River drainage reorganization and reticulate evolution in the Two-Lined Salamander (Eurycea bislineata) species complex.

The origin and eventual loss of biogeographic barriers can create alternating periods of allopatry and secondary contact, facilitating gene flow among distinct metapopulations and generating reticulate evolutionary histories that are not adequately described by a bifurcating evolutionary tree. One such example may exist in the two-lined salamander (Eurycea bislineata) species complex, where discordance among morphological and molecular datasets has created a "vexing taxonomic challenge". Previous phylogeographic analyses of mitochondrial DNA (mtDNA) suggested that the reorganization of Miocene paleodrainages drove vicariance and dispersal, but the inherent limitations of a single-locus dataset precluded the evaluation of subsequent gene flow. Here, we generate triple-enzyme restriction site-associated DNA sequencing (3RAD) data for >100 individuals representing all major mtDNA lineages and use a suite of complementary methods to demonstrate that discordance among earlier datasets is best explained by a reticulate evolutionary history influenced by river drainage reorganization. Systematics of such groups should acknowledge these complex histories and relationships that are not strictly hierarchical.

Developmental life history is associated with variation in rates of climatic niche evolution in a salamander adaptive radiation.

Rates of climatic niche evolution vary widely across the tree of life and are strongly associated with rates of diversification among clades. However, why the climatic niche evolves more rapidly in some clades than others remains unclear. Variation in life history traits often plays a key role in determining the environmental conditions under which species can survive, and therefore, could impact the rate at which lineages can expand in available climatic niche space. Here, we explore the relationships among life-history variation, climatic niche breadth, and rates of climatic niche evolution. We reconstruct a phylogeny for the genus Desmognathus, an adaptive radiation of salamanders distributed across eastern North America, based on nuclear and mitochondrial genes. Using this phylogeny, we estimate rates of climatic niche evolution for species with long, short, and no aquatic larval stage. Rates of climatic niche evolution are unrelated to the mean climatic niche breadth of species with different life histories. Instead, we find that the evolution of a short larval period promotes greater exploration of climatic space, leading to increased rates of climatic niche evolution across species having this trait. We propose that morphological and physiological differences associated with variation in larval stage length underlie the heterogeneous ability of lineages to explore climatic niche space. Rapid rates of climatic niche evolution among species with short larval periods were an important dimension of the clade's adaptive radiation and likely contributed to the rapid rate of lineage accumulation following the evolution of an aquatic life history in this clade. Our results show how variation in a key life-history trait can constrain or promote divergence of the climatic niche, leading to variation in rates of climatic niche evolution among species.

Morphological Polymorphism Associated with Alternative Reproductive Tactics in a Plethodontid Salamander.

Understanding polymorphism is a central problem in evolution and ecology, and alternative reproductive tactics (ARTs) provide compelling examples for studying the origin and maintenance of behavioral and morphological variation. Much attention has been given to examples where "parasitic" individuals exploit the reproductive investment of "bourgeois" individuals, but some ARTs are instead maintained by environmental heterogeneity, with alternative tactics exhibiting differential fitness in discontinuous reproductive niches. We use genomic, behavioral, karyological, and field observational data to demonstrate one such example in plethodontid salamanders. These ARTs ("searching" and "guarding" males) are associated with different reproductive niches and, unlike most other examples in amphibians, demonstrate substantial morphological differences and inflexibility within a reproductive season. Evidence suggests the existence of these ARTs within three putative species in the two-lined salamander (Eurycea bislineata) species complex, with other members of this clade fixed for one of the two tactics. We highlight directions for future research in this system, including the relationship between these ARTs and parental care.

Low acclimation capacity of narrow-ranging thermal specialists exposes susceptibility to global climate change.

