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Species delimitation

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https://www.readbyqxmd.com/read/28219759/reevaluating-species-number-distribution-and-endemism-of-the-coral-genus-pocillopora-lamarck-1816-using-species-delimitation-methods-and-microsatellites
#1
P Gélin, B Postaire, C Fauvelot, H Magalon
Species delimitation methods based on genetic information, notably using single locus data, have been proposed as means of increasing the rate of biodiversity description, but can also be used to clarify complex taxonomies. In this study, we explore the species diversity within the cnidarian genus Pocillopora, widely distributed in the tropical belt of the Indo-Pacific Ocean. From 943 Pocillopora colonies sampled in the Western Indian Ocean, the Tropical Southwestern Pacific and Southeast Polynesia, representing a huge variety of morphotypes, we delineated Primary Species Hypotheses (PSH) applying the Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule-coalescent model on two mitochondrial markers (Open Reading Frame and Dloop) and reconstructing a haploweb using one nuclear marker (Internal Transcribed Spacer 2)...
February 17, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28219669/combined-phylogenetic-and-morphometric-information-to-delimit-and-unify-the-triatoma-brasiliensis-species-complex-and-the-brasiliensis-subcomplex
#2
Jader Oliveira, Paula L Marcet, Daniela M Takiya, Vagner J Mendonça, Tiago Belintan, M D Bargues, Lucia Mateo, Vivian Chagas, Elaine Folly-Ramos, Pedro Cordeiro-Estrela, Rodrigo Gurgel-Gonçalves, Jane Costa, João A Rosa, Carlos E Almeida
"Triatoma brasiliensis species complex" was defined as a monophyletic group of the species: T. brasiliensis, T. juazeirensis, T. melanica, and T. sherlocki. An alternative grouping scheme proposed the concept of "Brasiliensis subcomplex" which included the former species together with T. melanocephala, T. petrocchiae, T. lenti, T. tibiamaculata, and T. vitticeps. To evaluate the relationship among these taxa we combined the results obtained with four mitochondrial genes (12S, 16S, COI and Cytb, adding to 1,811bp) and geometric morphometric analysis of wings and heads...
February 17, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28215350/species-delimitation-and-phylogeography-of-the-pectenia-species-complex-a-misunderstood-case-of-species-pairs-in-lichenized-fungi-where-reproduction-mode-does-not-delimit-lineages
#3
Mónica A G Otálora, Isabel Martínez, Gregorio Aragón, Mats Wedin
The main goal of this work was to study species boundaries in the genus Pectenia and elucidate the biogeographic history of the four currently accepted species. To accomplish this, we included 92 specimens across the range of Pectenia in Europe and northern Africa. We used three nuclear loci and assessed species circumscription using two Bayesian coalescent-based methods and the Bayes Factor approach. We reviewed the value of reproductive mode and other morphological features as predictors of monophyletic groups...
March 2017: Fungal Biology
https://www.readbyqxmd.com/read/28201983/comparative-analysis-of-the-mitochondrial-genomes-of-colletotrichum-gloeosporioides-sensu-lato-insights-into-the-evolution-of-a-fungal-species-complex-interacting-with-diverse-plants
#4
Xiaofei Liang, Xianglin Tian, Wenkui Liu, Tingyu Wei, Wei Wang, Qiuyue Dong, Bo Wang, Yanan Meng, Rong Zhang, Mark L Gleason, Guangyu Sun
BACKGROUND: The fungal species complex Colletotrichum gloeosporioides sensu lato contains over 20 plant-interacting species. These species exhibit different life styles (e.g., endophytes, foliar and fruit pathogens) and show considerable variation in host and tissue adaptation strategies. Accurate species delimitation in C. gloeosporioides s.l. is very challenging due to nascent lineage boundaries and phenotypic plasticity, which strongly impedes studies of the complex's host-interaction biology...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28188662/population-genetics-of-reef-coral-endosymbionts-symbiodinium-dinophyceae
#5
D J Thornhill, E J Howells, D C Wham, T D Steury, S R Santos
Symbiodinium is a diverse genus of unicellular dinoflagellate symbionts associating with various marine protists and invertebrates. Although the broad-scale diversity and phylogenetics of the Symbiodinium complex is well established, there have been surprisingly few data on fine-scale population structure and biogeography of these dinoflagellates. Yet population level processes contribute strongly to the biology of Symbiodinium, including how anthropogenic-driven global climate change impacts these symbionts and their host associations...
