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Camacho-Sanchez M, Leonard JA. Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland. J Hered 2021; 111:392-404. [PMID: 32485737 PMCID: PMC7423070 DOI: 10.1093/jhered/esaa014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 05/25/2020] [Indexed: 01/16/2023] Open
Abstract
Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.
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Affiliation(s)
- Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
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2
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Pepato AR, Vidigal THDA, Klimov PB. Evaluating the boundaries of marine biogeographic regions of the Southwestern Atlantic using halacarid mites (Halacaridae), meiobenthic organisms with a low dispersal potential. Ecol Evol 2019; 9:13359-13374. [PMID: 31871650 PMCID: PMC6912894 DOI: 10.1002/ece3.5791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/05/2019] [Indexed: 11/07/2022] Open
Abstract
AIM We evaluated traditional biogeographic boundaries of coastal marine regions in Southwestern Atlantic using DNA sequence data from common, rocky-shore inhabiting, marine mites of the genera Agauopsis and Rhombognathus, family Halacaridae. METHODS We investigated geographic population genetic structure using CO1 gene sequences, estimated divergence times using a multigene dataset and absolute time-calibrated molecular clock analyses, and performed environmental niche modeling (ENM) of common marine mite species. RESULTS Agauopsis legionium has a shallow history (2.01 Ma) with four geographically differentiated groups. Two of them corresponded to the traditional Amazonian and Northeastern ecoregions, but the boundary between the two other groups was inferred at the Abrolhos Plateau, not Cabo Frio. Rhombognathus levigatoides s. lat. was represented by two cryptic species that diverged 7.22 (multilocus data) or 10.01 Ma (CO1-only analyses), with their boundary, again at the Abrolhos Plateau. ENM showed that A. legionium has suitable habitats scattered along the coast, while the two R. levigatoides cryptic species differ considerably in their niches, especially in parameters related to upwelling. This indicates that genetic isolation associated with the Abrolhos Plateau occurred in both lineages, but for the R. levigatoides species complex, ecological niche specialization was also an important factor. MAIN CONCLUSIONS Our study suggests that the major biogeographic boundary in the Southwestern Atlantic lies not at Cabo Frio but at the Abrolhos Plateau. There two biogeographically relevant factors meet (a) changes in current directions (which limit dispersal) and (b) abrupt changes in environmental parameters associated with the South Atlantic Central Waters (SACW) upwelling (offering distinct ecological niches). We suggest that our result represents a general biogeographic pattern because a barrier at the Abrolhos Plateau was found previously for the fish genus Macrodon (phylogeographic data), prosobranch mollusks, ascidians, and reef fishes (community-level data).
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Affiliation(s)
- Almir R. Pepato
- Departamento de ZoologiaInstituto de Ciências BiológicasUFMGBelo HorizonteBrazil
- Tyumen State UniversityTyumenRussia
| | | | - Pavel B. Klimov
- Tyumen State UniversityTyumenRussia
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMIUSA
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3
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Crisp MD, Cook LG, Bowman DMJS, Cosgrove M, Isagi Y, Sakaguchi S. Turnover of southern cypresses in the post-Gondwanan world: extinction, transoceanic dispersal, adaptation and rediversification. THE NEW PHYTOLOGIST 2019; 221:2308-2319. [PMID: 30367483 PMCID: PMC6587739 DOI: 10.1111/nph.15561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/15/2018] [Indexed: 05/23/2023]
Abstract
Cupressaceae subfamily Callitroideae has been an important exemplar for vicariance biogeography, but its history is more than just disjunctions resulting from continental drift. We combine fossil and molecular data to better assess its extinction and, sometimes, rediversification after past global change. Key fossils were reassessed and their phylogenetic placement for calibration was determined using trait mapping and Bayes Factors. Five vicariance hypotheses were tested by comparing molecular divergence times with the timing of tectonic rifting. The role of adaptation to fire (serotiny) in its spread across a drying Australia was tested for Callitris. Our findings suggest that three transoceanic disjunctions within the Callitroideae probably arose from long-distance dispersal. A signature of extinction, centred on the end-Eocene global climatic chilling and drying, is evident in lineages-through-time plots and in the fossil record. Callitris, the most diverse extant callitroid genus, suffered extinctions but surviving lineages adapted and re-radiated into dry, fire-prone biomes that expanded in the Neogene. Serotiny, a key adaptation to fire, likely evolved in Callitris coincident with the biome shift. Both extinction and adaptive shifts have probably played major roles in this chronicle of turnover and renewal, but better understanding of biogeographical history requires improved taxonomy of fossils.