Thermal acclimation is hypothesized to offer a selective advantage in seasonal habitats and may underlie disparities in geographic range size among closely-related species with similar ecologies. Understanding this relationship is also critical for identifying species that are more sensitive to warming climates. Here, we study North American plethodontid salamanders to investigate whether acclimation ability is associated with species' latitudinal extents and the thermal range of the environments they inhabit. We quantified variation in thermal physiology by measuring standard metabolic rate (SMR) at different test and acclimation temperatures for 16 species of salamanders with varying latitudinal extents. A phylogenetically-controlled Markov chain Monte Carlo generalized linear mixed model (MCMCglmm) was then employed to determine whether there are differences in SMR between wide- and narrow-ranging species at different acclimation temperatures. In addition, we tested for a relationship between the acclimation ability of species and the environmental temperature ranges they inhabit. Further, we investigated if there is a trade-off between critical thermal maximum (CTMax) and thermal acclimation ability. MCMCglmm results show a significant difference in acclimation ability between wide and narrow-ranging temperate salamanders. Salamanders with wide latitudinal distributions maintain or slightly increase SMR when subjected to higher test and acclimation temperatures, whereas several narrow-ranging species show significant metabolic depression. We also found significant, positive relationships between acclimation ability and environmental thermal range, and between acclimation ability and CTMax. Wide-ranging salamander species exhibit a greater capacity for thermal acclimation than narrow-ranging species, suggesting that selection for acclimation ability may have been a key factor enabling geographic expansion into areas with greater thermal variability. Further, given that narrow-ranging salamanders are found to have both poor acclimation ability and lower tolerance to warm temperatures, they are likely to be more susceptible to environmental warming associated with anthropogenic climate change.

What explains patterns of species richness? The relative importance of climatic-niche evolution, morphological evolution, and ecological limits in salamanders.

A major goal of evolutionary biology and ecology is to understand why species richness varies among clades. Previous studies have suggested that variation in richness among clades might be related to variation in rates of morphological evolution among clades (e.g., body size and shape). Other studies have suggested that richness patterns might be related to variation in rates of climatic-niche evolution. However, few studies, if any, have tested the relative importance of these variables in explaining patterns of richness among clades. Here, we test their relative importance among major clades of Plethodontidae, the most species-rich family of salamanders. Earlier studies have suggested that climatic-niche evolution explains patterns of diversification among plethodontid clades, whereas rates of morphological evolution do not. A subsequent study stated that rates of morphological evolution instead explained patterns of species richness among plethodontid clades (along with "ecological limits" on richness of clades, leading to saturation of clades with species, given limited resources). However, they did not consider climatic-niche evolution. Using phylogenetic multiple regression, we show that rates of climatic-niche evolution explain most variation in richness among plethodontid clades, whereas rates of morphological evolution do not. We find little evidence that ecological limits explain patterns of richness among plethodontid clades. We also test whether rates of morphological and climatic-niche evolution are correlated, and find that they are not. Overall, our results help explain richness patterns in a major amphibian group and provide possibly the first test of the relative importance of climatic niches and morphological evolution in explaining diversity patterns.

Testing the Relationships between Diversification, Species Richness, and Trait Evolution.

