Testing for changes in rate of evolution and position of the climatic niche of clades

1. There is solid recognition that phylogenetic effects must be acknowledged to appreciate climatic niche variability among species clades properly. Yet, most currently available methods either work at the intra- specific level (hence they ignore phylogeny) or rely on the Brownian motion model of evolution to estimate phylogenetic effects on climatic niche variation. The Brownian mo-tion model may be inappropriate to describe niche evolution in several cases, and even a significant phylogenetic signal in climatic variables does not in-dicate that the effect of shared ancestry was relevant to niche evolution.2. We introduce a new phylogenetic comparative method which describes sig-nificant changes in the width and position of the climatic niche at the inter-specific (clade) level, while making no a priori assumption about how niche evolution took place.3. We devised the R function phylo.niche.shift to estimate whether the climatic niches of individual clades in the tree are either wider or narrower than expected, and whether the niche occupies unexpected climates. We tested phylo.niche.shift on realistic virtual species’ distribution patterns applied to a phylogeny of 365 extant primate species.4. We demonstrate via simulations that the new method is fast and accurate under widely different climatic niche evolution scenarios. phylo.niche.shift showed that the capuchin monkeys and langurs occupy much wider, and prosimian much narrower, climatic niche space than expected by their phylogenetic positions.5. phylo.niche.shift may help to improve research on niche evolution by allow-ing researchers to test specific hypotheses on the factors affecting clades’ realised niche width and position, and the potential effects of climate change on species’ distribution

Target Deformation of the Equus stenonis Holotype Skull : A Virtual Reconstruction

Equus stenonis is one of the most prevalent European Pleistocene fossil horses. It is believed to be the possible ancestor of all Old World Early Pleistocene Equus, extant zebras and asses, and as such provides insights into Equus evolution and its biogeography and paleoecology. The Equus stenonis holotype skull (IGF560) was first described by Igino Cocchi in 1867, from the Early Pleistocene locality of Terranuova (Upper Valdarno basin, Italy). IGF560 is a nearly complete, although medio-laterally crushed and badly compressed skull. Here we provide the first application of a new virtual reconstruction protocol, termed Target Deformation, to the Equus stenonis holotype. The protocol extends beyond classic retrodeformation by using target specimens as a guide for the virtual reconstruction. The targets used as a reference are two fragmentary, yet well-preserved E. stenonis skulls, coming from Olivola (Italy; IGF11023) and Dmanisi (Georgia; Dm 5/154.3/4.A4.5), both Early Pleistocene in age. These two specimens do not display any major deformation, but preserve different, only slightly overlapping portions of the skull. The virtual reconstruction protocol we carried out has shown its feasibility, by producing two 3D models whose final morphology is perfectly congruent with the natural variability of a comparative sample of E. stenonis specimens. This study shows the potential of using even broken or otherwise fragmentary specimens to guide retrodeformation in badly distorted and damaged specimens. The application of Target Deformation will allow us to increase the availability of comparative specimens in studies of fossil species morphology and evolution, as well as to the study of taphonomic processes

A new, fast method to search for morphological convergence with shape data

Morphological convergence is an intensely studied macroevolutionary phenomenon. It refers to the morphological resemblance between phylogenetically distant taxa. Currently available methods to explore evolutionary convergence either: rely on the analysis of the phenotypic resemblance between sister clades as compared to their ancestor, fit different evolutionary regimes to different parts of the tree to see whether the same regime explains phenotypic evolution in phylogenetically distant clades, or assess deviations from the congruence between phylogenetic and phenotypic distances. We introduce a new test for morphological convergence working directly with non-ultrametric (i.e. paleontological) as well as ultrametric phylogenies and multivariate data. The method (developed as the function search.conv within the R package RRphylo) tests whether unrelated clades are morphologically more similar to each other than expected by their phylogenetic distance. It additionally permits using known phenotypes as the most recent common ancestors of clades, taking full advantage of fossil information. We assessed the power of search.conv and the incidence of false positives by means of simulations, and then applied it to three well-known and long-discussed cases of (purported) morphological convergence: the evolution of grazing adaptation in the mandible of ungulates with high-crowned molars, the evolution of mandibular shape in sabertooth cats, and the evolution of discrete ecomorphs among anoles of Caribbean islands. The search.conv method was found to be powerful, correctly identifying simulated cases of convergent morphological evolution in 95% of the cases. Type I error rate is as low as 4-6%. We found search.conv is some three orders of magnitude faster than a competing method for testing convergence