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Affiliation(s)
- Michael D. Crisp
- Research School of BiologyThe Australian National UniversityRN Robertson Building, 46 Sullivans Creek RoadActon (Canberra)ACT2601Australia
| | - Lyn G. Cook
- School of Biological SciencesThe University of QueenslandBrisbaneQld4072Australia
| | - David M. J. S. Bowman
- School of Natural SciencesThe University of TasmaniaPrivate Bag 55HobartTas7001Australia
| | - Meredith Cosgrove
- Research School of BiologyThe Australian National UniversityRN Robertson Building, 46 Sullivans Creek RoadActon (Canberra)ACT2601Australia
| | - Yuji Isagi
- Graduate School of AgricultureKyoto UniversityKyoto606‐8502Japan
| | - Shota Sakaguchi
- Graduate School of Human and Environmental StudiesKyoto UniversityKyoto606‐8501Japan
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4
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Tiley GP, Barker MS, Burleigh JG. Assessing the Performance of Ks Plots for Detecting Ancient Whole Genome Duplications. Genome Biol Evol 2018; 10:2882-2898. [PMID: 30239709 PMCID: PMC6225891 DOI: 10.1093/gbe/evy200] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2018] [Indexed: 02/06/2023] Open
Abstract
Genomic data have provided evidence of previously unknown ancient whole genome duplications (WGDs) and highlighted the role of WGDs in the evolution of many eukaryotic lineages. Ancient WGDs often are detected by examining distributions of synonymous substitutions per site (Ks) within a genome, or “Ks plots.” For example, WGDs can be detected from Ks plots by using univariate mixture models to identify peaks in Ks distributions. We performed gene family simulation experiments to evaluate the effects of different Ks estimation methods and mixture models on our ability to detect ancient WGDs from Ks plots. The simulation experiments, which accounted for variation in substitution rates and gene duplication and loss rates across gene families, tested the effects of WGD age and gene retention rates following WGD on inferring WGDs from Ks plots. Our simulations reveal limitations of Ks plot analyses. Strict interpretations of mixture model analyses often overestimate the number of WGD events, and Ks plot analyses typically fail to detect WGDs when ≤10% of the duplicated genes are retained following the WGD. However, WGDs can accurately be characterized over an intermediate range of Ks. The simulation results are supported by empirical analyses of transcriptomic data, which also suggest that biases in gene retention likely affect our ability to detect ancient WGDs. Although our results indicate mixture model results should be interpreted with great caution, using node-averaged Ks estimates and applying more appropriate mixture models can improve the accuracy of detecting WGDs.
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Affiliation(s)
- George P Tiley
- Department of Biology, University of Florida.,Department of Biology, Duke University
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona
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5
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Warnock RCM, Yang Z, Donoghue PCJ. Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution. Proc Biol Sci 2018. [PMID: 28637852 PMCID: PMC5489717 DOI: 10.1098/rspb.2017.0227] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions.
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Affiliation(s)
- Rachel C M Warnock
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK .,Department of Paleobiology, National Museum of Natural History, The Smithsonian Institution, Washington, DC 20560, USA.,Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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6
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Krysko KL, Nuñez LP, Newman CE, Bowen BW. Phylogenetics of Kingsnakes, Lampropeltis getula Complex (Serpentes: Colubridae), in Eastern North America. J Hered 2017; 108:226-238. [PMID: 28119446 DOI: 10.1093/jhered/esw086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/08/2016] [Indexed: 01/25/2023] Open
Abstract
Kingsnakes of the Lampropeltis getula complex range throughout much of temperate and subtropical North America. Studies over the last century have used morphology and color pattern to describe numerous subspecies. More recently, DNA analyses have made invaluable contributions to our understanding of their evolution and taxonomy. We use genetic and ecological methods to test previous hypotheses of distinct evolutionary lineages by examining 66 total snakes and 1) analyzing phylogeographic structure using 2 mtDNA loci and 1 nuclear locus, 2) estimating divergence dates and historical demography among lineages in a Bayesian coalescent framework, and 3) applying ecological niche modeling (ENM). Our molecular data and ENMs illustrate that 3 previously recognized subspecies in the eastern United States comprise well-supported monophyletic lineages that diverged during the Pleistocene. The geographic boundaries of these 3 lineages correspond closely to known biogeographic barriers (Florida peninsula, Appalachian Mountains, and Apalachicola River) previously identified for other plants and animals, indicating shared geographic influences on evolutionary history. We conclude that genetic, ecological, and morphological data support recognition of these 3 lineages as distinct species (Lampropeltis floridana, Lampropeltis getula, and Lampropeltis meansi).
