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Species delimitation

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https://www.readbyqxmd.com/read/28108445/multi-rate-poisson-tree-processes-for-single-locus-species-delimitation-under-maximum-likelihood-and-markov-chain-monte-carlo
#1
P Kapli, S Lutteropp, J Zhang, K Kobert, P Pavlidis, A Stamatakis, T Flouri
MOTIVATION: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28103805/evolutionary-history-of-podarcis-tiliguerta-on-corsica-and-sardinia
#2
V Rodríguez, J M Buades, R P Brown, B Terrasa, V Pérez-Mellado, C Corti, M Delaugerre, J A Castro, A Picornell, M M Ramon
BACKGROUND: Podarcis tiliguerta is a wall lizard endemic to the Mediterranean islands of Corsica and Sardinia. Previous findings of high mtDNA and morphological diversity have led to the suggestion that it may represent a species complex. Here, we analysed mitochondrial and nuclear markers (mtDNA, 3110 bp; 6 nDNA loci, 3961 bp) in P. tiliguerta sampled from thirty-two localities across Corsica and Sardinia. RESULTS: We find much greater intraspecific genetic divergence than between sister species of other Mediterranean island Podarcis, i...
January 19, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28094568/barcode-based-species-delimitation-in-the-marine-realm-a-test-using-hexanauplia-multicrustacea-thecostraca-and-copepoda
#3
Robert G Young, Cathryn L Abbott, Thomas W Therriault, Sarah J Adamowicz
DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an optimal threshold value...
October 21, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28090412/development-characterization-and-cross-amplification-of-microsatellite-markers-in-the-understudied-african-genus-anthonotha-fabaceae
#4
Boris B Demenou, Olivier J Hardy
PREMISE OF THE STUDY: Anthonotha macrophylla (Fabaceae) is a common tree species throughout the Guineo-Congolian forest that is sometimes confounded with other congeneric species; it is expected to be an interesting phylogeographical model to infer the history of the African dense forests. We developed 18 microsatellite markers from this species and tested their transferability in 15 congeneric species. METHODS AND RESULTS: A genomic library was obtained using the Illumina platform, and 18 polymorphic microsatellite loci were developed...
January 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28089841/the-birth-of-aposematism-high-phenotypic-divergence-and-low-genetic-diversity-in-a-young-clade-of-poison-frogs
#5
Rebecca Dent Tarvin, Emily A Powell, Juan C Santos, Santiago R Ron, David C Cannatella
Rapid radiation coupled with low genetic divergence often hinders species delimitation and phylogeny estimation even if putative species are phenotypically distinct. Some aposematic species, such as poison frogs (Dendrobatidae), have high levels of intraspecific color polymorphism, which can lead to overestimation of species when phenotypic divergence primarily guides species delimitation. We explored this possibility in the youngest origin of aposematism (3-7 MYA) in poison frogs, Epipedobates, by comparing genetic divergence with color and acoustic divergence...
January 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28089840/biogeography-and-diversification-dynamics-of-the-african-woodpeckers
#6
Jérôme Fuchs, Jean-Marc Pons, Rauri C K Bowie
The dynamics of species accumulation of African terrestrial vertebrates over time remains underexplored in comparison with those in the New World, despite Africa hosting about 25% of the world's avian diversity. This lack of knowledge hampers our understanding of the fundamental processes that drive biodiversity and the dynamics of speciation. To begin to address this gap, we reconstructed species-level phylogenies of two unrelated clades of African woodpeckers (12 species of Geocolaptes/Campethera and 13 species of Chloropicus/ Mesopicos/ Dendropicos/Ipophilus) that diverged from their closest Indo-Malayan relatives at similar times...
January 12, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28074845/local-coexistence-and-genetic-isolation-of-three-pollinator-species-on-the-same-fig-tree-species
#7
T L Sutton, J L DeGabriel, M Riegler, J M Cook
Molecular tools increasingly reveal cryptic lineages and species that were previously unnoticed by traditional taxonomy. The discovery of cryptic species in sympatry prompts the question of how they coexist in the apparent absence of ecological divergence. However, this assumes first that the molecular taxonomy used to identify cryptic lineages delimits species boundaries accurately. This issue is important, because many diversity studies rely heavily or solely on data from mitochondrial DNA sequences for species delimitation, and several factors may lead to poor identification of species boundaries...
