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Molecular Phylogenetics and Evolution

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https://www.readbyqxmd.com/read/28646639/corrigendum-to-molecular-phylogenetic-relationships-reveal-contrasting-evolutionary-patterns-in-gorgoniidae-octocorallia-in-the-eastern-pacific-molec-phylogenet-evol-111-2017-219-230
#1
M M Soler-Hurtado, P J López-González, A Machordom
No abstract text is available yet for this article.
June 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28600183/integrative-species-delimitation-of-the-widespread-north-american-jumping-mice-zapodinae
#2
Jason L Malaney, John R Demboski, Joseph A Cook
Delimiting species can be challenging, but is a key step for the critical examination of evolutionary history and for prioritizing conservation efforts. Because systematic relationships are often determined iteratively using tests based on taxonomy, such methods can fail to detect cryptic variation and result in biased conclusions. Conversely, discovery-based approaches provide a powerful way to define operational taxonomic units and test species boundaries. We compare both approaches (taxonomy-based delimitation - TBD and discovery-based delimitation - DBD) within North American jumping mice (Zapodinae) using broad sampling, multilocus analyses, and ecological tests...
June 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28645767/assessing-the-potential-of-rad-sequencing-to-resolve-phylogenetic-relationships-within-species-radiations-the-fly-genus-chiastocheta-diptera-anthomyiidae-as-a-case-study
#3
Tomasz Suchan, Anahí Espíndola, Sereina Rutschmann, Brent C Emerson, Kevin Gori, Christophe Dessimoz, Nils Arrigo, Michał Ronikier, Nadir Alvarez
Determining phylogenetic relationships among recently diverged species has long been a challenge in evolutionary biology. Cytoplasmic markers, which have been widely used notably in the context of molecular barcoding, have not always proved successful in resolving such phylogenies, but phylogenies for closely related species have been resolved at a much higher detail in the last couple of years with the advent of next-generation-sequencing technologies and associated techniques of reduced genome representation...
June 20, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28645766/phylogenomic-analysis-supports-multiple-instances-of-polyphyly-in-the-oomycete-peronosporalean-lineage
#4
Marina S Ascunce, Jose C Huguet-Tapia, Almudena Ortiz-Urquiza, Nemat O Keyhani, Edward L Braun, Erica M Goss
The study of biological diversification of oomycetes has been a difficult task for more than a century. Pioneer researchers used morphological characters to describe this heterogeneous group, and physiological and genetic tools expanded knowledge of these microorganisms. However, research on oomycete diversification is limited by conflicting phylogenies. Using whole genomic data from 17 oomycete taxa, we obtained a dataset of 277 core orthologous genes shared among these genomes. Analyses of this dataset resulted in highly congruent and strongly supported estimates of oomycete phylogeny when we used concatenated maximum likelihood and coalescent-based methods; the one important exception was the position of Albugo...
June 20, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28642015/convergent-and-unidirectional-evolution-of-extremely-long-aedeagi-in-the-largest-feather-mite-genus-proctophyllodes-acari-proctophyllodidae-evidence-from-comparative-molecular-and-morphological-phylogenetics
#5
Pavel B Klimov, Sergey V Mironov, Barry M OConnor
Proctophyllodid feather mites (400+ species) are permanent (full-time) symbionts commonly occurring on passerine birds. Phenotypic evolution of these mites appears to be greatly influenced by characters related to reproduction (>87.5% of a total of 32 taxonomically important discrete characters) and male genitalic characters (21.9%). Because sexual selection could the major evolutionary driver in this system, we test the theoretical expectation that genitalic or sexually dimorphic characters should evolve more rapidly and divergently then other characters...
