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https://www.readbyqxmd.com/read/27905886/multi-locus-phylogeny-using-topotype-specimens-sheds-light-on-the-systematics-of-niviventer-rodentia-muridae-in-china
#1
Bin Zhang, Kai He, Tao Wan, Peng Chen, Guozheng Sun, Shaoying Liu, Truong Son Nguyen, Liangkong Lin, Xuelong Jiang
BACKGROUND: Niviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4)...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27904060/causative-agents-of-aspergillosis-including-cryptic-aspergillus-species-and-a-fumigatus
#2
Takahito Toyotome
Aspergillosis is an important deep mycosis. The causative agents are Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, and Aspergillus terreus, of which A. fumigatus is the most prevalent. Cryptic Aspergillus spp., which morphologically resemble representative species of each Aspergillus section, also cause aspergillosis. Most of the cryptic species reveal different susceptibility patterns and/or different secondary metabolite profiles, also called exometabolome in this manuscript, from those representative species...
2016: Medical Mycology Journal
https://www.readbyqxmd.com/read/27903261/discrete-phenotypes-are-not-underpinned-by-genome-wide-genetic-differentiation-in-the-squat-lobster-munida-gregaria-crustacea-decapoda-munididae-a-multi-marker-study-covering-the-patagonian-shelf
#3
Chen Wang, Shobhit Agrawal, Jürgen Laudien, Vreni Häussermann, Christoph Held
BACKGROUND: DNA barcoding has demonstrated that many discrete phenotypes are in fact genetically distinct (pseudo)cryptic species. Genetically identical, isogenic individuals, however, can also express similarly different phenotypes in response to a trigger condition, e.g. in the environment. This alternative explanation to cryptic speciation often remains untested because it requires considerable effort to reject the hypothesis that the observed underlying genetic homogeneity of the different phenotypes may be trivially caused by too slowly evolving molecular markers...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27903256/revealing-hidden-species-diversity-in-closely-related-species-using-nuclear-snps-ssrs-and-dna-sequences-a-case-study-in-the-tree-genus-milicia
#4
Kasso Daïnou, Céline Blanc-Jolivet, Bernd Degen, Priscilla Kimani, Dyana Ndiade-Bourobou, Armel S L Donkpegan, Félicien Tosso, Esra Kaymak, Nils Bourland, Jean-Louis Doucet, Olivier J Hardy
BACKGROUND: Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27902302/polynucleobacter-wuianus-sp-nov-a-free-living-freshwater-bacterium-affiliated-with-the-cryptic-species-complex-pnecc
#5
Martin W Hahn, Lesley R Huymann, Ulrike Koll, Johanna Schmidt, Elke Lang, Matthias Hoetzinger
Strain QLW-P1FAT50C-4T, isolated from a shallow acidic freshwater pond located in the Austrian Alps at an altitude of 1300 m, was characterized by investigation of phenotypic, chemotaxonomic and genomic traits. As shown previously, phylogenetic analyses based on 16S rRNA gene sequences place the strain in the cryptic species complex PnecC within the genus Polynucleobacter. The major fatty acids of the strain were C16:1 ω7c and C18:1 ω7c. The strain has a genome of 2.23 Mbp with a GC content of 44.9 mol%. The strain encodes a seemingly complete gene cluster for anoxygenic photosynthesis but lacks typical genes for CO2 assimilation...
November 2, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27901268/forecasting-pollination-declines-through-dna-barcoding-the-potential-contributions-of-macroecological-and-macroevolutionary-scales-of-inquiry
#6
Jana C Vamosi, Yan-Bing Gong, Sarah J Adamowicz, Laurence Packer
While pollinators are widely acknowledged as important contributors to seed production in plant communities, we do not yet have a good understanding of the importance of pollinator specialists for this ecosystem service. Determination of the prevalence of pollinator specialists is often hindered by the occurrence of cryptic species and the limitations of observational data on pollinator visitation rates, two areas where DNA barcoding of pollinators and pollen can be useful. Further, the demonstrated adequacy of pollen DNA barcoding from historical records offers opportunities to observe the effects of pollinator loss over longer timescales, and phylogenetic approaches can elucidate the historical rates of extinction of specialist lineages...
November 30, 2016: New Phytologist
https://www.readbyqxmd.com/read/27894994/a-new-genus-of-anostomidae-ostariophysi-characiformes-diversity-phylogeny-and-biogeography-based-on-cytogenetic-molecular-and-morphological-data
#7
Jorge L Ramirez, José L O Birindelli, Pedro M Galetti
A new genus of Anostomidae (Characiformes) is described to include ten valid extant species previously classified in Leporinus or Hypomasticus and distributed throughout most major river basins in South America: L. brinco, L. conirostris, L. elongatus, H. garmani, L. macrocephalus, L. muyscorum, L. obtusidens, L. piavussu, L. reinhardti, and L. trifasciatus. The monophyly of Megaleporinus is well-supported in a phylogenetic analysis based on two mitochondrial and three nuclear genes, as well as its sister group relationship to Abramites...
