1055-7903/$ see front matter 2008 Elsevier Inc. A doi:10.1016/j.ympev.2008.04.003 * Corresponding author. Fax: +33 01 40 79 38 44. E-mail address: [email protected] (A. Dettaï). The interphotoreceptor retinoid-binding protein (IRBP) coding gene has been used with success for the large-scale phylogeny of mammals. However, its phylogenetic worth had not been explored in Actinopterygians. We explore...

Closure operations are a useful device in both the theory and practice of tree reconstruction in biology and other areas of classification. These operations take a collection of trees (rooted or unrooted) that classify overlapping sets of objects at their leaves, and infer further tree-like relationships. In this paper we investigate closure operations on phylogenetic trees; both rooted and unr...

DNA-based taxonomy provides a convenient and reliable tool for species delimitation, especially in organisms in which morphological discrimination is difficult or impossible, such as many algal taxa. A group with a long history of confusing species circumscriptions is the morphologically plastic Boodlea complex, comprising the marine green algal genera Boodlea, Cladophoropsis, Phyllodictyon and...

From 1971 to 1985, Carl Woese and colleagues generated oligonucleotide catalogs of 16S/18S rRNAs from more than 400 organisms. Using these incomplete and imperfect data, Carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large RNA components of the translational apparatus. They recognized a third domain of life, revealed the phylogenetic ...

Evolution by natural selection is responsible for the divergence of species populations through three primary mechanisms: populations being altered over evolutionary time and speciating into separate branches, hybridization of two previously distinct species into one, or termination by extinction. Given the vastness of time elapsed since life first emerged on this planet, many distinct species ...

This is a time of unprecedented transition in DNA sequencing technologies. Next-generation sequencing (NGS) clearly holds promise for fast and cost-effective generation of multilocus sequence data for phylogeography and phylogenetics. However, the focus on non-model organisms, in addition to uncertainty about which sample preparation methods and analyses are appropriate for different research q...

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Knowledge of phylogeny is of fundamental importance for understanding evolution. It has become an indispensable tool in modern genomics as a framework for interpreting genomes and metagenomes, for understanding evolution of genes, proteins, and noncoding RNAs as well as different types of regulations including secondary RNA and protein structures, and for reconstructing ancestral genomes [1]. T...

In their article titled ‘‘Estimating species trees using approximate Bayesian computation’’ Fan and Kubatko present an algorithm called ST-ABC to sample the posterior distribution of species trees (Molecular Phylogenetics and Evolution 59: 354– 363). The authors claim that ST-ABC is an approximate Bayesian computation (ABC) algorithm. Here, I argue that one of the steps in their algorithm diffe...

I. Continuous characters – ancestral states Many traits of interest are measured on continuous or metric scales – size and shape, physiological rates, etc. Continuous traits are often useful for species identification and taxonomic descriptions; historically, they were also used in phylogenetic analysis through the use of clustering algorithms that can group taxa based on multivariate phenetic ...