scholarly journals Verticillium Systematics and Evolution: How Confusion Impedes Verticillium Wilt Management and How to Resolve It

2014 ◽  
Vol 104 (6) ◽  
pp. 564-574 ◽  
Author(s):  
Patrik Inderbitzin ◽  
Krishna V. Subbarao
Keyword(s):  
Plant Pathogens ◽  
Sequence Data ◽  
Current System ◽  
Species Boundaries ◽  
Individual Species ◽  
Distribution Data ◽  
Dna Sequence Data ◽  
Taxonomic History ◽  
History Of ◽  
Taxonomic Changes

Verticillium wilts are important vascular wilt diseases that affect many crops and ornamentals in different regions of the world. Verticillium wilts are caused by members of the ascomycete genus Verticillium, a small group of 10 species that are related to the agents of anthracnose caused by Colletotrichum species. Verticillium has a long and complicated taxonomic history with controversies about species boundaries and long overlooked cryptic species, which confused and limited our knowledge of the biology of individual species. We first review the taxonomic history of Verticillium, provide an update and explanation of the current system of classification and compile host range and geographic distribution data for individual species from internal transcribed spacer (ITS) GenBank records. Using Verticillium as an example, we show that species names are a poor vehicle for archiving and retrieving information, and that species identifications should always be backed up by DNA sequence data and DNA extracts that are made publicly available. If such a system were made a prerequisite for publication, all species identifications could be evaluated retroactively, and our knowledge of the biology of individual species would be immune from taxonomic changes, controversy and misidentification. Adoption of this system would improve quarantine practices and the management of diseases caused by various plant pathogens.

scholarly journals Model-Based Species Delimitation: Are Coalescent Species Reproductively Isolated?

2019 ◽  
Vol 69 (4) ◽  
pp. 708-721 ◽  
Author(s):  
Luke C Campillo ◽  
Anthony J Barley ◽  
Robert C Thomson
Keyword(s):  
Reproductive Isolation ◽  
Dna Sequence ◽  
Sequence Data ◽  
Species Recognition ◽  
Species Boundaries ◽  
Simultaneous Estimation ◽  
Dna Sequence Data ◽  
Multispecies Coalescent ◽  
Species Pairs ◽  
History Of

Abstract A large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question and a subject of vigorous debate. Here, we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation-based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed. [BPP; Drosophila speciation; genetic distance; multispecies coalescent.]

scholarly journals The Crematogaster (Hymenoptera, Formicidae, Myrmicinae) of Costa Rica

Zootaxa ◽  
2003 ◽  
Vol 151 (1) ◽  
pp. 1 ◽  
Author(s):  
JOHN T. LONGINO
Keyword(s):  
New Species ◽  
Natural History ◽  
Entire Range ◽  
Costa Rican ◽  
Species Boundaries ◽  
Additional Species ◽  
Taxonomic History ◽  
History Of ◽  
Taxonomic Changes ◽  
The Many