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Affiliation(s)
- Kenneth L Krysko
- Division of Herpetology, Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL, USA
| | - Leroy P Nuñez
- Division of Herpetology, Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL, USA.,School of Natural Resources and Environment, University of Florida, Gainesville, FL, USA
| | - Catherine E Newman
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Brian W Bowen
- Hawaii Institute of Marine Biology, University of Hawaii, Kaneohe, Hawaii, USA
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7
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Genetic diversity and divergence in the endangered Cape Verde warbler Acrocephalus brevipennis. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0909-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Eberle J, Fabrizi S, Lago P, Ahrens D. A historical biogeography of megadiverse Sericini-another story “out of Africa”? Cladistics 2016; 33:183-197. [DOI: 10.1111/cla.12162] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2016] [Indexed: 02/04/2023] Open
Affiliation(s)
- Jonas Eberle
- Centre of Taxonomy and Evolutionary Research; Zoologisches Forschungsmuseum Alexander Koenig Bonn; Adenauerallee 160 53113 Bonn Germany
| | - Silvia Fabrizi
- Centre of Taxonomy and Evolutionary Research; Zoologisches Forschungsmuseum Alexander Koenig Bonn; Adenauerallee 160 53113 Bonn Germany
| | - Paul Lago
- Department of Biology; University of Mississippi; University MS 38677 USA
| | - Dirk Ahrens
- Centre of Taxonomy and Evolutionary Research; Zoologisches Forschungsmuseum Alexander Koenig Bonn; Adenauerallee 160 53113 Bonn Germany
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9
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Krysko KL, Nuñez LP, Lippi CA, Smith DJ, Granatosky MC. Pliocene-Pleistocene lineage diversifications in the Eastern Indigo Snake (Drymarchon couperi) in the Southeastern United States. Mol Phylogenet Evol 2016; 98:111-22. [PMID: 26778258 DOI: 10.1016/j.ympev.2015.12.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/04/2015] [Accepted: 12/30/2015] [Indexed: 11/18/2022]
Abstract
Indigo Snakes (Drymarchon; with five currently recognized species) occur from northern Argentina, northward to the United States in southern Texas and eastward in disjunct populations in Florida and Georgia. Based on this known allopatry and a difference in supralabial morphology the two United States taxa previously considered as subspecies within D. corais (Boie 1827), the Western Indigo Snake, D. melanurus erebennus (Cope 1860), and Eastern Indigo Snake, D. couperi (Holbrook 1842), are currently recognized as separate species. Drymarchon couperi is a Federally-designated Threatened species by the United States Fish and Wildlife Service under the Endangered Species Act, and currently being incorporated into a translocation program. This, combined with its disjunct distribution makes it a prime candidate for studying speciation and genetic divergence. In this study, we (1) test the hypothesis that D. m. erebennus and D. couperi are distinct lineages by analyzing 2411 base pairs (bp) of two mitochondrial (mtDNA) loci and one single copy nuclear (scnDNA) locus; (2) estimate the timing of speciation using a relaxed phylogenetics method to determine if Milankovitch cycles during the Pleistocene might have had an influence on lineage diversifications; (3) examine historical population demography to determine if identified lineages have undergone population declines, expansions, or remained stable during the most recent Milankovitch cycles; and (4) use this information to assist in an effective and scientifically sound translocation program. Our molecular data support the initial hypothesis that D. melanurus and D. couperi should be recognized as distinct species, but further illustrate that D. couperi is split into two distinct genetic lineages that correspond to historical biogeography and sea level changes in peninsular Florida. These two well-supported genetic lineages (herein termed Atlantic and Gulf lineages) illustrate a common biogeographic distributional break previously identified for other plants and animals, suggesting that these organisms might have shared a common evolutionary history related to historic sea level changes caused by Milankovitch cycles. Our estimated divergence times suggest that the most recent common ancestor (MRCA) between D. melanurus and southeastern United States Drymarchon occurred ca. 5.9Ma (95% HPD=2.5-9.8Ma; during the late Blancan of the Pleistocene through the Hemphillian of the Miocene), whereas the MRCA between the Atlantic and Gulf lineages in the southeastern United States occurred ca. 2.0Ma (95% HPD=0.7-3.7Ma; during the Irvingtonian of the Pleistocene through the Blancan of the Pliocene). During one or more glacial intervals within these times, these two lineages must have become separated and evolved independently. Despite numerous Milankovitch cycles along with associated forming of physical barriers (i.e., sea level fluctuations, high elevation sand ridges, clayey soils, and/or insufficient habitats) since their initial lineage diversification, these two lineages have likely come in and out of contact with each other many times, yet today they still illustrate near discrete geographic distributions. Although the Atlantic and Gulf lineages appear to be cryptic, a thorough study examining morphological characters should be conducted. We believe that our molecular data is crucial and should be incorporated in making conscious decisions in the management of a translocation program. We suggest that source populations for translocations include maintaining the integrity of the known genetic lineages found herein, as well as those coming from the closest areas that currently support sizable Drymarchon populations.