Understanding which traits drive species diversification is essential for macroevolutionary studies and to understand patterns of species richness among clades. An important tool for testing if traits influence diversification is to estimate rates of net diversification for each clade, and then test for a relationship between traits and diversification rates among clades. However, this general approach has become very controversial. Numerous papers have now stated that it is inappropriate to analyze net diversification rates in groups in which clade richness is not positively correlated with clade age. Similarly, some have stated that variation in net diversification rates does not explain variation in species richness patterns among clades across the Tree of Life. Some authors have also suggested that strong correlations between richness and diversification rates are a statistical artifact and effectively inevitable. If this latter point is true, then correlations between richness and diversification rates would be uninformative (or even misleading) for identifying how much variation in species richness among clades is explained by variation in net diversification rates. Here, we use simulations (based on empirical data for plethodontid salamanders) to address three main questions. First, how is variation in net diversification rates among clades related to the relationship between clade age and species richness? Second, how accurate are these net diversification rate estimators, and does the age-richness relationship have any relevance to their accuracy? Third, is a relationship between species richness and diversification rates an inevitable, statistical artifact? Our simulations show that strong, positive age-richness relationships arise when diversification rates are invariant among clades, whereas realistic variation in diversification rates among clades frequently disrupts this relationship. Thus, a significant age-richness relationship should not be a requirement for utilizing net diversification rates in macroevolutionary studies. Moreover, we find no difference in the accuracy of net diversification rate estimators between conditions in which there are strong, positive relationships between clade age and richness and conditions in which these strong relationships are absent. We find that net diversification rate estimators are reasonably accurate under many conditions (true and estimated rates are strongly corrrelated, and typically differ by ∼10-20%), but become more accurate when clades are older and less accurate when using incorrect assumptions about extinction. We also find that significant relationships between richness and diversification rates fail to arise under many conditions, especially when there are faster rates in younger clades. Therefore, a significant relationship between richness and diversification rates is not inevitable. Given this latter result, we suggest that relationships between richness and diversification should be tested for when attempting to explain the causes of richness patterns, to avoid potential misinterpretations (e.g., high diversification rates associated with low-richness clades). Similarly, our results also provide some support for previous studies suggesting that variation in diversification rates might explain much of the variation in species richness among major clades, based on strong relationships between clade richness and diversification rates.

Diversity and niche evolution along aridity gradients in north american lizards (phrynosomatidae).

Deserts occupy approximately 12% of the Earth's land surface, and are thought to have species poor but highly specialized biotas. However, few studies have examined the evolutionary origins of desert biotas and of diversity patterns along aridity gradients. Further, it is unclear if species occurring in more extreme conditions on a given niche axis (i.e., precipitation) are more specialized for those conditions (i.e., have narrower niche breadths). We address these questions here using a time-calibrated phylogeny and climatic data for 117 species of phrynosomatid lizards. Phrynosomatids are the most species-rich family of lizards in North America, and are found from deserts to rainforests. Surprisingly, we find that phrynosomatids have higher richness in more arid environments. This pattern occurs seemingly because they have been present in more arid habitats longer (~55 million years), and lineages in mesic environments are recently derived from more arid-dwelling ancestors. We find little support for the hypothesis that species in more extreme environments are more specialized. Instead, many desert-dwelling species are broadly distributed, and species in the most mesic environments have the broadest niche breadths. In summary, phrynosomatids offer a counterexample to the idea that arid regions are inhabited by a small number of recent and highly specialized lineages.

How is the rate of climatic-niche evolution related to climatic-niche breadth?

The rate of climatic-niche evolution is important to many research areas in ecology, evolution, and conservation biology, including responses of species to global climate change, spread of invasive species, speciation, biogeography, and patterns of species richness. Previous studies have implied that clades with higher rates of climatic-niche evolution among species should have species with narrower niche breadths, but there is also evidence suggesting the opposite pattern. However, the relationships between rate and breadth have not been explicitly analyzed. Here, we examine the relationships between the rate of climatic-niche evolution and climatic-niche breadth using phylogenetic and climatic data for 250 species in the salamander family Plethodontidae, a group showing considerable variation in both rates of climatic-niche evolution and climatic-niche breadths. Contrary to some expectations, we find no general relationship between climatic-niche breadth and the rate of climatic-niche evolution. Climatic-niche breadths for some ecologically important climatic variables considered separately (temperature seasonality and annual precipitation) do show significant relationships with the rate of climatic-niche evolution, but rates are faster in clades in which species have broader (not narrower) niche breadths. In summary, our results show that narrower niche breadths are not necessarily associated with faster rates of niche evolution.

Latitude, elevational climatic zonation and speciation in New World vertebrates.