January 11, 2017: Heredity
https://www.readbyqxmd.com/read/28069534/genetic-spatial-structure-of-an-anchialine-cave-annelid-indicates-connectivity-within-but-not-between-islands-of-the-great-bahama-bank
#8
Brett C Gonzalez, Alejandro Martínez, Elizabeth Borda, Thomas M Iliffe, Diego Fontaneto, Katrine Worsaae
Land-locked anchialine blue holes are karstic sinkholes and caves with tidally influenced, vertically stratified water bodies that harbor endemic fauna exhibiting variable troglomorphic features. These habitats represent island-like systems, which can serve to elucidate evolutionary and biogeographic processes at local scales. We investigated whether the 'continuous spelean corridor' hypothesis may elucidate the biogeographical distributions of the stygobitic annelid Pelagomacellicephala iliffei (Polynoidae) collected from the Great Bahama and Caicos Banks of the Bahamas Archipelago...
January 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28056060/intraspecific-variation-and-phylogenetic-relationships-are-revealed-by-its1-secondary-structure-analysis-and-single-nucleotide-polymorphism-in-ganoderma-lucidum
#9
Xiuqing Zhang, Zhangyang Xu, Haisheng Pei, Zhou Chen, Xiaoyan Tan, Jing Hu, Bin Yang, Junshe Sun
Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS) sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1-3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia...
2017: PloS One
https://www.readbyqxmd.com/read/28053146/molecular-identification-of-chromoblastomycosis-clinical-isolates-in-guangdong
#10
Cindy Fransisca, Ya He, Zhiwen Chen, Hongfang Liu, Liyan Xi
Chromoblastomycosis is a chronic fungal infection of the skin and subcutaneous tissue. The most common etiologic agent encountered in Southern China is from the genus Fonsecaea. Fonsecaea species are often misidentified due to indistinct morphology features; furthermore, recent taxonomy revision was done on the fungi genus. Herein, a comprehensive evaluation with molecular sequencing data based on internal transcribed spacer (ITS) ribosomal DNA regions as molecular targets were implemented to 37 clinical isolates from chromoblastomycosis patients...
January 3, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/28050055/dna-barcoding-analysis-of-more-than-9%C3%A2-000-yeast-isolates-contributes-to-quantitative-thresholds-for-yeast-species-and-genera-delimitation
#11
D Vu, M Groenewald, S Szöke, G Cardinali, U Eberhardt, B Stielow, M de Vries, G J M Verkleij, P W Crous, T Boekhout, V Robert
DNA barcoding is a global initiative for species identification through sequencing of short DNA sequence markers. Sequences of two loci, ITS and LSU, were generated as barcode data for all (ca. 9k) yeast strains included in the CBS collection, originally assigned to ca. 2 000 species. Taxonomic sequence validation turned out to be the most severe bottleneck due to the large volume of generated trace files and lack of reference sequences. We have analysed and validated CBS strains and barcode sequences automatically...
September 2016: Studies in Mycology
https://www.readbyqxmd.com/read/28046038/species-delimitation-and-phylogenetic-relationships-in-ectobiid-cockroaches-dictyoptera-blattodea-from-china
#12
Yanli Che, Shunhua Gui, Nathan Lo, Andrew Ritchie, Zongqing Wang
We collected Ectobiidae cockroach specimens from 44 locations in the south of the Yangtze valley. We obtained 297 COI sequences specimens and carried out phylogenetic and divergence dating analyses, as well as species delimitation analysis using a General Mixed Yule Coalescent (GMYC) framework. The intraspecific and interspecific sequence divergence in Ectobiidae cockroaches ranged from 0.0 to 7.0% and 4.6 to 30.8%, respectively. GMYC analysis resulted in 53 (confidence interval: 37-65) entities (likelihood ratio = 103...
2017: PloS One
https://www.readbyqxmd.com/read/28043876/the-syllis-gracilis-species-complex-a-molecular-approach-to-a-difficult-taxonomic-problem-annelida-syllidae
#13
Patricia Álvarez-Campos, Gonzalo Giribet, Ana Riesgo
Syllis gracilis is an emblematic member of the subfamily Syllinae (Syllidae, Annelida), which inhabits shallow, temperate coastal waters and can be found on algae, coral rubble, and sponges. Their distinctive ypsiloid chaetae, usually found in specimens from populations all around the world, led to the consideration of the species as cosmopolitan, even though four other species have similar chaetae: Syllis magellanica, S. picta, S. mayeri and S. ypsiloides. The discovery of deeply divergent lineages in the Mediterranean Sea, that were morphologically similar, questioned the cosmopolitanism of S...
December 31, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28028478/reappraisal-of-europe-s-most-complete-early-cretaceous-plesiosaurian-brancasaurus-brancai-wegner-1914-from-the-wealden-facies-of-germany
#14
Sven Sachs, Jahn J Hornung, Benjamin P Kear
The holotype of Brancasaurus brancai is one of the most historically famous and anatomically complete Early Cretaceous plesiosaurian fossils. It derived from the Gerdemann & Co. brickworks clay pit near Gronau (Westfalen) in North Rhine-Westphalia, northwestern Germany. Stratigraphically this locality formed part of the classic European "Wealden facies," but is now more formally attributed to the upper-most strata of the Bückeberg Group (upper Berriasian). Since its initial description in 1914, the type skeleton of B...
