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Species delimitation

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https://www.readbyqxmd.com/read/29165655/expression-atlas-gene-and-protein-expression-across-multiple-studies-and-organisms
#1
Irene Papatheodorou, Nuno A Fonseca, Maria Keays, Y Amy Tang, Elisabet Barrera, Wojciech Bazant, Melissa Burke, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Nancy George, Laura Huerta, Satu Koskinen, Suhaib Mohammed, Matthew Geniza, Justin Preece, Pankaj Jaiswal, Andrew F Jarnuczak, Wolfgang Huber, Oliver Stegle, Juan Antonio Vizcaino, Alvis Brazma, Robert Petryszak
Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage, disease or cell type. The available public and controlled access data sets from different sources are curated and re-analysed using standardized, open source pipelines and made available for queries, download and visualization. As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29162552/the-challenge-of-species-delimitation-in-the-diploid-polyploid-complex-veronica-subsection-pentasepalae
#2
Nélida Padilla-García, Blanca M Rojas-Andrés, Noemí López-González, Mariana Castro, Sílvia Castro, João Loureiro, Dirk C Albach, Nathalie Machon, M Montserrat Martínez-Ortega
A reliable taxonomic framework and the identification of evolutionary lineages are essential for effective decisions in conservation biodiversity programs. However, phylogenetic reconstruction becomes extremely difficult when polyploidy and hybridization are involved. Veronica subsection Pentasepalae is a diploid-polyploid complex of ca. 20 species with ploidy levels ranging from 2x to 10x. Here, DNA-ploidy level estimations and AFLP fingerprinting were used to determine the evolutionary history, and species boundaries were reviewed in an integrated approach including also previous data (mainly morphology and sequence-based phylogenetic reconstructions)...
November 18, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29158611/phylogeny-of-xerophilic-aspergilli-subgenus-aspergillus-and-taxonomic-revision-of-section-restricti
#3
F Sklenář, Ž Jurjević, P Zalar, J C Frisvad, C M Visagie, M Kolařík, J Houbraken, A J Chen, N Yilmaz, K A Seifert, M Coton, F Déniel, N Gunde-Cimerman, R A Samson, S W Peterson, V Hubka
Aspergillus section Restricti together with sister section Aspergillus (formerly Eurotium) comprises xerophilic species, that are able to grow on substrates with low water activity and in extreme environments. We adressed the monophyly of both sections within subgenus Aspergillus and applied a multidisciplinary approach for definition of species boundaries in sect. Restricti. The monophyly of sections Aspergillus and Restricti was tested on a set of 102 isolates comprising all currently accepted species and was strongly supported by Maximum likelihood (ML) and Bayesian inferrence (BI) analysis based on β-tubulin (benA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) loci...
September 2017: Studies in Mycology
https://www.readbyqxmd.com/read/29158032/resolving-taxonomic-turbulence-and-uncovering-cryptic-diversity-in-the-musk-turtles-sternotherus-using-robust-demographic-modeling
#4
Peter A Scott, Travis C Glenn, Leslie J Rissler
Accurate and consistent delimitation of species and their relationships provides a necessary framework for comparative studies, understanding evolutionary relationships, and informing conservation management. Despite the ever-increasing availability of genomic data, evolutionary dynamics can still render some relationships exceedingly difficult to resolve, including underlying speciation events that are rapid, recent, or confounded by post-speciation introgression. Here we present an empirical study of musk turtles (Sternotherus) which illustrates approaches to resolve difficult nodes in the Tree of Life that robust species-tree methods fail to resolve...
November 17, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29153398/maximizing-power-in-phylogenetics-and-phylogenomics-a-perspective-illuminated-by-fungal-big-data
#5
Alex Dornburg, Jeffrey P Townsend, Zheng Wang
Since its original inception over 150 years ago by Darwin, we have made tremendous progress toward the reconstruction of the Tree of Life. In particular, the transition from analyzing datasets comprised of small numbers of loci to those comprised of hundreds of loci, if not entire genomes, has aided in resolving some of the most vexing of evolutionary problems while giving us a new perspective on biodiversity. Correspondingly, phylogenetic trees have taken a central role in fields that span ecology, conservation, and medicine...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29151883/speciation-history-of-a-species-complex-of-primulina-eburnea-gesneriaceae-from-limestone-karsts-of-southern-china-a-biodiversity-hot-spot
#6
Jing Wang, Bin Ai, Hanghui Kong, Ming Kang
Limestone karsts in southern China are characterized by high edaphic and topographic heterogeneity and host high levels of species richness and endemism. However, the evolutionary mechanisms for generating such biodiversity remain poorly understood. Here, we performed species delimitation, population genetic analyses, simulations of gene flow and analyses of floral morphological traits to infer the geographic history of speciation in a species complex of Primulina eburnea from limestone karsts of southern China...
