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Species delimitation

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https://www.readbyqxmd.com/read/28338346/chemical-variability-in-essential-oils-from-ruta-species-among-seasons-and-its-taxonomic-and-ecological-significance
#1
Zineb Bennaoum, Hachemi Benhassaini, Danilo Falconieri, Alessandra Piras, Silvia Porcedda
Leaf essential oils of 11 samples from Ruta montana, Ruta chalepensis subsp. latifolia and Ruta chalepensis subsp. angustifolia collected from two sites have been studied by GC/MS that allowed to identify 22, 25 and 12 components, respectively. The variability in the composition of essential oils among species and seasons was very high, and hence the existence of different chemotypes has been inferred. The major components were 2-undecanone, (E) caryophyllene, 2-nonanone and 2-methyloctyl acetate. Multivariate analysis of the 11 samples suggest that the main factors capable to influence the chemical composition of leaf essential oils was both the collection period and the geographical origin...
March 24, 2017: Natural Product Research
https://www.readbyqxmd.com/read/28332322/design-of-character-based-dna-barcode-motif-for-species-identification-a-computational-approach-and-its-validation-in-fishes
#2
Mohua Chakraborty, Bishal Dhar, Sankar Kumar Ghosh
The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa since the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters...
March 23, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28331401/dna-barcoding-and-species-delimitation-of-chaitophorinae-hemiptera-aphididae
#3
Xi-Chao Zhu, Jing Chen, Rui Chen, Li-Yun Jiang, Ge-Xia Qiao
Chaitophorinae aphids are widespread across Eurasia and North America, and include some important agricultural and horticultural pests. So, accurate rapid species identification is very important. Here, we used three mitochondrial genes and one endosymbiont gene to calculate and analyze the genetic distances within different datasets. For species delimitation, two distance-based methods were employed, threshold with NJ (neighbor-joining) and ABGD (Automatic Barcode Gap Discovery), and two tree-based approaches, GMYC (General Mixed Yule Coalescent) and PTP (Poisson Tree Process)...
2017: ZooKeys
https://www.readbyqxmd.com/read/28325976/arthropod-and-oligochaete-assemblages-from-grasslands-of-the-southern-kenai-peninsula-alaska
#4
Matthew L Bowser, John M Morton, John Delton Hanson, Dawn R Magness, Mallory Okuly
BACKGROUND: By the end of this century, the potential climate-biome of the southern Kenai Peninsula is forecasted to change from transitional boreal forest to prairie and grasslands, a scenario that may already be playing out in the Caribou Hills region. Here, spruce (Picea × lutzii Little [glauca × sitchensis]) forests were heavily thinned by an outbreak of the spruce bark beetle (Dendroctonus rufipennis (Kirby, 1837)) and replaced by the native but invasive grass species, Calamagrostis canadensis (Michx...
2017: Biodiversity Data Journal
https://www.readbyqxmd.com/read/28325372/is-predominant-clonal-evolution-a-common-evolutionary-adaptation-to-parasitism-in-pathogenic-parasitic-protozoa-fungi-bacteria-and-viruses
#5
M Tibayrenc, F J Ayala
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge...
2017: Advances in Parasitology
https://www.readbyqxmd.com/read/28323053/species-delimitation-and-phylogenetic-reconstruction-of-the-sinipercids-perciformes-sinipercidae-based-on-target-enrichment-of-thousands-of-nuclear-coding-sequences
#6
Shuli Song, Jinliang Zhao, Chenhong Li
The sinipercids are freshwater fishes endemic to East Asia, mainly in China. Phylogenetic studies on the sinipercids have made great progress in the last decades, but interspecific relationships and evolutionary history of the sinipercids remain unresolved. Lack of distinctive morphological characters leads to problems in validating of some species, such as Siniperca loona. Moreover, genetic data are needed to delimitate species pairs with explicit hypothesis testing, such as in S. chuatsi vs. S. kneri and Coreoperca whiteheadi vs...
