Biomedical subjects

Pierre Legendre

Publications and source records attributed to Pierre Legendre.

8 recordsLinked to original sources

PubMed2006

Are algal communities driven toward maximum biomass?

In this continental-scale study, we show that in major benthic and planktonic stream habitats, algal biovolume--a proxy measure of biomass--is a unimodal function of species richness (SR). The biovolume peak is observed at intermediate to high SR in the benthos but at low richness in the phytoplankton. The unimodal nature of the biomass-diversity relationship implies that a decline in algal biomass with potential harmful effects on all higher trophic levels, from invertebrates to fish, can result from either excessive species gain or species loss, both being common consequences of human-induced habitat alterations. SR frequency distributions indicate that the most frequent richness is habitat-specific and significantly higher in the benthos than in the plankton. In all studied stream environments, the most frequent SR is lower than the SR that yields the highest biovolume, probably as a result of anthropogenic influences, but always within one standard deviation from it, i.e. they are statistically indistinguishable. This suggests that algal communities may be driven toward maximum biomass.

Biodiversity↗

PubMed2006

Variation partitioning of species data matrices: estimation and comparison of fractions.

Establishing relationships between species distributions and environmental characteristics is a major goal in the search for forces driving species distributions. Canonical ordinations such as redundancy analysis and canonical correspondence analysis are invaluable tools for modeling communities through environmental predictors. They provide the means for conducting direct explanatory analysis in which the association among species can be studied according to their common and unique relationships with the environmental variables and other sets of predictors of interest, such as spatial variables. Variation partitioning can then be used to test and determine the likelihood of these sets of predictors in explaining patterns in community structure. Although variation partitioning in canonical analysis is routinely used in ecological analysis, no effort has been reported in the literature to consider appropriate estimators so that comparisons between fractions or, eventually, between different canonical models are meaningful. In this paper, we show that variation partitioning as currently applied in canonical analysis is biased. We present appropriate unbiased estimators. In addition, we outline a statistical test to compare fractions in canonical analysis. The question addressed by the test is whether two fractions of variation are significantly different from each other. Such assessment provides an important step toward attaining an understanding of the factors patterning community structure. The test is shown to have correct Type I. error rates and good power for both redundancy analysis and canonical correspondence analysis.

Animals↗

PubMed2006

Sonar backscatter differentiation of dominant macrohabitat types in a hydrothermal vent field.

Over the past 20 years, sonar remote sensing has opened ways of acquiring new spatial information on seafloor habitat and ecosystem properties. While some researchers are presently working to improve sonar methods so that broad-scale high-definition surveys can be effectively conducted for management purposes, others are trying to use these surveying techniques in more local areas. Because ecosystem management is scale-dependent, there is a need to acquire spatiotemporal knowledge over various scales to bridge the gap between already-acquired point-source data and information available at broader scales. Using a 675-kHz single-pencil-beam sonar mounted on the remotely operated vehicle ROPOS, 2200 m deep on the Juan de Fuca Ridge, East Pacific Rise, five dominant habitat types located in a hydrothermal vent field were identified and characterized by their sonar signatures. The data, collected at different altitudes from 1 to 10 m above the seafloor, were depth-normalized. We compared three ways of handling the echoes embedded in the backscatters to detect and differentiate the five habitat types; we examined the influence of footprint size on the discrimination capacity of the three methods; and we identified key variables, derived from echoes that characterize each habitat type. The first method used a set of variables describing echo shapes, and the second method used as variables the power intensity values found within the echoes, whereas the last method combined all these variables. Canonical discriminant analysis was used to discriminate among the five habitat types using the three methods. The discriminant models were constructed using 70% of the data while the remaining 30% were used for validation. The results showed that footprints 20-30 cm in diameter included a sufficient amount of spatial variation to make the sonar signatures sensitive to the habitat types, producing on average 82% correct classification. Smaller footprints produced lower percentages of correct classification; instead of the habitat types, the sonar data responded to intrapatch roughness and hardness characteristics. The sonar variables used in this study and the methods for extracting and transforming them are fully described in this paper and available in the public domain.

Animals↗

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↗