October 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/29151630/juglanconis-gen-nov-on-juglandaceae-and-the-new-family-juglanconidaceae-diaporthales
#7
H Voglmayr, L A Castlebury, W M Jaklitsch
Molecular phylogenetic analyses of ITS-LSU rDNA sequence data demonstrate that Melanconis species occurring on Juglandaceae are phylogenetically distinct from Melanconis s.str., and therefore the new genus Juglanconis is described. Morphologically, the genus Juglanconis differs from Melanconis by light to dark brown conidia with irregular verrucae on the inner surface of the conidial wall, while in Melanconis s.str. they are smooth. Juglanconis forms a separate clade not affiliated with a described family of Diaporthales, and the family Juglanconidaceae is introduced to accommodate it...
June 2017: Persoonia
https://www.readbyqxmd.com/read/29151627/a-multi-gene-phylogeny-of-lactifluus-basidiomycota-russulales-translated-into-a-new-infrageneric-classification-of-the-genus
#8
E De Crop, J Nuytinck, K Van de Putte, K Wisitrassameewong, J Hackel, D Stubbe, K D Hyde, M Roy, R E Halling, P-A Moreau, U Eberhardt, A Verbeken
Infrageneric relations of the genetically diverse milkcap genus Lactifluus (Russulales, Basidiomycota) are poorly known. Currently used classification systems still largely reflect the traditional, mainly morphological, characters used for infrageneric delimitations of milkcaps. Increased sampling, combined with small-scale molecular studies, show that this genus is underexplored and in need of revision. For this study, we assembled an extensive dataset of the genus Lactifluus, comprising 80 % of all known species and 30 % of the type collections...
June 2017: Persoonia
https://www.readbyqxmd.com/read/29143146/screening-transferable-microsatellite-markers-across-genus-phalaenopsis-orchidaceae
#9
Ya-Zhu Ko, Huei-Chuan Shih, Chi-Chu Tsai, Hsing-Hua Ho, Pei-Chun Liao, Yu-Chung Chiang
BACKGROUND: Molecular identification based on microsatellite loci is an important technology to improve the commercial breeding of the moth orchid. There are more than 30,000 cultivars have been enrolled at the Royal Horticultural Society (RHS). In this study, genomic microsatellite primer sets were developed from Phalaenopsis aphrodite subsp. formosana to further examine the transferability of across 21 Phalaenopsis species. METHODS AND RESULTS: Twenty-eight polymorphic microsatellite markers were obtained using the magnetic bead enrichment method, with high transferability of the 21 species of the genus Phalaenopsis, especially in the subgenus Phalaenopsis...
November 15, 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/29134240/fine-mapping-of-a-male-sterility-gene-ms-3-in-a-novel-cucumber-cucumis-sativus-l-mutant
#10
Yike Han, Fengyue Zhao, Shang Gao, Xianyun Wang, Aimin Wei, Zhengwu Chen, Nan Liu, Xueqiang Tong, Xinmeng Fu, Changlong Wen, Zhenxian Zhang, Ningning Wang, Shengli Du
The cucumber male sterility gene ms - 3 was fine mapped in a 76 kb region harboring an MMD1 -like gene Csa3M006660 that may be responsible for the male sterile in cucumber. A cucumber (Cucumis sativus L.) male sterile mutant (ms-3) in an advanced-generation inbred line was identified, and genetic analysis revealed that the male sterility trait was controlled by a recessive nuclear gene, ms-3, which was stably inherited. Histological studies suggested that the main cause of the male sterility was defective microsporogenesis, resulting in no tetrad or microspores being formed...
November 13, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29133994/a-commentary-on-the-practice-of-using-the-so-called-typeless-species
#11
Anatoly I Shatalkin, Tatiana V Galinskaya
The fears expressed by Santos et al. (2016) that description of typeless species (new species described based on field photographs) can be fatal for the practice of taxonomy which will succumb to an uncontrollable stream of "species of questionable delimitation" are, in our opinion, exaggerated. The Code already protects taxonomic practice from subjectivity quite well by limiting opportunities for descriptions of new species based on field photos by rigid requirements, and only skilled taxonomists with extensive knowledge of a group are capable of fulfilling them...
2017: ZooKeys
https://www.readbyqxmd.com/read/29116442/introduction
#12
Ricardo Gattass, Juliana G M Soares, Bruss Lima
The pulvinar can be subdivided into well-delimitated regions based on chemoarchitectural, cytoarchitectural, myeloarchitectural, connectivity, and electrophysiological criteria. Subdivisions of the pulvinar based on its chemoarchitectural features are the most consistently preserved across species of New and Old World monkeys. It is reasonable to speculate that the occurrence and distribution of calcium-binding proteins in the pulvinar, such as calbindin and parvalbumin, have been preserved along evolution...