March 17, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28322728/phlebotomine-sandflies-of-botswana-a-taxonomic-review-and-a-faunistic-update-with-the-first-record-of-genus-phlebotomus
#7
Andreas Krüger
The first records of phlebotomine sandflies from Botswana have been published only recently, comprising of four species of genus Sergentomyia. This update presents the first record of genus Phlebotomus, namely Ph. (Anaphlebotomus) rodhaini Parrot, which is also the first detection of a putative vector of leishmaniasis in Botswana. In addition, records of the Sergentomyia "bedfordi (Newstead) group" are reviewed, and the molecular taxonomy of all taxa known from Botswana is analysed based on three mitochondrial gene fragments (mtDNA)...
March 18, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28317541/mating-type-genes-in-the-genus-neofusicoccum-mating-strategies-and-usefulness-in-species-delimitation
#8
Anabela Lopes, Alan J L Phillips, Artur Alves
The genus Neofusicoccum includes species with wide geographical and plant host distribution, some of them of economic importance. The genus currently comprises 27 species that are difficult to identify based on morphological features alone. Thus, species differentiation is based on phylogenetic species recognition using multigene genealogies. In this study, we characterised the mating type genes of Neofusicoccum species. Specific primers were designed to amplify and sequence MAT genes in several species and a PCR-based mating type diagnostic assay was developed...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28317538/families-genera-and-species-of-botryosphaeriales
#9
Tao Yang, Johannes Z Groenewald, Ratchadawan Cheewangkoon, Fahimeh Jami, Jafar Abdollahzadeh, Lorenzo Lombard, Pedro W Crous
Members of Botryosphaeriales are ecologically diverse, but most commonly associated with leaf spots, fruit and root rots, die-back or cankers of diverse woody hosts. Based on morphology and DNA sequence data, the Botryosphaeriales have to date been shown to contain eight families, with an additional two, Endomelanconiopsisaceae (Endomelanconiopsis) and Pseudofusicoccumaceae (Pseudofusicoccum) being newly described in this study. Furthermore, Oblongocollomyces is introduced as new genus, while Spencermartinsia is reduced to synonymy under Dothiorella...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28303008/an-analysis-of-echinacea-chloroplast-genomes-implications-for-future-botanical-identification
#10
Ning Zhang, David L Erickson, Padmini Ramachandran, Andrea R Ottesen, Ruth E Timme, Vicki A Funk, Yan Luo, Sara M Handy
Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28296890/re-establishment-of-species-from-synonymies-based-on-dna-barcoding-and-phylogenetic-analysis-using-diplopterygium-simulans-gleicheniaceae-as-an-example
#11
Jiang-Ping Shu, Hui Shang, Dongmei Jin, Hong-Jin Wei, Xi-Le Zhou, Hong-Mei Liu, Yu-Feng Gu, Ying Wang, Fa-Guo Wang, Hui Shen, Rui Zhang, Bayu Adjie, Yue-Hong Yan
Because synonymy treatment traditionally relies on morphological judgments, it usually causes many problems in species delimitation and in the biodiversity catalogue. For example, Diplopterygium simulans, which belongs to the Gleicheniaceae family, has been considered to be synonymous with D. glaucum or D. giganteum based mainly on the morphology of its pinna rachis and blade. In the absence of molecular evidence, these revisions remain doubtful. DNA barcoding, which is considered to be a powerful method for species-level identification, was employed to assess the genetic distance among 9 members of the Diplopterygium genus...
2017: PloS One
https://www.readbyqxmd.com/read/28288945/species-level-phylogeny-fruit-evolution-and-diversification-history-of-geranium-geraniaceae
#12
Thomas Marcussen, Andrea S Meseguer
The cosmopolitan genus Geranium L. (Geraniaceae) consists of c. 350 species distributed in temperate habitats worldwide, with most of its diversity concentrated in the Mediterranean region. Unlike other genera in Geraniaceae, the species of Geranium present contrasting seed discharge syndromes, i.e. the 'Erodium-type' (ET), the 'carpel-projection type' (CP), the 'seed-ejection type' (SE), and the 'inoperative type' (IT), which have been used to delimit major groups within the genus. However, phylogenetic relationships within Geranium are unknown and so is the evolution of the different seed discharge mechanisms...
