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Molecular Phylogenetics and Evolution

M M Soler-Hurtado, P J López-González, A Machordom
The description and delimitation of species in an evolutionary framework is essential for understanding patterns of biodiversity and distribution, and in the assessment of conservation strategies for natural resources. This study seeks to clarify the evolutionary history and genetic variation within and between closely related octocoral species that are fundamental to benthic marine ecosystems for harbouring a high diversity of associated fauna. For our study system, we focused on members of the Gorgoniidae family in the Eastern Pacific, particularly of the Ecuadorian littoral, a less studied marine ecosystem...
March 24, 2017: Molecular Phylogenetics and Evolution
Meng Li, Ohi-Toma Tetsuo, Yun-Dong Gao, Bo Xu, Zhang-Ming Zhu, Wen-Bin Ju, Xin-Fen Gao
Explaining how plants from eastern Asia migrated to other Northern Hemisphere regions is still challenging. The genus Sorbus sensu stricto (including c. 88 species) is considered as a good example to illuminate this scenario, due to the wide distribution in the temperate zone and high diversity in the Himalayas and Hengduan Mountains. Based on four nuclear markers (LEAFY-2, GBSSI-1, SBEI and WD) and one chloroplast marker (rps16-trnK), we reconstructed the phylogenetic relationship of Sorbus using 54 taxa (60% of the genus representing all subgenera, sections, or series and geographical areas in the previous classifications), and estimated divergence time and historical biogeography of the genus...
March 23, 2017: Molecular Phylogenetics and Evolution
Pedro L V Peloso, Christopher J Raxworthy, Ward C Wheeler, Darrel R Frost
Peloso et al. (2015: PELOSO) published a comprehensive phylogenetic study of the frog family Microhylidae, which resulted in the discovery that several taxa were not monophyletic. To remedy this, a series of nomenclatural changes were proposed (several generic synonymies and two new subfamilies named). A recent study published in this journal by Scherz et al. (2016: SCHERZ), provided a novel phylogeny for the Malagasy subfamily Cophylinae. SCHERZ dispute the analyses and taxonomic conclusions of PELOSO. Their study is, however, based on substantial reduction of data from the PELOSO study, limited addition of new data, and different analytical methods...
March 20, 2017: Molecular Phylogenetics and Evolution
Ray C Schmidt, Henry L Bart, Wanja Dorothy Nyingi
The phylogenetics and taxonomic status of small African barbs (Cyprininae: Smiliogastrini) remains unresolved despite the recent decision to elevate the genus name Enteromius for the group. The main barrier to understanding the origin of African small barbs and evolutionary relationships within the group is the poor resolution of phylogenies published to date. These phylogenies usually rely on mitochondrial markers and have limited taxon sampling. Here we investigate the phylogenetic relationships of small barbs of Kenya utilizing cytochrome b, Growth Hormone (GH) intron 2, and RAG1 markers from multiple populations of many species in the region...
March 18, 2017: Molecular Phylogenetics and Evolution
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
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
Heather R Kates, Pamela S Soltis, Douglas E Soltis
Phylogenetics can facilitate the study of plant domestication by resolving sister relationships between crops and their wild relatives, thereby identifying the ancestors of cultivated plants. Previous phylogenetic studies of the six Cucurbita crop lineages (pumpkins and squashes) and their wild relatives suggest histories of deep coalescence that complicate uncovering the genetic origins of the six crop taxa. We investigated the evolution of wild and domesticated Cucurbita using the most comprehensive and robust molecular-based phylogeny for Cucurbita to date based on 44 loci derived from introns of single-copy nuclear genes...
March 10, 2017: Molecular Phylogenetics and Evolution
Emily D Fountain, Jonathan N Pauli, Jorge E Mendoza, Jenna Carlson, M Zachariah Peery
Specialized species, like arboreal folivores, often develop beneficial relationships with symbionts to exploit ecologically constrained lifestyles. Although coevolution can drive speciation by specialization of a symbiont to a host, a symbiotic relationship is not indicative of coevolution between host and symbiont. We tested for coevolved relationships between highly specialized two- and three-toed sloths (Choloepus spp. and Bradypus spp., respectively) and their symbiotic algae using cophylogenies and phylogeography...
