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The extent to which closely related species share similar niches remains highly debated. Ecological niches are increasingly analysed by combining distribution records with broad-scale climatic variables, but interactions between species and their environment often occur at fine scales. The idea that macroscale analyses correctly represent fine-scale processes relies on the assumption that average climatic variables are meaningful predictors of processes determining species persistence, but tests of this hypothesis are scarce. We compared broad- and fine-scale (microhabitat) approaches by analyzing the niches of European plethodontid salamanders. Both the microhabitat and the macroecological approaches identified niche differences among species, but the correspondence between micro- and macroecological niches was weak. When exploring niche evolution, the macroecological approach suggested a close relationship between niche and phylogenetic history, but this relationship did not emerge in fine-scale analyses. The apparent pattern of niche evolution emerging in broad-scale analyses likely was the by-product of related species having closely adjacent ranges. The environment actually experienced by most of animals is more heterogeneous than what is apparent from macro-scale predictors, and a better combination between macroecological and fine-grained data may be a key to obtain robust ecological generalizations.

Despite the importance of plethodontid salamanders and their vulnerability to ongoing environmental change, they are inherently difficult to monitor due to their cryptic nature. Recent advances in genomics have created new opportunities for monitoring of populations and their responses to environmental perturbations. In this study, we developed a new target capture-based genomic panel for the purposes of genetic monitoring in plethodontid salamanders. We demonstrate its utility in several distantly related species and present an example application in two representative species with co-occurring distributions but different ecological attributes and expected patterns of population structure: Plethodon jordani and Desmognathus wrighti . Although the number of successfully assembled loci declined with phylogenetic distance from the original reference species ( Desmognathus spp), we obtained high-quality data from thousands of loci from species in all four genera tested ( Desmognathus , Plethodon , Eurycea , and Gyrinophilus ), which span the deepest split in Plethodontidae. Landscape genetic analyses detected weak but statistically significant geographic structure in P. jordani , and much stronger geographic structure in D. wrighti , as expected based on the lower population density and likely lower dispersal ability of D. wrighti . Our target capture panel is broadly applicable across salamanders in Plethodontidae and has the potential to provide data for a wide range of phylogenetic, biogeographic, and population genetics research questions.

The transition from aquatic to terrestrial eggs is a key evolutionary change that has allowed vertebrates to successfully colonize and exploit the land. Although most amphibians retain the primitive biphasic life cycle (eggs deposited in water that hatch into free‐living aquatic larvae), direct development of terrestrial eggs has evolved repeatedly and may have been critical to the evolutionary success of several amphibian groups. We provide the first conclusive evidence for evolutionary reversal of direct development in vertebrates. The family Plethodontidae (lungless salamanders) contains the majority of salamander species, including major radiations of direct developers. We reconstruct the higher level phylogenetic relationships of plethodontid salamanders using molecular and morphological data and use this phylogeny to examine the evolution of direct development. We show that the predominantly biphasic desmognathines, previously considered the sister group of other plethodontids, are nested inside a group of directdeveloping species (Plethodontini) and have re‐evolved the aquatic larval stage. Rather than being an evolutionary dead end, the reversal from direct developing to biphasic life history may have helped communities in eastern North America to achieve the highest local diversity of salamander species in the world.

Metazoans display a tremendous diversity of developmental patterns, including complex life cycles composed of morphologically disparate stages. In this regard, the evolution of life cycle complexity promotes phenotypic diversity. However, correlations between life cycle stages can constrain the evolution of some structures and functions. Despite the potential macroevolutionary consequences, few studies have tested the impacts of life cycle evolution on broad-scale patterns of trait diversification. Here we show that larval and adult salamanders with a simple, aquatic-only (paedomorphic) life cycle had an increased rate of vertebral column and body form diversification compared to lineages with a complex, aquatic-terrestrial (biphasic) life cycle. These differences in life cycle complexity explain the variations in vertebral number and adult body form better than larval ecology. In addition, we found that lineages with a simple terrestrial-only (direct developing) life cycle also had a higher rate of adult body form evolution than biphasic lineages, but still 10-fold lower than aquatic-only lineages. Our analyses demonstrate that prominent shifts in phenotypic evolution can follow long-term transitions in life cycle complexity, which may reflect underlying stage-dependent constraints.