March 10, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28286714/true-s-beaked-whale-mesoplodon-mirus-in-macaronesia
#13
Natacha Aguilar de Soto, Vidal Martín, Monica Silva, Roland Edler, Cristel Reyes, Manuel Carrillo, Agustina Schiavi, Talia Morales, Belen García-Ovide, Anna Sanchez-Mora, Nerea Garcia-Tavero, Lisa Steiner, Michael Scheer, Roland Gockel, Dylan Walker, Enrico Villa, Petra Szlama, Ida K Eriksson, Marisa Tejedor, Monica Perez-Gil, João Quaresma, Wojtek Bachara, Emma Carroll
The True's beaked whale (Mesoplodon mirus, True 1913) is a poorly known member of the Ziphiidae family. Its distribution in the northern hemisphere is thought to be restricted to the temperate or warm temperate waters of the North Atlantic, while a few stranding records from the southern hemisphere suggest a wider and antitropical distribution, extending to waters from the Atlantic coast of Brazil to South Africa, Mozambique, Australia and the Tasman Sea coast of New Zealand. This paper (i) reports the first molecular confirmation of the occurrence of the True's beaked whale at the southern limit of its distribution recorded in the northeast Atlantic: the Azores and Canary Islands (macaronesian ecoregion); (ii) describes a new colouration for this species using evidence from a whale with molecular species confirmation; and (iii) contributes to the sparse worldwide database of live sightings, including the first underwater video recording of this species and close images of a calf...
2017: PeerJ
https://www.readbyqxmd.com/read/28281309/bayesian-species-identification-under-the-multispecies-coalescent-provides-significant-improvements-to-dna-barcoding-analyses
#14
Ziheng Yang, Bruce Rannala
DNA barcoding methods use a single locus (usually the mitochondrial COI gene) to assign unidentified specimens to known species in a library based on a genetic distance threshold that distinguishes between-species divergence from within-species diversity. Recently developed species delimitation methods based on the multispecies coalescent (MSC) model offer an alternative approach to individual assignment using either single-locus or multi-loci sequence data. Here we use simulations to demonstrate three features of an MSC method implemented in the program bpp...
March 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28274202/identification-of-constraints-influencing-the-bacterial-genomes-evolution-in-the-pvc-super-phylum
#15
Sandrine Pinos, Pierre Pontarotti, Didier Raoult, Vicky Merhej
BACKGROUND: Horizontal transfer plays an important role in the evolution of bacterial genomes, yet it obeys several constraints, including the ecological opportunity to meet other organisms, the presence of transfer systems, and the fitness of the transferred genes. Bacteria from the Planctomyctetes, Verrumicrobia, Chlamydiae (PVC) super-phylum have a compartmentalized cell plan delimited by an intracytoplasmic membrane that might constitute an additional constraint with particular impact on bacterial evolution...
March 9, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28273098/phylogenetic-relationships-of-vepris-rutaceae-inferred-from-chloroplast-nuclear-and-morphological-data
#16
Cynthia M Morton
The tribe Toddalieae Hook. F. (Rutaceae) has been controversial since its inception by Bentham and Hooker. The nine taxa examined, Acronychia J.R. & G.Foster, Diphasia Pierre, Diphasiopsis Mendonca, Fagaropsis Mildbr.ex. Siebenl., Oricia Pierre, Teclea Delile, Toddaliopsis Engl., Toddalia Juss. and Vepris Comm. ex. A. Juss, have been recognized under the tribe Toddalieae or Tribes Acronychia, Phellodendron and Toddalia. More recently Araliopsis Engl., Diphasia, Diphasiopsis, Oricia, Teclea, and Toddaliopsis have been incorporated into the genus Vepris, while Toddalia and Fagaropsis have continued to be recognized as closely related...