2018: Advances in Anatomy, Embryology, and Cell Biology
https://www.readbyqxmd.com/read/29114162/a-new-cave-centipede-from-croatia-eupolybothrus-liburnicus-sp-n-with-notes-on-the-subgenus-schizopolybothrus-verhoeff-1934-chilopoda-lithobiomorpha-lithobiidae
#13
Nesrine Akkari, Ana Komerički, Alexander M Weigand, Gregory D Edgecombe, Pavel Stoev
A new species of Eupolybothrus Verhoeff, 1907 discovered in caves of Velebit Mountain in Croatia is described. E. liburnicussp. n. exhibits a few morphological differences from its most similar congeners, all of which are attributed to the subgenus Schizopolybothrus Verhoeff, 1934, and two approaches to species delimitation using the COI barcode region identify it as distinct from the closely allied E. cavernicolus Stoev & Komerički, 2013. E. spiniger (Latzel, 1888) is redescribed and a lectotype is designated for it as well as E...
2017: ZooKeys
https://www.readbyqxmd.com/read/29107618/impact-of-tree-priors-in-species-delimitation-and-phylogenetics-of-the-genus-oligoryzomys-rodentia-cricetidae
#14
Marcos de O R da Cruz, Marcelo Weksler
The use of genetic data and tree-based algorithms to delimit evolutionary lineages is becoming an important practice in taxonomic identification, especially in morphologically cryptic groups. The effects of different phylogenetic and/or coalescent models in the analyses of species delimitation, however, are not clear. In this paper, we assess the impact of different evolutionary priors in phylogenetic estimation, species delimitation, and molecular dating of the genus Oligoryzomys (Mammalia: Rodentia), a group with complex taxonomy and morphological cryptic species...
October 28, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29084279/testing-efficacy-of-distance-and-tree-based-methods-for-dna-barcoding-of-grasses-poaceae-tribe-poeae-in-australia
#15
Joanne L Birch, Neville G Walsh, David J Cantrill, Gareth D Holmes, Daniel J Murphy
In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test the efficacy of DNA barcoding methods. A reference library was generated that included 93.9% of species in Australia (408 individuals, [Formula: see text] = 3.7 individuals per species)...
2017: PloS One
https://www.readbyqxmd.com/read/29075476/phylogeographic-and-phylogenetic-analysis-for-tripterygium-species-delimitation
#16
Baowei Ma, Tianyuan Hu, Pei Li, Qingjun Yuan, Zhaoshou Lin, Yuhe Tu, Jia Li, Xianan Zhang, Xiaoyi Wu, Xiujuan Wang, Luqi Huang, Wei Gao
Tripterygium wilfordii (Celastraceae) is a traditional Chinese medicine; and the dried root and rhizome constitute the main officinal parts. Tripterygium wilfordii has been identified as a potential candidate for the treatment of systemic lupus erythematosus, rheumatoid arthritis, nephritis, asthma, leprosy, and cancer. The phylogenetic relationships within the Tripterygium genus are ambiguous; thus, our aim is to clarify the relationships within this genus using phylogeographic and phylogenetic analyses. Here, we first sequenced three plastid DNA regions (i...
October 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29074460/molecular-and-morphological-data-reveal-non-monophyly-and-speciation-in-imperiled-freshwater-mussels-anodontoides-and-strophitus
#17
Chase H Smith, Nathan A Johnson, John M Pfeiffer, Michael M Gangloff
Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and has been petitioned for listing under the Endangered Species Act. We set out to resolve the evolutionary history of A. radiatus, primarily generic placement and species boundaries, using phylogenetic, morphometric, and geographic information...
October 23, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29070094/molecular-systematics-biogeography-and-colony-fusion-in-the-european-dry-wood-termites-kalotermes-spp-blattodea-termitoidae-kalotermitidae
#18
V Scicchitano, F Dedeine, B Mantovani, A Luchetti
European dry-wood termites belong to the genus Kalotermes (Kalotermitidae), one of the two termite genera in Europe. Until the recent description of two new species, Kalotermes italicus in Italy and Kalotermes phoenicae in the eastern Mediterranean area, Kalotermes flavicollis was the only taxon known in this region. The presence of additional entities, suggested by morphological and physiological variation observed in K. flavicollis, was supported by molecular studies revealing four distinct genetic lineages: lineage A, K...
October 26, 2017: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/29051971/fine-mapping-of-the-brassica-napus-bnsdt1-gene-associated-with-determinate-growth-habit
#19
Kaixiang Li, Yanmei Yao, Lu Xiao, Zhigang Zhao, Shaomin Guo, Zhong Fu, Dezhi Du
The newly discovered determinate plant growth habit of Brassica napus is a potential trait that might contribute to the genetic improvement of rapeseed. Brassica napus is an important species of rapeseed and has an indeterminate growth habit. However, a determinate inflorescence strain (4769) has been discovered among doubled haploid (DH) lines obtained from a spring B. napus × winter B. napus cross. We assessed the effect of the determinate growth habit on agronomic traits. The results showed that determinacy is beneficial for reducing plant height and flowering time, advancing maturity and maintaining productivity...
October 19, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29049373/barcoding-the-butterflies-of-southern-south-america-species-delimitation-efficacy-cryptic-diversity-and-geographic-patterns-of-divergence
#20
Pablo D Lavinia, Ezequiel O Núñez Bustos, Cecilia Kopuchian, Darío A Lijtmaer, Natalia C García, Paul D N Hebert, Pablo L Tubaro
Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America...
2017: PloS One
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