Many biodiversity hotspots are located in montane regions, especially in the tropics. A possible explanation for this pattern is that the narrow thermal tolerances of tropical species and greater climatic stratification of tropical mountains create more opportunities for climate-associated parapatric or allopatric speciation in the tropics relative to the temperate zone. However, it is unclear whether a general relationship exists among latitude, climatic zonation and the ecology of speciation. Recent taxon-specific studies obtained different results regarding the role of climate in speciation in tropical versus temperate areas. Here, we quantify overlap in the climatic distributions of 93 pairs of sister species of mammals, birds, amphibians and reptiles restricted to either the New World tropics or to the Northern temperate zone. We show that elevational ranges of tropical- and temperate-zone species do not differ from one another, yet the temperature range experienced by species in the temperate zone is greater than for those in the tropics. Moreover, tropical sister species tend to exhibit greater similarity in their climatic distributions than temperate sister species. This pattern suggests that evolutionary conservatism in the thermal niches of tropical taxa, coupled with the greater thermal zonation of tropical mountains, may result in increased opportunities for allopatric isolation, speciation and the accumulation of species in tropical montane regions. Our study exemplifies the power of combining phylogenetic and spatial datasets of global climatic variation to explore evolutionary (rather than purely ecological) explanations for the high biodiversity of tropical montane regions.

Accelerated rates of climatic-niche evolution underlie rapid species diversification.

A major goal of ecology is to explain differences in species richness between regions and among clades. The diversification rate of clades is a key parameter for understanding both patterns. Here, we combine phylogenetic and climatic data for 250 species of plethodontid salamanders and show for the first time that rapid species diversification is associated with accelerated climatic-niche evolution among species. Both rates are particularly rapid in tropical regions, and where few clades geographically overlap. These results offer a surprising ecological explanation for why diversification rates are often higher in the tropics: rapid shifts between climatic regimes, rather than specific environmental conditions (e.g. high productivity, energy) drive higher diversity. They also suggest that climatic-niche evolution may be particularly rapid in regions where climate is particularly stable. Finally, these results indicate that evolutionary conservatism in climatic niches may be influenced by interactions between species and clades, rather than physiological tolerances alone.

Early bursts of body size and shape evolution are rare in comparative data.

George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations-more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early-burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long-term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data.

Niche conservatism drives elevational diversity patterns in Appalachian salamanders.

Many biodiversity hotspots are in montane regions, and many plant and animal groups have their highest species richness at intermediate elevations. Yet, the explanation for this hump-shaped diversity pattern has remained unclear because no studies have addressed both the ecological and evolutionary causes. Here, we address these causes in North American plethodontid salamanders, using a near-comprehensive phylogeny and environmental data. We develop a null model for assessing the relationship between the time that an area has been occupied and its species richness, and we apply a new approach that tests whether clades exhibit long-term stasis in their climatic niches (niche conservatism). Evolutionarily, the midelevation peak in species richness is explained by the time-for-speciation effect, with intermediate-elevation habitats seemingly being inhabited longest and accumulating more species. We find that this pattern is associated with evolutionary stasis in species' climatic niches, driving the midelevation peak by constraining the dispersal of lineages to environments at lower and higher elevations. These processes may help explain elevational diversity patterns in many montane regions around the world. The results also suggest that montane biotas may harbor high levels of both species diversity and phylogenetic diversity but may be particularly susceptible to rapid climate change.

Recent range-wide demographic expansion in a Taiwan endemic montane bird, Steere's Liocichla (Liocichla steerii).

