No abstract

Phylogeneticists have long understood that several biological processes can cause a gene tree to disagree with its species tree. In recent years, molecular phylogeneticists have increasingly foregone traditional supermatrix approaches in favor of species tree methods that account for one such source of error, incomplete lineage sorting (ILS). While gene tree-species tree discordance no doubt poses a significant challenge to phylogenetic inference with molecular data, researchers have only recently begun to systematically evaluate the relative accuracy of traditional and ILS-sensitive methods. Here, we report on simulations demonstrating that concatenation can perform as well or better than methods that attempt to account for sources of error introduced by ILS. Based on these and similar results from other researchers, we argue that concatenation remains a useful component of the phylogeneticist’s toolbox and highlight that phylogeneticists should continue to make explicit comparisons of results produced by contemporaneous and classical methods.

We assess whether correlative paleoclimatic models of species ranges accurately predict genetic diversity patterns in species of distinct life histories traits in the Atlantic Forest (AF) of Brazil. To this end, we use sequences of the mitochondrial gene ND2 from Dendropsophus elegans and Chiasmocleis carvalhoi – summarized in the shape of phylogenies and population genetic statistics – and maximum entropy models of species distributions under current, 21 kya BP and 120 kya BP climatic reconstructions. The two target species have distinct ranges, habitat tolerances, rates of reproduction and dispersal abilities, yet are endemic to the AF. Although the more restricted and semi‐fossorial C. carvalhoi is associated with forested habitats and thought to be a poor disperser, the widely ranged arboreal D. elegans inhabits open areas such as pastures and human‐impacted regions of the AF, and is easily found perched on herbaceous vegetation in inundated areas. We had anticipated that correlative distribution models of the broadly distributed D. elegans would perform better then models of the narrowly ranged C. carvalhoi, thus better predicting current patterns of genetic diversity. The results demonstrate poor predictive ability of climate‐based models of C. carvalhoi under current climatic conditions, suggesting that factors such as biotic interactions or dispersal ability may be playing a central role in defining this species distribution – both now and in the recent past. Models under current climate are nonetheless accurate in the broadly ranged D. elegans. As a corollary, paleoclimatic models accurately predicted patterns of diversity of the ND2 mitochondrial gene in D. elegans, but not in C. carvalhoi. We attribute these distinct responses to the poor explanatory power of paleodistributions models when applied to species that violate the basic assumption of the environment as main driver of distribution patterns. This calls for a careful use of distribution models for the purpose of evolutionary biogeographical inference. Like C. carvalhoi, other species whose ranges are not yet at equilibrium, or which are impacted by competitor, parasite or pathogen presence, may not be suitable to the combined use of paleoclimatic‐model based phylogeographic inference, as here implemented – despite relatively high area under the curve values.

Factors driving the spatial configuration of centres of endemism have long been a topic of broad interest and debate. Due to different eco-evolutionary processes, these highly biodiverse areas may harbour different amounts of ancient and recently diverged organisms (paleo-and neo-endemism, respectively). Patterns of endemism still need to be measured at distinct phylogenetic levels for most clades and, consequently, little is known about the distribution, the age and the causes of such patterns. Here we tested for the presence of centres with high phylogenetic endemism (PE) in the highly diverse Neotropical snakes, testing the age of these patterns (paleo-or neoendemism), and the presence of PE centres with distinct phylogenetic composition. We then tested whether PE is predicted by topography, by climate (seasonality, stability, buffering and relictualness), or biome size. We found that most areas of high PE for Neotropical snakes present a combination of both ancient and recently diverged diversity, which is distributed mostly in the Caribbean region, Central America, the Andes, the Atlantic Forest and on scattered highlands in central Brazil. Turnover of lineages is higher across Central America, resulting in more phylogenetically distinct PE centres compared to South America, which presents a more phylogenetically uniform snake Research * equally contributed. 329fauna. Finally, we found that elevational range (topographic roughness) is the main predictor of PE, especially for paleoendemism, whereas low paleo-endemism levels coincide with areas of high climatic seasonality. Our study highlights the importance of mountain systems to both ancient and recent narrowly distributed diversity. Mountains are both museums and cradles of snake diversity in the Neotropics, which has important implications for conservation in this region.

