Information Content of Trees: Three-taxon Statements Inference Rules and Dependency

ABSTRACTThe three-taxon statement (also called triplet) is the fundamental unit of rooted trees in phylogenetic systematics. Various supertree and phylogenetic methods use three-taxon statements that are minimal rooted statements of degree of kinship relationships. Because of their fundamental role in phylogenetics, three-taxon statements are present in methodological research of various disciplines in evolutionary biology, as in consensus methods, supertree methods, species-tree methods, distance metrics, phylogenetics, and cladistic biogeography. Three-taxon statements are thus widely used. However, their theoretical properties have been poorly investigated. As a result, three-taxon statements methods are subject to important flaws related to information redundancy. Correcting these biases is essential to improve the efficiency of methods using three-taxon statements. Our aim is to study the behavior of three-taxon statements and the interactions among them in order to enhance their performance in phylogenetic studies. We have identified new types of very specific interactions between three-taxon statements responsible of the emergence of redundancy and dependency in trees. We propose for the first time a classification of three-taxon statements interactions and trace the link between those and the emergence of dependency and redundancy. A new fractional weighting procedure for suppressing redundancy of three-taxon statements is proposed. Our method is subsequently empirically tested in the supertree framework using simulations. We show that three-taxon statements using fractional weights perform drastically better than classical supertree methods such as MRP or methods using unweighted three-taxon statements. Our study shows that appropriate fractional weighting of three taxon statements is an efficient measure of phylogenetic information content for rooted trees. Fractional weighting is of critical importance for removing redundancy in any method using three-taxon statements, as in consensus, supertrees, distance metrics, and phylogenetic or biogeographic analyses.

Areas of endemism of hummingbirds (Aves: Apodiformes: Trochilidae) in the Andean and Neotropical regions

Using track analysis and cladistic biogeography, we identified areas of endemism of hummingbirds in the Andean and Neotropical regions. Our results point out that the current areas of endemism of hummingbirds occur in the Andes, Guiana Shield, the Lesser Antilles, western Central and North America and the Chiapas Highlands. The cladistic biogeographic analysis suggests a hummingbird distribution shaped mainly by dispersal events.

Areas of endemism of hummingbirds (Aves: Apodiformes: Trochilidae) in the Andean and Neotropical regions

Using track analysis and cladistic biogeography, we identified areas of endemism of hummingbirds in the Andean and Neotropical regions. Our results point out that the current areas of endemism of hummingbirds occur in the Andes, Guiana Shield, the Lesser Antilles, western Central and North America and the Chiapas Highlands. The cladistic biogeographic analysis suggests a hummingbird distribution shaped mainly by dispersal events.

Where is historical biogeography going? The evolution of the discipline in the first decade of the 21st century

It has been argued that historical biogeography, the study of how processes that occur over long periods of time influence the distribution of life forms, is in the midst of a scientific revolution. The aim of this paper is to analyze the evolution of historical biogeography during the first decade of the 21st century and to identify major trends for the near future. We constructed a database containing all articles which dealt with historical biogeography published in the Journal of Biogeography during 1998–2010. The database included 610 contributions. Our results indicated that historical biogeography is going through a growth period. The papers analyzed were written by 2018 authors, with a mean of 3.3 authors per paper. Authors from 62 countries were involved, and most of them worked in Europe or North America. The Palearctic was the most analyzed region. Most contributions dealt with terrestrial habitats and were devoted to animal (especially Chordata) and plant taxa. Phylogeography was the most used approach (35%), followed by biota similarity and PAE (13%) and molecular biogeography (12%), with cladistic biogeography and event-based methods at 6% each. Some of the future challenges that historical biogeography faces are summarized: (1) to increase the study of taxa which are underrepresented according to the segment of biodiversity they represent; (2) to balance the amount of work devoted to different biogeographical regions; (3) to increase biogeographical knowledge of aquatic habitats; (4) to maintain the diversity of approaches, preventing the reduction of time, spatial, and taxonomic scales addressed by the discipline; and (5) to continue integrating historical biogeography along with other sources of information from other disciplines (e.g. ecology, paleontology, geology, isotope chemistry, remote sensing) into a richer context for explaining past, present, and future patterns of biodiversity on Earth.