February 11, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28187641/cryptic-within-cryptic-genetics-morphometrics-and-bioacoustics-delimitate%C3%A2-a-new-species-of-i-eleutherodactylus-i-anura-eleutherodactylidae-from-eastern-cuba
#6
Ariel Rodríguez, Álvaro Dugo-Cota, Santiago Montero-Mendieta, Alejandro Gonzalez-Voyer, Roberto Alonso Bosch, Miguel Vences, Carles Vilà
We studied the variation in genetics, bioacustics, and morphology in Eleutherodactylus glamyrus, a regionally endemic frog species restricted to high elevations in the Sierra Maestra Massif, Western Cuba that was originally described as a cryptic species hidden under the name E. auriculatus. Genetic analysis of mtDNA sequences of the 16S and cob genes identify two allopatric and strongly supported mitochondrial clades (phylogroups) which also showed no haplotype sharing in the nuclear Rag-1 gene. Bioacustic, and morphological comparisons concordantly identify these two phylogroups as independent evolutionary lineages...
January 20, 2017: Zootaxa
https://www.readbyqxmd.com/read/28187182/delimiting-priority-areas-for-the-conservation-of-endemic-and-threatened-neotropical-birds-using-a-niche-based-gap-analysis
#7
Dorinny Lisboa de Carvalho, Tiago Sousa-Neves, Pablo Vieira Cerqueira, Gustavo Gonsioroski, Sofia Marques Silva, Daniel Paiva Silva, Marcos Pérsio Dantas Santos
Knowledge of spatiotemporal distribution of biodiversity is still very incomplete in the tropics. This is one of the major problems preventing the assessment and effectiveness of conservation actions. Mega-diverse tropical regions are being exposed to fast and profound environmental changes, and the amount of resources available to describe the distribution of species is generally limited. Thus, the tropics is losing species at unprecedented rates, without a proper assessment of its biodiversity. Species distribution models (SDMs) can be used to fill such biogeographic gaps within a species' range and, when allied with systematic conservation planning (e...
2017: PloS One
https://www.readbyqxmd.com/read/28185948/unpacking-boxes-integration-of-molecular-morphological-and-ecological-approaches-reveals-extensive-patterns-of-reticulate-evolution-in-the-box-eucalypts
#8
Flores-Rentería Lluvia, Rymer Paul, Riegler Markus
Reticulate evolution by hybridization is considered a common process shaping the evolution of many plant species, however, reticulation could also be due to incomplete lineage sorting in biodiverse systems. For our study we selected a group of closely related plant taxa with contrasting yet partially overlapping geographic distributions and different population sizes, to distinguish between reticulated patterns due to hybridization and incomplete lineage sorting. We predicted that sympatric or proximal populations of different species are more likely to have gene flow than geographically distant populations of the same widespread species...
February 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28183833/cytogeography-of-the-subalpine-marsh-marigold-polyploid-complex-caltha-leptosepala-s-l-ranunculaceae
#9
Keir M Wefferling, Sílvia Castro, João Loureiro, Mariana Castro, Daniela Tavares, Sara B Hoot
PREMISE OF THE STUDY: Unrecognized variation in ploidy level can lead to an underestimation of species richness and a misleading delineation of geographic range. Caltha leptosepala (Ranunculaceae) comprises a complex of hexaploids (6x), rare nonaploids (9x), and dodecaploids (12x), all with unknown distributions. We delineate the geographic distribution and contact zones of the cytotypes, investigate morphologies of cytotypes and subspecies, and discuss the biogeography and evolutionary history of the polyploid complex...
February 9, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28161911/cryptic-diversity-and-discordance-in-single-locus-species-delimitation-methods-within-horned-lizards-phrynosomatidae-phrynosoma
#10
Christopher Blair, Robert W Bryson
Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data...
February 4, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28157656/integration-of-gold-sputtered-electrofluidic-paper-on-wire-included-analytical-platforms-for-glucose-biosensing
#11
Estefanía Núnez-Bajo, M Carmen Blanco-López, Agustín Costa-García, M Teresa Fernández-Abedul
This work describes the fabrication and evaluation of an electroanalytical paper-based platform based on the combination of both, reusable and disposable materials in order to generate simple, versatile and low-cost microfluidic devices. With this aim, a holder containing metal wires that act as reusable reference and counter electrodes has been developed. The gold-sputtered paper electrode is disposable and easily interchangeable, meanwhile the platform that includes reference and counter electrodes can be reused...
May 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28144174/an-early-record-of-meloidogyne-fallax-from-ireland
#12
Olivera Topalović, John F Moore, Toon Janssen, Wim Bert, Gerrit Karssen
Root-knot nematodes, Meloidogyne spp., cause huge economic losses worldwide. Currently, three Meloidogyne spp. are present on the quarantine A2 list of EPPO, Meloidogyne chitwoodi, Meloidogyne fallax and Meloidogyne enterolobii. As a quarantine organism, Meloidogyne fallax has been detected in England and Northern Ireland on sport turf in 2011, and in England on leek in 2013. However, its presence in Ireland has probably been overlooked since 1965, when Mr. John F. Moore and Dr. Mary T. Franklin had detected a new Meloidogyne species for that time...
