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Species delimitation

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https://www.readbyqxmd.com/read/28412535/complex-biogeographic-scenarios-revealed-in-the-diversification-of-the-largest-woodpecker-radiation-in-the-new-world
#1
Adolfo G Navarro-Sigüenza, Hernán Vázquez-Miranda, Germán Hernández-Alonso, Erick A García-Trejo, Luis A Sánchez-González
Phylogenetic relationships and patterns of evolution within Melanerpes, one of the most diverse groups of New World woodpeckers (22-23 lineages), have been complicated due to complex plumages and morphological adaptations. In an attempt to resolve these issues, we obtained sequence data from four nuclear introns and two mitochondrial protein-coding genes for 22 of the 24 currently recognized species in the genus. We performed phylogenetic analyses involving Maximum Likelihood and Bayesian Inference, species-tree divergence dating, and biogeographic reconstructions...
April 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28401612/co-diversification-of-gastrointestinal-microbiota-and-phylogeny-in-passerines-is-not-explained-by-ecological-divergence
#2
Lucie Kropáčková, Martin Těšický, Tomáš Albrecht, Jan Kubovčiak, Dagmar Čížková, Oldřich Tomášek, Jean-François Martin, Lukáš Bobek, Tereza Králová, Petr Procházka, Jakub Kreisinger
Vertebrate gut microbiota (GM) is comprised of a taxonomically diverse consortium of symbiotic and commensal microorganisms that have a pronounced effect on host physiology, immune system function and health status. Despite much research on interactions between hosts and their GM, the factors affecting inter- and intra-specific GM variation in wild populations are still poorly known. We analyzed data on fecal microbiota composition in 51 passerine species (319 individuals) using Illumina MiSeq sequencing of bacterial 16S rRNA (V3-V4 variable region)...
April 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28400268/genetic-evidence-supporting-the-taxonomic-separation-of-the-arabian-and-northwest-african-subspecies-of-the-desert-hedgehog-paraechinus-aethiopicus
#3
Louiza Derouiche, Paul Vercammen, Rachid Bouhadad, Carlos Fernandes
Traditional subspecies call attention to differences between geographic populations with research potential, but their value is often in need of revision. Genetic data can be useful for evaluating the taxonomic validity of historical species and subspecies designations or for identifying morphologically cryptic divergent lineages worthy of further in-depth taxonomic study. The desert hedgehog (Paraechinus aethiopicus) has a wide but fragmented distribution in arid and semi-arid habitats from the northwest to the northeast of Africa and southwestern Asia, and its taxonomy is still unclear...
April 8, 2017: Gene
https://www.readbyqxmd.com/read/28393289/practically-delineating-bacterial-species-with-genealogical-concordance
#4
Stephanus N Venter, Marike Palmer, Chrizelle W Beukes, Wai-Yin Chan, Giyoon Shin, Elritha van Zyl, Tarren Seale, Teresa A Coutinho, Emma T Steenkamp
Bacterial species are commonly defined by applying a set of predetermined criteria, including DNA-DNA hybridization values, 16S rRNA gene sequence similarity, phenotypic data as well as genome-based criteria such as average nucleotide identity or digital DNA-DNA hybridization. These criteria mostly allow for the delimitation of taxa that resemble typical bacterial species. Their application is often complicated when the objective is to delineate new species that are characterized by significant population-level diversity or recent speciation...
April 9, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28392486/species-delimitation-of-the-blue-spotted-spiny-lizard-within-a-multilocus-multispecies-coalescent-framework-results-in-the-recognition-of-a-new-sceloporus-species
#5
Brenda Díaz-Cárdenas, Eduardo Ruiz-Sanchez, Patricia Castro-Felix, Gamaliel Castañeda-Gaytán, Sergio Ruiz-Santana, Héctor Gadsden
Species delimitation is a major topic in systematics. Species delimitation methods based on molecular data have become more common since this approach provides insights about species identification via levels of gene flow, the degree of hybridization and phylogenetic relationships. Also, combining multilocus mitochondrial and nuclear DNA leads to more reliable conclusions about species limits. Coalescent-based species delimitation methods explicitly reveal separately evolving lineages using probabilistic approaches and testing the delimitation hypotheses for several species...
April 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28391307/one-species-hypothesis-to-rule-them-all-consistency-is-essential-to-delimitate-species
#6
Erwan Delrieu-Trottin, Kang-Ning Shen, Chih-Wei Chang, Philippe Borsa
No abstract text is available yet for this article.
