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Species delimitation

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https://www.readbyqxmd.com/read/28539687/phylogenetic-analysis-of-monascus-and-new-species-from-honey-pollen-and-nests-of-stingless-bees
#1
R N Barbosa, S L Leong, O Vinnere-Pettersson, A J Chen, C M Souza-Motta, J C Frisvad, R A Samson, N T Oliveira, J Houbraken
The genus Monascus was described by van Tieghem (1884) to accommodate M. ruber and M. mucoroides, two species with non-ostiolate ascomata. Species delimitation in the genus is still mainly based on phenotypic characters, and taxonomic studies that include sequence data are limited. The genus is of economic importance. Species are used in fermented Asian foods as food colourants (e.g. 'red rice' (ang-kak, angka)) and found as spoilage organisms, and recently Monascus was found to be essential in the lifecycle of stingless bees...
March 2017: Studies in Mycology
https://www.readbyqxmd.com/read/28536444/the-geography-and-timing-of-genetic-divergence-in-the-lizard-phrynocephalus-theobaldi-on-the-qinghai-tibetan-plateau
#2
Yuanting Jin, Naifa Liu, Richard P Brown
The Qinghai-Tibetan Plateau (QTP) represents one of the earth's most significant physical features and there is increasing interest in the historical generation of biodiversity within this region. We hypothesized that there should be clear geographically coherent genetic structuring within one of the world's highest altitude lizards, Phrynocephalus theobaldi, due to considerable historical population fragmentation in this environment. This was tested using a major mitochondrial DNA (mtDNA) survey and sequencing of two nuclear markers (AME and RAG-1) from P...
May 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28533767/characterization-of-mycobacterium-chelonae-like-strains-by-comparative-genomics
#3
Christiane L Nogueira, Luiz G P de Almeida, Maria C Menendez, Maria J Garcia, Luciano A Digiampietri, Erica Chimara, Margo Cnockaert, Juan C Palomino, Françoise Portaels, Anandi Martin, Peter Vandamme, Sylvia C Leão
Isolates of the Mycobacterium chelonae-M. abscessus complex are subdivided into four clusters (CHI to CHIV) in the INNO-LiPA® Mycobacterium spp DNA strip assay. A considerable phenotypic variability was observed among isolates of the CHII cluster. In this study, we examined the diversity of 26 CHII cluster isolates by phenotypic analysis, drug susceptibility testing, whole genome sequencing and single-gene analysis. Pairwise genome comparisons were performed using several approaches, including average nucleotide identity (ANI) and genome-to-genome distance (GGD) among others...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28512377/species-delimitation-and-description-of-mesocriconema-nebraskense-n-sp-nematoda-criconematidae-a-morphologically-cryptic-parthenogenetic-species-from-north-american-grasslands
#4
Magdalena Olson, Timothy Harris, Rebecca Higgins, Peter Mullin, Kirsten Powers, Sean Olson, Thomas O Powers
Nematode surveys of North American grasslands conducted from 2010 to 2015 frequently recovered a species of criconematid nematode morphologically resembling Mesocriconema curvatum. These specimens were recovered from remnant native prairies in the central tallgrass ecoregion of North America, and not from surrounding agroecosystems. Historical records indicate that M. curvatum is a cosmopolitan species feeding on a wide range of agronomic and native plants. DNA barcoding indicates North American grasslands contain at least 10 phylogenetically distinct lineages of Mesocriconema that resemble, but are not, M...
March 2017: Journal of Nematology
https://www.readbyqxmd.com/read/28510191/taxonomy-of-cyrtochilum-alliance-orchidaceae-in-the-light-of-molecular-and-morphological-data
#5
Dariusz L Szlachetko, Marta Kolanowska, Aleksandra Naczk, Marcin Górniak, Magdalena Dudek, Piotr Rutkowski, Guy Chiron
BACKGROUND: The generic separateness and specific composition of the orchid genus Cyrtochilum was discussed for almost two centuries. Over the years several smaller taxa were segregated from this taxon, but their separateness was recently questioned based on molecular studies outcomes. The aim of our study was to revise concepts of morphological-based generic delimitation in Cyrtochilum-alliance and to compare it with the results of genetic analysis. We used phylogenetic framework in combination with phenetical analysis to provide proposal of the generic delimitation within Cyrtochilum-alliance...
December 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/28502764/cryptic-speciation-and-gene-flow-in-a-migratory-songbird-species-complex-insights-from-the-red-eyed-vireo-vireo-olivaceus
#6
C J Battey, John Klicka
Migratory species that alternate between sympatry and allopatry over the course of an annual cycle are promising subjects for studies seeking to understand the process of speciation in the absence of strict geographic isolation. Here we sought to identify cryptic species and assess rates of gene flow in a clade of neotropical migrant songbirds in which geography and taxonomy are currently out of sync: the Red-Eyed Vireo (V. olivaceus) Species Complex. Phylogenetic, clustering, and statistical species delimitation analyses found that V...
