Trees of Unusual Size: Biased Inference of Early Bursts from Large Molecular Phylogenies

Trees of Unusual Size: Biased Inference of Early Bursts from Large Molecular Phylogenies

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive radiations. One often-overlooked source of bias in these studies is that of sampling at the level of whole clades, as researchers tend to choose large, speciose cla...

Inference of Large Phylogenies Using Neighbour-Joining

The neighbour-joining method is a widely used method for phylogenetic reconstruction which scales to thousands of taxa. However, advances in sequencing technology have made data sets with more than 10,000 related taxa widely available. Inference of such large phylogenies takes hours or days using the Neighbour-Joining method on a normal desktop computer because of the O(n) running time. RapidNJ...

Inference and Applications of Molecular Phylogenies: An Introductory Guide

Inference of Evolutionary Jumps in Large Phylogenies using Lévy Processes

Although it is now widely accepted that the rate of phenotypic evolution may not necessarily be constant across large phylogenies, the frequency and phylogenetic position of periods of rapid evolution remain unclear. In his highly influential view of evolution, G. G. Simpson supposed that such evolutionary jumps occur when organisms transition into so-called new adaptive zones, for instance aft...

Estimating divergence times in large molecular phylogenies.

Molecular dating of species divergences has become an important means to add a temporal dimension to the Tree of Life. Increasingly larger datasets encompassing greater taxonomic diversity are becoming available to generate molecular timetrees by using sophisticated methods that model rate variation among lineages. However, the practical application of these methods is challenging because of th...