June 19, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28634150/molecular-phylogenetics-and-biogeography-of-the-ambush-bugs-hemiptera-reduviidae-phymatinae
#6
Paul Masonick, Amy Michael, Sarah Frankenberg, Wolfgang Rabitsch, Christiane Weirauch
The ambush bugs (Heteroptera: Reduviidae: Phymatinae) are a diverse clade of predators known for their cryptic hunting behavior and morphologically diverse raptorial forelegs. Despite their striking appearance, role as pollinator predators, and intriguing biogeographic distribution, phylogenetic relationships within Phymatinae are largely unknown and the evolutionary history of the subfamily has remained in the dark. We here utilize the most extensive molecular phylogeny of ambush bugs to date, generated from a 3,328 base pair molecular dataset, to refine our understanding of phymatine relationships, estimate dates of divergence (BEAST 2), and uncover historical biogeographic patterns (S-DIVA and DEC)...
June 17, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28625763/effects-of-tectonics-and-large-scale-climatic-changes-on-the-evolutionary-history-of-hyalomma-ticks
#7
Arthur F Sands, Dmitry A Apanaskevich, Sonja Matthee, Ivan G Horak, Alan Harrison, Shahid Karim, Mohammad K Mohammad, Kosta Y Mumcuoglu, Rupika S Rajakaruna, Maria M Santos-Silva, Conrad A Matthee
HyalommaKoch, 1844 are ixodid ticks that infest mammals, birds and reptiles, to which 27 recognized species occur across the Afrotropical, Palearctic and Oriental regions. Despite their medical and veterinary importance, the evolutionary history of the group is enigmatic. To investigate various taxonomic hypotheses based on morphology, and also some of the mechanisms involved in the diversification of the genus, we sequenced and analysed data derived from two mtDNA fragments, three nuclear DNA genes and 47 morphological characters...
June 15, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28624516/pleistocene-range-shifts-refugia-and-the-origin-of-widespread-species-in-western-palaearctic-water-beetles
#8
David García-Vázquez, David T Bilton, Garth N Foster, I Ribera
Quaternary glacial cycles drove major shifts in both the extent and location of the geographical ranges of many organisms. During glacial maxima, large areas of central and northern Europe were inhospitable to temperate species, and these areas are generally assumed to have been recolonized during interglacials by range expansions from Mediterranean refugia. An alternative is that this recolonization was from non-Mediterranean refugia, in central Europe or western Asia, but data on the origin of widespread central and north European species remain fragmentary, especially for insects...
June 15, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28602572/the-near-east-as-a-cradle-of-biodiversity-a-phylogeography-of-banded-newts-genus-ommatotriton-reveals-extensive-inter-and-intraspecific-genetic-differentiation
#9
Isolde van Riemsdijk, Jan W Arntzen, Sergé Bogaerts, Michael Franzen, Spartak N Litvinchuk, Kurtuluş Olgun, Ben Wielstra
The banded newt (genus Ommatotriton) is widely distributed in the Near East (Anatolia, Caucasus and the Levant) - an understudied region from the perspective of phylogeography. The genus is polytypic, but the number of species included and the phylogenetic relationships between them are not settled. We sequenced two mitochondrial and two nuclear DNA markers throughout the range of Ommatotriton. For mtDNA we constructed phylogenetic trees, estimated divergence times using fossil calibration, and investigated changes in effective population size with Bayesian skyline plots and mismatch analyses...
June 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28606445/multilocus-coalescent-species-delimitation-to-evaluate-traditionally-defined-morphotypes-in-hydrangea-sect-asperae-hydrangeaceae
#10
Yannick De Smet, Olivier De Clerck, Tatsuya Uemachi, Carolina Granados Mendoza, Stefan Wanke, Paul Goetghebeur, Marie-Stéphanie Samain
The number of species recognized in section Asperae of the flowering plant genus Hydrangea differs widely between subsequent revisions. This variation is largely centered around the H. aspera species complex, with numbers of recognized species varying from one to nearly a dozen. Despite indications of molecular variation in this complex, no sequence-based species delimitation methods have been employed to evaluate the primarily morphology-based species boundaries. In the present study, a multi-locus coalescent-based approach to species delimitation is employed in order to identify separate evolutionary lines within H...