May 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28502098/-fix-me-another-marguerite-species-delimitation-in-a-group-of-intensively-hybridising-lineages-of-ox-eye-daisies-leucanthemum-mill-compositae-anthemideae
#7
Florian Wagner, Sabine Härtl, Robert Vogt, Christoph Oberprieler
Delineating species boundaries in the framework of the multi-species coalescent (MSC) proves to be a reliable, objective, and reproducible method in an increasing number of studies. However, the underlying model assumes the lack of gene flow after speciation; an assumption which may be frequently violated in plant evolution. The present study evaluates the robustness of currently available species delimitation methods implemented in beast (BFD, BFD*, and dissect) in the closely-knit ox-eye daisy group around Leucanthemum ageratifolium Pau...
May 14, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28487706/evolution-and-expression-patterns-of-cyc-tb1-genes-in-anacyclus-phylogenetic-insights-for-floral-symmetry-genes-in-asteraceae
#8
María A Bello, Pilar Cubas, Inés Álvarez, Guillermo Sanjuanbenito, Javier Fuertes-Aguilar
Homologs of the CYC/TB1 gene family have been independently recruited many times across the eudicots to control aspects of floral symmetry The family Asteraceae exhibits the largest known diversification in this gene paralog family accompanied by a parallel morphological floral richness in its specialized head-like inflorescence. In Asteraceae, whether or not CYC/TB1 gene floral symmetry function is preserved along organismic and gene lineages is unknown. In this study, we used phylogenetic, structural and expression analyses focused on the highly derived genus Anacyclus (tribe Anthemidae) to address this question...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28487260/pinpointing-cryptic-borders-fine-scale-phylogeography-and-genetic-landscape-analysis-of-the-hormogaster-elisae-complex-oligochaeta-hormogastridae
#9
Daniel F Marchán, Rosa Fernández, Irene de Sosa, Darío J Díaz Cosín, Marta Novo
Spatial and temporal aspects of the evolution of cryptic species complexes have received less attention than species delimitation within them. The phylogeography of the cryptic complex Hormogaster elisae (Oligochaeta, Hormogastridae) lacks knowledge on several aspects, including the small-scale distribution of its lineages or the palaeogeographic context of their diversification. To shed light on these topics, a dense specimen collection was performed in the center of the Iberian Peninsula - resulting in 28 new H...
May 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28481646/barcode-index-number-taxonomic-rank-and-modes-of-speciation-examples-from-fish
#10
Yuri Phedorovich Kartavtsev
Species delimitation by DNA sequence data or DNA barcoding is successful, as confirmed by the vast BOLD data base. However, the theory that would explain this fact has not been developed yet. An approach based on Barcoding Index Number (BIN), suggested in the assignment, allows delimiting of taxa of three ranks (species, genera, and families) and statistical validation with a high precision of delimiting (over 80%), as well as shows for majority of Co-1-based single gene trees good correspondence between their topology and conventional taxa content for analyzed fish species (R(2) ≈ 0...
May 8, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28469025/genetic-diversity-is-largely-unpredictable-but-scales-with-museum-occurrences-in-a-species-rich-clade-of-australian-lizards
#11
Sonal Singhal, Huateng Huang, Pascal O Title, Stephen C Donnellan, Iris Holmes, Daniel L Rabosky
Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based species delimitation to delineate 83 species-level lineages within the genus for downstream analyses...
May 17, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28467886/species-boundaries-in-the-absence-of-morphological-ecological-or-geographical-differentiation-in-the-red-sea-octocoral-genus-ovabunda-alcyonacea-xeniidae
#12
Catherine S McFadden, Roxanne Haverkort-Yeh, Alexandra M Reynolds, Anna Halàsz, Andrea M Quattrini, Zac H Forsman, Yehuda Benayahu, Robert J Toonen
The development of coalescent-based and other multilocus methods for species delimitation has facilitated the identification of cryptic species complexes across the tree of life. A recent taxonomic revision of the ecologically important soft coral genus Ovabunda validated 11morphospecies, all with type localities and overlapping geographic ranges in the Red Sea. A subsequent molecular phylogenetic analysis using mitochondrial and 28S nrDNA genes divided the genus into just two clades, with no apparent genetic distinctions among morphospecies...
April 30, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28467409/a-pilot-study-to-delimit-tsetse-target-populations-in-zimbabwe
#13
Gerald Chikowore, Ahmadou H Dicko, Peter Chinwada, Moses Zimba, William Shereni, François Roger, Jérémy Bouyer, Laure Guerrini
BACKGROUND: Tsetse (Glossina sensu stricto) are cyclical vectors of human and animal trypanosomoses, that are presently targeted by the Pan African Tsetse and Trypanosomiasis Eradication Campaign (PATTEC) coordinated by the African Union. In order to achieve effective control of tsetse, there is need to produce elaborate plans to guide intervention programmes. A model intended to aid in the planning of intervention programmes and assist a fuller understanding of tsetse distribution was applied, in a pilot study in the Masoka area, Mid-Zambezi valley in Zimbabwe, and targeting two savannah species, Glossina morsitans morsitans and Glossina pallidipes...
