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Article
Anomalous networks under the multispecies coalescent: theory and prevalence
Reticulations in a phylogenetic network represent processes such as gene flow, admixture, recombination and hybrid speciation. Extending definitions from the tree setting, an anomalous network is one in which som...
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Article
Open AccessEcophysiological adaptations shape distributions of closely related trees along a climatic moisture gradient
Tradeoffs between the energetic benefits and costs of traits can shape species and trait distributions along environmental gradients. Here we test predictions based on such tradeoffs using survival, growth, an...
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Article
Identifiability of local and global features of phylogenetic networks from average distances
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks f...
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Article
Phase transition on the convergence rate of parameter estimation under an Ornstein–Uhlenbeck diffusion on a tree
Diffusion processes on trees are commonly used in evolutionary biology to model the joint distribution of continuous traits, such as body mass, across species. Estimating the parameters of such processes from ...
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Article
Open AccessSingle copy nuclear gene analysis of polyploidy in wild potatoes (Solanum section Petota)
Recent genomic studies have drastically altered our knowledge of polyploid evolution. Wild potatoes (Solanum section Petota) are a highly diverse and economically important group of about 100 species widely distr...
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Article
Open AccessDo potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?
Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage so...
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Article
Groves of Phylogenetic Trees
A major challenge in biological sciences is the reconstruction of the Tree of Life. To this effect, large genomic databases like GenBank and SwissProt are being mined for clusters from which phylogenies can be...
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Article
On logarithmic Sobolev inequalities for continuous time random walks on graphs
We establish modified logarithmic Sobolev inequalities for the path distributions of some continuous time random walks on graphs, including the simple examples of the discrete cube and the lattice ZZ ...
