DOES NICHE DIVERGENCE ACCOMPANY ALLOPATRIC DIVERGENCE IN APHELOCOMA JAYS AS PREDICTED UNDER ECOLOGICAL SPECIATION?: INSIGHTS FROM TESTS WITH NICHE MODELS

The role of ecology in the origin of species has been the subject of long‐standing interest to evolutionary biologists. New sources of spatially explicit ecological data allow for large‐scale tests of whether speciation is associated with niche divergence or whether closely related species tend to be similar ecologically (niche conservatism). Because of the confounding effects of spatial autocorrelation of environmental variables, we generate null expectations for niche divergence for both an ecological‐niche modeling and a multivariate approach to address the question: do allopatrically distributed taxa occupy similar niches? In a classic system for the study of niche evolution—the Aphelocoma jays—we show that there is little evidence for niche divergence among Mexican Jay (A. ultramarina) lineages in the process of speciation, contrary to previous results. In contrast, Aphelocoma species that exist in partial sympatry in some regions show evidence for niche divergence. Our approach is widely applicable to the many cases of allopatric lineages in the beginning stages of speciation. These results do not support an ecological speciation model for Mexican Jay lineages because, in most cases, the allopatric environments they occupy are not significantly more divergent than expected under a null model.     

Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake, Lampropeltis getula

Niche conservatism and niche divergence are both important ecological mechanisms associated with promoting allopatric speciation across geographical barriers. However, the potential for variable responses in widely distributed organisms has not been fully investigated. For allopatric sister lineages, three patterns for the interaction of ecological niche preference and geographical barriers are possible: (i) niche conservatism at a physical barrier; (ii) niche divergence at a physical barrier; and (iii) niche divergence in the absence of a physical barrier. We test for the presence of these patterns in a transcontinentally distributed snake species, the common kingsnake ( Lampropeltis getula ), to determine the relative frequency of niche conservatism or divergence in a single species complex inhabiting multiple distinct ecoregions. We infer the phylogeographic structure of the kingsnake using a range-wide data set sampled for the mitochondrial gene cytochrome b . We use coalescent simulation methods to test for the presence of structured lineage formation vs. fragmentation of a widespread ancestor. Finally, we use statistical techniques for creating and evaluating ecological niche models to test for conservatism of ecological niche preferences. Significant geographical structure is present in the kingsnake, for which coalescent tests indicate structured population division. Surprisingly, we find evidence for all three patterns of conservatism and divergence. This suggests that ecological niche preferences may be labile on recent phylogenetic timescales, and that lineage formation in widespread species can result from an interaction between inertial tendencies of niche conservatism and natural selection on populations in ecologically divergent habitats.     

Niche divergence builds the case for ecological speciation in skinks of the Plestiodon skiltonianus species complex

Adaptation to different thermal environments has the potential to cause evolutionary changes that are sufficient to drive ecological speciation. Here, we examine whether climate‐based niche divergence in lizards of the Plestiodon skiltonianus species complex is consistent with the outcomes of such a process. Previous work on this group shows that a mechanical sexual barrier has evolved between species that differ mainly in body size and that the barrier may be a by‐product of selection for increased body size in lineages that have invaded xeric environments; however, baseline information on niche divergence among members of the group is lacking. We quantified the climatic niche using mechanistic physiological and correlative niche models and then estimated niche differences among species using ordination techniques and tests of niche overlap and equivalency. Our results show that the thermal niches of size‐divergent, reproductively isolated morphospecies are significantly differentiated and that precipitation may have been as important as temperature in causing increased shifts in body size in xeric habitats. While these findings alone do not demonstrate thermal adaptation or identify the cause of speciation, their integration with earlier genetic and behavioral studies provides a useful test of phenotype–environment associations that further support the case for ecological speciation in these lizards.     

RIVERSCAPE GENETICS IDENTIFIES REPLICATED ECOLOGICAL DIVERGENCE ACROSS AN AMAZONIAN ECOTONE

Ecological speciation involves the evolution of reproductive isolation and niche divergence in the absence of a physical barrier to gene flow. The process is one of the most controversial topics of the speciation debate, particularly in tropical regions. Here, we investigate ecologically based divergence across an Amazonian ecotone in the electric fish, Steatogenys elegans. We combine phylogenetics, genome scans, and population genetics with a recently developed individual‐based evolutionary landscape genetics approach that incorporates selection. This framework is used to assess the relative contributions of geography and divergent natural selection between environments as biodiversity drivers. We report on two closely related and sympatric lineages that exemplify how divergent selection across a major Amazonian aquatic ecotone (i.e., between rivers with markedly different hydrochemical properties) may result in replicated ecologically mediated speciation. The results link selection across an ecological gradient with reproductive isolation and we propose that assortative mating based on water color may be driving the divergence. Divergence resulting from ecologically driven selection highlights the importance of considering environmental heterogeneity in studies of speciation in tropical regions. Furthermore, we show that framing ecological speciation in a spatially explicit evolutionary landscape genetics framework provides an important first step in exploring a wide range of the potential effects of spatial dependence in natural selection.     