May 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28467369/developmental-control-of-nramp1-slc11a1-expression-in-professional-phagocytes
#14
Mathieu F M Cellier
NRAMP1 (SLC11A1) is a professional phagocyte membrane importer of divalent metals that contributes to iron recycling at homeostasis and to nutritional immunity against infection. Analyses of data generated by several consortia and additional studies were integrated to hypothesize mechanisms restricting NRAMP1 expression to mature phagocytes. Results from various epigenetic and transcriptomic approaches were collected for mesodermal and hematopoietic cell types and compiled for combined analysis with results of genetic studies associating single nucleotide polymorphisms (SNPs) with variations in NRAMP1 expression (eQTLs)...
May 3, 2017: Biology
https://www.readbyqxmd.com/read/28466109/fine-mapping-identifies-csgcn5-encoding-a-histone-acetyltransferase-as-putative-candidate-gene-for-tendril-less1-mutation-td-1-in-cucumber
#15
Feifan Chen, Bingbing Fu, Yupeng Pan, Chaowen Zhang, Haifan Wen, Yiqun Weng, Peng Chen, Yuhong Li
Next-generation sequencing-aided map-based cloning delimited the cucumber tendril - less1 ( td - 1 ) locus into a 190.7-kb region in chromosome 6 harboring a putative, novel-function candidate gene encoding a histone acetyltransferase ( CsGCN5 ). The tendril initiated from the lateral meristem is an important and characteristic organ for the species in the Cucurbitaceae family including cucumber (Cucumis sativus L.). While the tendril has its evolutionary significance, it also poses a nuisance in cucumber cultivation under protected environments in which tendril-less cucumber has its advantages...
May 2, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28459805/species-delimitation-in-asexual-insects-of-economic-importance-the-case-of-black-scale-parasaissetia-nigra-a-cosmopolitan-parthenogenetic-pest-scale-insect
#16
Yen-Po Lin, Robert D Edwards, Takumasa Kondo, Thomas L Semple, Lyn G Cook
Asexual lineages provide a challenge to species delimitation because species concepts either have little biological meaning for them or are arbitrary, since every individual is monophyletic and reproductively isolated from all other individuals. However, recognition and naming of asexual species is important to conservation and economic applications. Some scale insects are widespread and polyphagous pests of plants, and several species have been found to comprise cryptic species complexes. Parasaissetia nigra (Nietner, 1861) (Hemiptera: Coccidae) is a parthenogenetic, cosmopolitan and polyphagous pest that feeds on plant species from more than 80 families...
2017: PloS One
https://www.readbyqxmd.com/read/28453569/molecular-exploration-of-hidden-diversity-in-the-indo-west-pacific-sciaenid-clade
#17
Pei-Chun Lo, Shu-Hui Liu, Siti Azizah Mohd Nor, Wei-Jen Chen
The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa...
2017: PloS One
https://www.readbyqxmd.com/read/28448639/cryptic-diversity-of-the-subfamily-calaphidinae-hemiptera-aphididae-revealed-by-comprehensive-dna-barcoding
#18
Yerim Lee, Wonhoon Lee, Mariusz Kanturski, Robert G Foottit, Shin-Ichi Akimoto, Seunghwan Lee
Aphids are a species rich group comprising many important pests. However, species identification can be very difficult for aphids due to their morphological ambiguity. DNA barcoding has been widely adopted for rapid and reliable species identification as well as cryptic species detection. In this study, we investigated cryptic diversity in the subfamily Calaphidinae (Hemiptera: Aphididae) based on 899 sequences of cytochrome c oxidase I (COI) for 115 morphospecies (78 species collected in this study and sequences of 73 species downloaded from Genbank)...
2017: PloS One
https://www.readbyqxmd.com/read/28448491/relevant-units-of-analysis-for-applied-and-basic-research-dealing-with-neglected-transmissible-diseases-the-predominant-clonal-evolution-model-of-pathogenic-microorganisms
#19
REVIEW
Michel Tibayrenc, Francisco J Ayala
The predominant clonal evolution (PCE) model seeks to formulate a common population genetics framework for all micropathogens (namely, parasitic protozoa, fungi and yeasts, bacteria, and viruses). It relies on a definition of clonality that is only based on population structure features (namely, strongly restrained genetic recombination). Its clear-cut properties make it of strong interest for applied and basic research, since it permits the definition of stable, clearly delimited units of analysis below the species level: clonal genotypes and discrete genetic subdivisions ("near-clades")...
April 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28412535/complex-biogeographic-scenarios-revealed-in-the-diversification-of-the-largest-woodpecker-radiation-in-the-new-world
#20
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 13, 2017: Molecular Phylogenetics and Evolution
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