2016: PeerJ
https://www.readbyqxmd.com/read/28028461/an-integrative-systematic-revision-and-biogeography-of-rhynchocalamus-snakes-reptilia-colubridae-with-a-description-of-a-new-species-from-israel
#15
Karin Tamar, Jiří Šmíd, Bayram Göçmen, Shai Meiri, Salvador Carranza
BACKGROUND: The colubrid snakes of the genus Rhynchocalamus are seldom studied and knowledge of their ecology and life history is scarce. Three species of Rhynchocalamus are currently recognized, R. satunini (from Turkey eastwards to Iran), R. arabicus (Yemen and Oman), and R. melanocephalus (from the Sinai Peninsula northwards to Turkey). All are slender, secretive, mainly nocturnal and rare fossorial snakes. This comprehensive study is the first to sample all known Rhynchocalamus species in order to review the intra-generic phylogenetic relationships and historical biogeography of the genus...
2016: PeerJ
https://www.readbyqxmd.com/read/28011338/phylogenetic-relationships-of-burmeistera-campanulaceae-lobelioideae-combining-whole-plastome-with-targeted-loci-data-in-a-recent-radiation
#16
Simon Uribe-Convers, Monica M Carlsen, Laura P Lagomarsino, Nathan Muchhala
The field of molecular systematics has benefited greatly with the advent of high-throughput sequencing (HTS), making large genomic datasets commonplace. However, a large number of targeted Sanger sequences produced by many studies over the last two decades are publicly available and should not be overlooked. In this study, we elucidate the phylogenetic relationships of the plant genus Burmeistera (Campanulaceae: Lobelioideae), while investigating how to best combine targeted Sanger loci with HTS data. We sequence, annotate, and analyze complete to nearly complete plastomes for a subset of the genus...
December 21, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28007567/global-phylogeography-of-oithona-similis-s-l-crustacea-copepoda-oithonidae-a-cosmopolitan-plankton-species-or-a-complex-of-cryptic-lineages
#17
Astrid Cornils, Britta Wend-Heckmann, Christoph Held
Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae...
December 19, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28007566/by-how-much-do-we-underestimate-species-diversity-of-liverworts-using-morphological-evidence-an-example-from-australasian-plagiochila-plagiochilaceae-jungermanniopsida
#18
Matt A M Renner, Margaret M Heslewood, Simon D F Patzak, Alfons Schäfer-Verwimp, Jochen Heinrichs
As a framework for revisionary study of the leafy liverwort Plagiochila in Australia, two methods for species delimitation on molecular sequence data, General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) were applied to a dataset including 265 individuals from Australia, New Zealand, and the Pacific. Groups returned by GMYC and ABGD were incongruent in some lineages, and ABGD tended to lump groups. This may reflect underlying heterogeneity in the history of diversification within different lineages of Plagiochila...
December 19, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28006793/a-revision-of-the-neogene-conidae-and-conorbidae-gastropoda-of-the-paratethys-sea
#19
Mathias Harzhauser, Bernard Landau
The Miocene Conidae and Conorbidae of the central- and south-eastern European Paratethys Sea are revised. In total, 74 species are described of which 10 are new species and 5 are documented for the first time from Paratethyan localities. Species descriptions and delimitations are partly based on morphometric data. In addition, colour patterns are described for the first time for the majority of species. In respect to the ongoing discussion on the supraspecific treatment of extant Conidae, we strongly focus on generic allocations and provide a key for the genera as understood herein...
December 22, 2016: Zootaxa
https://www.readbyqxmd.com/read/28006700/detection-of-different-microenvironments-and-lactobacillus-sakei-biotypes-in-ventricina-a-traditional-fermented-sausage-from-central-italy
#20
Patrizio Tremonte, Elena Sorrentino, Gianfranco Pannella, Luca Tipaldi, Marina Sturchio, Armando Masucci, Lucia Maiuro, Raffaele Coppola, Mariantonietta Succi
The present study evaluated the physico-chemical and microbiological features of Ventricina, considering for the first time the presence of different compartments deriving from the technology of production. In fact meat pieces (pork muscle and fat cut into cubes of about 10-20cm(3)), mixed with other ingredients and then stuffed into pig bladder, are still distinguishable at the end of the ripening. They appear delimited on the outside by the casing and inside by thin layers consisting of spices (mainly red pepper powder), salt and meat juices...
February 2, 2017: International Journal of Food Microbiology
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