November 25, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27886423/an-approach-for-identifying-cryptic-barriers-to-gene-flow-that-limit-species-geographic-ranges
#8
Steven J Micheletti, Andrew Storfer
Species' geographic range limits are most often not demarcated by obvious dispersal barriers. Poor quality habitat at the edge of a species' range can prevent range expansion by preventing outward migration or through reducing adaptive potential resulting from decreased genetic diversity. We identified habitat variables that constrain gene flow across the entire geographic range of an endemic salamander (Ambystoma barbouri) in the eastern United States, and we tested whether increased resistance resulting from these variables provides cryptic dispersal barriers at the range edges...
November 25, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27884104/phylogeography-reveals-an-ancient-cryptic-radiation-in-east-asian-tree-frogs-hyla-japonica-group-and-complex-relationships-between-continental-and-island-lineages
#9
Christophe Dufresnes, Spartak N Litvinchuk, Amaël Borzée, Yikweon Jang, Jia-Tang Li, Ikuo Miura, Nicolas Perrin, Matthias Stöck
BACKGROUND: In contrast to the Western Palearctic and Nearctic biogeographic regions, the phylogeography of Eastern-Palearctic terrestrial vertebrates has received relatively little attention. In East Asia, tectonic events, along with Pleistocene climatic conditions, likely affected species distribution and diversity, especially through their impact on sea levels and the consequent opening and closing of land-bridges between Eurasia and the Japanese Archipelago. To better understand these effects, we sequenced mitochondrial and nuclear markers to determine phylogeographic patterns in East-Asian tree frogs, with a particular focus on the widespread H...
November 23, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27875982/comparative-genomics-to-explore-phylogenetic-relationship-cryptic-sexual-potential-and-host-specificity-of-rhynchosporium-species-on-grasses
#10
Daniel Penselin, Martin Münsterkötter, Susanne Kirsten, Marius Felder, Stefan Taudien, Matthias Platzer, Kevin Ashelford, Konrad H Paskiewicz, Richard J Harrison, David J Hughes, Thomas Wolf, Ekaterina Shelest, Jenny Graap, Jan Hoffmann, Claudia Wenzel, Nadine Wöltje, Kevin M King, Bruce D L Fitt, Ulrich Güldener, Anna Avrova, Wolfgang Knogge
BACKGROUND: The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young age of the five species currently known, this genus appears to be well-suited to address the question at the molecular level of how pathogenic fungi adapt to their hosts...
November 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27870312/mixed-pollen-load-and-late-acting-self-incompatibility-flexibility-in-adenocalymma-peregrinum-miers-l-g-lohmann-bignonieae-bignoniaceae
#11
Mariana Oliveira Duarte, Clesnan Mendes-Rodrigues, Mariana Ferreira Alves, Paulo Eugênio Oliveira, Diana Salles Sampaio
Mixed cross and self-pollen load in the stigma (mixed pollination) in species with late-acting self-incompatibility system (LSI) can lead to self-fertilized seed production. This "cryptic self-fertility" may allow selfed seedling development in populations of otherwise largely self-sterile species. Our aims were to check if mixed pollinations would lead to fruit set in LSI Adenocalymma peregrinum, and test for evidence of early-acting inbreeding depression in putative selfed seeds from mixed pollinations. Experimental pollinations and tests for germination were carried out in a natural population...
November 21, 2016: Plant Biology
https://www.readbyqxmd.com/read/27870044/foliar-bacteria-and-soil-fertility-mediate-seedling-performance-a-new-and-cryptic-dimension-of-niche-differentiation
#12
Eric A Griffin, M Brian Traw, Peter J Morin, Jonathan N Pruitt, S Joseph Wright, Walter P Carson
The phyllosphere (comprising the leaf surface and interior) is one of the world's largest microbial habitats and is host to an abundant and diverse array of bacteria. Nonetheless, the degree to which bacterial communities are benign, harmful, or beneficial to plants in situ is unknown. We tested the hypothesis that the net effect of reducing bacterial abundance and diversity would vary substantially among host species (from harmful to beneficial) and this would be strongly mediated by soil resource availability...
November 2016: Ecology
https://www.readbyqxmd.com/read/27870036/seedling-performance-covaries-with-dormancy-thresholds-maintaining-cryptic-seed-heteromorphism-in-a-fire-prone-system
#13
Ganesha S Liyanage, David J Ayre, Mark K J Ooi
The production of morphologically different seeds or fruits by the same individual plant is known as seed heteromorphism. Such variation is expected to be selected for in disturbance-prone environments to allow germination into inherently variable regeneration niches. However, there are few demonstrations that heteromorphic seed characteristics should be favored by selection or how they may be maintained. In fire-prone ecosystems, seed heteromorphism is found in the temperatures needed to break physical dormancy, with seeds responding to high or low temperatures, ensuring emergence under variable fire-regime-related soil heating...