The taxonomy and natural history of the ant genus Crematogaster are reviewed for the Costa Rican fauna. Thirtyone species are known, and a key is provided for these and two additional species from adjacent regions of Panama. Species boundaries are evaluated over their entire range when possible. The taxonomic history of the genus is one of unbridled naming of new species and subspecies, with no synthetic works or keys. Major taxonomic changes are proposed, with the recognition of several polytypic species with very broad ranges and the synonymization of the many names associated with them. Crematogaster pygmaea Forel 1904, suturalis Forel 1912, ornatipilis Wheeler 1918, erici Santschi 1929, and chacoana Santschi 1933 are synonymized under abstinens Forel 1899; centralis Santschi 1932 under acuta (Fabricius 1804); aruga Forel 1913 under arcuata Forel 1899; ludio Forel 1912, armandi Forel 1921, inca Wheeler 1925, and cocciphila Borgmeier 1934 under brasiliensis Mayr 1878; parabiotica Forel 1904 under carinata Mayr 1862; brevispinosa Mayr 1870, minutior Forel 1893, schuppi Forel 1901, recurvispina Forel 1912, sampaioi Forel 1912, striatinota Forel 1912, townsendi Wheeler 1925, and chathamensis Wheeler 1933 under crinosa Mayr 1862; barbouri Weber 1934 under cubaensis Mann 1920; antillana Forel 1893, sculpturata Pergande 1896, kemali Santschi 1923, accola Wheeler 1934, phytoeca Wheeler 1934, panamana Wheeler 1942, and obscura Santschi 1929 under curvispinosa Mayr 1870; descolei Kusnezov 1949 under distans Mayr 1870; projecta Santschi 1925 under erecta Mayr 1866; carbonescens Forel 1913 under evallans Forel 1907; palans Forel 1912, ascendens Wheeler 1925, and dextella Santschi 1929 under limata F. Smith 1858; agnita Wheeler 1934 under obscurata Emery 1895; amazonensis Forel 1905, autruni Mann 1916, and guianensis Crawley 1916 under stollii Forel 1885; surdior Forel 1885, atitlanica Wheeler 1936, and maya Wheeler 1936 under sumichrasti Mayr 1870; tumulifera Forel 1899 and arizonensis Wheeler 1908 under torosa Mayr 1870. The following taxa are raised to species: ampla Forel 1912, brevidentata Forel 1912, chodati Forel 1921, crucis Forel 1912, cubaensis Mann 1920, goeldii Forel 1903, malevolens Santschi 1919, mancocapaci Santschi 1911, moelleri Forel 1912, montana Borgmeier 1939, obscurata Emery 1895, rochai Forel 1903, russata Wheeler 1925, sericea Forel 1912, stigmatica Forel 1911, sub-tonsa Santschi 1925, tenuicula Forel 1904, thalia Forel 1911, uruguayensis Santschi 1912, and vicina Andre 1893. The following new species are described: bryophilia, flavomicrops, flavosensitiva, foliocrypta, jardinero, levior, monteverdensis, raptor, snellingi, sotobosque, and wardi.

scholarly journals Model-based species delimitation: are coalescent species reproductively isolated?

2019 ◽  
Author(s):  
Luke C. Campillo ◽  
Anthony J. Barley ◽  
Robert C. Thomson
Keyword(s):  
Reproductive Isolation ◽  
Dna Sequence ◽  
Sequence Data ◽  
Species Recognition ◽  
Species Boundaries ◽  
Simultaneous Estimation ◽  
Dna Sequence Data ◽  
Multispecies Coalescent ◽  
Species Pairs ◽  
History Of

ABSTRACTA large and growing fraction of systematists define species as independently evolving lineages that may be recognized by analyzing the population genetic history of alleles sampled from individuals belonging to those species. This has motivated the development of increasingly sophisticated statistical models rooted in the multispecies coalescent process. Specifically, these models allow for simultaneous estimation of the number of species present in a sample of individuals and the phylogenetic history of those species using only DNA sequence data from independent loci. These methods hold extraordinary promise for increasing the efficiency of species discovery, but require extensive validation to ensure that they are accurate and precise. Whether the species identified by these methods correspond to the species that would be recognized by alternative species recognition criteria (such as measurements of reproductive isolation) is currently an open question, and a subject of vigorous debate. Here we perform an empirical test of these methods by making use of a classic model system in the history of speciation research, flies of the genus Drosophila. Specifically, we use the uniquely comprehensive data on reproductive isolation that is available for this system, along with DNA sequence data, to ask whether Drosophila species inferred under the multispecies coalescent model correspond to those recognized by many decades of speciation research. We found that coalescent based and reproductive isolation based methods of inferring species boundaries are concordant for 77% of the species pairs. We explore and discuss potential explanations for these discrepancies. We also found that the amount of prezygotic isolation between two species is a strong predictor of the posterior probability of species boundaries based on DNA sequence data, regardless of whether the species pairs are sympatrically or allopatrically distributed.

scholarly journals Phylogeography of two Andean frogs: Test of vicariance versus elevational gradient models of diversification

2019 ◽  
Author(s):  
Daria Koscinski ◽  
Paul Handford ◽  
Pablo L. Tubaro ◽  
Peiwen Li ◽  
Stephen C. Lougheed
Keyword(s):  
Sequence Data ◽  
Environmental Gradients ◽  
Spatial Scales ◽  
Elevational Gradient ◽  
Northwestern Argentina ◽  
Dna Sequence Data ◽  
The Andes ◽  
Common Causes ◽  
History Of ◽  
Historical Range

