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Phylogenetic and phylogeographic approaches have become widespread in evolutionary biology, ecology, and biogeography.  However, analyses that incorporate inferences from historical biogeography (e.g. timing of colonization of a region) may be essential to answer the most important large-scale questions in these fields, but they remain infrequently used.  I focus on two examples here.  First, I argue that understanding the origins of biodiversity hotspots (and other high-diversity regions) requires comparing the timing of biogeographic colonization and diversification rates among regions.  In contrast, phylogeographic studies (analyses within species within a region) may themselves say little about why a region is diverse relative to others.  Second, incorporating historical biogeograpy can help address the processes that determine community species richness and structure, such as dispersal, in-situ trait evolution, and in-situ speciation.  In contrast, the widespread “community phylogenetics” approach (focusing on relatedness of species in communities) may have limited ability to explain community richness and structure.

Niche breadth is a unifying concept spanning diverse aspects of ecology, evolution, and conservation biology. Niche breadth usually refers to the diversity of resources used or environments tolerated by an individual, population, species, or clade. Here we review key research in ecology, evolution, and conservation biology in light of niche breadth. Namely, we explore the role of niche breadth in shaping geographic distributions and species richness from local to landscape scales, how niche breadth evolves and influences lineage diversification, and its use for understanding species invasions, responses to climate change, vulnerability to extinction, and ecosystem functioning. This diverse literature informs a research agenda that identifies focused needs for further progress: testing the hierarchical nature of niche breadth (e.g., of individuals, populations, and species); quantifying correlations in niche breadth among different niche axes and the role of environmental drivers and organismal constraints in generating these correlations; and evaluating the factors that decouple fundamental and realized niches. We describe how this research agenda could help unify disparate subdisciplines and shed light on key questions in ecology, evolution, and conservation. [ABSTRACT FROM AUTHOR]

Aim: Are different fruit colours related to large‐scale patterns of dispersal, distribution and diversification? Here, we investigate this question for the first time, using phylogenetic approaches in the tribe Gaultherieae (Ericaceae). We test relationships between fruit colour and (a) biogeographic dispersal, (b) elevational and latitudinal species distributions and (c) rates of diversification. Location: Global. Time period: Recent to 30 million years ago. Major taxa studied: The plant tribe Gaultherieae in the family Ericaceae (blueberries and relatives). Methods: We estimated a new time‐calibrated phylogeny for Gaultherieae. Data on fruit colours and geographic distributions for each species were compiled from published sources and field observations. Using phylogenetic methods, we estimated major dispersal events across the tree and the most likely fruit colour associated with each dispersal event, and tested whether dispersal between major biogeographic regions was equally likely for different fruit colours, and whether dispersal distances were larger for certain colours. We then tested the relationships between fruit colours and geographic variables (latitude, elevation) and diversification rates. Results: Large‐scale dispersal events were significantly associated with red‐fruited lineages, even though red‐fruited species were relatively uncommon. Further, different fruit colours were associated with different elevations and latitudes (e.g. red at lower elevations, violet at lower latitudes, white at higher elevations). Violet colour was related to increased diversification rates, leading to more violet‐fruited species globally. Main conclusions: Overall, we show that different fruit colours can significantly impact the large‐scale dispersal, distribution and diversification of plant clades. Furthermore, the interplay between biogeography and fruit‐colour evolution seems to generate "taxon cycles" in fruit colour that may drive variation in fruit colour over macroevolutionary time‐scales. [ABSTRACT FROM AUTHOR]

