Codiversification of gut microbiota with humans
The gut microbiomes of human populations worldwide have many core microbial species in
common. However, within a species, some strains can show remarkable population …
common. However, within a species, some strains can show remarkable population …
Bayesian inference of ancestral dates on bacterial phylogenetic trees
The sequencing and comparative analysis of a collection of bacterial genomes from a single
species or lineage of interest can lead to key insights into its evolution, ecology or …
species or lineage of interest can lead to key insights into its evolution, ecology or …
Quartet sampling distinguishes lack of support from conflicting support in the green plant tree of life
Premise of the Study Phylogenetic support has been difficult to evaluate within the green
plant tree of life partly due to a lack of specificity between conflicted versus poorly informed …
plant tree of life partly due to a lack of specificity between conflicted versus poorly informed …
Using the BirdTree. org website to obtain robust phylogenies for avian comparative studies: a primer
Comparative studies of trait evolution require accounting for the shared evolutionary history.
This is done by including phylogenetic hypotheses into statistical analyses of species' traits …
This is done by including phylogenetic hypotheses into statistical analyses of species' traits …
Microevolutionary analysis of Clostridium difficile genomes to investigate transmission
Abstract Background The control of Clostridium difficile infection is a major international
healthcare priority, hindered by a limited understanding of transmission epidemiology for …
healthcare priority, hindered by a limited understanding of transmission epidemiology for …
Analysis of a rapid evolutionary radiation using ultraconserved elements: evidence for a bias in some multispecies coalescent methods
Rapid evolutionary radiations are expected to require large amounts of sequence data to
resolve. To resolve these types of relationships many systematists believe that it will be …
resolve. To resolve these types of relationships many systematists believe that it will be …
Modeling protein evolution with several amino acid replacement matrices depending on site rates
Most protein substitution models use a single amino acid replacement matrix summarizing
the biochemical properties of amino acids. However, site evolution is highly heterogeneous …
the biochemical properties of amino acids. However, site evolution is highly heterogeneous …
Phylogenetic paleoecology: tree-thinking and ecology in deep time
The new and emerging field of phylogenetic paleoecology leverages the evolutionary
relationships among species to explain temporal and spatial changes in species diversity …
relationships among species to explain temporal and spatial changes in species diversity …
[HTML][HTML] Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions
Phylogeneticists have long understood that several biological processes can cause a gene
tree to disagree with its species tree. In recent years, molecular phylogeneticists have …
tree to disagree with its species tree. In recent years, molecular phylogeneticists have …
[HTML][HTML] The phylogenetics of Teleosauroidea (Crocodylomorpha, Thalattosuchia) and implications for their ecology and evolution
Teleosauroidea was a clade of ancient crocodylomorphs that were a key element of coastal
marine environments during the Jurassic. Despite a 300-year research history and a recent …
marine environments during the Jurassic. Despite a 300-year research history and a recent …