March 10, 2017: Molecular Phylogenetics and Evolution
Christine D Bacon, Monica Moraes R, Carlos Jaramillo, Alexandre Antonelli
Species expansions into new habitats are often associated with physiological adaptations, for instance when rain forest lineages colonize dry habitats. Although such shifts have been documented for the Brazilian savanna (Cerrado), little is known about the biogeographic origin of species occupying an extreme South American habitat type, the coastal dunes (Restinga). We examined the formation of this poorly known, endangered habitat by reconstructing the evolutionary history of two endemic species. Due to the proposed recency and uniqueness of this habitat, we hypothesized that Restinga species of the palm genus Allagoptera to be recently evolved and to present derived morphological characters...
March 10, 2017: Molecular Phylogenetics and Evolution
Shannon Corrigan, Pierpaolo Maisano Delser, Corey Eddy, Clinton Duffy, Lei Yang, Chenhong Li, Adam L Bazinet, Stefano Mona, Gavin J P Naylor
We use a genomic sampling of both nuclear and mitochondrial DNA markers to examine a pattern of genetic admixture between Carcharhinus galapagensis (Galapagos sharks) and Carcharhinus obscurus (dusky sharks), two well-known and closely related sharks that have been recognized as valid species for more than 100years. We describe widespread mitochondrial-nuclear discordance in which these species are readily distinguishable based on 2152 nuclear single nucleotide polymorphisms from 910 independent autosomal regions, but show pervasive mitochondrial admixture...
March 10, 2017: Molecular Phylogenetics and Evolution
Luciana F Santoferrara, Viviana V Alder, George B McManus
Ciliated protists in the subclasses Choreotrichia and Oligotrichia are major components of marine plankton. Despite their ecological relevance, there are uncertainties in their systematics and diversity. We retrieved and curated all the GenBank ribosomal DNA (rDNA) sequences from these groups, which were analyzed in two ways. The first approach was based on morphologically-identified sequences (including those of two families and six genera newly studied here by single-cell sequencing), and aimed at improving phylogenetic inferences using concatenated sequences of three rDNA loci...
March 9, 2017: Molecular Phylogenetics and Evolution
Ke He, Hong-Yi Liu, Yun-Fa Ge, Shao-Ying Wu, Qiu-Hong Wan
Major histocompatibility complex (MHC) is a good marker system for geographical genetics since they are functional genes in the immune system that are likely to affect the fitness of the individual, and the survival and evolutionary potential of a population in a changing environment. Golden pheasant (Chrysolophus pictus) is a wild Phasianidae distributed in central and north China. In this study, we used a locus-specific genotyping technique for MHC IIB genes of golden pheasant. Combining with microsatellites (simple sequence repeat, SSR) and mitochondrial DNA (mtDNA) D-loop region, we investigated the demographic history and illuminate genetic structure of this bird in detail...
March 7, 2017: Molecular Phylogenetics and Evolution
Luis Sandoval, Kevin L Epperly, John Klicka, Daniel J Mennill
The large number of endemic species in Middle America is frequently attributed to the interplay of geographical barriers and historical climatic changes in the region. This process promotes genetic divergence between populations, and given enough time, may yield new species. Animals that inhabit mid-elevation or highland habitats may be disproportionately affected in this way. Genetic analyses of animals in this region allow us to better understand how historical patterns of isolation have influenced the generation of new species in this biodiversity hotspot...
March 7, 2017: Molecular Phylogenetics and Evolution
Lucie Bauret, Myriam Gaudeul, Michael A Sundue, Barbara S Parris, Tom A Ranker, France Rakotondrainibe, Sabine Hennequin, Jaona Ranaivo, Marc-André Selosse, Germinal Rouhan
Based on a worldwide phylogenetic framework filling the taxonomic gap of Madagascar and surrounding islands of the Western Indian Ocean (WIO), we revisited the systematics of grammitid fern species (Polypodiaceae). We also investigated the biogeographic origin of the extant diversity in Madagascar and estimated the relative influence of vicariance, long-distance dispersals (LDD) and in situ diversification. Phylogenetic inferences were based on five plastid DNA regions (atpB, rbcL, rps4-trnS, trnG-trnR, trnL-trnF) and the most comprehensive taxonomic sampling ever assembled (224 species belonging to 31 out of 33 recognized grammitids genera)...