2017: ZooKeys
https://www.readbyqxmd.com/read/28137871/multispecies-coalescent-delimits-structure-not-species
#13
Jeet Sukumaran, L Lacey Knowles
The multispecies coalescent model underlies many approaches used for species delimitation. In previous work assessing the performance of species delimitation under this model, speciation was treated as an instantaneous event rather than as an extended process involving distinct phases of speciation initiation (structuring) and completion. Here, we use data under simulations that explicitly model speciation as an extended process rather than an instantaneous event and carry out species delimitation inference on these data under the multispecies coalescent...
January 30, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28135280/predicting-river-macroinvertebrate-communities-distributional-shifts-under-future-global-change-scenarios-in-the-spanish-mediterranean-area
#14
Javier Alba-Tercedor, Marta Sáinz-Bariáin, José Manuel Poquet, Roberto Rodríguez-López
Several studies on global change over the next century predict increases in mean air temperatures of between 1°C to 5°C that would affect not only water temperature but also river flow. Climate is the predominant environmental driver of thermal and flow regimes of freshwater ecosystems, determining survival, growth, metabolism, phenology and behaviour as well as biotic interactions of aquatic fauna. Thus, these changes would also have consequences for species phenology, their distribution range, and the composition and dynamics of communities...
2017: PloS One
https://www.readbyqxmd.com/read/28131362/phylogenetic-pattern-evolutionary-processes-and-species-delimitation-in-the-genus-echinococcus
#15
A J Lymbery
An accurate and stable alpha taxonomy requires a clear conception of what constitutes a species and agreed criteria for delimiting different species. An evolutionary or general lineage concept defines a species as a single lineage of organisms with a common evolutionary trajectory, distinguishable from other such lineages. Delimiting evolutionary species is a two-step process. In the first step, phylogenetic reconstruction identifies putative species as groups of organisms that are monophyletic (share a common ancestor) and exclusive (more closely related to each other than to organisms outside the group)...
2017: Advances in Parasitology
https://www.readbyqxmd.com/read/28122738/heteroploid-reticulate-evolution-and-taxonomic-status-of-an-endemic-species-with-bicentric-geographical-distribution
#16
Kai Uwe Nierbauer, Juraj Paule, Georg Zizka
Reticulate evolution is considered to be among the main mechanisms of plant evolution, often leading to the establishment of new species. However, complex evolutionary scenarios result in a challenging definition of evolutionary and taxonomic units. In the present study, we aimed to examine the evolutionary origin and revise the species status of Campanula baumgartenii, a rare endemic species from the polyploid complex Campanula section Heterophylla. Morphometry, flow cytometric ploidy estimation, AFLPs, as well as chloroplast and nuclear DNA sequence markers were used to assess the morphological and genetic differentiation among C...
January 24, 2017: AoB Plants
https://www.readbyqxmd.com/read/28122062/hedysarum-l-fabaceae-hedysareae-is-not-monophyletic-evidence-from-phylogenetic-analyses-based-on-five-nuclear-and-five-plastid-sequences
#17
Pei-Liang Liu, Jun Wen, Lei Duan, Emine Arslan, Kuddisi Ertuğrul, Zhao-Yang Chang
The legume family (Fabaceae) exhibits a high level of species diversity and evolutionary success worldwide. Previous phylogenetic studies of the genus Hedysarum L. (Fabaceae: Hedysareae) showed that the nuclear and the plastid topologies might be incongruent, and the systematic position of the Hedysarum sect. Stracheya clade was uncertain. In this study, phylogenetic relationships of Hedysarum were investigated based on the nuclear ITS, ETS, PGDH, SQD1, TRPT and the plastid psbA-trnH, trnC-petN, trnL-trnF, trnS-trnG, petN-psbM sequences...
2017: PloS One
https://www.readbyqxmd.com/read/28114901/cryptic-diversity-geographical-endemism-and-allopolyploidy-in-ne-pacific-seaweeds
#18
João Neiva, Ester A Serrão, Laura Anderson, Peter T Raimondi, Neusa Martins, Licínia Gouveia, Cristina Paulino, Nelson C Coelho, Kathy Ann Miller, Daniel C Reed, Lydia B Ladah, Gareth A Pearson
BACKGROUND: Molecular markers are revealing a much more diverse and evolutionarily complex picture of marine biodiversity than previously anticipated. Cryptic and/or endemic marine species are continually being found throughout the world oceans, predominantly in inconspicuous tropical groups but also in larger, canopy-forming taxa from well studied temperate regions. Interspecific hybridization has also been found to be prevalent in many marine groups, for instance within dense congeneric assemblages, with introgressive gene-flow being the most common outcome...
January 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28108445/multi-rate-poisson-tree-processes-for-single-locus-species-delimitation-under-maximum-likelihood-and-markov-chain-monte-carlo
#19
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
#20
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
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