ABSTRACTThe tropical and subtropical Andes have among the highest levels of biodiversity in the world. Understanding the forces that underlie speciation and diversification in the Andes is a major focus of research. Here we tested two hypotheses of species origins in the Andes: 1. Vicariance mediated by orogenesis or shifting habitat distribution. 2. Parapatric diversification along elevational environmental gradients. We also sought insights on the factors that impacted the phylogeography of co-distributed taxa, and the influences of divergent species ecology on population genetic structure. We used phylogeographic and coalescent analyses of nuclear and mitochondrial DNA sequence data to compare genetic diversity and evolutionary history of two frog species: Pleurodema borellii (Family: Leiuperidae, 130 individuals; 20 sites), and Hypsiboas riojanus (Family: Hyllidae, 258 individuals; 23 sites) across their shared range in northwestern Argentina. The two showed concordant phylogeographic structuring, and our analyses support the vicariance model over the elevational gradient model. However, Pleurodema borellii exhibited markedly deeper temporal divergence (≥4 Ma) than H. riojanus (1-2 Ma). The three main mtDNA lineages of P. borellii were nearly allopatric and diverged between 4-10 Ma. At similar spatial scales, differentiation was less in the putatively more habitat-specialized H. riojanus than in the more generalist P. borellii. Similar allopatric distributions of major lineages for both species implies common causes of historical range fragmentation and vicariance. However, different divergence times among clades presumably reflect different demographic histories, permeability of different historical barriers at different times, and/or difference in life history attributes and sensitivities to historical environmental change. Our research enriches our understanding of the phylogeography of the Andes in northwestern Argentina.

Taxonomic revision of the Neotropical genus Parastagmatoptera Saussure, 1871 (Dictyoptera, Mantidae, Stagmatopterinae) with a biogeographic comment

2015 ◽  
Vol 46 (3) ◽  
pp. 221-267 ◽  
Author(s):  
Francesco Lombardo ◽  
Rita Umbriaco ◽  
Salvatrice Ippolito
Keyword(s):  
New Species ◽  
Taxonomic Revision ◽  
Valid Species ◽  
Full Description ◽  
Distribution Data ◽  
Species Status ◽  
Two New Species ◽  
Taxonomic History ◽  
History Of ◽  
Previously Treated

A full taxonomic revision of the Neotropical genusParastagmatopteraSaussure is presented, including the description of two new species:Parastagmatoptera bororoisp.n. andParastagmatoptera sottileisp.n.The following species are synonyms:Parastagmatoptera tessellataSaussure & Zehntnersyn.n.(male nec female) andParastagmatoptera hoorieCaudellsyn.n.ofParastagmatoptera flavoguttata(Serville);Parastagmatoptera confusaG.-Tossyn.n.ofParastagmatoptera pellucidaG.-Tos;Parastagmatoptera tessellataSaussure & Zehntnersyn.n.(female nec male),Parastagmatoptera serricornisKirbysyn.n.andParastagmatoptera vitrepennisBrunersyn.n.ofParastagmatoptera unipunctata(Burmeister);Parastagmatoptera concolorJantschsyn.n.ofParastagmatoptera theresopolitanaG.-Tos.Parastagmatoptera vitreola(Stål), previously treated as a synonym ofParastagmatoptera flavoguttatais returned to species status;P. flavoguttata var. immaculataChopard is recognized as a valid species.Parastagmatoptera amazonicaWerner andParastagmatoptera glauca(Rehn) are transferred to the subfamily Photinainae. In total, nine species are recognized, each of which is presented with a diagnosis, a full description, assessments, distribution data and a comprehensive bibliography. A taxonomic history of the genus and its species is provided. A key to allParastagmatopteraspecies is included and each is fully illustrated. Comments about the biogeography ofParastagmatopteraare also presented.

scholarly journals Genome-scale DNA sequence data and the evolutionary history of placental mammals

Data in Brief ◽  
2018 ◽  
Vol 18 ◽  
pp. 1972-1975 ◽  
Author(s):  
Shaoyuan Wu ◽  
Scott Edwards ◽  
Liang Liu
Keyword(s):  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
History Of ◽  
Genome Scale