Rethinking adaptation: the niche-construction perspective

Niche construction refers to the capacity of organisms to construct, modify, and select important components of their local environments, such as nests, burrows, pupal cases, chemicals, and nutrients. A small but increasing number of evolutionary biologists regard niche construction as an evolutionary process in its own right, rather than as a mere product of natural selection. Through niche construction organisms not only influence the nature of their world, but also in part determine the selection pressures to which they and their descendants are exposed, and they do so in a non-random manner. Mathematical population genetics analyses have revealed that niche construction is likely to be evolutionarily consequential because of the feedback that it generates in the evolutionary process. A parallel movement has emerged in ecosystem ecology, where researchers stress the utility of regarding organisms as ecosystem engineers, who partly control energy and matter flows. From the niche construction standpoint, the evolving complementary match between organisms and environments is the product of reciprocal interacting processes of natural selection and niche construction. This essay reviews the arguments put forward in favor of the niche-construction perspective.     

Synergistic selection between ecological niche and mate preference primes diversification

The ecological niche and mate preferences have independently been shown to be important for the process of speciation. Here, we articulate a novel mechanism by which ecological niche use and mate preference can be linked to promote speciation. The degree to which individual niches are narrow and clustered affects the strength of divergent natural selection and population splitting. Similarly, the degree to which individual mate preferences are narrow and clustered affects the strength of divergent sexual selection and assortative mating between diverging forms. This novel perspective is inspired by the literature on ecological niches; it also explores mate preferences and how they may contribute to speciation. Unlike much comparative work, we do not search for evolutionary patterns using proxies for adaptation and sexual selection, but rather we elucidate how ideas from niche theory relate to mate preference, and how this relationship can foster speciation. Recognizing that individual and population niches are conceptually and ecologically linked to individual and population mate preference functions will significantly increase our understanding of rapid evolutionary diversification in nature. It has potential to help solve the difficult challenge of testing the role of sexual selection in the speciation process. We also identify ecological factors that are likely to affect individual niche and individual mate preference in synergistic ways and as a consequence to promote speciation. The ecological niche an individual occupies can directly affect its mate preference. Clusters of individuals with narrow, differentiated niches are likely to have narrow, differentiated mate preference functions. Our approach integrates ecological and sexual selection research to further our understanding of diversification processes. Such integration may be necessary for progress because these processes seem inextricably linked in the natural world.     

Climatic niche conservatism and ecological opportunity in the explosive radiation of arvicoline rodents (Arvicolinae,Cricetidae)

Climatic niche conservatism shapes patterns of diversity in many taxonomic groups, while ecological opportunity (EO) can trigger rapid speciation that is less constrained by the amount of time a lineage has occupied a given habitat. These two processes are well studied, but limited research has considered their joint and relative roles in shaping diversity patterns. We characterized climatic and biogeographic variables for 102 species of arvicoline rodents (Arvicolinae, Cricetidae), testing the effects of climatic niche conservatism and EO on arvicoline diversification as lineages transitioned between biogeographic regions. We found that the amount of time a lineage has occupied a precipitation niche is positively correlated with diversity along a precipitation gradient, suggesting climatic niche conservatism. In contrast, shift in diversification rate explained diversity patterns along a temperature gradient. Our results suggest that an indirect relationship exists between temperature and diversification that is associated with EO as arvicoline rodents colonized warm Palearctic environments. Climatic niche conservatism alone did not fully explain diversity patterns under density‐dependence, highlighting the additional importance of EO‐related processes in promoting the explosive radiation in arvicoline rodents and shaping diversity pattern among biogeographic regions and along climatic gradients.     

