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Species delimitation

Erinn P Fagan-Jeffries, Steven J B Cooper, Terry Bertozzi, Tessa M Bradford, Andrew D Austin
The Microgastrinae are a hugely diverse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents, and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Northern Hemisphere, the Australian fauna has received little attention. In total, 100 species have been described from or have been introduced into Australia, but the real species diversity for the region is clearly much larger than this...
May 23, 2018: Molecular Ecology Resources
Arántzazu Molins, Patricia Moya, Francisco J García-Breijo, José Reig-Armiñana, Eva Barreno
Three vagrant (Circinaria hispida, Circinaria gyrosa, Circinaria sp. 'paramerae') and one crustose (semi-vagrant, Circinaria sp.'oromediterranea') lichens growing in very continental areas in the Iberian Peninsula were selected to study the phycobiont diversity. Mycobiont identification was checked using nrITS DNA barcoding: Circinaria sp.'oromediterranea' and Circinaria sp. 'paramerae' formed a new clade. Phycobiont diversity was analyzed in 50 thalli of Circinaria spp. using nrITS DNA and LSU rDNA, with microalgae coexistence being found in all the species analyzed by Sanger sequencing...
May 23, 2018: Journal of Phycology
Astrid Tempestini, Søren Rysgaard, France Dufresne
Monitoring the distribution of marine biodiversity is a crucial step to better assess the impacts of global changes. Arctic marine fauna is dominated by amphipods in terms of abundance and biomass. These peracarids are an important marine order of crustaceans but the number of species found in the different Canadian oceans is currently unknown. Furthermore, most species are difficult to identify due to poor taxonomic descriptions and morphological convergence. The aim of this study was to assess the species diversity of marine amphipods in the three Canadian oceans using DNA barcoding...
2018: PloS One
Ewelina Klichowska, Monika Ślipiko, Marcin Nobis, Monika Szczecińska
Stipa pennata (Poaceae), has become a rare and endangered species in Central Europe due habitat loss and fragmentation. This species is characterized by high morphological variability, which has resulted in the description of numerous intraspecific taxa. The aim of present work is to develop microsatellite markers useful in population genetics studies as well as in intraspecific taxonomy of S. pennata s.l. We developed ten microsatellite markers using Illumina high-throughput. Polymorphism at each marker was evaluated using 4-15 individuals from four morphotypes of S...
May 21, 2018: Molecular Biology Reports
I Kelnarova, E Jendek, V V Grebennikov, L Bocak
All more than 3000 species of Agrilus beetles are phytophagous and some cause economically significant damage to trees and shrubs. Facilitated by international trade, Agrilus species regularly invade new countries and continents. This necessitates a rapid identification of Agrilus species, as the first step for subsequent protective measures. This study provides the first DNA reference library for ~100 Agrilus species from the Northern Hemisphere based on three mitochondrial markers: cox1-5' (DNA barcode fragment), cox1-3', and rrnL...
May 22, 2018: Bulletin of Entomological Research
Carlos Daniel Pinacho-Pinacho, Martín García-Varela, Ana L Sereno-Uribe, Gerardo Pérez-Ponce de León
The genus Neoechinorhynchus represents a hyper-diverse group of acanthocephalans, parasites of fresh and brackish water fish and freshwater turtles, with approximately 116 species described worldwide. Forty-nine species have been recorded in the Americas, nine of them in Middle America. Even though species delimitation methods using DNA sequences have been rarely used for parasitic helminths, the genetic library for species of Neoechinorhynchus has grown in the past few years, enhancing the possibility of using these methods for inferring evolutionary relationships and for establishing more robust species boundaries...
May 18, 2018: Molecular Phylogenetics and Evolution
Devina Sharma, Nirbhay K Singh, Harkirat Singh, Anja Joachim, Shitanshu S Rath, Damer P Blake
Infections with Eimeria spp. are common in pigs worldwide, occasionally affecting animals clinically after weaning or during the fattening period when diarrhoea and weight loss can be observed upon infection with the more pathogenic species. Molecular characterization of pathogens is valuable to accurately delimit species and development novel diagnostics, although sequences which define Eimeria species that infect pigs are scarce. Only three of the eight common species are currently represented in GenBank...