Around the world, many species are confined to "Sky Islands," with different populations in isolated patches of montane habitat. How does this pattern arise? One scenario is that montane species were widespread in lowlands when climates were cooler, and were isolated by local extinction caused by warming conditions. This scenario implies that many montane species may be highly susceptible to anthropogenic warming. Here, we test this scenario in a montane lizard (Sceloporus jarrovii) from the Madrean Sky Islands of southeastern Arizona. We combined data from field surveys, climate, population genomics, and physiology. Overall, our results support the hypothesis that this species' current distribution is explained by local extinction caused by past climate change. However, our results for this species differ from simple expectations in several ways: (a) their absence at lower elevations is related to warm winter temperatures, not hot summer temperatures; (b) they appear to exclude a low‐elevation congener from higher elevations, not the converse; (c) they are apparently absent from many climatically suitable but low mountain ranges, seemingly "pushed off the top" by climates even warmer than those today; (d) despite the potential for dispersal among ranges during recent glacial periods (~18,000 years ago), populations in different ranges diverged ~4.5–0.5 million years ago and remained largely distinct; and (e) body temperatures are inversely related to climatic temperatures among sites. These results may have implications for many other Sky Island systems. More broadly, we suggest that Sky Island species may be relevant for predicting responses to future warming. [ABSTRACT FROM AUTHOR]

Most groups of organisms occur in multiple regions and have different numbers of species in different regions. These richness patterns are directly explained by speciation, extinction, and dispersal. Thus, regional richness patterns may be explained by differences in when regions were colonized (more time for speciation in regions colonized earlier), differences in how often they were colonized, or differences in diversification rates (speciation minus extinction) among regions (with diversification rates potentially influenced by area, climate, and/or many other variables). Few studies have tested all three factors, and most that did examined them only in individual clades. Here, we analyze a diverse set of 15 clades of plants and animals to test the causes of regional species richness patterns within clades. We find that time was the sole variable significantly explaining richness patterns in the best-fitting models for most clades (10/15), whereas time combined with other factors explained richness in all others. Time was the most important factor explaining richness in 13 of 15 clades, and it explained 72% of the variance in species richness among regions across all 15 clades (on average). Surprisingly, time was increasingly important in older and larger clades. In contrast, the area of the regions was relatively unimportant for explaining these regional richness patterns. A systematic review yielded 15 other relevant studies, which also overwhelmingly supported time over diversification rates (13 to 1, with one study supporting both diversification rates and time). Overall, our results suggest that colonization time is a major factor explaining regional-scale richness patterns within clades (e.g., families). [ABSTRACT FROM AUTHOR]

For most marine organisms, species richness peaks in the Central Indo- Pacific region and declines longitudinally, a striking pattern that remains poorly understood. Here, we used phylogenetic approaches to address the causes of richness patterns among global marine regions, comparing the relative importance of colonization time, number of colonization events, and diversification rates (speciation minus extinction). We estimated regional richness using distributional data for almost all percomorph fishes (17 435 species total, including approximately 72% of all marine fishes and approximately 33% of all freshwater fishes). The high diversity of the Central Indo-Pacific was explained by its colonization by many lineages 5.3-34 million years ago. These relatively old colonizations allowed more time for richness to build up through in situ diversification compared to other warm-marine regions. Surprisingly, diversification rates were decoupled from marine richness patterns, with clades in low-richness cold-marine habitats having the highest rates. Unlike marine richness, freshwater diversity was largely derived from a few ancient colonizations, coupled with high diversification rates. Our results are congruent with the geological history of the marine tropics, and thus may apply to many other organisms. Beyond marine biogeography, we add to the growing number of cases where colonization and time-for-speciation explain large-scale richness patterns instead of diversification rates. [ABSTRACT FROM AUTHOR]

Summary: What causes the disparity in biodiversity among regions is a fundamental question in biogeography, ecology, and evolutionary biology. Evolutionary and biogeographic processes (speciation, extinction, dispersal) directly determine species richness patterns, and can be studied using integrative phylogenetic approaches. However, the strikingly high richness of East Asia relative to other Northern Hemisphere regions remains poorly understood from this perspective. Here, for the first time, we test two general hypotheses (older colonization time, faster diversification rate) to explain this pattern, using the plant tribe Lysimachieae (Primulaceae) as a model system. We generated a new time‐calibrated phylogeny for Lysimachieae (13 genes, 126 species), to estimate colonization times and diversification rates for each region and to test the relative importance of these two factors for explaining regional richness patterns. We find that neither time nor diversification rates alone explain richness patterns among regions in Lysimachieae. Instead, a new index that combines both factors explains global richness patterns in the group and their high East Asian biodiversity. Based on our results from Lysimachieae, we suggest that the high richness of plants in East Asia may be explained by a combination of older colonization times and faster diversification rates in this region. [ABSTRACT FROM AUTHOR]

