Biomedical subjects

Pierre Legendre

Publications and source records attributed to Pierre Legendre.

5 recordsLinked to original sources

PubMed2004

From a phylogenetic tree to a reticulated network.

In many phylogenetic problems, assuming that species have evolved from a common ancestor by a simple branching process is unrealistic. Reticulate phylogenetic models, however, have been largely neglected because the concept of reticulate evolution have not been supported by using appropriate analytical tools and software. The reticulate model can adequately describe such complicated mechanisms as hybridization between species or lateral gene transfer in bacteria. In this paper, we describe a new algorithm for inferring reticulate phylogenies from evolutionary distances among species. The algorithm is capable of detecting contradictory signals encompassed in a phylogenetic tree and identifying possible reticulate events that may have occurred during evolution. The algorithm produces a reticulate phylogeny by gradually improving upon the initial solution provided by a phylogenetic tree model. The new algorithm is compared to the popular SplitsGraph method in a reanalysis of the evolution of photosynthetic organisms. A computer program to construct and visualize reticulate phylogenies, called T-Rex (Tree and Reticulogram Reconstruction), is available to researchers at the following URL: www.fas.umontreal.ca/biol/casgrain/en/labo/t-rex.

Algorithms↗

PubMed2003

Quantifying phylogenetically structured environmental variation.

Comparative analysis methods control for the variation linked to phylogeny before attempting to correlate the remaining variation of a trait to present-day conditions (i.e., ecology and/or environment). A portion of the phylogenetic variation of the trait may be related to ecology, however; this portion is called "phylogenetic niche conservatism." We propose a method of variation partitioning that allows users to quantify this portion of the variation, called the "phylogenetically structured environmental variation." The new method is applied to published data to study, in a phylogenetic framework, the link between body mass and population density in 79 species of mammals. The results suggest that an important part of the variation of mammal body mass is related to the common influence of phylogeny and population density.

Analysis of Variance↗

PubMed2002

Reconstruction of biogeographic and evolutionary networks using reticulograms.

A reticulogram is a general network capable of representing a reticulate evolutionary structure. It is particularly useful for portraying relationships among organisms that may be related in a nonunique way to their common ancestor - relationships that cannot be represented by a dendrogram or a phylogenetic tree. We propose a new method for constructing reticulograms that represent a given distance matrix. Reticulate evolution applies first to phylogenetic problems; it has been found in nature, for example, in the within-species microevolution of eukaryotes and in lateral gene transfer in bacteria. In this paper, we propose a new method for reconstructing reticulation networks and we develop applications of the reticulate evolution model to ecological biogeographic, population microevolutionary, and hybridization problems. The first example considers a spatially constrained reticulogram representing the postglacial dispersal of freshwater fishes in the Québec peninsula; the reticulogram provides a better model of postglacial dispersal than does a tree model. The second example depicts the morphological similarities among local populations of muskrats in a river valley in Belgium; adding supplementary branches to a tree depicting the river network leads to a better representation of the morphological distances among local populations of muskrats than does a tree structure. A third example involves hybrids between plants of the genus Aphelandra.

Algorithms↗

PubMed2002

A statistical test for host-parasite coevolution.

A new method, ParaFit, has been developed to test the significance of a global hypothesis of coevolution between parasites and their hosts. Individual host-parasite association links can also be tested. The test statistics are functions of the host and parasite phylogenetic trees and of the set of host-parasite association links. Numerical simulations are used to show that the method has correct rate of type I error and good power except under extreme error conditions. An application to real data (pocket gophers and chewing lice) is presented.

Animals↗

PubMed2002

Coevolution between Lamellodiscus (Monogenea: Diplectanidae) and Sparidae (Teleostei): the study of a complex host-parasite system.

Host-parasite coevolution was studied between Sparidae (Teleostei) fishes and their parasites of the genus Lamellodiscus (Monogenea, Diplectanidae) in the northwestern Mediterranean Sea. Molecular phylogenies were reconstructed for both groups. The phylogenctic tree of the Sparidae was obtained from previously published 16S mitochondrial DNA (mtDNA) sequences associated with new cytochrome-b mtDNA sequences via a "total evidence" procedure. The phylogeny of Lamellodiscus species was reconstructed from 18S rDNA sequences that we obtained. Host-parasite coevolution was studied through different methods: TreeFitter, TreeMap, and a new method, ParaFit. If the cost of a host switch is not assumed to be high for parasites, all methods agree on the absence of widespread cospeciation processes in this host-parasite system. Host-parasite associations were interpreted to be due more to ecological factors than to coevolutionary processes. Host specificity appeared not to be related to host-parasite cospeciation.

Animals↗