May 15, 2018: Veterinary Parasitology
Qian Tang, Scott V Edwards, Frank E Rheindt
Multi-locus data have proven invaluable in phylogenetic reconstruction and species delimitation. However, the mixed genetic signal from different loci can make inference of evolutionary history challenging and may produce incongruences depending on analytical and marker choice. Aside from incomplete lineage sorting (ILS) following diversification events that have had little time for deep differentiation, the most common causes of incongruent phylogenies are genetic introgression confounding a bifurcating evolutionary trajectory...
May 11, 2018: Molecular Phylogenetics and Evolution
Richard H Adams, Drew R Schield, Daren C Card, Todd A Castoe
The assumption of strictly neutral evolution is fundamental to the multispecies coalescent model and permits the derivation of gene tree distributions and coalescent times conditioned on a given species tree. In this study, we conduct computer simulations to explore the effects of violating this assumption in the form of species-specific positive selection when estimating species trees, species delimitations, and coalescent parameters under the model. We simulated datasets under an array of evolutionary scenarios that differ in both speciation parameters (i...
May 11, 2018: Systematic Biology
Alba Pérez-Cataluña, Luis Collado, Oscar Salgado, Violeta Lefiñanco, María J Figueras
The species Arcobacter cryaerophilus is found in many food products of animal origin and is the dominating species in wastewater. In addition, it is associated with cases of farm animal and human infectious diseases,. The species embraces two subgroups i.e., 1A (LMG 24291T = LMG 9904T ) and 1B (LMG 10829) that can be differentiated by their 16S rRNA-RFLP pattern. However, some authors, on the basis of the shared intermediate levels of DNA-DNA hybridization, have suggested abandoning the subgroup classification...
2018: Frontiers in Microbiology
Adam D Leaché, Matthew T McElroy, Anna Trinh
Determining the boundaries between species and deciding when to describe new species are challenging practices that are particularly difficult in groups with high levels of geographic variation. The coast horned lizards (Phrynosoma blainvillii, P. cerroense, and P. coronatum) have an extensive geographic distribution spanning many distinctive ecological regions ranging from northern California to the Cape Region of Baja California, Mexico, and populations differ substantially with respect to external morphology across much of this range...
May 9, 2018: Molecular Ecology
Owen S Wangensteen, Creu Palacín, Magdalena Guardiola, Xavier Turon
Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the "Leray fragment" of mitochondrial cytochrome c oxidase (COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied...
2018: PeerJ
J G Lorén, Maribel Farfán, M C Fusté
The definition of species boundaries constitutes an important challenge in biodiversity studies. In this work we applied the Generalized Mixed Yule Coalescent (GMYC) method, which determines a divergence threshold to delimit species in a phylogenetic tree. Based on the tree branching pattern, the analysis fixes the transition threshold between speciation and the coalescent process associated with the intra-species diversification. This approach has been widely used to delineate eukaryote species and establish their diversification process from sequence data...
2018: Frontiers in Microbiology
Ittai Renan, Thorsten Assmann, Amnon Freidberg
The south-west Palaearctic Graphipterus serrator group is revised. The systematic concept of the G. serrator group has undergone many changes during the last two centuries, and several different classifications have been published in recent decades. Here, the numerical taxonomy approach is used with the morphological characterization similarity level of the sympatric taxa in order to delimit allopatrically occurring taxa at the species and subspecies level. A key to the species and distribution maps are provided along with analyses of the conservation status and habitat preferences of the taxa...