Saturation is the idea that a community is effectively filled with species, such that no more can be added without extinctions. This concept has important implications for many areas of ecology, such as species richness, community assembly, invasive species and climate change. Here, we illustrate how biogeography can be used to test for community saturation, when combined with data on local species richness, phylogeny and climate. We focus on a clade of frogs (Terrarana) and the impact of the Great American Biotic Interchange on patterns of local richness in Lower Middle America and adjacent regions. We analyse data on species richness at 83 sites and a time-calibrated phylogeny for 363 species. We find no evidence for saturation, and show instead that biotic interchange dramatically increased local richness in the region. We suggest that historical biogeography offers thousands of similar long-term natural experiments that can be used to test for saturation. [ABSTRACT FROM AUTHOR]

Life-history modes can profoundly impact the biology of a species, and a classic example is the dichotomy between metamorphic (biphasic) and paedomorphic (permanently aquatic) life-history strategies in salamanders. However, despite centuries of research on this system, several basic questions about the evolution of paedomorphosis in salamanders have not been addressed. Here, we use a nearly comprehensive, time-calibrated phylogeny of spelerpine plethodontids to reconstruct the evolution of paedomorphosis and to test if paedomorphosis is (1) reversible; (2) associated with living in caves; (3) associated with relatively dry climatic conditions on the surface; and (4) correlated with limited range size and geographic dispersal. We find that paedomorphosis arose multiple times in spelerpines. We also find evidence for re-evolution of metamorphosis after several million years of paedomorphosis in a lineage of Eurycea from the Edwards Plateau region of Texas. We also show for the first time using phylogenetic comparative methods that paedomorphosis is highly correlated with cave-dwelling, arid surface environments, and small geographic range sizes, providing insights into both the causes and consequences of this major life history transition. [ABSTRACT FROM AUTHOR]

Many clades contain ecologically and phenotypically similar species across continents, yet the processes generating this similarity are largely unstudied, leaving fundamental questions unanswered. Is similarity in morphology and performance across assemblages caused by evolutionary convergence or by biogeographic dispersal of evolutionarily conserved ecotypes? Does convergence to new ecological conditions erase evidence of past adaptation? Here, we analyse ecology, morphology and performance in frog assemblages from three continents (Asia, Australia and SouthAmerica), assessing the importance of dispersal and convergent evolution in explaining similarity across regions. We find three striking results. First, species using the same microhabitat type are highly similar in morphology and performance across both clades and continents. Second, some species on different continents owe their similarity to dispersal and evolutionary conservatism (rather than evolutionary convergence), even over vast temporal and spatial scales. Third, in one case, an ecologically specialized ancestor radiated into diverse ecotypes that have converged with those on other continents, largely erasing traces of past adaptation to their ancestral ecology. Overall, our study highlights the roles of both evolutionary conservatism and convergence in explaining similarity in species traits over large spatial and temporal scales and demonstrates a statistical framework for addressing these questions in other systems. [ABSTRACT FROM AUTHOR]

Speciation is often categorized based on geographic modes (allopatric, parapatric or sympatric). Although it is widely accepted that species can arise in allopatry and then later become sympatrically or parapatrically distributed, patterns in the opposite direction are also theoretically possible (e.g. sympatric lineages or ecotypes becoming parapatric), but such patterns have not been shown at a macrogeographic scale. Here, we analyse genetic, climatic, ecological and morphological data and show that two typically sympatric colour morphs of the salamander Plethodon cinereus (redback and leadback) appear to have become parapatrically distributed on Long Island, New York, with pure-redback populations in the west and pure-leadback populations in the east (and polymorphic populations in between and on the mainland). In addition, the pure-leadback populations in eastern Long Island are genetically, ecologically and morphologically divergent from both mainland and other Long Island populations, suggesting the possibility of incipient speciation. This parapatric separation seems to be related to the different ecological preferences of the two morphs, preferences which are present on the mainland and across Long Island. These results potentially support the idea that spatial segregation of sympatric ecotypes may sometimes play an important part in parapatric speciation. [ABSTRACT FROM AUTHOR]