Recent speciation research has generally focused on how lineages that originate in allopatry evolve intrinsic reproductive isolation, or how ecological divergence promotes nonallopatric speciation. However, the ecological basis of allopatric isolation, which underlies the most common geographic mode of speciation, remains poorly understood and largely unstudied. Here, we explore the ecological and evolutionary factors that promote speciation in Desmognathus and Plethodon salamanders from temperate eastern North America. Based on published molecular phylogenetic estimates and the degree of geographic range overlap among extant species, we find strong evidence for a role for geographic isolation in speciation. We then examine the relationship between climatic variation and speciation in 16 sister‐taxon pairs using geographic information system maps of climatic variables, new methods for modeling species' potential geographic distributions, and data on geographic patterns of genetic variation. In contrast to recent studies in tropical montane regions, we found no evidence for parapatric speciation along climatic gradients. Instead, many montane sister taxa in the Appalachian Highlands inhabit similar climatic niches and seemingly are allopatric because they are unable to tolerate the climatic conditions in the intervening lowlands. This temporal and spatial‐ecological pattern suggests that niche conservatism, rather than niche divergence, plays the primary role in promoting allopatric speciation and montane endemism in this species‐rich group of vertebrates. Our results demonstrate that even the relatively subtle climatic differences between montane and lowland habitats in eastern North America may play a key role in the origin of new species.

Macroclimatic niches are indirect and potentially inadequate predictors of the realized environmental conditions that many species experience. Consequently, analyses of niche evolution based on macroclimatic data alone may incompletely represent the evolutionary dynamics of species niches. Yet, understanding how an organisms’climatic (Grinnellian) niche responds to changing macroclimatic conditions is of vital importance for predicting their potential response to global change. In this study, we integrate microclimatic and macroclimatic data across 26 species of plethodontid salamanders to portray the relationship between microclimatic niche evolution in response to changing macroclimate. We demonstrate stronger phylogenetic signal in microclimatic niche variables than at the macroclimatic scale. Even so, we find that the microclimatic niche tracks climatic changes at the macroscale, but with a phylogenetic lag at million-year timescales. We hypothesize that behavioral tracking of the microclimatic niche over space and phenology generates the lag: salamanders preferentially select microclimates similar to their ancestral conditions rather than adapting with changes in physiology. We demonstrate that macroclimatic variables are weak predictors of niche evolution and that incorporating spatial scale into analyses of niche evolution is critical for predicting responses to climate change.

Aim: Studies of environmental niche shift/niche conservatism that are based on species distribution modelling require a quantification of niche purity and potential overlap. Although various metrics have been proposed for this task, no comparisons of their performance are available yet that express the linearity of range shifts and error-proneness. Herein, we assess the performance of six niche overlap metrics using three sister pairs of plethodontid salamanders as well as artificial species to test for linearity of overlap curves, impacts of varying potential distribution sizes and study area sizes. Location: North America, artificial environments. Methods: Species distribution models for the salamanders were performed with Maxent, and artificial species were created in the R environment. Potential distributions of species with varying range sizes and extents of the study area were compared using the Bray-Curtis distance BC, Schoener's D, two different modifications of the Hellinger distance I mod, I cor, Pianka's O and Horn's R. Niche overlaps in ecological space were compared using linear discriminant analyses based on principal components. Results: Simulations of niche overlaps revealed strong variations in the performance of the niche overlap metrics. In artificial species, BC and D performed best, followed by O, R and I cor , but the modified Hellinger distance I mod showed a nonlinear slope and a truncated range. Furthermore, the simulations suggest that, in proportionally small potential distributions on large grids, an inclusion of a high proportion of grid cells with low occurrence probabilities representing background noise may bias assessments of niche overlaps. Main conclusions: Both the salamander examples and simulations suggest that Schoener's D and the Bray-Curtis distance BC are best suited to compute niche overlaps from potential distributions derived from species distribution models. However, like all analysed metrics, both D and BC are seriously affected by the inclusion of high numbers of grid cells where the species are probably absent, i. e. with low occurrence probabilities. Therefore, pre-processing to eliminate background noise in the potential distribution grids is highly recommended.

The evolution of ballistic tongue projection in plethodontid salamanders—a high-performance and thermally robust musculo-skeletal system—is ideal for examining how the components required for extreme performance in animal movement are assembled in evolution. Our comparative data on whole-organism performance measured across a range of temperatures and the musculoskeletal morphology of the tongue apparatus were examined in a phylogenetic framework and combined with data on muscle contractile physiology and neural control. Our analysis reveals that relatively minor evolutionary changes in morphology and neural control have transformed a muscle-powered system with modest performance and high thermal sensitivity into a spring-powered system with extreme performance and functional robustness in the face of evolutionarily conserved muscle contractile physiology. Furthermore, these changes have occurred in parallel in both major clades of this largest family of salamanders. We also find that high-performance tongue projection that exceeds available muscle power and thermal robustness of performance coevolve, both being emergent properties of the same elastic-recoil mechanism. Among the taxa examined, we find muscle-powered and fully fledged elastic systems with enormous performance differences, but no intermediate forms, suggesting that incipient elastic mechanisms do not persist in evolutionary time. A growing body of data from other elastic systems suggests that similar coevolution of traits may be found in other ectothermic animals with high performance, particularly those for which thermoregulation is challenging or ecologically costly.