2018: ZooKeys
Ana L Sereno-Uribe, Martín García-Varela, Carlos D Pinacho-Pinacho, Gerardo Pérez-Ponce de León
We recently engaged in a two-part study of Clinostomum Leidy, 1856 across a geographic range comprising central Mexico southwards to Costa Rica, in Central America. In the first study, we investigated the species boundaries by using DNA sequences of mitochondrial and nuclear molecular markers, implementing several analytical tools and species delimitation methods. The result of that approach revealed five highly divergent genetic lineages that were interpreted as independent evolutionary units, or species. Here, we present the second part of the study, where we describe three of the five species for which we have sexually mature adult specimens obtained from the mouth cavity of fish-eating birds...
May 5, 2018: Parasitology Research
Rohan S Mehta, Noah A Rosenberg
Reciprocal monophyly, a feature of a genealogy in which multiple groups of descendant lineages each consist of all of the descendants of their respective most recent common ancestors, has been an important concept in studies of species delimitation, phylogeography, population history reconstruction, systematics, and conservation. Computations involving the probability that reciprocal monophyly is observed in a genealogy have played a key role in criteria for defining taxonomic groups and inferring divergence times...
May 3, 2018: Theoretical Population Biology
Manuel de la Estrella, Félix Forest, Bente Klitgård, Gwilym P Lewis, Barbara A Mackinder, Luciano P de Queiroz, Jan J Wieringa, Anne Bruneau
Detarioideae (81 genera, c. 760 species) is one of the six Leguminosae subfamilies recently reinstated by the Legume Phylogeny Working Group. This subfamily displays high morphological variability and is one of the early branching clades in the evolution of legumes. Using previously published and newly generated sequences from four loci (matK-trnK, rpL16, trnG-trnG2G and ITS), we develop a new densely sampled phylogeny to assess generic relationships and tribal delimitations within Detarioideae. The ITS phylogenetic trees are poorly resolved, but the plastid data recover several strongly supported clades, which also are supported in a concatenated plastid + ITS sequence analysis...
May 2, 2018: Scientific Reports
Florian M Steiner, Sándor Csősz, Bálint Markó, Alexander Gamisch, Lukas Rinnhofer, Clemens Folterbauer, Sarina Hammerle, Christian Stauffer, Wolfgang Arthofer, Birgit C Schlick-Steiner
Seed harvesting ants are ecosystem engineers that shape vegetation, nutrient cycles, and microclimate. Progress in ecological research is, however, slowed down by poor species delimitation. For example, it has not been resolved to date, how many species the European harvester ant Messor "structor" (Latreille, 1798) represents. Since its first description, splitting into additional taxa was often proposed but not accepted later on due to inconsistent support from morphology and ecology. Here, we took an iterative integrative-taxonomy approach - comparing multiple, independent data sets of the same sample - and used traditional morphometrics, Wolbachia symbionts, mitochondrial DNA, amplified fragment length polymorphism, and ecological niche modelling...
April 27, 2018: Molecular Phylogenetics and Evolution
Jonah M Ulmer, Istvan Miko, Andrew R Deans
Background: Male genitalia phenotypes of Ceraphron (Jurine, 1807) are informative for species delimitation, but due to their minute size, these characters have not been used extensively. Recent developments in visualisation techniques, e.g. confocal laser scanning microscopy and high resolution bright field imaging, allow for more thorough examination of these minute anatomical structures and the development of a robust, male genitalia-based taxonomic system. We also establish a character set, a template, that will facilitate future revisions of these wasps...
2018: Biodiversity Data Journal
Scott Schuette, Ryan A Folk, Jason T Cantley, Christopher T Martine
The genus Heuchera is recognized as one of the most diverse endemic radiations of Saxifragaceae in North America, yet species delimitation and geographic distribution within the group remain controversial. Many species remain difficult to identify, including Heuchera alba , a narrow Appalachian endemic and globally imperiled (G2) taxon recorded only from West Virginia and Virginia that occurs in sympatry with H. pubescens and H. americana . A recent survey of the cliffside flora of the Shikellamy Bluffs, PA recorded dozens of Heuchera individuals that, through the use of social media, were positively identified as H...
2018: PhytoKeys
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