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Detecting Darwinian Shortfalls in the Amazonian Odonata
Among the oldest winged insects, odonates are a monophyletic order that have become important models for ecological studies because of their highly...
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Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation
One of the Grand Challenges in Science is the construction of the Tree of Life , an evolutionary tree containing several million species, spanning all...
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EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets
BackgroundGenome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still...
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Rapid divergence of a gamete recognition gene promoted macroevolution of Eutheria
BackgroundSpeciation genes contribute disproportionately to species divergence, but few examples exist, especially in vertebrates. Here we test...
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A simpler linear-time algorithm for the common refinement of rooted phylogenetic trees on a common leaf set
BackgroundThe supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical...
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Testing the agreement of trees with internal labels
BackgroundA semi-labeled tree is a tree where all leaves as well as, possibly, some internal nodes are labeled with taxa. Semi-labeled trees...
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Low morphological disparity and decelerated rate of limb size evolution close to the origin of birds
The origin of birds from theropod dinosaurs involves many changes in musculoskeletal anatomy and epidermal structures, including multiple instances...
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A Guide to Phylogenomic Inference
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes....
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Heuristic algorithms for best match graph editing
BackgroundBest match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics as a representation of the...
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Global phylogenetic analysis reveals multiple origins and correlates of genital mutilation/cutting
Genital mutilation/cutting is costly in terms of health, survival and reproduction, and the long-term maintenance of these practices is an...
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Revised molecular phylogeny, global biogeography, and diversification of palms subfamily Coryphoideae (Arecaceae) based on low copy nuclear and plastid regions
Coryphoideae are palmate-leaved palms from the family Arecaceae consisting of 46 genera representing 421 species. Although several phylogenetic...
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The Performance of Two Supertree Schemes Compared Using Synthetic and Real Data Quartet Input
Despite impressive advancements in technological and theoretical tools, construction of phylogenetic (evolutionary) trees is still a challenging...
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The compact genome of Caenorhabditis niphades n. sp., isolated from a wood-boring weevil, Niphades variegatus
BackgroundThe first metazoan genome sequenced, that of Caenorhabditis elegans , has motivated animal genome evolution studies. To date > 50 species...
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SHOOT: phylogenetic gene search and ortholog inference
Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here, we present SHOOT. SHOOT searches a...
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Wood Density Variations
WD is highly conserved across seed plant species. Variation in WD is primarily attributable to genera within a family, followed by family, order, and...
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Description of Nocardioides jiangsuensis sp. nov., and Proposal for Reclassification of the Genus Marmoricola as Nocardioides
A Gram-staining-positive, non-motile, aerobic, spherical actinobacterium, designated WL0053 T , was isolated from the coastal sediment of Nantong City,...
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Decoupling speciation and extinction reveals both abiotic and biotic drivers shaped 250 million years of diversity in crocodile-line archosaurs
Whereas living representatives of Pseudosuchia, crocodylians, number fewer than 30 species, more than 700 pseudosuchian species are known from their...
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Extended embryo retention and viviparity in the first amniotes
The amniotic egg with its complex fetal membranes was a key innovation in vertebrate evolution that enabled the great diversification of reptiles,...
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Phylogenomics provides robust support for a two-domains tree of life
Hypotheses about the origin of eukaryotic cells are classically framed within the context of a universal ‘tree of life’ based on conserved core...
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Rooting Species Trees Using Gene Tree-Species Tree Reconciliation
Interpreting phylogenetic trees requires a root, which provides the direction of evolution and polarizes ancestor-descendant relationships. But...