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Molecular Phylogenetics and Evolution

Valentin De Mazancourt, Werner Klotz, Gerard Marquet, Benjamin Mos, D Christopher Rogers, Philippe Keith
Atyid shrimps, a key component of tropical freshwater ecosystems, face multiple anthropogenic threats and thus need special attention. With more than 300 described species, the genus Caridina is the most speciose of all the Caridea infra-order. Caridina spp. occupy diverse habitats in tropical freshwaters of the Indo-West Pacific region. Several species complexes have been recognized, based on common morphological features, but little is known about how well these morphological characteristics align with phylogenetic characteristics...
November 10, 2018: Molecular Phylogenetics and Evolution
Gabriele Margos, Noémie S Becker, Volker Fingerle, Andreas Sing, Jaime Albino Ramos, Isabel Lopes de Carvalho, Ana Claudia Norte
Borrelia burgdorferi sensu lato comprises a species complex of tick-transmitted bacteria that includes the agents of human Lyme borreliosis. Borrelia turdi is a genospecies of this complex that exists in cryptic transmission cycles mainly between ornithophilic tick vectors and their avian hosts. The species has been originally discovered in avian transmission cycles in Asia but has increasingly been found in Europe. Next generation sequencing was used to sequence the genome of B. turdi isolates obtained from ticks feeding on birds in Portugal to better understand the evolution and phylogenetic relationship of this avian and ornithophilic tick-associated genospecies...
November 10, 2018: Molecular Phylogenetics and Evolution
Nina T Mikkelsen, Christiane Todt, Kevin M Kocot, Kenneth M Halanych, Endre Willassen
The shell-less, worm-shaped Caudofoveata (=Chaetodermomorpha) is one of the least known group of molluscs. The taxon consists of 141 recognized species found from intertidal environments to the deep-sea where they live burrowing in sediment. Evolutionary relationships of the group have been debated, but few studies based on morphological or molecular data have investigated the phylogeny of the group. Here we use molecular phylogenetics to resolve relationships among and within families of Caudofoveata. Phylogenetic analyses were performed using selected mitochondrial and nuclear genes from species from all recognized families of Caudofoveata...
November 10, 2018: Molecular Phylogenetics and Evolution
Marianne Espeland, Jesse Breinholt, Eduardo P Barbosa, Mirna Casagrande, Blanca Huertas, Gerardo Lamas, Mario A Marín, Olaf H H Mielke, Jacqueline Y Miller, Shinichi Nakahara, Denise Tan, Andrew D Warren, Thamara Zacca, Akito Y Kawahara, André L V Freitas, Keith R Willmott
Relationships within satyrine butterflies have been notoriously difficult to resolve using both morphology and Sanger sequencing methods, and this is particularly true for the mainly Neotropical subtribe Euptychiina, which contains about 400 described species. Larvae of Euptychiina feed on grasses and sedges, with the exception of the genus Euptychia, which feed on mosses and lycopsids, and the butterflies occur widely in rainforest, cloudforest and grassland habitats, where they are often abundant. Several previous molecular and morphological studies have made significant progress in tackling the systematics of the group, but many relationships remain unresolved, with analytical challenges such as long-branch-attraction being a major problem...
November 10, 2018: Molecular Phylogenetics and Evolution
Božo Frajman, Eliška Záveská, Alexander Gamisch, Tim Moser, Peter Schönswetter
Next generation sequencing has revolutionised biology. Restriction-associated DNA sequencing (RADseq) has primarily been used to study infraspecific relationships but has also been applied in multi-species phylogenomic analyses. In this study, we used a combination of phylogenomic (with RADseq data) and phylogenetic (with sequences of the nuclear internal transcribed spacer, ITS) methods to explore relationships within the taxonomically intricate Euphorbia seguieriana s. l., one of the most widespread Euphorbia taxa inhabiting zonal and extrazonal steppes from Iberia to Central Asia...
November 8, 2018: Molecular Phylogenetics and Evolution
Martin Schnittler, Karsten Horn, Rico Kaufmann, Radvilė Rimgailė-Voicik, Anja Klahr, Manuela Bog, Jörg Fuchs, H Wilfried Bennert
In Europe, the genus Diphasiastrum (Lycopodiophyta) forms a reticulate network of six diploid taxa, including three parent species (D. alpinum, D. complanatum and D. tristachyum) and three hybrids (D. × issleri, D. × oellgaardii and D. × zeilleri). It was not clear if the hybrids arose once or repeatedly, if they have reproductive competence and if backcrossing occurs. We addressed these questions by analysing 209 accessions for chloroplast microsatellites (cp), two nuclear markers (introns of the RPB and LFY genes) and AFLP...