BACKGROUND: The subtropical island of Taiwan is an area of high endemism and a complex topographic environment. Phylogeographic studies indicate that vicariance caused by Taiwan's mountains has subdivided many taxa into genetic phylogroups. We used mitochondrial DNA sequences and nuclear microsatellites to test whether the evolutionary history of an endemic montane bird, Steere's Liocichla (Liocichla steerii), fit the general vicariant paradigm for a montane organism. RESULTS: We found that while mountains appear to channel gene flow they are not a significant barrier for Steere's Liocichla. Recent demographic expansion was evident, and genetic diversity was relatively high across the island, suggesting expansion from multiple areas rather than a few isolated refugia. Ecological niche modeling corroborated the molecular results and suggested that populations of Steere's Liocichla are connected by climatically suitable habitat and that there was less suitable habitat during the Last Glacial Maximum. CONCLUSIONS: Genetic and ecological niche modeling data corroborate a single history--Steere's Liocichla was at lower density during the Last Glacial Maximum and has subsequently expanded in population density. We suggest that such a range-wide density expansion might be an overlooked cause for the genetic patterns of demographic expansion that are regularly reported. We find significant differences among some populations in FST indices and an admixture analysis. Though both of these results are often used to suggest conservation action, we affirm that statistically significant results are not necessarily biologically meaningful and we urge caution when interpreting highly polymorphic data such as microsatellites.

The merging of community ecology and phylogenetic biology.

The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.

Can parallel diversification occur in sympatry? Repeated patterns of body-size evolution in coexisting clades of North American salamanders.

A classic paradigm in evolutionary biology is that geographically isolated clades inhabiting similar selective regimes will diversify to create similar sets of phenotypes in different locations (e.g., similar stickleback species in different lakes, similar Anolis ecomorphs on different islands). Such parallel radiations are not generally expected to occur in sympatry because the available niche space would be filled by whichever clade is diversified first. Here, we document a very different pattern, the parallel evolution of similar body-size morphs in three sympatric clades of plethodontid salamanders (Desmognathus, Plethodon, Spelerpinae) in eastern North America. Using a comprehensive, time-calibrated phylogeny of North American plethodontids from nuclear and mitochondrial DNA sequences, we show that these three clades have undergone replicated patterns of evolution in body size and that this parallel diversification occurred in broad-scale sympatry. At the local scale, we find that coexisting species from these clades are more similar in body size than expected under a null model in which species are randomly assembled into communities. These patterns are particularly surprising in that competition is known to be important in driving phenotypic diversification and limiting local coexistence of similar-sized species within these clades. Although parallel diversification of sympatric clades may seem counterintuitive, we discuss several ecological and evolutionary factors that may allow the phenomenon to occur.

Are rates of species diversification correlated with rates of morphological evolution?

Some major evolutionary theories predict a relationship between rates of proliferation of new species (species diversification) and rates of morphological divergence between them. However, this relationship has not been rigorously tested using phylogeny-based approaches. Here, we test this relationship with morphological and phylogenetic data from 190 species of plethodontid salamanders. Surprisingly, we find that rates of species diversification and morphological evolution are not significantly correlated, such that rapid diversification can occur with little morphological change, and vice versa. We also find that most clades have undergone remarkably similar patterns of morphological evolution (despite extensive sympatry) and that those relatively novel phenotypes are not associated with rapid diversification. Finally, we find a strong relationship between rates of size and shape evolution, which has not been previously tested.

Integrating GIS-based environmental data into evolutionary biology.

Many evolutionary processes are influenced by environmental variation over space and time, including genetic divergence among populations, speciation and evolutionary change in morphology, physiology and behaviour. Yet, evolutionary biologists have generally not taken advantage of the extensive environmental data available from geographic information systems (GIS). For example, studies of phylogeography, speciation and character evolution often ignore or use only crude proxies for environmental variation (e.g. latitude and distance between populations). Here, we describe how the integration of GIS-based environmental data, along with new spatial tools, can transform evolutionary studies and reveal new insights into the ecological causes of evolutionary patterns.

The importance of comparative phylogeography in diagnosing introduced species: a lesson from the seal salamander, Desmognathus monticola.