The invasive coconut mite Aceria guerreronis (Acari: Eriophyidae): origin and invasion sources inferred from mitochondrial (16S) and nuclear (ITS) sequences

2005 ◽  
Vol 95 (6) ◽  
pp. 505-516 ◽  
Author(s):  
D. Navia ◽  
G.J. de Moraes ◽  
G. Roderick ◽  
M. Navajas
Keyword(s):  
Sequence Data ◽  
Common Source ◽  
Aceria Guerreronis ◽  
Dna Sequence Data ◽  
Coconut Mite ◽  
Ocean Region ◽  
Invasion Routes ◽  
History Of ◽  
Nuclear Its ◽  
Production Areas

AbstractOver the past 30 years the coconut mite Aceria guerreronis Keifer has emerged as one of the most important pests of coconut and has recently spread to most coconut production areas worldwide. The mite has not been recorded in the Indo-Pacific region, the area of origin of coconut, suggesting that it has infested coconut only recently. To investigate the geographical origin, ancestral host associations, and colonization history of the mite, DNA sequence data from two mitochondrial and one nuclear region were obtained from samples of 29 populations from the Americas, Africa and the Indo-ocean region. Mitochondrial DNA 16S ribosomal sequences were most diverse in Brazil, which contained six of a total of seven haplotypes. A single haplotype was shared by non-American mites. Patterns of nuclear ribosomal internal transcribed spacer (ITS) variation were similar, again with the highest nucleotide diversity found in Brazil. These results suggest an American origin of the mite and lend evidence to a previous hypothesis that the original host of the mite is a non-coconut palm. In contrast to the diversity in the Americas, all samples from Africa and Asia were identical or very similar, consistent with the hypothesis that the mite invaded these regions recently from a common source. Although the invasion routes of this mite are still only partially reconstructed, the study rules out coconut as the ancestral host of A. guerreronis, thus prompting a reassessment of efforts using quarantine and biological control to check the spread of the pest.

Cryptic species, biogeographic complexity and the evolutionary history of theEctemnorhinusgroup in the sub-Antarctic, including a description ofBothrometopus huntleyi, n. sp.

2011 ◽  
Vol 23 (3) ◽  
pp. 211-224 ◽  
Author(s):  
G.C. Grobler ◽  
A.D.S. Bastos ◽  
A.M. Treasure ◽  
S.L. Chown
Keyword(s):  
Sequence Data ◽  
Morphological Data ◽  
Early Pleistocene ◽  
Dna Sequence Data ◽  
Prince Edward Islands ◽  
South Indian ◽  
Prevailing Wind Direction ◽  
Previous Hypothesis ◽  
Molecular Phylogenetic ◽  
History Of

AbstractThe biogeography of the South Indian Ocean Province (SIP) biotas has long been controversial. Much of the discussion has been based on interpretation of species distributions, based on morphological or anatomical delimitations. However, molecular phylogenetic approaches elsewhere have recently shown that interpretations based solely on morphological data may be misleading. Nonetheless, few studies have employed molecular phylogenetic approaches to understand the biogeography of the SIP biotas. We do so here for theEctemnorhinusgroup of genera, a monophyletic unit of weevils endemic to the region. We use mitochondrial cytochrome oxidase I DNA sequence data to reconstruct relationships among 13 species and 22 populations in the generaPalirhoeus,BothrometopusandEctemnorhinus. On the basis of this analysis we find little support for separating the genusPalirhoeusfromBothrometopus, and little support for the morphologically-based species groups currently recognized withinBothrometopus. Using a molecular clock we show that dispersal among islands probably took place against the prevailing wind direction. These data also support a previous hypothesis of radiation of the epilithic generaBothrometopusandPalirhoeusduring the Pliocene/early Pleistocene, but reject the hypothesis that the genusEctemnorhinusradiated following the last glacial maximum. We show thatBothrometopus parvulus(C.O. Waterhouse) on the Prince Edward Islands comprises two species that are not sister taxa. We name the second speciesBothrometopus huntleyin. sp. and provide a description thereof.

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