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Species delimitation

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https://www.readbyqxmd.com/read/27918622/fungal-algal-association-patterns-in-lichen-symbiosis-linked-to-macroclimate
#1
Garima Singh, Francesco Dal Grande, Pradeep K Divakar, Jürgen Otte, Ana Crespo, Imke Schmitt
Both macroclimate and evolutionary events may influence symbiont association and diversity patterns. Here we assess how climatic factors and evolutionary events shape fungal-algal association patterns in the widely distributed lichen-forming fungal genus Protoparmelia. Multilocus phylogenies of fungal and algal partners were generated using 174 specimens. Coalescent-based species delimitation analysis suggested that 23 fungal hosts are associating with 20 algal species. Principal component analysis (PCA) was performed to infer how fungal-algal association patterns varied with climate...
December 5, 2016: New Phytologist
https://www.readbyqxmd.com/read/27916935/genome-wide-survey-reveals-transcriptional-differences-underlying-the-contrasting-trichome-phenotypes-of-two-sister-desert-poplars
#2
Jianchao Ma, Xiaodong He, Xiaotao Bai, Zhimin Niu, Bingbing Duan, Ningning Chen, Xuemin Shao, Dongshi Wan
Trichomes, which are widely used as an important diagnostic characteristic in plant species delimitation, play important roles in plant defense and adaptation to adverse environments. In this study, we used two sister poplar species, Populus pruinosa and Populus euphratica-which have, respectively, dense and sparse trichomes-to examine the genetic differences associated with these contrasting phenotypes. The results showed that 42 and 45 genes could be identified as candidate genes related to trichomes in P...
December 1, 2016: Genes
https://www.readbyqxmd.com/read/27915305/dna-barcoding-coupled-with-high-resolution-melting-analysis-enables-rapid-and-accurate-distinction-of-aspergillus-species
#3
Gabor Fidler, Sandor Kocsube, Eva Leiter, Sandor Biro, Melinda Paholcsek
We describe a high-resolution melting (HRM) analysis method that is rapid, reproducible, and able to identify reference strains and further 40 clinical isolates of Aspergillus fumigatus (14), A. lentulus (3), A. terreus (7), A. flavus (8), A. niger (2), A. welwitschiae (4), and A. tubingensis (2). Asp1 and Asp2 primer sets were designed to amplify partial sequences of the Aspergillus benA (beta-tubulin) genes in a closed-, single-tube system. Human placenta DNA, further Aspergillus (3), Candida (9), Fusarium (6), and Scedosporium (2) nucleic acids from type strains and clinical isolates were also included in this study to evaluate cross reactivity with other relevant pathogens causing invasive fungal infections...
December 3, 2016: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/27905886/multi-locus-phylogeny-using-topotype-specimens-sheds-light-on-the-systematics-of-niviventer-rodentia-muridae-in-china
#4
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/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
#5
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
#6
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/27900472/tissue-specific-expression-of-telomerase-reverse-transcriptase-gene-variants-in-nicotiana-tabacum
#7
Jana Fišerová Jurečková, Eva Sýkorová, Said Hafidh, David Honys, Jiří Fajkus, Miloslava Fojtová
In tobacco, three sequence variants of the TERT gene have been described. We revealed unbalanced levels of TERT variant transcripts in vegetative tobacco tissues and enhanced TERT transcription and telomerase activity in reproductive tissues. Telomerase is a ribonucleoprotein complex responsible for the maintenance of telomeres, structures delimiting ends of linear eukaryotic chromosomes. In the Nicotiana tabacum (tobacco) allotetraploid plant, three sequence variants (paralogs) of the gene coding for the telomerase reverse transcriptase subunit (TERT) have been described, two of them derived from the maternal N...