2017: PloS One
https://www.readbyqxmd.com/read/28264411/a-new-species-and-locality-record-for-i-pseudopsyra-i-katydid-orthoptera-phaneropterinae
#17
Ming Kai Tan, Pattarawich Dawwrueng, Taksin Artchawakom
Pseudopsyra is a genus of Phaneropterinae katydid (Orthoptera: Tettigoniidae), currently comprising of four species - two species each from southern China and Peninsular Malaysia (Hebard, 1922; Liu & Kang, 2006; Tan & Kamaruddin, 2013, 2014). The revision of Pseudopsyra by Liu & Kang (2006) provided a redescription of the genus, a new diagnosis and a key to known species. Subsequently, more surveys were conducted in Peninsular Malaysia and yield another species, representing the lowest latitudinal limits of this genus thus far (Tan & Kamaruddin, 2013)...
February 13, 2017: Zootaxa
https://www.readbyqxmd.com/read/28264311/cryptic-diversity-in-the-azorean-beetle-genus-i-tarphius-i-erichson-1845-coleoptera-zopheridae-an-integrative-taxonomic-approach-with-description-of-four-new-species
#18
Paulo A V Borges, Isabel R Amorim, Sofia Terzopoulou, François Rigal, Brent C Emerson, Artur R M Serrano
Recent findings based on molecular data support the occurrence in the Azores of several independently evolving lineages of the beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae Solier, 1834) and higher species richness masked by cryptic diversity, needing formal taxonomic description. All Tarphius from the Azores are revised using an integrative taxonomic approach, using evidence from morphology, morphometrics and molecular data to delimit species. Our results reveal that Azorean Tarphius comprise at least five phyletic lineages, two of which share a similar morphology, despite being divergent at the molecular level...
February 23, 2017: Zootaxa
https://www.readbyqxmd.com/read/28264253/taxonomic-revision-of-the-malagasy-i-camponotus-i-i-grandidieri-i-and-i-niveosetosus-i-species-groups-hymenoptera-formicidae-using-qualitative-and-quantitative-morphology
#19
Jean Claude Rakotonirina, Sándor Csősz, Brian L Fisher
The Camponotus grandidieri species group and Camponotus niveosetosus species group of the Malagasy region are revised. Species delimitation was inferred from the evidence of both qualitative morphological analysis and multivariate morphometry. The multivariate method combined the Nest Centroid (NC)-clustering method and Partitioning Algorithm based on Recursive Thresholding (PART) function to generate hypotheses about species boundaries (clusters) based on 19 continuous morphological traits of minor workers...
March 2, 2017: Zootaxa
https://www.readbyqxmd.com/read/28238365/the-well-sorted-fine-sand-community-from-the-western-mediterranean-sea-a-resistant-and-resilient-marine-habitat-under-diverse-human-pressures
#20
Jean-Claude Dauvin, Ali Bakalem, Alexandrine Baffreau, Claire Delecrin, Gérard Bellan, Claudio Lardicci, Elena Balestri, Rafael Sardá, Samir Grimes
The Biocoenosis of Well Sorted Fine Sands (WSFS) (SFBC, Sables Fins Bien Calibrés in French) is a Mediterranean community very well delimited by bathymetry (2-25 m) and sedimentology (>90% of fine sand) occurring in zones with relatively strong hydrodynamics. In this study focused on sites located along the Algerian, French, Italian and Spanish coasts of the Western Basin of the Mediterranean Sea (WBMS) we aim to compare the structure, ecological status and diversity of the macrofauna of the WSFS and examine the effects of recent human pressures on the state of this shallow macrobenthic community...
February 18, 2017: Environmental Pollution
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