March 6, 2017: Molecular Phylogenetics and Evolution
Christophe Vieira, Olga Camacho, Zhongmin Sun, Suzanne Fredericq, Frederik Leliaert, Claude Payri, Olivier De Clerck
The tropical to warm-temperate marine brown macroalgal genus Lobophora (Dictyotales, Phaeophyceae) recently drew attention because of its striking regional diversity. In this study we reassess Lobophora global species diversity, and species distributions, and explore how historical factors have shaped current diversity patterns. We applied a series of algorithmic species delineation techniques on a global mitochondrial cox3 dataset of 598 specimens, resulting in an estimation of 98-121 species. This diversity by far exceeds traditional diversity estimates based on morphological data...
March 6, 2017: Molecular Phylogenetics and Evolution
Ângela Brito, Vitor Ramos, Rita Mota, Steeve Lima, Arlete Santos, Jorge Vieira, Cristina P Vieira, Jan Kaštovský, Vitor M Vasconcelos, Paula Tamagnini
Aiming at increasing the knowledge on marine cyanobacteria from temperate regions, we previously isolated and characterized 60 strains from the Portuguese foreshore and evaluate their potential to produce secondary metabolites. About 15% of the obtained 16S rRNA gene sequences showed less than 97% similarity to sequences in the databases revealing novel biodiversity. Herein, seven of these strains were extensively characterized and their classification was re-evaluated. The present study led to the proposal of five new taxa, three genera (Geminobacterium, Lusitaniella, and Calenema) and two species (Hyella patelloides and Jaaginema litorale)...
March 6, 2017: Molecular Phylogenetics and Evolution
Julieta M Manrique, Leandro R Jones
No abstract text is available yet for this article.
March 6, 2017: Molecular Phylogenetics and Evolution
S T Williams, P G Foster, C Hughes, E M Harper, J D Taylor, D T J Littlewood, P Dyal, K P Hopkins, A G Briscoe
Mitogenomic trees for Bivalvia have proved problematic in the past, but several highly divergent lineages were missing from these analyses and increased representation of these groups may yet improve resolution. Here, we add seven new sequences from the Anomalodesmata and one unidentified semelid species (Bryopa lata, Euciroa cf. queenslandica, Laternula elliptica, Laternula truncata, Lyonsia norwegica, Myadora brevis, Tropidomya abbreviata, "Abra" sp.). We show that relationships in a mitogenomic tree for the Class are improved by the addition of seven anomalodesmatans from this highly divergent clade, but are still not completely consistent with relationships recovered in studies of nuclear genes...
March 6, 2017: Molecular Phylogenetics and Evolution
Allison K Miller, Alexander M Kerr, Gustav Paulay, Mike Reich, Nerida G Wilson, Jose I Carvajal, Greg W Rouse
Sea cucumbers (Holothuroidea) are a morphologically diverse, ecologically important, and economically valued clade of echinoderms; however, the understanding of the overall systematics of the group remains controversial. Here, we present a phylogeny of extant Holothuroidea assessed with maximum parsimony, maximum likelihood, and Bayesian approaches using approximately 4.3 kb of mt- (COI, 16S, 12S) and nDNA (H3, 18S, 28S) sequences from 82 holothuroid terminals representing 23 of the 27 widely-accepted family-ranked taxa...
March 2, 2017: Molecular Phylogenetics and Evolution
Andrés A Ojanguren-Affilastro, Renzo S Adilardi, Camilo I Mattoni, Martín J Ramírez, F Sara Ceccarelli
A dated molecular phylogeny of the southernmost American species of the family Buthidae, based on two nuclear and two mitochondrial genes, is presented. Based on this study, analyzed species of the subgenus Tityus (Archaeotityus) are neither sister to the remaining species of the genus Tityus, nor are they closely related to the New World microbuthids with decreasing neobothriotaxy. Analyzed species of the subgenus Tityus do not form a monophyletic group. Based on ancestral area estimation analyses, known geoclimatic events of the region and comparisons to the diversification processes of other epigean groups from the area, a generalized hypothesis about the patterns of historical colonization processes of the family Buthidae in southern South America is presented...
March 1, 2017: Molecular Phylogenetics and Evolution
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