November 29, 2016: Planta
https://www.readbyqxmd.com/read/27890091/lactarius-subgenus-russularia-basidiomycota-russulales-novel-asian-species-worldwide-phylogeny-and-evolutionary-relationships
#8
Komsit Wisitrassameewong, Brian P Looney, Huyen T Le, Eske De Crop, Kanad Das, Kobeke Van de Putte, Ursula Eberhardt, Guo Jiayu, Dirk Stubbe, Kevin D Hyde, Annemieke Verbeken, Jorinde Nuytinck
Lactarius subg. Russularia is a large group of milkcaps occurring almost worldwide and dominant in many ecosystems. In this study we focus on new diversity, evolutionary relationships, divergence time, and origin of the subgenus. Six conifer symbionts are described as new to science: Lactarius atrii, L. aurantionitidus, L. dombangensis, L. flavigalactus, L. lachungensis, and L. sikkimensis. Species delimitation is assessed based on the concordance between morphological characteristics and an ITS phylogeny. Infrageneric relationships were studied using a phylogeny constructed from concatenated ITS-rpb2 data using Maximum Likelihood and Bayesian inference...
December 2016: Fungal Biology
https://www.readbyqxmd.com/read/27889831/an-ecophysiological-background-for-biogeographic-patterns-of-two-island-lizards
#9
Miguel A Carretero, Evandro P Lopes, Raquel Vasconcelos
Distributions of sedentary ectotherms are dependent on temperature and humidity due to their low homeostatic and dispersal abilities. Lizards are strongly conditioned by temperature, but hydric environment may be also important, at least in arid environments. Biotic interactions may also play a role in range patterns, but they are of minor importance in islands where native species monopolize well-delimited niche spaces. On the arid island of São Vicente (Cabo Verde), two endemic lizards display different spatial patterns...
December 2016: Die Naturwissenschaften
https://www.readbyqxmd.com/read/27878089/phylogenetic-relationships-of-freshwater-fishes-of-the-genus-capoeta-actinopterygii-cyprinidae-in-iran
#10
Hamid Reza Ghanavi, Elena G Gonzalez, Ignacio Doadrio
The Middle East contains a great diversity of Capoeta species, but their taxonomy remains poorly described. We used mitochondrial history to examine diversity of the algae-scraping cyprinid Capoeta in Iran, applying the species-delimiting approaches General Mixed Yule-Coalescent (GMYC) and Poisson Tree Process (PTP) as well as haplotype network analyses. Using the BEAST program, we also examined temporal divergence patterns of Capoeta. The monophyly of the genus and the existence of three previously described main clades (Mesopotamian, Anatolian-Iranian, and Aralo-Caspian) were confirmed...
November 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/27872558/taxonomic-revision-and-distribution-of-herbaceous-paramollugo-molluginaceae-in-the-eastern-hemisphere
#11
Alexander P Sukhorukov, Maria Kushunina
The genus Paramollugo with the type species Paramollugo nudicaulis (≡Mollugo nudicaulis) has recently been described after molecular investigations. Here we report two new endemic Malagasy species: Paramollugo simulans and Paramollugo elliotii, and transfer a forgotten New Caledonian endemic Mollugo digyna to Paramollugo (Paramollugo digyna). Consequently, the number of Paramollugo species in the Eastern Hemisphere is increased from three to six. Almost all genus representatives (except Paramollugo nudicaulis, which has a wide distribution in Southern Asia, Arabia and tropical Africa) are endemic to Madagascar, Somalia, or New Caledonia...
2016: PhytoKeys
https://www.readbyqxmd.com/read/27870903/rdna-loci-evolution-in-the-genus-glechoma-lamiaceae
#12
Tae-Soo Jang, Jamie McCann, John S Parker, Koji Takayama, Suk-Pyo Hong, Gerald M Schneeweiss, Hanna Weiss-Schneeweiss
Glechoma L. (Lamiaceae) is distributed in eastern Asia and Europe. Understanding chromosome evolution in Glechoma has been strongly hampered by its small chromosomes, constant karyotype and polyploidy. Here phylogenetic patterns and chromosomal variation in Glechoma species are considered, using genome sizes, chromosome mapping of 5S and 35S rDNAs by fluorescence in situ hybridisation (FISH), and phylogenetic analyses of internal transcribed spacers (nrITS) of 35S rDNA and 5S rDNA NTS sequences. Species and populations of Glechoma are tetraploid (2n = 36) with base chromosome number of x = 9...
