Search Results - "BMC evolutionary biology"

Phylogenetic classification of bony fishes by Betancur-R, Ricardo, Wiley, Edward O, Arratia, Gloria, Acero, Arturo, Bailly, Nicolas, Miya, Masaki, Lecointre, Guillaume, Ortí, Guillermo

“…Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural…”
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bModelTest: Bayesian phylogenetic site model averaging and model comparison by Bouckaert, Remco R, Drummond, Alexei J

“…Reconstructing phylogenies through Bayesian methods has many benefits, which include providing a mathematically sound framework, providing realistic estimates…”
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A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes by Pyron, R Alexander, Burbrink, Frank T, Wiens, John J

“…The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no…”
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Selecting optimal partitioning schemes for phylogenomic datasets by Lanfear, Robert, Calcott, Brett, Kainer, David, Mayer, Christoph, Stamatakis, Alexandros

“…Partitioning involves estimating independent models of molecular evolution for different subsets of sites in a sequence alignment, and has been shown to…”
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Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants by Smith, Stephen A, Moore, Michael J, Brown, Joseph W, Yang, Ya

“…The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant…”
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From algae to angiosperms-inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes by Ruhfel, Brad R, Gitzendanner, Matthew A, Soltis, Pamela S, Soltis, Douglas E, Burleigh, J Gordon

“…Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although…”
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Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits by Kayal, Ehsan, Bentlage, Bastian, Sabrina Pankey, M, Ohdera, Aki H, Medina, Monica, Plachetzki, David C, Collins, Allen G, Ryan, Joseph F

“…Background: The phylogeny of Cnidaria has been a source of debate for decades, during which nearly all-possible relationships among the major lineages have…”
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Phylogenomic analysis of Apoidea sheds new light on the sister group of bees by Sann, Manuela, Niehuis, Oliver, Peters, Ralph S, Mayer, Christoph, Kozlov, Alexey, Podsiadlowski, Lars, Bank, Sarah, Meusemann, Karen, Misof, Bernhard, Bleidorn, Christoph, Ohl, Michael

“…Apoid wasps and bees (Apoidea) are an ecologically and morphologically diverse group of Hymenoptera, with some species of bees having evolved eusocial…”
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Going deeper in the automated identification of Herbarium specimens by Carranza-Rojas, Jose, Goeau, Herve, Bonnet, Pierre, Mata-Montero, Erick, Joly, Alexis

“…Hundreds of herbarium collections have accumulated a valuable heritage and knowledge of plants over several centuries. Recent initiatives started ambitious…”
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A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree by Särkinen, Tiina, Bohs, Lynn, Olmstead, Richard G, Knapp, Sandra

“…The Solanaceae is a plant family of great economic importance. Despite a wealth of phylogenetic work on individual clades and a deep knowledge of particular…”
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Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships by Huang, Hui, Shi, Chao, Liu, Yuan, Mao, Shu-Yan, Gao, Li-Zhi

“…Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is…”
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MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation by Hoang, Diep Thi, Vinh, Le Sy, Flouri, Tomáš, Stamatakis, Alexandros, von Haeseler, Arndt, Minh, Bui Quang

“…The nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains…”
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Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model by Reid, Noah M, Carstens, Bryan C

“…Species are considered the fundamental unit in many ecological and evolutionary analyses, yet accurate, complete, accessible taxonomic frameworks with which to…”
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Evolutionary dynamics of host specialization in wood-decay fungi by Krah, Franz-Sebastian, Bässler, Claus, Heibl, Christoph, Soghigian, John, Schaefer, Hanno, Hibbett, David S

“…The majority of wood decomposing fungi are mushroom-forming Agaricomycetes, which exhibit two main modes of plant cell wall decomposition: white rot, in which…”
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Origin and diversification of leucine-rich repeat receptor-like protein kinase (LRR-RLK) genes in plants by Liu, Ping-Li, Du, Liang, Huang, Yuan, Gao, Shu-Min, Yu, Meng

“…Leucine-rich repeat receptor-like protein kinases (LRR-RLKs) are the largest group of receptor-like kinases in plants and play crucial roles in development and…”
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Home-field advantage? evidence of local adaptation among plants, soil, and arbuscular mycorrhizal fungi through meta-analysis by Rúa, Megan A, Antoninka, Anita, Antunes, Pedro M, Chaudhary, V Bala, Gehring, Catherine, Lamit, Louis J, Piculell, Bridget J, Bever, James D, Zabinski, Cathy, Meadow, James F, Lajeunesse, Marc J, Milligan, Brook G, Karst, Justine, Hoeksema, Jason D

“…Local adaptation, the differential success of genotypes in their native versus foreign environment, arises from various evolutionary processes, but the…”
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BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments by Criscuolo, Alexis, Gribaldo, Simonetta

“…The quality of multiple sequence alignments plays an important role in the accuracy of phylogenetic inference. It has been shown that removing ambiguously…”
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Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life by Hamilton, Chris A, Lemmon, Alan R, Lemmon, Emily Moriarty, Bond, Jason E

“…Despite considerable effort, progress in spider molecular systematics has lagged behind many other comparable arthropod groups, thereby hindering family-level…”
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Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating by Condamine, Fabien L, Nagalingum, Nathalie S, Marshall, Charles R, Morlon, Hélène

“…Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution. This approach requires the use of priors on…”
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A glimpse on the pattern of rodent diversification: a phylogenetic approach by Fabre, Pierre-Henri, Hautier, Lionel, Dimitrov, Dimitar, Douzery, Emmanuel J P

“…Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of…”
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