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Affiliation(s)
- Kenneth L Krysko
- Florida Museum of Natural History, Museum Road, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA.
| | - Leroy P Nuñez
- Florida Museum of Natural History, Museum Road, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA; School of Natural Resources and Environment, 103 Black Hall, University of Florida, Gainesville, FL 32611, USA.
| | - Catherine A Lippi
- Department of Epidemiology and Biostatistics, College of Public Health, University of South Florida, 13201 Bruce B Downs, MDC56, Tampa, FL 33612, USA.
| | - Daniel J Smith
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
| | - Michael C Granatosky
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
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10
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Vanneste K, Sterck L, Myburg AA, Van de Peer Y, Mizrachi E. Horsetails Are Ancient Polyploids: Evidence from Equisetum giganteum. THE PLANT CELL 2015; 27:1567-78. [PMID: 26002871 PMCID: PMC4498207 DOI: 10.1105/tpc.15.00157] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/03/2015] [Accepted: 04/28/2015] [Indexed: 05/18/2023]
Abstract
Horsetails represent an enigmatic clade within the land plants. Despite consisting only of one genus (Equisetum) that contains 15 species, they are thought to represent the oldest extant genus within the vascular plants dating back possibly as far as the Triassic. Horsetails have retained several ancient features and are also characterized by a particularly high chromosome count (n = 108). Whole-genome duplications (WGDs) have been uncovered in many angiosperm clades and have been associated with the success of angiosperms, both in terms of species richness and biomass dominance, but remain understudied in nonangiosperm clades. Here, we report unambiguous evidence of an ancient WGD in the fern lineage, based on sequencing and de novo assembly of an expressed gene catalog (transcriptome) from the giant horsetail (Equisetum giganteum). We demonstrate that horsetails underwent an independent paleopolyploidy during the Late Cretaceous prior to the diversification of the genus but did not experience any recent polyploidizations that could account for their high chromosome number. We also discuss the specific retention of genes following the WGD and how this may be linked to their long-term survival.
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Affiliation(s)
- Kevin Vanneste
- Department of Plant Systems Biology, VIB, Ghent B-9052, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
| | - Lieven Sterck
- Department of Plant Systems Biology, VIB, Ghent B-9052, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
| | - Alexander Andrew Myburg
- Department of Genetics, Forestry, and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent B-9052, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Eshchar Mizrachi
- Department of Genetics, Forestry, and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
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11
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ur Rehman I, Vaughan G, Purdy MA, Xia GL, Forbi JC, Rossi LMG, Butt S, Idrees M, Khudyakov YE. Genetic history of hepatitis C virus in Pakistan. INFECTION GENETICS AND EVOLUTION 2014; 27:318-24. [PMID: 25131452 DOI: 10.1016/j.meegid.2014.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/26/2014] [Accepted: 08/05/2014] [Indexed: 12/13/2022]
Abstract
Hepatitis C virus (HCV) genotype 3a accounts for ∼80% of HCV infections in Pakistan, where ∼10 million people are HCV-infected. Here, we report analysis of the genetic heterogeneity of HCV NS3 and NS5b subgenomic regions from genotype 3a variants obtained from Pakistan. Phylogenetic analyses showed that Pakistani genotype 3a variants were as genetically diverse as global variants, with extensive intermixing. Bayesian estimates showed that the most recent ancestor for genotype 3a in Pakistan was last extant in ∼1896-1914 C.E. (range: 1851-1932). This genotype experienced a population expansion starting from ∼1905 to ∼1970 after which the effective population leveled. Death/birth models suggest that HCV 3a has reached saturating diversity with decreasing turnover rate and positive extinction. Taken together, these observations are consistent with a long and complex history of HCV 3a infection in Pakistan.