BACKGROUND: In most regions of the world human influences on the distribution of flora and fauna predate complete biotic surveys. In some cases this challenges our ability to discriminate native from introduced species. This distinction is particularly critical for isolated populations, because relicts of native species may need to be conserved, whereas introduced species may require immediate eradication. Recently an isolated population of seal salamanders, Desmognathus monticola, was discovered on the Ozark Plateau, approximately 700 km west of its broad continuous distribution in the Appalachian Mountains of eastern North America. Using Nested Clade Analysis (NCA) we test whether the Ozark isolate results from population fragmentation (a natural relict) or long distance dispersal (a human-mediated introduction). RESULTS: Despite its broad distribution in the Appalachian Mountains, the primary haplotype diversity of D. monticola is restricted to less than 2.5% of the distribution in the extreme southern Appalachians, where genetic diversity is high for other co-distributed species. By intensively sampling this genetically diverse region we located haplotypes identical to the Ozark isolate. Nested Clade Analysis supports the hypothesis that the Ozark population was introduced, but it was necessary to include haplotypes that are less than or equal to 0.733% divergent from the Ozark population in order to arrive at this conclusion. These critical haplotypes only occur in < 1.2% of the native distribution and NCA excluding them suggest that the Ozark population is a natural relict. CONCLUSION: Our analyses suggest that the isolated population of D. monticola from the Ozarks is not native to the region and may need to be extirpated rather than conserved, particularly because of its potential negative impacts on endemic Ozark stream salamander communities. Diagnosing a species as introduced may require locating nearly identical haplotypes in the known native distribution, which may be a major undertaking. Our study demonstrates the importance of considering comparative phylogeographic information for locating critical haplotypes when distinguishing native from introduced species.

Climatic zonation drives latitudinal variation in speciation mechanisms.

Many groups of organisms show greater species richness in the tropics than in the temperate zone, particularly in tropical montane regions. Forty years ago, Janzen suggested that more limited temperature seasonality in the tropics leads to greater climatic zonation and more climatic barriers to organismal dispersal along elevational gradients in the tropics relative to temperate regions. These factors could lead to differences in how species arise in tropical versus temperate regions and possibly contribute to greater tropical diversity. However, no studies have compared the relationships among climate, elevational distribution and speciation in a group inhabiting both tropical and temperate regions. Here, we compare elevational and climatic divergence among 30 sister-species pairs (14 tropical, 16 temperate) within a single family of salamanders (Plethodontidae) that reaches its greatest species richness in montane Mesoamerica. In support of Janzen's hypothesis, we find that sister species are more elevationally and climatically divergent in the tropics than in the temperate zone. This pattern seemingly reflects regional variation in the role of climate in speciation, with niche conservatism predominating in the temperate zone and niche divergence in the tropics. Our study demonstrates how latitudinal differences in elevational climatic zonation may increase opportunities for geographical isolation, speciation and the associated build-up of species diversity in the tropics relative to the temperate zone.

Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon).

Adaptive radiations have served as model systems for quantifying the build-up of species richness. Few studies have quantified the tempo of diversification in species-rich clades that contain negligible adaptive disparity, making the macroevolutionary consequences of different modes of evolutionary radiation difficult to assess. We use mitochondrial-DNA sequence data and recently developed phylogenetic methodologies to explore the tempo of diversification of eastern North American Plethodon, a species-rich clade of woodland salamanders exhibiting only limited phenotypic disparity. Lineage-through-time analysis reveals a high rate of lineage accumulation, 0.8 species per million years, occurring 11-8 million years ago in the P. glutinosus species group, followed by decreasing rates. This high rate of lineage accumulation is exceptional, comparable to the most rapid of adaptive radiations. In contrast to classic models of adaptive radiation where ecological niche divergence is linked to the origin of species, we propose that phylogenetic niche conservatism contributes to the rapid accumulation of P. glutinosus-group lineages by promoting vicariant isolation and multiplication of species across a spatially and temporally fluctuating environment. These closely related and ecologically similar lineages persist through long-periods of evolutionary time and form strong barriers to the geographic spread of their neighbours, producing a subsequent decline in lineage accumulation. Rapid diversification among lineages exhibiting long-term maintenance of their bioclimatic niche requirements is an under-appreciated phenomenon driving the build-up of species richness.