November 8, 2018: Molecular Phylogenetics and Evolution
Jin Il Kim, Sehee Park, Hyuk Chu, Ilseob Lee, Joon-Yong Bae, Kirim Yoo, Juwon Kim, Joo-Yeon Lee, Namju Lee, Miseon Kim, Jun-Sub Kim, Kyung Wook Hong, Kyung Ran Jun, Jeong Nyeo Lee, Kisoon Kim, Man-Seong Park
Influenza virus is a respiratory pathogen that causes seasonal epidemics by resulting in a considerable number of influenza-like illness (ILI) patients. During the 2016/17 season, ILI rates increased unusually earlier and higher than previous seasons in Korea, and most viral isolates were subtyped as H3N2 strains. Notably, the hemagglutinin (HA) of most Korean H3N2 strains retained newly introduced lysine signatures in HA antigenic sites A and D, compared with that of clade 3C.2a vaccine virus, which might affect antigenic distances to the standard vaccine antisera in a hemagglutination inhibition assay...
November 3, 2018: Molecular Phylogenetics and Evolution
Pu Tang, Jia-Chen Zhu, Bo-Yin Zheng, Shu-Jun Wei, M Sharkey, Xue-Xin Chen, A P Vogler
The insect order Hymenoptera presents marvelous morphological and ecological diversity. Higher-level hymenopteran relationships remain controversial, even after recent phylogenomic analyses, as their taxon sampling was limited. To shed light on the origin and diversification of Hymenoptera, in particular the poorly studied Parasitica, we undertook phylogenetic analyses of 40 newly and 43 previously sequenced mitochondrial genomes representing all major clades of Hymenoptera. Various Bayesian inferences using different data partitions and phylogenetic methods recovered similar phylogenetic trees with strong statistical support for almost all nodes...
November 3, 2018: Molecular Phylogenetics and Evolution
Karola Maul, Michael Krug, Daniel L Nickrent, Kai F Müller, Dietmar Quandt, Susann Wicke
Besides their alleged therapeutic effects, mistletoes of the genus Viscum L. (Viscaceae) are keystone species in many ecosystems across Europe, Africa, Asia and Australia because of their complex faunal interactions. We here reconstructed the evolutionary history of Viscum based on plastid and nuclear DNA sequence data. We obtained a highly resolved phylogenetic tree with ten well-supported clades, which we used to understand the spatio-temporal evolution of these aerial parasites and evaluate the contribution of reproductive switches and shifts in host ranges to their distribution and diversification...
November 3, 2018: Molecular Phylogenetics and Evolution
Juan D Gaitán-Espitia, Claudio A González-Wevar, Elie Poulin, Leyla Cardenas
Mitochondrial genomes (mitogenomes) provide valuable phylogenetic information and genome-level characters that are useful in resolving evolutionary relationships within major lineages of gastropods. However, for more than one decade, these relationships and the phylogenetic position of Patellogastropoda have been inferred based on the genomic architecture as well as the nucleotide and protein sequences of a single representative, the limpet Lottia digitalis. This mitogenome exhibits extensive rearrangements and several repetitive units that may not represent universal features for Patellogastropoda...
November 2, 2018: Molecular Phylogenetics and Evolution
P V Bruyns, P Hanáček, C Klak
The Crassulaceae is an important family in the Greater Cape Floristic Region of southern Africa and is the seventh largest family in the arid Succulent Karoo Biome. After the Aizoaceae it is the largest group of leaf-succulents in southern Africa. This is the first investigation of a broad selection (68%) of the ± 170 species of Crassula. We used data from three chloroplast and two nuclear gene-regions, which yielded many informative characters and provided good resolution among the species. We show that only five of the 20 sections in Crassula are monophyletic...
November 1, 2018: Molecular Phylogenetics and Evolution
Mark P Simmons, Daniel B Sloan, Mark S Springer, John Gatesy
In summary ("two-step") coalescent analyses of empirical data, researchers typically apply the bootstrap to quantify branch support for clades inferred on the optimal species tree. We tested whether site-wise bootstrap analyses provide consistently more conservative support than gene-wise bootstrap analyses. We did so using data from three empirical phylogenomic studies and employed four coalescent methods (ASTRAL, MP-EST, NJst, and STAR). We demonstrate that application of site-wise bootstrapping generally resulted in gene-trees with substantial additional conflicts relative to the original data and this approach therefore cannot be relied upon to provide conservative support...