November 2016: Ecology
https://www.readbyqxmd.com/read/27863094/resources-for-phylogenomic-analyses-of-australian-terrestrial-vertebrates
#14
Jason G Bragg, Sally Potter, Ke Bi, Renee Catullo, Stephen C Donnellan, Mark D B Eldridge, Leo Joseph, J Scott Keogh, Paul Oliver, Kevin C Rowe, Craig Moritz
High throughput sequencing methods promise to improve our ability to infer the evolutionary histories of lineages and to delimit species. These are exciting prospects for the study of Australian vertebrates, a group comprised of many globally unique lineages with a long history of isolation. The evolutionary relationships within many of these lineages have been difficult to resolve with small numbers of loci and we now know that many lineages also exhibit substantial cryptic diversity. Here, we present a set of phylogenetically diverse transcriptome resources to enable exon-based sequence capture studies of Australian vertebrates, including transcriptome sequences for 4 species of birds, 4 frogs, 7 lizards and 7 mammals...
November 8, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27862533/phylogeography-of-the-heavily-poached-african-common-pangolin-pholidota-manis-tricuspis-reveals-six-cryptic-lineages-as-traceable-signatures-of-pleistocene-diversification
#15
Philippe Gaubert, Flobert Njiokou, Gabriel Ngua, Komlan Afiademanyo, Sylvain Dufour, Jean Malekani, Sery Gonedelé Bi, Christelle Tougard, Ayodeji Olayemi, Emmanuel Danquah, Chabi A M S Djagoun, Prince Kaleme, Casimir Nebesse Mololo, William Stanley, Shu-Jin Luo, Agostinho Antunes
Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins...
December 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27862524/sequence-capture-and-next-generation-sequencing-of-ultraconserved-elements-in-a-large-genome-salamander
#16
Catherine E Newman, Christopher C Austin
Amidst the rapid advancement in next-generation sequencing (NGS) technology over the last few years, salamanders have been left behind. Salamanders have enormous genomes - up to 40 times the size of the human genome - and this poses challenges to generating NGS data sets of quality and quantity similar to those of other vertebrates. However, optimization of laboratory protocols is time-consuming and often cost prohibitive, and continued omission of salamanders from novel phylogeographic research is detrimental to species facing decline...
November 14, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27861481/-presence-of-lactoferrin-lf-in-lymphocutaneous-sporotrichosis-yeast-bound-antimicrobial-peptide
#17
Alejandro Palma-Ramos, Laura E Castrillón-Rivera, María Elisa Vega-Mémije, Roberto Arenas-Guzmán, Lucía Rangel-Gamboa
: Sporotrichosis is a common subcutaneous mycosis in Latin America, produced by dimorphic fungi belong to Sporothrix schenckii complex of cryptic species. Infection is acquired by traumatic inoculation with contaminated organic material. Host immune response includes polymorphonuclear neutrophils chemotaxis and release of granular components. Lactoferrin is a protein member of the transferrin family of iron-binding proteins, present inside polymorphonuclear granular structure, and has been reported to affect growth and development of infectious agents, including fungal organisms...
November 2016: Gaceta Médica de México
https://www.readbyqxmd.com/read/27859102/large-herbivores-promote-habitat-specialization-and-beta-diversity-of-african-savanna-trees
#18
Robert M Pringle, Kirsten M Prior, Todd M Palmer, Truman P Young, Jacob R Goheen
Edaphic variation in plant community composition is widespread, yet its underlying mechanisms are rarely understood and often assumed to be physiological. In East African savannas, Acacia tree species segregate sharply across soils of differing parent material: the ant-defended whistling thorn, A. drepanolobium (ACDR), is monodominant on cracking clay vertisols that are nutrient rich but physically stressful, whereas poorly defended species such as A. brevispica (ACBR) dominate on nutrient-poor but otherwise less-stressful sandy loams...
October 2016: Ecology
https://www.readbyqxmd.com/read/27855726/helminth-parasites-of-south-american-fishes-current-status-and-characterization-as-a-model-for-studies-of-biodiversity
#19
J L Luque, F B Pereira, P V Alves, M E Oliva, J T Timi
The South American subcontinent supports one of the world's most diverse and commercially very important ichthyofauna. In this context, the study of South American fish parasites is of increased relevance in understanding their key roles in ecosystems, regulating the abundance or density of host populations, stabilizing food webs and structuring host communities. It is hard to estimate the number of fish parasites in South America. The number of fish species studied for parasites is still low (less than 10%), although the total number of host-parasite associations (HPAs) found in the present study was 3971...
November 18, 2016: Journal of Helminthology
https://www.readbyqxmd.com/read/27855173/global-population-structure-of-a-worldwide-pest-and-virus-vector-genetic-diversity-and-population-history-of-the-bemisia-tabaci-sibling-species-group
#20
Margarita Hadjistylli, George K Roderick, Judith K Brown
The whitefly Bemisia tabaci sibling species (sibsp.) group comprises morphologically indiscernible lineages of well-known exemplars referred to as biotypes. It is distributed throughout tropical and subtropical latitudes and includes the contemporary invasive haplotypes, termed B and Q. Several well-studied B. tabaci biotypes exhibit ecological and biological diversity, however, most members are poorly studied or completely uncharacterized. Genetic studies have revealed substantial diversity within the group based on a fragment of the mitochondrial cytochrome oxidase I (mtCOI) sequence (haplotypes), with other tested markers being less useful for deep phylogenetic comparisons...
2016: PloS One
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