2016: PloS One
https://www.readbyqxmd.com/read/27863094/resources-for-phylogenomic-analyses-of-australian-terrestrial-vertebrates
#13
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
#14
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
#15
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/27851754/complex-within-a-complex-integrative-taxonomy-reveals-hidden-diversity-in-cicadetta-brevipennis-hemiptera-cicadidae-and-unexpected-relationships-with-a-song-divergent-relative
#16
Thomas Hertach, Stéphane Puissant, Matija Gogala, Tomi Trilar, Reto Hagmann, Hannes Baur, Gernot Kunz, Elizabeth J Wade, Simon P Loader, Chris Simon, Peter Nagel
Multiple sources of data in combination are essential for species delimitation and classification of difficult taxonomic groups. Here we investigate a cicada taxon with unusual cryptic diversity and we attempt to resolve seemingly contradictory data sets. Cicada songs act as species-specific premating barriers and have been used extensively to reveal hidden taxonomic diversity in morphologically similar species. The Palaearctic Cicadetta montana species complex is an excellent example where distinct song patterns have disclosed multiple recently described species...
2016: PloS One
https://www.readbyqxmd.com/read/27851742/demographic-costs-associated-with-differences-in-habitat-space-occupancy
#17
Kelly A Williams, Donald B Miles
Delimiting the habitat characteristics describing the environmental conditions required by a species has become a critical tool for predicting organismal responses to environmental change. Grinnell emphasized the effects of environmental factors on the ability of a population to maintain a positive growth rate, yet few studies have included demographic or reproductive data in analyses of the Grinnellian niche. Identifying differences in habitat exploitation patterns in response to structural variation in the environment presents an incomplete description of the ability of species to adapt to changing habitats if demographic traits are not included...
2016: PloS One
https://www.readbyqxmd.com/read/27834678/receptor-species-dependent-desensitization-controls-kcnq1-kcne1-k-channels-as-downstream-effectors-of-gq-protein-coupled-receptors
#18
Marie-Cécile Kienitz, Dilyana Vladimirova, Christian Müller, Lutz Pott, Andreas Rinne
Activation of Gq protein-coupled receptors (GqPCRs) might induce divergent cellular responses, related to receptor-specific activation of different branches of the Gq-signaling pathway. Receptor-specific desensitization provides a mechanism of effector modulation by restricting the spatiotemporal activation of signaling components downstream of Gq We quantified signaling events downstream to GqPCR activation with Foerster resonance energy transfer (FRET)-based biosensors in CHO and HEK 293 cells. KCNQ1/KCNE1 channels (IKs) were measured as a functional readout of receptor-specific activation...
November 10, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27829048/remarkable-diversity-and-prevalence-of-dagger-nematodes-of-the-genus-xiphinema-cobb-1913-nematoda-longidoridae-in-olives-revealed-by-integrative-approaches
#19
Antonio Archidona-Yuste, Juan A Navas-Cortés, Carolina Cantalapiedra-Navarrete, Juan E Palomares-Rius, Pablo Castillo
The genus Xiphinema includes a remarkable group of invertebrates of the phylum Nematoda comprising ectoparasitic animals of many wild and cultivated plants. Damage is caused by direct feeding on root cells and by vectoring nepoviruses that cause diseases on several crops. Precise identification of Xiphinema species is critical for launching appropriate control measures. We make available the first detailed information on the diversity and distribution of Xiphinema species infesting wild and cultivated olive in a wide-region in southern Spain that included 211 locations from which 453 sampling sites were analyzed...
2016: PloS One
https://www.readbyqxmd.com/read/27828951/limitations-of-species-delimitation-based-on-phylogenetic-analyses-a-case-study-in-the-hypogymnia-hypotrypa-group-parmeliaceae-ascomycota
#20
Xinli Wei, Bruce McCune, H Thorsten Lumbsch, Hui Li, Steven Leavitt, Yoshikazu Yamamoto, Svetlana Tchabanenko, Jiangchun Wei
Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H...
2016: PloS One
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