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Affiliation(s)
- Irshad ur Rehman
- National Centre of Excellence in Molecular Biology, Division of Molecular Virology and Molecular Diagnostics, University of the Punjab, Genome Center for Molecular Diagnosis & Research, Lahore, Pakistan
| | - Gilberto Vaughan
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Michael A Purdy
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Guo-liang Xia
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joseph C Forbi
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Livia Maria Gonçalves Rossi
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA; Department of Biology, Institute of Bioscience, Language and Exact Science, São Paulo State University, São José do Rio Preto, SP, Brazil
| | - Sadia Butt
- National Centre of Excellence in Molecular Biology, Division of Molecular Virology and Molecular Diagnostics, University of the Punjab, Genome Center for Molecular Diagnosis & Research, Lahore, Pakistan
| | - Muhammad Idrees
- National Centre of Excellence in Molecular Biology, Division of Molecular Virology and Molecular Diagnostics, University of the Punjab, Genome Center for Molecular Diagnosis & Research, Lahore, Pakistan
| | - Yury E Khudyakov
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
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12
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Morrison DA. The Monkey's Voyage: How Improbable Journeys Shaped the History of Life.—By Alan de Queiroz. Syst Biol 2014. [DOI: 10.1093/sysbio/syu045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- David A. Morrison
- Systematic Biology, Evolutionary Biology Centre, Norbyvägen 18D, 752 36 Uppsala, Sweden
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13
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Vanneste K, Van de Peer Y, Maere S. Inference of genome duplications from age distributions revisited. Mol Biol Evol 2012; 30:177-90. [PMID: 22936721 DOI: 10.1093/molbev/mss214] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Whole-genome duplications (WGDs), thought to facilitate evolutionary innovations and adaptations, have been uncovered in many phylogenetic lineages. WGDs are frequently inferred from duplicate age distributions, where they manifest themselves as peaks against a small-scale duplication background. However, the interpretation of duplicate age distributions is complicated by the use of K(S), the number of synonymous substitutions per synonymous site, as a proxy for the age of paralogs. Two particular concerns are the stochastic nature of synonymous substitutions leading to increasing uncertainty in K(S) with increasing age since duplication and K(S) saturation caused by the inability of evolutionary models to fully correct for the occurrence of multiple substitutions at the same site. K(S) stochasticity is expected to erode the signal of older WGDs, whereas K(S) saturation may lead to artificial peaks in the distribution. Here, we investigate the consequences of these effects on K(S)-based age distributions and WGD inference by simulating the evolution of duplicated sequences according to predefined real age distributions and re-estimating the corresponding K(S) distributions. We show that, although K(S) estimates can be used for WGD inference far beyond the commonly accepted K(S) threshold of 1, K(S) saturation effects can cause artificial peaks at higher ages. Moreover, K(S) stochasticity and saturation may lead to confounded peaks encompassing multiple WGD events and/or saturation artifacts. We argue that K(S) effects need to be properly accounted for when inferring WGDs from age distributions and that the failure to do so could lead to false inferences.
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Affiliation(s)
- Kevin Vanneste
- Department of Plant Systems Biology, VIB, Ghent, Belgium
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14
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Extreme habitats that emerged in the Pleistocene triggered divergence of weedy Youngia (Asteraceae) in Taiwan. Mol Phylogenet Evol 2012; 63:486-99. [DOI: 10.1016/j.ympev.2012.01.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 01/29/2012] [Accepted: 01/30/2012] [Indexed: 11/23/2022]
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15
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Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ, Wu X, Zhang Y, Wang J, Zhang Y, Carpenter EJ, Deyholos MK, Kutchan TM, Chanderbali AS, Soltis PS, Stevenson DW, McCombie R, Pires JC, Wong GKS, Soltis DE, Depamphilis CW. A genome triplication associated with early diversification of the core eudicots. Genome Biol 2012; 13:R3. [PMID: 22280555 PMCID: PMC3334584 DOI: 10.1186/gb-2012-13-1-r3] [Citation(s) in RCA: 286] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/26/2012] [Indexed: 11/23/2022] Open
Abstract
Background Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. Results To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago. Conclusions The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis.