June 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28606444/comparative-mitochondrial-genomics-among-spirometra-cestoda-diphyllobothriidae-and-the-molecular-phylogeny-of-related-tapeworms
#11
Xi Zhang, Jiang Yang Duan, Ya Li Shi, Peng Jiang, De Jun Zeng, Zhong Quan Wang, Jing Cui
The larva of Spirometra erinaceieuropaei can parasitize humans, causing a serious parasitic zoonosis known as sparganosis. Although it is medically important, our knowledge about the phylogenetic position of S. erinaceieuropaei and its evolutionary history is fragmentary. In this study, complete mitochondrial (mt) genomes of 4 geographically distinct isolates of S. erinaceieuropaei spargana collected from 4 frog hosts (Hylarana guentheri, Rana nigromaculata, R. rugulosa, R. temporaria) were characterized using an Illumina sequencing platform...
June 9, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28603037/species-boundaries-in-the-astragalus-cusickii-complex-delimited-using-molecular-phylogenetic-techniques
#12
J C Zimmers, M Thomas, L Yang, A Bombarely, M M Mancuso, M F Wojciechowski, J F Smith
Understanding the source of phenotypic variability is a challenge in the biological sciences. Variation in phenotypes is the result of variation in the genetics and environment the organism experiences, but elucidating the relative contribution of these two parameters can pose problems, especially in the field of systematics. Systematists are challenged to classify biological diversity into groups that share common ancestry. Phenotypic variation can be useful to demonstrate common ancestry, but only when the primary contributor to the variation is under strong genetic control, and thus heritable...
June 8, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28603036/canine-parvovirus-type-2-cpv-2-and-feline-panleukopenia-virus-fpv-codon-bias-analysis-reveals-a-progressive-adaptation-to-the-new-niche-after-the-host-jump
#13
Giovanni Franzo, Claudia Maria Tucciarone, Mattia Cecchinato, Michele Drigo
Based on virus dependence from host cell machinery, their codon usage is expected to show a strong relation with the host one. Even if this association has been stated, especially for bacteria viruses, the linkage is considered to be less consistent for more complex organisms and a codon bias adaptation after host jump has never been proven. Canine parvovirus type 2 (CPV-2) was selected as a model because it represents a well characterized case of host jump, originating from Feline panleukopenia virus (FPV)...
June 8, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28603035/evolution-of-the-mir5200-flowering-locus-t-flowering-time-regulon-in-the-temperate-grass-subfamily-pooideae
#14
Meghan McKeown, Marian Schubert, Jill C Preston, Siri Fjellheim
Flowering time is a carefully regulated trait controlled primarily through the action of the central genetic regulator, FLOWERING LOCUS T (FT). Recently it was demonstrated that a microRNA, miR5200, targets the end of the second exon of FT under short-day photoperiods in the grass subfamily Pooideae, thus preventing FT transcripts from reaching threshold levels under non-inductive conditions. Pooideae are an interesting group in that they rapidly diversified from the tropics into the northern temperate region during a major global cooling event spanning the Eocene-Oligocene transition...
June 8, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28602622/homoeologous-chromosome-pairing-across-the-eukaryote-phylogeny
#15
REVIEW
Amanda L Grusz, Erin M Sigel, Colby Witherup
During the past quarter century, molecular phylogenetic inferences have significantly resolved evolutionary relationships spanning the eukaryotic tree of life. With improved phylogenies in hand, the focus of systematics will continue to expand from estimating species relationships toward examining the evolution of specific, fundamental traits across the eukaryotic tree. Undoubtedly, this will expose knowledge gaps in the evolution of key traits, particularly with respect to non-model lineages. Here, we examine one such trait across eukaryotes-the regulation of homologous chromosome pairing during meiosis-as an illustrative example...
