.pone.0017704] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 02/08/2011] [Indexed: 11/19/2022] Open
Abstract
Observed patterns of genetic structure result from the interactions of demographic, physical, and historical influences on gene flow. The particular strength of various factors in governing gene flow, however, may differ between species in biologically relevant ways. We investigated the role of demographic factors (population size and sex-biased dispersal) and physical features (geographic distance, island size and climatological winds) on patterns of genetic structure and gene flow for two lineages of Greater Antillean bats. We used microsatellite genetic data to estimate demographic characteristics, infer population genetic structure, and estimate gene flow among island populations of Erophylla sezekorni/E. bombifrons and Macrotus waterhousii (Chiroptera: Phyllostomidae). Using a landscape genetics approach, we asked if geographic distance, island size, or climatological winds mediate historical gene flow in this system. Samples from 13 islands spanning Erophylla's range clustered into five genetically distinct populations. Samples of M. waterhousii from eight islands represented eight genetically distinct populations. While we found evidence that a majority of historical gene flow between genetic populations was asymmetric for both lineages, we were not able to entirely rule out incomplete lineage sorting in generating this pattern. We found no evidence of contemporary gene flow except between two genetic populations of Erophylla. Both lineages exhibited significant isolation by geographic distance. Patterns of genetic structure and gene flow, however, were not explained by differences in relative effective population sizes, island area, sex-biased dispersal (tested only for Erophylla), or surface-level climatological winds. Gene flow among islands appears to be highly restricted, particularly for M. waterhousii, and we suggest that this species deserves increased taxonomic attention and conservation concern.
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Chan LM, Goodman SM, Nowak MD, Weisrock DW, Yoder AD. Increased population sampling confirms low genetic divergence among Pteropus (Chiroptera: Pteropodidae) fruit bats of Madagascar and other western Indian Ocean islands. PLOS CURRENTS 2011; 3:RRN1226. [PMID: 21479256 PMCID: PMC3064450 DOI: 10.1371/currents.rrn1226] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/22/2011] [Indexed: 11/28/2022]
Abstract
Fruit bats of the genus Pteropus occur throughout the Austral-Asian region west to islands off the eastern coast of Africa. Recent phylogenetic analyses of Pteropus from the western Indian Ocean found low sequence divergence and poor phylogenetic resolution among several morphologically defined species. We reexamine the phylogenetic relationships of these taxa by using multiple individuals per species. In addition, we estimate population genetic structure in two well-sampled taxa occurring on Madagascar and the Comoro Islands (P. rufus and P. seychellensis comorensis). Despite finding a similar pattern of low sequence divergence among species, increased sampling provides insight into the phylogeographic history of western Indian Ocean Pteropus, uncovering high levels of gene flow within species.
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Affiliation(s)
- Lauren M Chan
- Department of Biology, Box 90338, Duke University, Durham, NC 27708; Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA, and Vahatra, BP 3972, Antananarivo 101, Madagascar; Centro de Ciências do Mar do Algarve, Universidade do Algarve, Campus de Gambelas 8005-139, Faro, Portugal and Department of Biology, University of Kentucky, 101 TH Morgan Building, Lexington KY 40506
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Linkem CW, Hesed KM, Diesmos AC, Brown RM. Species boundaries and cryptic lineage diversity in a Philippine forest skink complex (Reptilia; Squamata; Scincidae: Lygosominae). Mol Phylogenet Evol 2010; 56:572-85. [DOI: 10.1016/j.ympev.2010.03.043] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 02/04/2010] [Accepted: 03/24/2010] [Indexed: 10/19/2022]
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19
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Phylogeny and biogeography of Philippine bent-toed geckos (Gekkonidae: Cyrtodactylus) contradict a prevailing model of Pleistocene diversification. Mol Phylogenet Evol 2010; 55:699-710. [DOI: 10.1016/j.ympev.2010.01.027] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 01/26/2010] [Accepted: 01/27/2010] [Indexed: 11/19/2022]
