The influence of domestication, insularity and sociality on the tempo and mode of brain size evolution in mammals

The ability to develop complex social bonds and an increased capacity for behavioural flexibility in novel environments have both been forwarded as selective forces favouring the evolution of a large brain in mammals. However, large brains are energetically expensive, and in circumstances in which selective pressures are relaxed, e.g. on islands, smaller brains are selected for. Similar reasoning has been offered to explain the reduction of brain size in domestic species relative to their wild relatives. Herein, we assess the effect of domestication, insularity and sociality on brain size evolution at the macroevolutionary scale. Our results are based on analyses of a 426-taxon tree, including both wild species and domestic breeds. We further develop the phylogenetic ridge regression comparative method (RRphylo) to work with discrete variables and compare the rates (tempo) and direction (mode) of brain size evolution among categories within each of three factors (sociality, insularity and domestication). The common assertion that domestication increases the rate of brain size evolution holds true. The same does not apply to insularity. We also find support for the suggested but previously untested hypothesis that species living in medium-sized groups exhibit faster rates of brain size evolution than either solitary or herding taxa

A 450 million years long latitudinal gradient in age-dependent extinction.

Leigh Van Valen famously stated that under constant conditions extinction probability is independent of species age. To test this 'law of constant extinction', we developed a new method using deep learning to infer age-dependent extinction and analysed 450 myr of marine life across 21 invertebrate clades. We show that extinction rate significantly decreases with age in > 90% of the cases, indicating that most species died out soon after their appearance while those which survived experienced ever decreasing extinction risk. This age-dependent extinction pattern is stronger towards the Equator and holds true when the potential effects of mass extinctions and taxonomic inflation are accounted for. These results suggest that the effect of biological interactions on age-dependent extinction rate is more intense towards the tropics. We propose that the latitudinal diversity gradient and selection at the species level account for this exceptional, yet little recognised, macroevolutionary and macroecological pattern

A 450 million years long latitudinal gradient in age-dependent extinction

Leigh Van Valen famously stated that under constant conditions extinction probability is independent of species age. To test this 'law of constant extinction', we developed a new method using deep learning to infer age-dependent extinction and analysed 450 myr of marine life across 21 invertebrate clades. We show that extinction rate significantly decreases with age in > 90% of the cases, indicating that most species died out soon after their appearance while those which survived experienced ever decreasing extinction risk. This age-dependent extinction pattern is stronger towards the Equator and holds true when the potential effects of mass extinctions and taxonomic inflation are accounted for. These results suggest that the effect of biological interactions on age-dependent extinction rate is more intense towards the tropics. We propose that the latitudinal diversity gradient and selection at the species level account for this exceptional, yet little recognised, macroevolutionary and macroecological pattern

Assessment of the current distribution of free-living parrots and parakeets (Aves: Psittaciformes) in Italy: A synthesis of published data and new records

Parrot species are often introduced outside of their native distribution range, as they are among the most popular pets worldwide. Releases, and particularly unplanned escapes, have resulted in the establishment of many naturalised populations in Europe, including Italy. Many parrot species present wide ecological tolerance and high synanthropy, but the knowledge of their distribution in the areas of introduction is limited. The introduction of these species may have a negative impact on local biodiversity, particularly in terms of competition with hole-nesting birds and bats, crop damage and epidemiology, so that it has become crucial to provide accurate and up-to-date research on the distribution of these taxa. This work aimed at reporting the occurrence points of the various Psittaciformes species in Italy. Records for 21 species (72.41% of those reported for all of Europe) were collected, with five of them breeding, always close to urban centres. © 2013 Copyright 2013 Unione Zoologica Italiana

What's hot in conservation biogeography in a changing climate? Going beyond species range dynamics

International audienceIn recent decades Earth's rapidly changing climate, driven by anthropogenic greenhouse gas emissions, has affected species distributions and phenology, ecological communities and ecosystem processes, effects that are increasingly being observed globally (Allen et al., 2010; Doney et al., 2012; Franklin, Serra‐Diaz, Syphard, & Regan, 2016; Parmesan, 2006; Walther et al., 2002). Pleistocene shifts in species ranges during glacial–interglacial transitions reveal large‐scale biome shifts and no‐analog species assemblages (MacDonald et al., 2008; Nolan et al., 2018; Williams & Jackson, 2007); the pace of current anthropogenic warming outstrips past changes in the Earth system and climate, however, leading to new climate novelties and ecological communities (Ordonez, Williams, & Svenning, 2016). Global scientific consensus now emphasizes that global warming should be kept to 1.5°C to avoid catastrophic changes in ecosystems and the services they provide to people (IPCC, 2018), and climate change threats to biodiversity are being prioritized in international policy response (Ferrier et al., 2016)

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

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 motion model may be inappropriate to describe niche evolution in several cases, and even a significant phylogenetic signal in climatic variables does not indicate that the effect of shared ancestry was relevant to niche evolution. We introduce a new phylogenetic comparative method which describes significant 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. 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. 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. phylo.niche.shift may help to improve research on niche evolution by allowing researchers to test specific hypotheses on the factors affecting clades' realised niche width and position, and the potential effects of climate change on species' distributions

ENphylo: A new method to model the distribution of extremely rare species

Species distribution models (SDMs) are a useful mean to understand how environmental variation influences species geographical distribution. SDMs are implemented by several different algorithms. Unfortunately, these algorithms consistently lose accuracy exactly when they are needed the most, that is with rare species, originating the so-called rare-species modelling paradox. Although approaches exist to tackle this problem, most notably by performing and then averaging a number of bivariate models, they are usually computationally intensive and were never shown to apply successfully to the rarest species (i.e. with less than 20 geographical occurrences). Here, we present a new algorithm, ENphylo, embedded in the readily-available R package RRdtn, which couples Environmental Niche Factor Analysis (ENFA) and phylogenetic imputation to model the distribution of rare species. Using the fossil record of 31 species of large mammals that lived during the late Pleistocene as the source data to sample from, we demonstrate ENphylo provides good SDM evaluation scores, with area under the curve and Sørensen Index both consistently above 0.75, True Skills Statistics above 0.4 and Boyce Index above 0.5 in most cases, when just 10 fossil occurrences are randomly drawn from their respective fossil records. ENphylo proved significantly more accurate than ENFA and the ensemble of bivariate models using Maxent, Generalized Linear Model and Random Forest algorithms. Intriguingly, we found that randomly drawing as little as 10 occurrence data points per species allows ENphylo to perform equally well as Maxent run using the entire fossil record of these same species and data. ENphylo provides a fast and accurate solution to perform species distribution modelling with rare species, which will help predicting their distribution in the light of climate change, and to delineate how rare extinct species reacted to past climatic variation

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011