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Species delimitation

Abdullah M S Al-Hatmi, Sarah A Ahmed, Anne D van Diepeningen, Miranda Drogari-Apiranthitou, Paul E Verweij, Jacques F Meis, G Sybren de Hoog
The Fusarium solani species complex (FSSC) is the most common group of fusaria associated with superficial and life-threatening infections in humans. Here we formally introduce Fusarium metavorans sp. nov., widely known as FSSC6 (Fusarium solani species complex lineage 6), one of the most frequent agents of human opportunistic infections. The species is described with multilocus molecular data including sequences of internal transcribed spacer region (ITS), portions of the translation elongation factor 1-a gene (TEF1), and the partial RNA polymerase II gene (rPB2)...
April 1, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
Jennifer A Sheridan, Bryan L Stuart
Accurately delimiting species and their geographic ranges is imperative for conservation, especially in areas experiencing rapid habitat loss. Southeast Asia currently has one of the highest rates of deforestation in the world, is home to multiple biodiversity hotspots, and the majority of its countries have developing economies with limited resources for biodiversity conservation. Thus, accurately delimiting species and their ranges is particularly important in this region. We examined genetic and morphological variation in the widespread frog species Sylvirana nigrovittata (and its long-treated junior synonym S...
2018: PloS One
Maria Soledad Morales-Covarrubias, María Del Carmen Bolan-Mejía, Ana Isabel Vela Alonso, Jose F Fernandez-Garayzabal, Bruno Gomez-Gil
Strain CAIM 1838T , isolated from the hepatopancreas of a cultured diseased Pacific white shrimp (Penaeusvannamei), was subjected to characterization by a polyphasic taxonomic approach. On the basis of 16S rRNA gene sequence analysis, strain CAIM 1838T was most closely related to Streptococcus bovimastitidis 99.3 % and to other species of the Pyogenes clade of Streptococcus with lower similarity values. Average nucleotide identity values and the genome-to-genome distance of strain CAIM 1838T , as compared with the type strains, confirmed the separate species status with closely related species of the genus Streptococcus and were all below the thresholds to delimit a species, 93...
March 13, 2018: International Journal of Systematic and Evolutionary Microbiology
Steven D Leavitt, Martin Westberg, Matthew P Nelsen, John A Elix, Einar Timdal, Mohammad Sohrabi, Larry L St Clair, Laura Williams, Mats Wedin, H T Lumbsch
Multiple drivers shape the spatial distribution of species, including dispersal capacity, niche incumbency, climate variability, orographic barriers, and plate tectonics. However, biogeographic patterns of fungi commonly do not fit conventional expectations based on studies of animals and plants. Fungi, in general, are known to occur across exceedingly broad, intercontinental distributions, including some important components of biological soil crust communities (BSCs). However, molecular data often reveal unexpected biogeographic patterns in lichenized fungal species that are assumed to have cosmopolitan distributions...
2018: Frontiers in Microbiology
Petter Z Marki, Jon Fjeldså, Martin Irestedt, Knud A Jønsson
Detailed knowledge of species limits is an essential component of the study of biodiversity. Although accurate species delimitation usually requires detailed knowledge of both genetic and phenotypic variation, such variation may be limited or unavailable for some groups. In this study, we reconstruct a molecular phylogeny for all currently recognized species and subspecies of Australasian shrikethrushes (Colluricincla), including the first sequences of the poorly known C. tenebrosa. Using a novel method for species delimitation, the multi-rate Poisson Tree Process (mPTP), in concordance with the phylogenetic data, we estimate species limits in this genetically diverse, but phenotypically subtly differentiated complex of birds...
March 8, 2018: Molecular Phylogenetics and Evolution
Jin-Mei Zhang, Jordi López-Pujol, Xun Gong, Hua-Feng Wang, Roser Vilatersana, Shi-Liang Zhou
According to the present taxonomical treatment, Paeonia subsect. Delavayanae consists of only two species (P. delavayi and P. ludlowii) endemic to the Himalayan-Hengduan Mountains. Although P. ludlowii can be distinguished from P. delavayi on the basis of a series of morphological characters, the species delimitation remains controversial because the more widespread one, P. delavayi, exhibits considerable morphological diversity. Both chloroplast DNA markers and nuclear microsatellites or simple sequence repeats (nSSR) are used herein to reveal genetic diversity and relationships of the two taxa included in this subsection, and ecological niche modeling (ENM) is employed to get insights into their paleodistribution...
