Ecological niche differentiation is a process that accompanies lineage diversification and community assembly. Traditionally, the degree of niche differentiation is estimated by contrasting niche hypervolumes of two taxa, reconstructed using ecologically relevant variables. These methods disregard the fact that niches can shift in different ways and directions. Without means of discriminating between different types of niche differentiation, important evolutionary and ecological patterns may go unrecognized. Herein, we introduce a new conceptual and methodological framework that allows quantification and classification of niche differentiation and divergence between taxa along single niche axis. This new method, the Niche Divergence Plane, is based on species' responses to an underlying environmental gradient, from which we derive a two-dimensional plane defined by two indices, niche exclusivity and niche dissimilarity. These two indices identify the proportion of the environmental gradient that is unique to each species, that is, how much of the environmental gradient species do not share (niche breadth exclusivity) and how different the species' responses are along the environmental gradient (niche dissimilarity). Thus, the latter can also be seen as a measure of the differences in niche preference or importance, even when there is significant overlap in niche breadth (i.e., low niche exclusivity). Based on the position of the two indices on the divergence plane, we can distinguish niche conservatism from four other general types of niche divergence: hard, soft, weighted, and nested. We demonstrate that the Niche Divergence Plane complements traditional measures of niche similarity (e.g., Schoener's D or Hellinger's I). Additionally, we show an empirical comparison using the Niche Divergence Plane framework on two Ambystoma salamanders. Overall, we demonstrate that the Niche Divergence Plane is a versatile tool that can be used to complement and expand previous methods of ecological niche comparisons and the study of ecological niche divergence.

Hybridization can have a profound negative effect on population fitness when species exhibit divergence in adaptive traits. The Streamside salamander, Ambystoma barbouri, and the Smallmouth salamander, A. texanum, are closely related species differentiated primarily by breeding habitat and reproduction-related traits, but previous work suggests patterns of hybridization and introgression between them. Here we investigate whether 1) hybridization occurs between the two species in laboratory settings, 2) their divergent reproduction-related traits are retained under a common treatment, and 3) hybrid offspring exhibit similar fitness as their non-hybrid counterparts. We bred conspecific and heterospecific pairs of A. barbouri and A. texanum and raised hybrid and non-hybrid offspring to metamorphosis. Reproduction-related traits such as oviposition location and clutch size remained well differentiated between the two species. Heterospecific pairs hybridized readily, at similar rates to conspecific pairs. The hybrid larvae generally exhibited a maternal effect and, less frequently, intermediate phenotypes with respect to measured traits. Hybrid larvae did not exhibit reduced fitness as measured by survival to metamorphosis. Our results suggest that traits differentiating A. barbouri and A. texanum are likely genetically determined despite the lack of reproductive isolation between them. This suggests that the generally parapatric distribution of the two species, often paired with abrupt transition in traits, might be driven by selection on these traits in local habitats. Further, the maternal effect and consequent lack of intermediate phenotypes observed for several traits likely reduces the negative effect of hybridization in locally adapted populations.

Occurrence data used to build species distribution models often include historical records from locations in which the species no longer exists. When these records are paired with contemporary environmental values that no longer represent the conditions the species experienced, the model creates false associations that hurt predictive performance. The extent of mismatching increases with the number of historical occurrences and with inclusion of environmental variables that are prone to change over time. Indeed, the mismatch between occurrence data and contemporaneous environmental variables is a common dilemma when modeling rare or cryptic species, especially those of conservation concern that were once more abundant. Herein, we assess (1) the impact of historical occurrences on model performance across three sets of environmental variables of increasing persistency and (2) the performance of models built using selected-historical occurrences from locations that showed evidence of limited environmental change over time. Concepts are tested on federally listed flatwoods salamanders, reflecting real-world conservation management efforts. We predicted that, compared to other occurrence sets, (1) historical occurrences would perform best with environmental variables that were more persistent, (2) recent occurrences would perform best when the environmental variables were more impersistent, and that (3) our selected-historical occurrences would perform best with a combination of persistent and impersistent variables. Our results showed the expected inversion of model performance of recent and historical occurrences across environmental variables of increasing persistency when evaluated by correct predictions. However, the inversion was not seen in area under the curve performance, in which historical occurrences outperformed recent occurrence models across all variable sets. Selected-historical occurrences did not notably improve performance over all-historical occurrences in any metric or variable set. To maximize utility and performance, modelers could acknowledge potential trade-offs from inclusion of historical occurrences and consider number and age of recent and historical occurrences available, the persistency of environmental variables considered, and how their conservation goals are reflected in model design and evaluation, particularly with respect to sensitivity versus specificity. Our study lends support for inclusion of historical occurrences, with the potential exception of mostly impersistent variables when sensitivity is the highest priority.