May 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28391240/physical-confirmation-and-comparative-genomics-of-the-rat-mammary-carcinoma-susceptibility-3-quantitative-trait-locus
#7
Saasha Le, Zachary C Martin, David J Samuelson
Human breast and rat mammary cancer susceptibility are complex phenotypes where complete sets of risk associated loci remain to be identified for both species. We tested multiple congenic rat strains to physically confirm and positionally map rat Mammary carcinoma susceptibility 3 (Mcs3), a mammary cancer resistance allele previously predicted at Rattus norvegicus chromosome 1 (RNO1). The mammary cancer susceptible Wistar Furth (WF) strain was the recipient, and the mammary cancer resistant Copenhagen (Cop) strain was the RNO1-segment donor for congenics...
April 8, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28378799/non-photonic-sensing-of-membrane-delimited-reactive-species-with-a-na-channel-protein-containing-selenocysteine
#8
Navin K Ojha, Enrico Leipold, Roland Schönherr, Toshinori Hoshi, Stefan H Heinemann
Photonic experiments are of key importance in life sciences but light-induced side effects are serious confounding factors. Here we introduce roNaV2, an engineered voltage-gated Na(+) channel harboring a selenocysteine in its inactivation motif, as a non-photonic, sensitive, gateable, and reversible sensor for membrane-delimited reactive species. roNaV2 allows for the assessment of chemical modification induced in fluorescence microscopy settings with high sensitivity and time resolution and it demonstrates the usefulness of ion channels as highly sensitive reporters of membrane processes...
April 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28377782/species-delimitation-and-lineage-separation-history-of-a-species-complex-of-aspens-in-china
#9
Honglei Zheng, Liqiang Fan, Richard I Milne, Lei Zhang, Yaling Wang, Kangshan Mao
Species delimitation in tree species is notoriously challenging due to shared polymorphisms among species. An integrative survey that considers multiple operational criteria is a possible solution, and we aimed to test it in a species complex of aspens in China. Genetic [four chloroplast DNA (cpDNA) fragments and 14 nuclear microsatellite loci (nSSR)] and morphological variations were collected for 76 populations and 53 populations, respectively, covering the major geographic distribution of the Populus davidiana-rotundifolia complex...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28369873/a-comparison-of-molecular-markers-and-morphology-for-neidium-taxa-bacillariophyta-from-eastern-north-america
#10
Keely E Lefebvre, Paul B Hamilton, Frances R Pick
Historically a morphological species concept has applied shape subjectively in the delimitation of diatom species. This has led to confusion between taxa within the benthic diatom genus Neidium. Samples from Ontario, Quebec, Nova Scotia, Newfoundland (Canada) and New York, (USA) were examined for Neidium taxa under LM and SEM. Fourier shape analysis showed that shape as a taxonomic character was not able to discern all species. Isolated individuals from the samples were amplified and sequenced for three chloroplast molecular markers (rbcL, psbC, and psbA) and one nuclear ribosomal molecular marker (18S)...
March 31, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28347889/genome-wide-data-delimits-multiple-climate-determined-species-ranges-in-a-widespread-australian-fish-the-golden-perch-macquaria-ambigua
#11
Luciano B Beheregaray, Lauren V Pfeiffer, Catherine R M Attard, Jonathan Sandoval-Castillo, Fabricius M C B Domingos, Leanne K Faulks, Dean M Gilligan, Peter J Unmack
Species range limits often fluctuate in space and time in response to variation in environmental factors and to gradual niche evolution due to changes in adaptive traits. We used genome-wide data to investigate evolutionary divergence and species range limits in a generalist and highly dispersive fish species that shows an unusually wide distribution across arid and semi-arid regions of Australia. We generated ddRAD data (18,979 filtered SNPs and 1.725million bp of sequences) for samples from 27 localities spanning the native range of golden perch, Macquaria ambigua (Teleostei; Percichthyidae)...
March 24, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28344106/molecular-phylogenetic-relationships-reveal-contrasting-evolutionary-patterns-in-gorgoniidae-octocorallia-in-the-eastern-pacific
#12
M M Soler-Hurtado, P J López-González, A Machordom
The description and delimitation of species in an evolutionary framework is essential for understanding patterns of biodiversity and distribution, and in the assessment of conservation strategies for natural resources. This study seeks to clarify the evolutionary history and genetic variation within and between closely related octocoral species that are fundamental to benthic marine ecosystems for harbouring a high diversity of associated fauna. For our study system, we focused on members of the Gorgoniidae family in the Eastern Pacific, particularly of the Ecuadorian littoral, a less studied marine ecosystem...
March 24, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28338346/chemical-variability-in-essential-oils-from-ruta-species-among-seasons-and-its-taxonomic-and-ecological-significance
#13
Zineb Bennaoum, Hachemi Benhassaini, Danilo Falconieri, Alessandra Piras, Silvia Porcedda
Leaf essential oils of 11 samples from Ruta montana, Ruta chalepensis subsp. latifolia and Ruta chalepensis subsp. angustifolia collected from two sites have been studied by GC/MS that allowed to identify 22, 25 and 12 components, respectively. The variability in the composition of essential oils among species and seasons was very high, and hence the existence of different chemotypes has been inferred. The major components were 2-undecanone, (E) caryophyllene, 2-nonanone and 2-methyloctyl acetate. Multivariate analysis of the 11 samples suggest that the main factors capable to influence the chemical composition of leaf essential oils was both the collection period and the geographical origin...