Male butterflies in the hyperdiverse tribe Eumaeini possess an unusually complex and diverse repertoire of secondary sexual characteristics involved in pheromone production and dissemination. Maintaining multiple sexually selected traits is likely to be metabolically costly, potentially resulting in trade-offs in the evolution of male signals. However, a phylogenetic framework to test hypotheses regarding the evolution and maintenance of male sexual traits in Eumaeini has been lacking. Here, we infer a comprehensive, time-calibrated phylogeny from 379 loci for 187 species representing 91% of the 87 described genera. Eumaeini is a monophyletic group that originated in the late Oligocene and underwent rapid radiation in the Neotropics. We examined specimens of 818 of the 1096 described species (75%) and found that secondary sexual traits are present in males of 91% of the surveyed species. Scent pads and scent patches on the wings and brush organs associated with the genitalia were probably present in the common ancestor of Eumaeini and are widespread throughout the tribe. Brush organs and scent pads are negatively correlated across the phylogeny, exhibiting a trade-off in which lineages with brush organs are unlikely to regain scent pads and vice versa . In contrast, scent patches seem to facilitate the evolution of scent pads, although they are readily lost once scent pads have evolved. Our results illustrate the complex interplay between natural and sexual selection in the origin and maintenance of multiple male secondary sexual characteristics and highlight the potential role of sexual selection spurring diversification in this lineage.

Reserva Biológica de Duas Bocas (2,910 ha) is one of the largest Atlantic forest remnants in the State of Espírito Santo, Southeastern Brazil. We recorded non-volant tetrapods in this area from May 2007 through April 2008, using pitfalls, live traps, camera traps, and diurnal and nocturnal opportunistic searches. In addition, we compiled available museum and literature records from this area. We documented 52 species of amphibians, 24 species of non-avian reptiles, and 39 species of non-volant mammals. Out of these 115 species, 47 are new records for this area and six other species had their geographic ranges expanded with the present study. Furthermore, we present the record of predation of the tree frog Hypsiboas faber by the snake Chironius bicarinatus. Out of the species listed, five species are listed as threatened with extinction in the State of Espírito Santo, and many others have uncertain conservation status. Reserva Biológica de Duas Bocas is an important wildlife refuge, especially considering the expansion of urban areas in its surroundings.

Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

Allometric constraint is a product of natural selection and physical laws, particularly with respect to body size and traits constrained by properties thereof, such as metabolism, longevity, and vocal frequency. Allometric relationships are often conserved across lineages, indicating that physical constraints dictate scaling patterns in deep time, despite substantial genetic and ecological divergence among organisms.In particular, acoustic allometry (sound frequency ~ body size) is conserved across frogs, in defiance of massive variation in both body size and frequency. Here, we ask how many instances of allometric escape have occurred across the frog tree of life using a Bayesian framework that estimates the location, number, and magnitude of shifts in the adaptive landscape of acoustic allometry. Moreover, we test whether ecology in terms of calling site could affect these relationships. We find that calling site has a major influence on acoustic allometry. Despite this, we identify only four major instances of allometric escape, potentially deriving from ecomorphological adaptations to new signal modalities. In these instances of allometric escape, the optima and strength of the scaling relationship are different than expected for most other frog species, representing new adaptive regimes of body size ~ call frequency.Allometric constraints on frog calls are highly conserved and have rarely allowed escape, despite frequent invasions of new adaptive regimes and dramatic ecomorphological divergence. Our results highlight the rare instances in which natural and sexual selection combined can overcome physical constraints on sound production. K E Y W O R D S adaptive evolution, advertisement call, anurans, evolution, phylogenetic comparative methods | 3687 TONINI eT al. S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section. How to cite this article: Tonini JFR, Provete DB, Maciel NM, et al. Allometric escape from acoustic constraints is rare for frog calls.