A stochastic, evolutionary model for range shifts and richness on tropical elevational gradients under Quaternary glacial cycles

Quaternary glacial-interglacial cycles repeatedly forced thermal zones up and down the slopes of mountains, at all latitudes. Although no one doubts that these temperature cycles have left their signature on contemporary patterns of geography and phylogeny, the relative roles of ecology and evolution are not well understood, especially for the tropics. To explore key mechanisms and their interactions in the context of chance events, we constructed a geographical range-based, stochastic simulation model that incorporates speciation, anagenetic evolution, niche conservatism, range shifts and extinctions under late Quaternary temperature cycles along tropical elevational gradients. In the model, elevational patterns of species richness arise from the differential survival of founder lineages, consolidated by speciation and the inheritance of thermal niche characteristics. The model yields a surprisingly rich variety of realistic patterns of phylogeny and biogeography, including close matches to a variety of contemporary elevational richness profiles from an elevational transect in Costa Rica. Mountaintop extinctions during interglacials and lowland extinctions at glacial maxima favour mid-elevation lineages, especially under the constraints of niche conservatism. Asymmetry in temperature (greater duration of glacial than of interglacial episodes) and in lateral area (greater land area at low than at high elevations) have opposing effects on lowland extinctions and the elevational pattern of species richness in the model--and perhaps in nature, as well.     

Out of the dark: 350 million years of conservatism and evolution in diel activity patterns in vertebrates

Many animals are active only during a particular time (e.g., day vs. night), a partitioning that may have important consequences for species coexistence. An open question is the extent to which this diel activity niche is evolutionarily conserved or labile. Here, we analyze diel activity data across a phylogeny of 1914 tetrapod species. We find strong phylogenetic signal, showing that closely related species tend to share similar activity patterns. Ancestral reconstructions show that nocturnality was the most likely ancestral diel activity pattern for tetrapods and many major clades within it (e.g., amphibians, mammals). Remarkably, nocturnal activity appears to have been maintained continuously in some lineages for ～350 million years. Thus, we show that traits involved in local‐scale resource partitioning can be conserved over strikingly deep evolutionary time scales. We also demonstrate a potentially important (but often overlooked) metric of niche conservatism. Finally, we show that diurnal lineages appear to have faster speciation and diversification rates than nocturnal lineages, which may explain why there are presently more diurnal tetrapod species even though diurnality appears to have evolved more recently. Overall, our results may have implications for studies of community ecology, species richness, and the evolution of diet and communication systems.     

Taxic evolutionary paleoecology and the ecological context of macroevolutionary change

Summary A traditional focus of evolutionary paleoecology has been the reconstruction of the selective forces that have affected evolving lineages through time. If the history of those lineages is dominated by stasis and punctuation, however, this is at best an inadequate and at worst a misdirected research strategy for macroevolution, because long-term stasis implies that environmental factors may have less influence on evolving lineages than previously believed. Such reasoning has led some proponents of punctuated views to reject ecological interactions as predominant or even significant forces in evolution. This is not a necessary conclusion. It is possible to accept the empirical predominance of stasis in evolution and at the same time the importance of ecology in affecting the course of evolutionary trends within lineages. If stasis prevails, ecology matters in the evolution of lineages if either (1) stabilizing selection is an important cause of stasis or (2) ecological interactions play an important role in controlling the speciation process. Viewing allopatric speciation explicitly as a three-stage process (consisting of formation, persistence and differentiation of isolated populations) clarifies testing of the role of ecology in speciation and may redirect clade-specific evolutionary paleoecology towards more enlightening interaction with other areas of macroevolutionary study.     

Cultural niche construction and human evolution

Organisms frequently choose, regulate, construct and destroy important components of their environments, in the process changing the selection pressures to which they and other organisms are exposed. We refer to these processes as niche construction. In humans, culture has greatly amplified our capacity for niche construction and our ability to modify selection pressures. We use gene‐culture coevolutionary models to explore the evolutionary consequences of culturally generated niche construction through human evolution. Our analysis suggests that where cultural traits are transmitted in an unbiased fashion from parent to offspring, cultural niche construction will have a similar effect to gene‐based niche construction. However, cultural transmission biases favouring particular cultural traits may either increase or reduce the range of parameter space over which niche construction has an impact, which means that niche construction with biased transmission will either have a much smaller or a much bigger effect than gene‐based niche construction. The analysis also reveals circumstances under which cultural transmission can overwhelm natural selection, accelerate the rate at which a favoured gene spreads, initiate novel evolutionary events and trigger hominid speciation. Because cultural processes typically operate faster than natural selection, cultural niche construction probably has more profound consequences than gene‐based niche construction, and is likely to have played an important role in human evolution.     

Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach

Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analysed inter‐ and intraspecific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models (SDMs) and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with SDMs and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors, have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process.     

