Search results for " modeling."
showing 10 items of 2251 documents
Efficient estimation of generalized linear latent variable models.
2019
Generalized linear latent variable models (GLLVM) are popular tools for modeling multivariate, correlated responses. Such data are often encountered, for instance, in ecological studies, where presence-absences, counts, or biomass of interacting species are collected from a set of sites. Until very recently, the main challenge in fitting GLLVMs has been the lack of computationally efficient estimation methods. For likelihood based estimation, several closed form approximations for the marginal likelihood of GLLVMs have been proposed, but their efficient implementations have been lacking in the literature. To fill this gap, we show in this paper how to obtain computationally convenient estim…
Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes
2008
The rate of mutation is central to evolution. Mutations are required for adaptation, yet most mutations with phenotypic effects are deleterious. As a consequence, the mutation rate that maximizes adaptation will be some intermediate value. Here, we used digital organisms to investigate the ability of natural selection to adjust and optimize mutation rates. We assessed the optimal mutation rate by empirically determining what mutation rate produced the highest rate of adaptation. Then, we allowed mutation rates to evolve, and we evaluated the proximity to the optimum. Although we chose conditions favorable for mutation rate optimization, the evolved rates were invariably far below the optimu…
Colour patch size and measurement error using reflectance spectrophotometry
2017
1 - Over the past twenty years, portable and relatively affordable spectrophotometers have greatly advanced the study of animal coloration. However, the small size of many colour patches poses methodological challenges that have not, to date, been assessed in the literature. Here, we tackle this issue for a reflectance spectrophotometry set-up widely used in ecology and evolution (the beam method). 2 - We reviewed the literature on animal coloration reporting the use of reflectance spectrophotometry to explore how the minimum measurable size of a colour patch is determined. We then used coloured plastic sheets to create artificial colour patches, and quantify the relationship between colour…
A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies).
2013
Background Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies. Methodology / Principal Findings 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even …
Assembling and testing a generic phenological model to predict Lobesia botrana voltinism for impact studies.
2020
13 pages; International audience; The physiological development of insect pests is driven by temperature and photoperiod. Geographic variations in the speed of growth reflect current patterns in thermal conditions as a function of latitude and altitude. Global warming will likely lead to shifts in pests’ phenology. Insects are expected to overwinter earlier and develop more generations, with implications for the risks of damage to agricultural crops. Understanding and monitoring of the voltinism of insect pests will be increasingly important to anticipate critical phases of pest development and devise options for adapting pest control measures. In this study, we describe a new generic pheno…
Effects of ocean acidification on embryonic respiration and development of a temperate wrasse living along a natural CO2gradient
2016
We assessed rising CO2 effects on metabolism and development of a nesting wrasse by reciprocal transplant experiments in the field. Offspring brooded under different CO2 conditions exhibited similar responses. However, embryos from High-CO2 site were resilient to a wider range of pCO2 levels than those belonging to current-day conditions.
An Empirical Evaluation of the Utility of Convex Hull and Standard Ellipse Areas for Assessing Population Niche Widths from Stable Isotope Data
2013
Stable isotope analyses are increasingly employed to characterise population niche widths. The convex hull area (TA) in a δ¹³C–δ¹⁵N biplot has been used as a measure of isotopic niche width, but concerns exist over its dependence on sample size and associated difficulties in among-population comparisons. Recently a more robust method was proposed for estimating and comparing isotopic niche widths using standard ellipse areas (SEA), but this approach has yet to be tested with empirical stable isotope data. The two methods measure different kind of isotopic niche areas, but both are now widely used to characterise isotopic niche widths of populations. We used simulated data and an extensive e…
Testing hypotheses in evolutionary ecology with imperfect detection: capture-recapture structural equation modeling.
2012
8 pages; International audience; Studying evolutionary mechanisms in natural populations often requires testing multifactorial scenarios of causality involving direct and indirect relationships among individual and environmental variables. It is also essential to account for the imperfect detection of individuals to provide unbiased demographic parameter estimates. To cope with these issues, we developed a new approach combining structural equation models with capture-recapture models (CR-SEM) that allows the investigation of competing hypotheses about individual and environmental variability observed in demographic parameters. We employ Markov chain Monte Carlo sampling in a Bayesian frame…
Human-associated migration of Holarctic Saccharomyces uvarum strains to Patagonia
2020
Our results show that the greatest S. uvarum population diversity worldwide is observed in Patagonia, where strains of this species can be isolated from industrial and traditional fermentations as well as from natural environments. This greater Patagonian diversity is due to the presence of strains belonging to two genetically differentiated populations, South America B (SA-B), and Holarctic/South America A (H/SA-A). The H/SA-A population of Patagonia is directly related to apple fermentation environments, mainly from cider fermentations but also, to a lesser extent, from traditional apple chicha. Our data suggest that strains from the Holarctic population colonized Patagonia. This is possi…
Ten principles for conservation translocations of threatened wood-inhabiting fungi
2020
Abstract Unlike for many other organism groups, conservation translocations of fungi are still rare. Encouraged by recent successful translocations, there is a growing interest in applying this conservation tool to threatened wood-inhabiting fungi. When combined with other conservation or restoration measures, translocation can be an effective measure for preventing further population decline in the short term, and species extinctions in the long term. Translocations can be appropriate for rare and specialist fungal species that occur as small local populations in isolated patches across fragmented landscapes, where there is a low likelihood of successful dispersal between distant host tree…