March 7, 2018: Molecular Phylogenetics and Evolution
John S Berriman, Ryan A Ellingson, Jaymes D Awbrey, Diane M Rico, Ángel A Valdés, Nerida G Wilson, Andres Aguilar, David G Herbert, Yayoi M Hirano, Cynthia D Trowbridge, Patrick J Krug
Predicting biotic resistance to highly invasive strains of "killer algae" (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates...
March 7, 2018: Molecular Phylogenetics and Evolution
Birthe Thormann, Dirk Ahrens, Carlos Iván Espinosa, Diego Marín Armijos, Thomas Wagner, Johann W Wägele, Marcell K Peters
Elevational diversity gradients are typically studied without considering the complex small-scale topography of large mountains, which generates habitats of strongly different environmental conditions within the same elevational zones. Here we analyzed the importance of small-scale topography for elevational diversity patterns of hyperdiverse tropical leaf beetles (Coleoptera: Chrysomelidae). We compared patterns of elevational diversity and species composition of beetles in two types of forests (on mountain ridges and in valleys) and analyzed whether differences in the rate of species turnover among forest habitats lead to shifts in patterns of elevational diversity when scaling up from the local study site to the elevational belt level...
March 9, 2018: Oecologia
P Fasura Amorim
The Jenynsia lineata species complex comprises J. lineata from Montevideo, Uruguay and Jenynsia multidentata, from coastal basins of Brazil, Uruguay and Argentina up to 1200 m a.s.l. Taxonomic divisions within this group were tested using three different species delimitation methods, which found the two existing names to be synonyms and revealed a new cryptic species. Jenynsia darwini sp. nov. is distinguished from all congeners by having a unique combination of character states, including the shape of the dorsal postcleithrum (three times higher than wide v...
March 7, 2018: Journal of Fish Biology
José Ferreira Saraiva, Raimundo Nonato Picanço Souto, Vera Margarete Scarpassa
Recent studies have shown that Anopheles oswaldoi sensu lato comprises a cryptic species complex in South America. Anopheles konderi, which was previously raised to synonymy with An. oswaldoi, has also been suggested to form a species complex. An. oswaldoi has been incriminated as a malaria vector in some areas of the Brazilian Amazon, Colombia, Peru and Venezuela, but was not recognized as a vector in the remaining regions in its geographic distribution. The role of An. konderi as a malaria vector is unknown or has been misattributed to An...
2018: PloS One
I Skrede, T Carlsen, T Schumacher
Helvella is a widespread, speciose genus of large apothecial ascomycetes ( Pezizomycete : Pezizales ) that are found in terrestrial biomes of the Northern and Southern Hemispheres. This study represents a beginning on assessing species limits and applying correct names for Helvella species based on type material and specimens in the university herbaria (fungaria) of Copenhagen (C), Harvard (FH) and Oslo (O). We use morphology and phylogenetic evidence from four loci - heat shock protein 90 ( hsp ), translation elongation factor alpha ( tef ), RNA polymerase II ( rpb2 ) and the nuclear large subunit ribosomal DNA (LSU) - to assess species boundaries in an expanded sample of Helvella specimens from Europe...
December 2017: Persoonia
M Wang, F Liu, P W Crous, L Cai
Species of Nigrospora commonly occur as plant pathogens, endophytes or saprobes, and have been shown to be extremely interesting for the discovery of novel metabolites. The familial placement, as well as phylogenetic relationships among Nigrospora species remain ambiguous. In this study, Nigrospora (= Khusia ) is confirmed as a monophyletic genus belonging to Apiosporaceae ( Xylariales ), based on a phylogeny inferred from LSU sequence data. A multi-locus phylogeny based on ITS, TEF1-α and TUB2 , in conjunction with morphological characters, host associations, and ecological data was employed for species delimitation in Nigrospora , as well as identification of 165 recently collected isolates from China, and three from Europe...
December 2017: Persoonia
Siddharthan Surveswaran, Vinita Gowda, Mei Sun
Spiranthes (∼ 36 species, Orchidaceae) is a small genus with a global distribution. It has a center of diversity in North America with only a few species occurring in Asia. This study focuses on the Asian Spiranthes with an emphasis on understanding their biogeographic relationships and species delimitations using molecular markers. Our phylogenetic trees based on nuclear (ITS) and chloroplast (trnL-trnLF, matK and trnS-G) sequences from samples across their range in Asia revealed the Asian Spiranthes are monophyletic...
