Emmanuel Paradis

UNLABELLED: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. AVAILABILITY: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.

Summary: After more than fifteen years of existence, the R package ape has continuously grown its contents, and has been used by a growing community of users. The release of version 5.0 has marked a leap towards a modern software for evolutionary analyses. Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use and quality check before a new release. These changes will hopefully make ape a useful software for the study of biodiversity and evolution in a context of increasing data quantity. Availability and implementation: ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/package=ape. Further information may be found at http://ape-package.ird.fr/.

SUMMARY: pegas (Population and Evolutionary Genetics Analysis System) is a new package for the analysis of population genetic data. It is written in R and is integrated with two other existing R packages (ape and adegenet). pegas provides functions for standard population genetic methods, as well as low-level functions for developing new methods. The flexible and efficient graphical capabilities of R are used for plotting haplotype networks as well as for other functionalities. pegas emphasizes the need to further develop an integrated-modular approach for software dedicated to the analysis of population genetic data. AVAILABILITY: pegas is distributed through the Comprehensive R Archive Network (CRAN): http://cran.r-project.org/web/packages/pegas/index.html. Further information may be found at: http://ape.mpl.ird.fr/pegas/.

1. Dispersal is of critical ecological and evolutionary importance for several issues of population biology, particularly population synchrony, colonization and range expansion, metapopulation and source–sink dynamics, and population genetic structure, but it has not previously been possible to compare dispersal patterns across a wide range of species or to study movement outside the confines of local study areas. 2. Using resampling methods, we verified that statistically unbiased estimates of average dispersal distance and of intraspecific variance in dispersal distance could be extracted from the bird ringing data of the British Trust for Ornithology. 3. Using data on 75 terrestrial bird species, we tested whether natal and breeding dispersal were influenced by a species’ habitat requirements, diet, geographical range, abundance, morphology, social system, life history or migratory status. We used allometric techniques to ascertain whether these relationships were independent of body size, and used the method of phylogenetically independent contrasts to ascertain whether they were independent of phylogeny. 4. Both natal and breeding dispersal distances were lower among abundant species and among species with large geographical ranges. Dispersal distances and life‐history variables were correlated independent of phylogeny, but these relationships did not persist after controlling for body size. All morphometrical variables (wing length, tarsus length and bill length) were not significantly correlated with dispersal distances after correcting for body size or phylogenetic relatedness. 5. Migrant species disperse further than resident ones, this relation was independent of body size but not of phylogeny. A significant positive relation was observed between breeding dispersal distance and long‐term population decline among migrants, but not among residents. 6. The species living in wet habitats disperse further than those living in dry habitats, which could be explained by the greater patchiness of wet habitats in space and/or time. This relationship was observed only for breeding dispersal, suggesting that this habitat variable does not impose the same constraint on natal dispersal.