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Silva-Iturriza A, Ketmaier V, Tiedemann R. Mitochondrial DNA suggests multiple colonizations of central Philippine islands (Boracay, Negros) by the sedentary Philippine bulbul Hypsipetes philippinus guimarasensis(Aves). J ZOOL SYST EVOL RES 2010. [DOI: 10.1111/j.1439-0469.2010.00566.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Phylogeography of Musonycteris harrisoni Along the Pacific Coast of Mexico. ACTA CHIROPTEROLOGICA 2009. [DOI: 10.3161/150811009x485503] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Almeida FC, Giannini NP, DeSalle R, Simmons NB. The phylogenetic relationships of cynopterine fruit bats (Chiroptera: Pteropodidae: Cynopterinae). Mol Phylogenet Evol 2009; 53:772-83. [PMID: 19660560 DOI: 10.1016/j.ympev.2009.07.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Revised: 07/25/2009] [Accepted: 07/29/2009] [Indexed: 10/20/2022]
Abstract
The subfamily Cynopterinae comprises ca. 24 species of pteropodid bats (Family Pteropodidae) distributed exclusively in South and Southeast Asia. Although some studies have supported monophyly of the subfamily, molecular analyses have produced contradictory results and there has been little agreement on relationships of cynopterines to other megabat groups. However, no previous studies have included a complete sampling of cynopterine genera. Here we describe a phylogenetic analysis of Cynopterinae based on more than 6000 bp from six different genes sampled in representatives of all 14 recognized genera. Our results support the monophyly of Cynopterinae but refute a close relationship of cynopterines with Nyctimeninae. Within Cynopterinae, our analyses consistently recovered two monophyletic clades, which we recommend be recognized formally as tribes: Cynopterini and Balionycterini. Biogeographic analyses indicate a Sundaland origin of the Cynopterinae and divergence date estimates suggest different timing of diversification of the two major cynopterine clades.
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Affiliation(s)
- Francisca C Almeida
- American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA.
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Meyer CFJ, Kalko EKV, Kerth G. Small-Scale Fragmentation Effects on Local Genetic Diversity in Two Phyllostomid Bats with Different Dispersal Abilities in Panama. Biotropica 2009. [DOI: 10.1111/j.1744-7429.2008.00443.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Esselstyn JA, Garcia HJD, Saulog MG, Heaney LR. A New Species ofDesmalopex(Pteropodidae) from the Philippines, with a Phylogenetic Analysis of the Pteropodini. J Mammal 2008. [DOI: 10.1644/07-mamm-a-285.1] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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25
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Crawford AJ, Bermingham E, Carolina PS. The role of tropical dry forest as a long-term barrier to dispersal: a comparative phylogeographical analysis of dry forest tolerant and intolerant frogs. Mol Ecol 2007; 16:4789-807. [PMID: 17908220 DOI: 10.1111/j.1365-294x.2007.03524.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We used a comparative phylogeographical approach to investigate the origins of the disjunct wet forest biota of the Golfo Dulce region along the Pacific slope of Costa Rica. This region is isolated by Pacific dry forests north and south and isolated from Caribbean wet forests by mountains. We studied three sympatric lowland frog species in the Craugastor fitzingeri species group that prefer wet forest but differ in their response to dry habitats. In dry forest, C. fitzingeri can survive along streams while C. crassidigitus and C. talamancae are entirely absent. We collected samples from across the ranges of all three species, and obtained mitochondrial DNA sequence data from the COI and cytochrome b genes. We observed significant phylogeographical structure in C. crassidigitus and C. talamancae, but much less in C. fitzingeri, demonstrating that mountain barriers and dry forest habitat have reduced mitochondrial gene flow in the strictly wet-forest species. Additionally, we discovered that the Golfo Dulce and Central Panama populations of C. crassidigitus appear to have diverged in the Pliocene or earlier, suggesting that the dry forest separating these populations is old. Our phylogenetic analysis of 12 of approximately 16 species of the C. fitzingeri species group suggests that the three lowland species are each other's closest relatives. Because of this shared phylogenetic history, we attribute the striking differences in phylogeographical structure to the different ecologies of the frogs. In summary, we find that what appear to be minor differences in the natural history of these three closely related species may profoundly impact the potential for dispersal, range size, and cladogenesis.
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Affiliation(s)
- Andrew J Crawford
- Smithsonian Tropical Research Institute, Apartado 0840-0309, Balboa, Ancón, Panama.
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Helgen KM, Kock D, Gomez RKSC, Ingle NR, Sinaga MH. Taxonomy and Natural History of the Southeast Asian Fruit-Bat GenusDyacopterus. J Mammal 2007. [DOI: 10.1644/06-mamm-a-276r.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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