Nucleotide sequence comparisons were used to investigate the evolution of P transposable elements and the possibility that horizontal transfer has played a role in their occurrence in natural populations of Drosophila and other Diptera. The phylogeny of P elements was examined using published sequences from eight dipteran taxa and a new, partial sequence from Scaptomyza elmoi. The results from ...

Researchers interested in the history of the Indo-European family of languages have used a variety of methods to estimate the phylogeny of the family, and have obtained widely differing results. In this paper we explore the reconstructions of the Indo-European phylogeny obtained by using the major phylogeny estimation procedures on an existing database of 336 characters (including lexical, phon...

Previous molecular phylogeny algorithms mainly rely onmulti-sequence alignments of cautiously selected characteristic sequences,thus not directly appropriate for whole genome phylogeny where eventssuch as rearrangements make full-length alignments impossible. Weintroduce here the concept of Complete Information Set (CIS) and itsmeasurement implementation as evolution distance without reference ...

Turtles (Testudines) form a monophyletic group with a highly distinctive body plan. The taxonomy and phylogeny of turtles are still under discussion, at least for some clades. Whereas in most previous studies, only a few species or genera were considered, we here use an extensive compilation of DNA sequences from nuclear and mitochondrial genes for more than two thirds of the total number of tu...

Molecular phylogenetics studies the hierarchical evolutionary relationships among organisms by means of molecular data. These relationships are typically described through a weighted tree, called phylogeny, whose leaves represent the observed organisms, internal vertices represent the intermediate ancestors, and the edges represent evolutionary relationships between pairs of organisms. Molecula...

1. Fumin Lei is no longer listed as an author of this article. Instead, his helpful input is noted in the acknowledgements section. 2. The provisional version of this article mistakenly stated that zebra finch belongs to the Paridae family. We have now corrected this error to reflect the classification of this species to the Estrildidae family. 3. In the abstract of the provisional version of t...

Lateral gene transfers are frequent among prokaryotes, although their detection remains difficult. If all genes are equally affected, this questions the very existence of an organismal phylogeny. The complexity hypothesis postulates the existence of a core of genes (those involved in numerous interactions) that are unaffected by transfers. To test the hypothesis, we studied all the proteins inv...

Our main demographic analysis is based on the Generalized Phylogenetic Coalescent Sampler (G-PhoCS) developed by Gronau et al. [1]. G-PhoCS performs demographic inference conditioned on a given population phylogeny augmented by a collection of migration bands (see Fig. S9.1.1). Migration bands describe scenarios of post-divergence gene flow in the demographic model, and are defined by ordered p...

In the Origin of Species, Darwin used the metaphor of a tree to describe the relationship of life; indeed a tree is famously the only illustration in the book. The origin of species didn’t include any explicit phylogeny of animal life, yet Darwin’s book is said to have prompted the German biologist Ernst Haeckel to abandon his medical practice and turn to the study of evolution. In 1866, Haecke...