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Affiliation(s)
- Yuannian Jiao
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Whittall JB, Syring J, Parks M, Buenrostro J, Dick C, Liston A, Cronn R. Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines. Mol Ecol 2010; 19 Suppl 1:100-14. [PMID: 20331774 DOI: 10.1111/j.1365-294x.2009.04474.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Critical to conservation efforts and other investigations at low taxonomic levels, DNA sequence data offer important insights into the distinctiveness, biogeographic partitioning and evolutionary histories of species. The resolving power of DNA sequences is often limited by insufficient variability at the intraspecific level. This is particularly true of studies involving plant organelles, as the conservative mutation rate of chloroplasts and mitochondria makes it difficult to detect polymorphisms necessary to track genealogical relationships among individuals, populations and closely related taxa, through space and time. Massively parallel sequencing (MPS) makes it possible to acquire entire organelle genome sequences to identify cryptic variation that would be difficult to detect otherwise. We are using MPS to evaluate intraspecific chloroplast-level divergence across biogeographic boundaries in narrowly endemic and widespread species of Pinus. We focus on one of the world's rarest pines - Torrey pine (Pinus torreyana) - due to its conservation interest and because it provides a marked contrast to more widespread pine species. Detailed analysis of nearly 90% ( approximately 105 000 bp each) of these chloroplast genomes shows that mainland and island populations of Torrey pine differ at five sites in their plastome, with the differences fixed between populations. This is an exceptionally low level of divergence (1 polymorphism/ approximately 21 kb), yet it is comparable to intraspecific divergence present in widespread pine species and species complexes. Population-level organelle genome sequencing offers new vistas into the timing and magnitude of divergence within species, and is certain to provide greater insight into pollen dispersal, migration patterns and evolutionary dynamics in plants.
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Affiliation(s)
- J B Whittall
- Department of Biology, Santa Clara University, CA 95053, USA
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Battistuzzi FU, Filipski A, Hedges SB, Kumar S. Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Mol Biol Evol 2010; 27:1289-300. [PMID: 20093431 DOI: 10.1093/molbev/msq014] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The rapid expansion of sequence data and the development of statistical approaches that embrace varying evolutionary rates among lineages have encouraged many more investigators to use DNA and protein data to time species divergences. Here, we report results from a systematic evaluation, by means of computer simulation, of the performance of two frequently used relaxed-clock methods for estimating these times and their credibility intervals (CrIs). These relaxed-clock methods allow rates to vary in a phylogeny randomly over lineages (e.g., BEAST software) and in autocorrelated fashion (e.g., MultiDivTime software). We applied these methods for analyzing sequence data sets simulated using naturally derived parameters (evolutionary rates, sequence lengths, and base substitution patterns) and assuming that clock calibrations are known without error. We find that the estimated times are, on average, close to the true times as long as the assumed model of lineage rate changes matches the actual model. The 95% CrIs also contain the true time for >or=95% of the simulated data sets. However, the use of incorrect lineage rate model reduces this frequency to 83%, indicating that the relaxed-clock methods are not robust to the violation of underlying lineage rate model. Because these rate models are rarely known a priori and are difficult to detect empirically, we suggest building composite CrIs using CrIs produced from MultiDivTime and BEAST analysis. These composite CrIs are found to contain the true time for >or=97% data sets. Our analyses also verify the usefulness of the common practice of interpreting the congruence of times inferred from different methods as a reflection of the accuracy of time estimates. Overall, our results show that simple strategies can be used to enhance our ability to estimate times and their CrIs when using the relaxed-clock methods.
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Affiliation(s)
- Fabia U Battistuzzi
- Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, USA
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Ho SYW, Phillips MJ. Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times. Syst Biol 2009; 58:367-80. [PMID: 20525591 DOI: 10.1093/sysbio/syp035] [Citation(s) in RCA: 521] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Simon Y. W. Ho
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - Matthew J. Phillips
- Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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