Tracking niche variation over millennial timescales in sympatric killer whale lineages

Niche variation owing to individual differences in ecology has been hypothesized to be an early stage of sympatric speciation. Yet to date, no study has tracked niche width over more than a few generations. In this study, we show the presence of isotopic niche variation over millennial timescales and investigate the evolutionary outcomes. Isotopic ratios were measured from tissue samples of sympatric killer whale Orcinus orca lineages from the North Sea, spanning over 10 000 years. Isotopic ratios spanned a range similar to the difference in isotopic values of two known prey items, herring Clupea harengus and harbour seal Phoca vitulina. Two proxies of the stage of speciation, lineage sorting of mitogenomes and genotypic clustering, were both weak to intermediate indicating that speciation has made little progress. Thus, our study confirms that even with the necessary ecological conditions, i.e. among-individual variation in ecology, it is difficult for sympatric speciation to progress in the face of gene flow. In contrast to some theoretical models, our empirical results suggest that sympatric speciation driven by among-individual differences in ecological niche is a slow process and may not reach completion. We argue that sympatric speciation is constrained in this system owing to the plastic nature of the behavioural traits under selection when hunting either mammals or fish.     

Non-ecological speciation, niche conservatism and thermal adaptation: how are they connected?

During the last decade, the ecological theory of adaptive radiation, and its corollary ??ecological speciation??, has been a major research theme in evolutionary biology. Briefly, this theory states that speciation is mainly or largely the result of divergent selection, arising from niche differences between populations or incipient species. Reproductive isolation evolves either as a result of direct selection on mate preferences (e.g. reinforcement), or as a correlated response to divergent selection (??by-product speciation??). Although there are now many tentative examples of ecological speciation, I argue that ecology??s role in speciation might have been overemphasised and that non-ecological and non-adaptive alternatives should be considered more seriously. Specifically, populations and species of many organisms often show strong evidence of niche conservatism, yet are often highly reproductively isolated from each other. This challenges niche-based ecological speciation and reveals partial decoupling between ecology and reproductive isolation. Furthermore, reproductive isolation might often evolve in allopatry before ecological differentiation between taxa or possibly through learning and antagonistic sexual interactions, either in allopatry or sympatry. Here I discuss recent theoretical and empirical work in this area, with some emphasis on odonates (dragonflies and damselflies) and suggest some future avenues of research. A main message from this paper is that the ecology of species differences is not the same as ecological speciation, just like the genetics of species differences does not equate to the genetics of speciation.     

Niche construction,human behavior,and the adaptive‐lag hypothesis

Niche construction is the process whereby organisms modify selective environments, thereby affecting evolution. The niche‐construction perspective is particularly relevant to researchers using evolutionary methods to interpret human behavior and society. On the basis of niche‐construction theory, we argue against the hypothesis that modern humans experience an atypically large adaptive lag. We stress that humans construct their world largely to suit themselves and frequently buffer adaptive lag through cultural niche construction. Where they are unable to do that, natural selection of genes rapidly ensues. Our argument has implications for evolutionary psychology and human behavioral ecology, and suggests that the methods of the latter are potentially applicable to all human societies, even postindustrial ones.     

Testing the role of climate in speciation: New methods and applications to squamate reptiles (lizards and snakes)

Climate may play important roles in speciation, such as causing the range fragmentation that underlies allopatric speciation (through niche conservatism) or driving divergence of parapatric populations along climatic gradients (through niche divergence). Here, we developed new methods to test the frequency of climate niche conservatism and divergence in speciation, and applied it to species pairs of squamate reptiles (lizards and snakes). We used a large‐scale phylogeny to identify 242 sister species pairs for analysis. From these, we selected all terrestrial allopatric pairs with sufficient occurrence records (n = 49 pairs) and inferred whether each originated via climatic niche conservatism or climatic niche divergence. Among the 242 pairs, allopatric pairs were most common (41.3%), rather than parapatric (19.4%), partially sympatric (17.7%), or fully sympatric species pairs (21.5%). Among the 49 selected allopatric pairs, most appeared to have originated via climatic niche divergence (61–76%, depending on the details of the methods). Surprisingly, we found greater climatic niche divergence between allopatric sister species than between parapatric pairs, even after correcting for geographic distance. We also found that niche divergence did not increase with time, further implicating niche divergence in driving lineage splitting. Overall, our results suggest that climatic niche divergence may often play an important role in allopatric speciation, and the methodology developed here can be used to address the generality of these findings in other organisms.     