June 8, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28579077/phylogenomic-analysis-of-lake-malawi-cichlid-fishes-further-evidence-that-the-three-stage-model-of-diversification-does-not-fit
#16
Christopher Darrin Hulsey, Jimmy Zheng, Brant C Faircloth, Axel Meyer, Michael E Alfaro
Adaptive radiations could often occur in discrete stages. For instance, the species flock of ∼1000 species of Lake Malawi cichlid fishes might have only diverged once between rocky and sandy environments during the initial stage of their diversification. All further diversification within the rock-dwelling (mbuna) or sand-dwelling (utaka) cichlids would have occurred during a subsequent second stage of extensive trophic evolution that was followed by a third stage of sexual trait divergence. We provide an improved phylogenetic framework for Malawi cichlids to test this three-stage hypothesis based on newly reconstructed phylogenetic relationships among 32 taxonomically disparate Malawi cichlids species...
June 1, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28578201/correlated-evolutionary-rates-across-genomic-compartments-in-annonaceae
#17
Paul H Hoekstra, Jan J Wieringa, Erik Smets, Rita D Brandão, Jenifer de Carvalho Lopes, Roy H J Erkens, Lars W Chatrou
The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models...
May 31, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28559213/phylogenomic-analysis-of-integral-diiron-membrane-histidine-motif-containing-enzymes-in-ciliates-provides-insights-into-their-function-and-evolutionary-relationships
#18
Nicolas G Cid, María L Sanchez Granel, María G Montes, María E Elguero, Clara B Nudel, Alejandro D Nusblat
The Integral Membrane Histidine Motif-containing Enzymes (IMHME) are a class of binuclear non-heme iron proteins widely distributed among prokaryotes and eukaryotes. They are characterized by a conserved tripartite motif consisting of eight to ten histidine residues. Their known function is the activation of the dioxygen moiety to serve as efficient catalysts for reactions of hydroxylation, desaturation or reduction. To date most studies on IMHME were carried out in metazoan, phototrophic or parasitic organisms, whereas genome-wide analysis in heterotrophic free living protozoa, such as the Ciliophora phylum, has not been undertaken...
May 27, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28559212/evolution-of-foraging-behaviour-deep-intra-generic-genetic-divergence-between-territorial-and-non-territorial-southern-african-patellid-limpets
#19
Kolobe L Mmonwa, Peter R Teske, Christopher D McQuaid, Nigel P Barker
Southern Africa is a biodiversity hotspot of patellid limpets, with three genera (Helcion, Cymbula and Scutellastra) identified and described in the region. Scutellastra is the most diverse and most frequently studied of these and, along with Cymbula, includes species with territorial and non-territorial foraging behaviours. We used three mitochondrial markers (12S rRNA, 16S rRNA and COI) and one nuclear marker (ATPSβ intron) to assess evolutionary relationships among species of Cymbula and Scutellastra with these two foraging behaviours and to identify which foraging mode is the more ancient...
May 27, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28552506/a-global-phylogeny-of-the-fern-genus-tectaria-tectariaceae-polypodiales-based-on-plastid-and-nuclear-markers-identifies-major-evolutionary-lineages-and-suggests-repeated-evolution-of-free-venation-from-anastomosing-venation
#20
Liang Zhang, Xin-Mao Zhou, De-Kui Chen, Eric Schuettpelz, Ralf Knapp, Ngan Thi Lu, Thien Tam Luong, Minh Tri Dang, Yi-Fan Duan, Hai He, Xin-Fen Gao, Li-Bing Zhang
Tectaria (Tectariaceae) is one of the most confusing fern genus in terms of its circumscription and phylogeny. Since its original description, a number of genera had been moved into or related with this genus, while others had been segregated from it. Tectaria is also among the largest fern genera, comprising 150-210 mostly tropical species. Previous molecular studies have been far from comprehensive (sampling no more than 76 accessions from 52 species), limited in geographic scope (mainly restricted to Asia), and based exclusively on plastid markers...
May 25, 2017: Molecular Phylogenetics and Evolution
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