March 1, 2018: Molecular Phylogenetics and Evolution
S Taheri, S James, V Roy, T Decaëns, B W Williams, F Anderson, R Rougerie, C-H Chang, G Brown, L Cunha, D W G Stanton, E Da Silva, J-H Chen, A R Lemmon, E Moriarty Lemmon, M Bartz, D Baretta, I Barois, E Lapied, M Coulis, L Dupont
Pontoscolex corethrurus is the most widespread earthworm species in tropical and sub-tropical zones and one of the most studied in soil science. Although, ecological interactions of P. corethrurus with its environment are well documented, the taxonomic status of the species remains unclear. In this study, we investigated phylogenetic relationships within the genus Pontoscolex, in particular focusing on morphologically indistinguishable (i.e., cryptic) lineages. A total of 792 specimens collected from 25 different countries and islands all over the world were analyzed using two mitochondrial (COI and 16S rDNA) and two nuclear (internal transcribed spacers 2 and 28S rDNA) markers, and a total of 11 morphological characters both internal and external were investigated in all genetically characterized lineages...
February 28, 2018: Molecular Phylogenetics and Evolution
Kathryn M Everson, Kyndall B P Hildebrandt, Steven M Goodman, Link E Olson
Madagascar is one of the world's foremost biodiversity hotspots, yet a large portion of its flora and fauna remains undescribed and the driving forces of in situ diversification are not well understood. Recent studies have identified a widespread, latitudinally structured phylogeographic pattern in Madagascar's humid-forest mammals, amphibians, reptiles, and insects. Several factors may be driving this pattern, namely biogeographic barriers (i.e., rivers or valleys) or past episodes of forest contraction and expansion...
February 28, 2018: Molecular Phylogenetics and Evolution
Noelia Martínez, Roberto Luque, Christian Milani, Marco Ventura, Oscar Bañuelos, Abelardo Margolles
Bifidobacteria are mutualistic intestinal bacteria and their presence in the human gut has been associated with health-promoting activities. The presence of antibiotic resistance genes in this genus is controversial, since, although bifidobacteria are non-pathogenic microorganisms, they could serve as reservoirs of resistance for intestinal pathogens. However, until now, few antibiotic resistance determinants have been functionally characterized in this genus. In this work, we show that Bifidobacterium breve CECT7263 displays atypical resistance to erythromycin and clindamycin...
March 2, 2018: Applied and Environmental Microbiology
Rosane Silva-Santos, Jorge L Ramirez, Pedro M Galetti, Patrícia D Freitas
The megadiversity of the neotropical ichthyofauna has been associated to recent diversification processes, reflecting in subtle or lacking morphological differentiation between species, challenging the classical taxonomic identification. Leporinus friderici occurs in several river basins of South America, and its nominal taxonomic validity has been questioned. Its wide distribution within the Brazilian Shield suggests that this species could be genetically structured among the hydrographic basins, despite a sharp morphological similarity...
2018: Frontiers in Genetics
Mark S Springer, John Gatesy
coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny...
February 26, 2018: Genes
Willie A S Vieira, Waléria G Lima, Eduardo S Nascimento, Sami J Michereff, Marcos P S Câmara, Vinson P Doyle
Developing a comprehensive and reliable taxonomy for the Colletotrichum gloeosporioides species complex will require adopting data standards on the basis of an understanding of how methodological choices impact morphological evaluations and phylogenetic inference. We explored the impact of methodological choices in a morphological and molecular evaluation of Colletotrichum species associated with banana in Brazil. The choice of alignment filtering algorithm has a significant impact on topological inference and the retention of phylogenetically informative sites...
January 16, 2018: Mycologia
Eglė Rudaitytė-Lukošienė, Petras Prakas, Dalius Butkauskas, Liuda Kutkienė, Iglė Vepštaitė-Monstavičė, Elena Servienė
Diaphragm muscles of 25 sika deer (Cervus nippon) farmed in Lithuania were examined for sarcocysts of Sarcocystis species. Two new Sarcocystis species, Sarcocystis frondea and Sarcocystis nipponi, were observed using light microscopy (LM) and transmission electron microscopy (TEM) and characterized by 18S ribosomal DNA (rDNA) and subunit I of cytochrome c oxidase (cox1) sequence analyses. By LM, sarcocysts of S. frondea and S. nipponi were ribbon-shaped and had finger-like sarcocyst wall protrusions, respectively...
February 26, 2018: Parasitology Research
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