Diversification in North American arid lands: Niche conservatism, divergence and expansion of habitat explain speciation in the genus Ephedra

A lineage of 12 arid land shrubby species in the gymnosperm genus Ephedra (Gnetales) from North America is used to evaluate the influence of climate on speciation. With a long evolutionary history, and a well documented fossil record this lineage is an ideal model for understanding the process of speciation under a niche conservatism scenario. Using seven DNA molecular markers, Bayesian inference is carried out to uncover sister species and to estimate time of divergence of the lineages. Ecological niche models are generated for four parapatric and sympatric sister species and two analyses of niche evolution are performed, one based on ecological niche models and another using raw data and multivariate analysis. As previous analyses suggest, the diversification of North America Ephedra species may be the result of a recent secondary radiation. Both parapatric and sympatric species diverged mostly in a scenario of climatic niche conservatism. However, we also found strong evidence for niche divergence for one of the sister species pairs (E. californica-E. trifurca). Moreover, the multivariate analysis found environmental differences for some variables between sister species. The estimated divergence time of three pairs of sister species distributed in southwestern North America (E. cutleri-E. aspera, E. californica-E. trifurca and E. torreyana-E. viridis) is inferred to have occurred in the Late Miocene to Pliocene and for the sister species pair E. antisyphilitica-E. coryi distributed in the southern United States and northeastern Mexico, it was inferred from the Pliocene to Pleistocene. The orogenetic and climatic changes documented for these regions related to expansion of arid lands, may have contributed to the diversification in North American Ephedra, rather than adaptations to new climatic conditions.     

Matching habitat choice causes directed gene flow: a neglected dimension in evolution and ecology

Gene flow among populations is typically thought to be antagonistic to population differentiation and local adaptation. However, this assumes that dispersing individuals disperse randomly with respect to their ability to use the environment. Yet dispersing individuals often sample and compare environments and settle in those environments that best match their phenotype, causing directed gene flow, which can in fact promote population differentiation and adaptation. We refer to this process as "matching habitat choice." Although this process has been acknowledged by several researchers, no synthesis or perspective on its potentially widespread importance exists. Here we synthesize empirical and theoretical studies, and offer a new perspective that matching habitat choice can have significant effects on important and controversial topics. We discuss the potential implications of matching habitat choice for the degree and rate of local adaptation, the evolution of niche width, adaptive peak shifts, speciation in the presence of gene flow, and on our view and interpretation of measures of natural selection. Because of its potential importance for such a wide range of topics, we call for heightened empirical and theoretical attention for this neglected dimension in evolutionary and ecological studies.     

The ecology of sexual conflict: ecologically dependent parallel evolution of male harm and female resistance in Drosophila melanogaster

The prevalence of sexual conflict in nature, along with the potentially stochastic nature of the resulting coevolutionary trajectories, makes it an important driver of phenotypic divergence and speciation that can operate even in the absence of environmental differences. The majority of empirical work investigating sexual conflict's role in population divergence/speciation has therefore been done in uniform environments and any role of ecology has largely been ignored. However, theory suggests that natural selection can constrain phenotypes influenced by sexual conflict. We use replicate populations of Drosophila melanogaster adapted to alternative environments to test how ecology influences the evolution of male effects on female longevity. The extent to which males reduce female longevity, as well as female resistance to such harm, both evolved in association with adaptation to the different environments. Our results demonstrate that ecology plays a central role in shaping patterns of population divergence in traits under sexual conflict.     

Genetic admixture in multidimensional environmental space: asymmetrical niche similarity promotes gene flow in armadillos (Dasypus novemcinctus)

We unite genetic data with a robust test of niche divergence to test the hypothesis that patterns of gene flow between two lineages of the nine-banded armadillo are influenced by their climatic niches. We collected Geographical Information System (GIS) data on climate using locality information from 111 individuals from two lineages that had associated genetic material. We tested whether niches of these lineages were more conserved or divergent than the background environments of their geographic ranges and found evidence for niche conservatism on two axes and no evidence for divergence on any axis. To address the role of niche similarity in gene flow, we genotyped the 111 individuals at five microsatellite loci and tested whether admixed individuals tended to be located in parts of multidimensional environmental space (E-space) shared between the two lineages. We observed an asymmetrical pattern of overlap, in which the West lineage's E-space was almost completely included inside East lineage's E-space. Genetic admixture levels were significantly higher in the West lineage and, for both lineages, in shared portions of E-space. This suggests that niche similarity can facilitate gene flow among disjunct groups with moderate-to-good dispersal capabilities, contrasting with the prevailing view of niche conservatism as a diversifying force.