March 24, 2017: Natural Product Research
https://www.readbyqxmd.com/read/28332322/design-of-character-based-dna-barcode-motif-for-species-identification-a-computational-approach-and-its-validation-in-fishes
#14
Mohua Chakraborty, Bishal Dhar, Sankar Kumar Ghosh
The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa since the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters...
March 23, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28331401/dna-barcoding-and-species-delimitation-of-chaitophorinae-hemiptera-aphididae
#15
Xi-Chao Zhu, Jing Chen, Rui Chen, Li-Yun Jiang, Ge-Xia Qiao
Chaitophorinae aphids are widespread across Eurasia and North America, and include some important agricultural and horticultural pests. So, accurate rapid species identification is very important. Here, we used three mitochondrial genes and one endosymbiont gene to calculate and analyze the genetic distances within different datasets. For species delimitation, two distance-based methods were employed, threshold with NJ (neighbor-joining) and ABGD (Automatic Barcode Gap Discovery), and two tree-based approaches, GMYC (General Mixed Yule Coalescent) and PTP (Poisson Tree Process)...
2017: ZooKeys
https://www.readbyqxmd.com/read/28325976/arthropod-and-oligochaete-assemblages-from-grasslands-of-the-southern-kenai-peninsula-alaska
#16
Matthew L Bowser, John M Morton, John Delton Hanson, Dawn R Magness, Mallory Okuly
BACKGROUND: By the end of this century, the potential climate-biome of the southern Kenai Peninsula is forecasted to change from transitional boreal forest to prairie and grasslands, a scenario that may already be playing out in the Caribou Hills region. Here, spruce (Picea × lutzii Little [glauca × sitchensis]) forests were heavily thinned by an outbreak of the spruce bark beetle (Dendroctonus rufipennis (Kirby, 1837)) and replaced by the native but invasive grass species, Calamagrostis canadensis (Michx...
2017: Biodiversity Data Journal
https://www.readbyqxmd.com/read/28325372/is-predominant-clonal-evolution-a-common-evolutionary-adaptation-to-parasitism-in-pathogenic-parasitic-protozoa-fungi-bacteria-and-viruses
#17
M Tibayrenc, F J Ayala
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge...
2017: Advances in Parasitology
https://www.readbyqxmd.com/read/28323053/species-delimitation-and-phylogenetic-reconstruction-of-the-sinipercids-perciformes-sinipercidae-based-on-target-enrichment-of-thousands-of-nuclear-coding-sequences
#18
Shuli Song, Jinliang Zhao, Chenhong Li
The sinipercids are freshwater fishes endemic to East Asia, mainly in China. Phylogenetic studies on the sinipercids have made great progress in the last decades, but interspecific relationships and evolutionary history of the sinipercids remain unresolved. Lack of distinctive morphological characters leads to problems in validating of some species, such as Siniperca loona. Moreover, genetic data are needed to delimitate species pairs with explicit hypothesis testing, such as in S. chuatsi vs. S. kneri and Coreoperca whiteheadi vs...
March 18, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28322728/phlebotomine-sandflies-of-botswana-a-taxonomic-review-and-a-faunistic-update-with-the-first-record-of-genus-phlebotomus
#19
Andreas Krüger
The first records of phlebotomine sandflies from Botswana have been published only recently, comprising of four species of genus Sergentomyia. This update presents the first record of genus Phlebotomus, namely Ph. (Anaphlebotomus) rodhaini Parrot, which is also the first detection of a putative vector of leishmaniasis in Botswana. In addition, records of the Sergentomyia "bedfordi (Newstead) group" are reviewed, and the molecular taxonomy of all taxa known from Botswana is analysed based on three mitochondrial gene fragments (mtDNA)...
March 18, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28317541/mating-type-genes-in-the-genus-neofusicoccum-mating-strategies-and-usefulness-in-species-delimitation
#20
Anabela Lopes, Alan J L Phillips, Artur Alves
The genus Neofusicoccum includes species with wide geographical and plant host distribution, some of them of economic importance. The genus currently comprises 27 species that are difficult to identify based on morphological features alone. Thus, species differentiation is based on phylogenetic species recognition using multigene genealogies. In this study, we characterised the mating type genes of Neofusicoccum species. Specific primers were designed to amplify and sequence MAT genes in several species and a PCR-based mating type diagnostic assay was developed...
April 2017: Fungal Biology
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