November 1, 2018: Molecular Phylogenetics and Evolution
Nicholas T Homziak, Jesse W Breinholt, Marc A Branham, Caroline G Storer, Akito Y Kawahara
The subfamily Erebinae (Lepidoptera, Erebidae) includes approximately 10,000 species with many still undescribed. It is one of the most diverse clades within the moth superfamily Noctuoidea and encompasses a diversity of ecological habits. Erebine caterpillars feed on a broad range of host plants including several economically important crops. Adults possess a unique array of adaptations for predator defense, including some of the most sensitive hearing organs (tympana) across the Lepidoptera and striking wing coloration to startle visual predators...
October 31, 2018: Molecular Phylogenetics and Evolution
Edyta Konecka, Ziemowit Olszanowski
The understanding of the biology of arthropods requires an understanding of their bacterial associates. We determined the distribution of bacteria Wolbachia sp., Rickettsia sp., Cardinium sp., Spiroplasma sp., Arsenophonus sp., Hamiltonella sp., and Flavobacterium in oribatid mites (Acari: Oribatida). We identified Cardinium sp. in Achipteria coleoptrata. This is the first report of this bacterium in A. coleoptrata. Approximately 30% of the mite population was infected by Cardinium sp. The Cardinium 16S rDNA was examined for the presence of two sequences unique for this microorganism...
October 31, 2018: Molecular Phylogenetics and Evolution
Edward A Myers, Robert W Bryson, Robert W Hansen, Matthew L Aardema, David Lazcano, Frank T Burbrink
Within many biomes, the cause of phylogeographic structure remains unknown even across regions throughout North America, including within the biodiverse Chihuahuan Desert. For example, little is known about population structure or the diming of diversification of Chihuahuan endemics. In part, this is due largely to the lack of population genomic studies within this region. We generated ultra-conserved element data for the gray-banded kingsnake (Lampropeltis alterna) to investigate lineage divergence and historical demography across the Chihuahuan Desert...
October 30, 2018: Molecular Phylogenetics and Evolution
Alice da Cruz Lima Gerlach, Zeynep Toprak, Yamama Naciri, Elena Araujo Caviró, Rosa Mara Borges da Silveira, Philippe Clerc
Biological processes such as hybridization, incomplete lineage sorting and gene flow can obscure the recognition of distinct evolutionary lineages, particularly in groups of organisms that have recently diverged. Therefore, compiling pieces of evidence from diverse data sources is critical to accurately assess species boundaries in such groups. The increasing availability of DNA sequence data allows for a much deeper understanding of diversification and speciation processes and their consequences on biodiversity...
October 29, 2018: Molecular Phylogenetics and Evolution
Nicholas M A Crouch, Karolis Ramanauskas, Boris Igić
Despite a relatively vast accumulation of molecular data, the timing of diversification of modern bird lineages remains elusive. Accurate dating of the origination of Telluraves-a clade of birds defined by their arboreality-is of particular interest, as it contains the most species-rich avian group, the passerines. Historically, neontological studies have estimated a Cretaceous origin for the group, but more recent studies have recovered Cenozoic dates, closer to the oldest known fossils for the group. We employ total-evidence dating to estimate divergence times that are expected to be both less sensitive to prior assumptions and more accurate...
October 29, 2018: Molecular Phylogenetics and Evolution
Jia-Shi Zhu, Yu-Ling Li, Yi-Sang Yao, Wei-Dong Xie
No abstract text is available yet for this article.
October 27, 2018: Molecular Phylogenetics and Evolution
Maryam Rabiee, Erfan Sayyari, Siavash Mirarab
Genome-wide phylogeny reconstruction is becoming increasingly common, and one driving factor behind these phylogenomic studies is the promise that the potential discordance between gene trees and the species tree can be modeled. Incomplete lineage sorting is one cause of discordance that bridges population genetic and phylogenetic processes. ASTRAL is a species tree reconstruction method that seeks to find the tree with minimum quartet distance to an input set of inferred gene trees. However, the published ASTRAL algorithm only works with one sample per species...
October 26, 2018: Molecular Phylogenetics and Evolution
Jinlong Liu, Xianguang Guo, Dali Chen, Jun Li, Bisong Yue, Xiaomao Zeng
Late Cenozoic stepwise aridification has transformed Central Asia into an arid environment, and the Pleistocene climatic oscillations exerted further ecological impact. Therefore, both aridification and glaciation would have considerably influenced the evolution of many midlatitude species in arid Central Asia (ACA). However, strong biotic evidence supporting this role is still lacking. Here, we test this perspective using a phylogeographic study of Eremias velox, which is an arid-adapted lizard, across ACA using sequences from mitochondrial cytochrome b and 12S rRNA genes...
October 26, 2018: Molecular Phylogenetics and Evolution
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