Clade diversification is a central topic in macroevolutionary studies. Recently, it has been shown that diversification rates appear to decelerate over time in many clades. What causes this deceleration remains unclear, but it has been proposed that competition for limited resources between sympatric, ecologically similar species slows diversification. Employing carnivoran mammals as a model system, we test this hypothesis using a comprehensive time-calibrated phylogeny. We also explore several conceptually related explanations including limited geographic area and limited rates of niche evolution. We find that diversification slowdowns are strong in carnivorans. Surprisingly, these slowdowns are independent of geographic range overlap between related species and are also decoupled from rates of niche evolution, suggesting that slowdowns are unrelated to competition and niche filling. When controlling for the effects of clade diversity, diversification slowdowns appear independent of geographic area. There is a significant effect of clade diversity on diversification slowdowns, but simulations show that this relationship may arise as a statistical artifact (i.e., greater clade diversity increases the ability of the gamma statistic to refute constant diversification). Overall, our results emphasize the need to test hypotheses about the causes of diversification slowdowns with ecological data, rather than assuming ecological processes from phylogenies alone. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Ecology and historical (phylogeny-based) biogeography have much to offer one another, but exchanges between these fields have been limited. Historical biogeography has become narrowly focused on using phylogenies to discover the history of geological connections among regions. Conversely, ecologists often ignore historical biogeography, even when its input can be crucial. Both historical biogeographers and ecologists have more-or-less abandoned attempts to understand the processes that determine the large-scale distribution of clades. Here, we describe the chasm that has developed between ecology and historical biogeography, some of the important questions that have fallen into it and how it might be bridged. To illustrate the benefits of an integrated approach, we expand on a model that can help explain the latitudinal gradient of species richness. [Copyright &y& Elsevier]

To understand speciation, we first need to know what species are. Yet debates over species concepts have seemed endless, with little obvious relevance to the study of speciation. Recently, there has been progress in resolving these debates, favoring a lineage-based, evolutionary species concept. This progress calls for reconsideration of the study of speciation. Traditional speciation research based on the biological species concept has led to great advances in understanding how nonallopatric speciation occurs and how species diverge and remain separate from each other. However, this research has neglected the question of how new species arise in the first place for the most common geographic mode (allopatric). A new and very different research program is needed to understand the ecological and evolutionary processes that split an ancestral species into new allopatric lineages. This research program will connect speciation to many other fundamental questions in evolutionary biology, ecology, biogeography, and conservation biology. [ABSTRACT FROM AUTHOR]

Phylogenomic approaches offer a wealth of data, but a bewildering diversity of methodological choices. These choices can strongly affect the resulting topologies. Here, we explore two controversial approaches (binning genes into “supergenes” and inclusion of only rapidly evolving sites), using new data from hyloid frogs. Hyloid frogs encompass ∼53% of frog species, including true toads (Bufonidae), glassfrogs (Centrolenidae), poison frogs (Dendrobatidae), and treefrogs (Hylidae). Many hyloid families are well-established, but relationships among these families have remained difficult to resolve. We generated a dataset of ultraconserved elements (UCEs) for 50 ingroup species, including 18 of 19 hyloid families and up to 2214 loci spanning >800,000 aligned base pairs. We evaluated these two general approaches (binning, rapid sites only) based primarily on their ability to recover and strongly support well-established clades. Data were analyzed using concatenated likelihood and coalescent species-tree methods (NJst, ASTRAL). Binning strongly affected inferred relationships, whereas use of only rapidly evolving sites did not (indicating ∼87% of the data contributed little information). The optimal approaches for maximizing recovery and support of well-established clades were concatenated likelihood analysis and the use of a limited number of naive bins (statistical binning gave more problematic results). These two optimal approaches converged on similar relationships among hyloid families, and resolved them with generally strong support. The relationships found were very different from most previous estimates of hyloid phylogeny, and a new classification is proposed. The new phylogeny also suggests an intriguing biogeographical scenario, in which hyloids originated in southern South America before radiating throughout the world. [ABSTRACT FROM AUTHOR]