AbstractThe southwestern and central United States serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate change, geographic features, and habitat heterogeneity on spatial patterns of genetic diversity. In this study, we combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA sequences (ND1) from the Texas horned lizard (Phrynosoma cornutum) to quantify relative support for different catalysts of diversification. Phylogenetic and clustering analyses of the GBS data indicate support for at least three primary populations. The spatial distribution of populations appears concordant with habitat type, with desert populations in AZ and NM showing the largest genetic divergence from the remaining populations. The mtDNA data also support a divergent desert population, but other relationships differ and suggest mtDNA introgression. Genotype–environment association with bioclimatic variables supports divergence along precipitation gradients more than along temperature gradients. Demographic analyses support a complex history, with introgression and gene flow playing an important role during diversification. Bayesian multispecies coalescent analyses with introgression (MSci) analyses also suggest that gene flow occurred between populations. Paleo-species distribution models support two southern refugia that geographically correspond to contemporary lineages. We find that divergence times are underestimated and population sizes are overestimated when introgression occurred and is ignored in coalescent analyses, and furthermore, inference of ancient introgression events and demographic history is sensitive to inclusion of a single recently admixed sample. Our analyses cannot refute the riverine barrier or glacial refugia hypotheses. Results also suggest that populations are continuing to diverge along habitat gradients. Finally, the strong evidence of admixture, gene flow, and mtDNA introgression among populations suggests that P. cornutum should be considered a single widespread species under the General Lineage Species Concept.

All output files generated by running the raw GBS data through the ipyad pipeline.

Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here, we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization routes. Based on our analyses of a large SNP data set, we find evidence that both climate and demographic history have shaped the genetic structure of populations. Pronounced genetic differentiation was evident between populations occupying cold versus hot deserts, and we detected numerous loci with significant associations with climate. The genetic signal of founder effects, however, is still present in the genomes of the recently expanded populations, which comprise subsets of genetic variation found in the southern populations.

Isolated populations of Cope's (Dicamptodon copei) and Coastal (D. tenebrosus) Giant Salamanders occur 30-50 km east of the Cascade Mountain crest in northern Oregon, USA. To date, only D. copei have been found in the White River basin that emanates from the southern flanks of Mount Hood. At 7.6-11.0 km east of D. copei, D. tenebrosus only occurs at two localities along the steep and xeric slopes of the Deschutes River canyon: Oak Springs and 4-5 km upriver at Maupin Spring. During surveys conducted from 28 July 2013 to 20 August 2015, we found D. tenebrosus at Oak Springs, but not at Maupin Spring or 12 additional sites in the Deschutes River basin. At Oak Springs, larval D. tenebrosus were described previously as having unique coloration. The dorsum of older larvae was light tan-brown with "peculiar" scattered yellow dots. We provide the first photographs and measurements of larval D. tenebrosus from Oak Springs. Dorsolateral coloration of three large larvae was reddish-brown with cream-yellowish flecks and small blotches that were most prevalent anterior on the dorsum. A large transformed adult was melanistic but had a marbled pattern beneath the outermost dermal layer. Unlike D. tenebrosus elsewhere, Oak Springs and Maupin Spring specimens had low fin height, similar to that typical of D. copei. The origins of these isolated populations of D. copei and D. tenebrosus are unknown. They appear to be distinct groups occurring in disjunct, small geographic areas. Their distinctive morphological characters indicate prolonged isolation and they merit conservation action.