Scaling between macro- to microscale climatic data reveals strong phylogenetic inertia in niche evolution in plethodontid salamanders

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

The adaptive dynamics of niche constructing traits in spatially subdivided populations: evolving posthumous extended phenotypes

Niche construction, by which organisms modify the environment in which they live, has been proposed to affect the evolution of many phenotypic traits. But what about the evolution of a niche constructing trait itself, whose expression changes the pattern of natural selection to which the trait is exposed in subsequent generations? This article provides an inclusive fitness analysis of selection on niche constructing phenotypes, which can affect their environment from local to global scales in arbitrarily spatially subdivided populations. The model shows that phenotypic effects of genes extending far beyond the life span of the actor can be affected by natural selection, provided they modify the fitness of those individuals living in the future that are likely to have inherited the niche construction lineage of the actor. Present benefits of behaviors are thus traded off against future indirect costs. The future costs will generally result from a complicated interplay of phenotypic effects, population demography and environmental dynamics. To illustrate these points, I derive the adaptive dynamics of a trait involved in the consumption of an abiotic resource, where resource abundance in future generations feeds back to the evolutionary dynamics of the trait.     

Biodiversity inhibits species' evolutionary responses to changing environments

Despite growing interplay between ecological and evolutionary studies, the question of how biodiversity influences evolutionary dynamics within species remains understudied. Here, using a classical model of phenotypic evolution in species occupying a patchy environment, but introducing global change affecting patch conditions, we show that biodiversity can inhibit species' evolution during global change. The presence of several species increases the chance that one or more species are pre-adapted to new conditions, which restricts the ecological opportunity for evolutionary responses in all the species. Consequently, environmental change tends to select for changes in species abundances rather than for changing phenotypes within each species. The buffering effects of species diversity that we describe might be one important but neglected explanation for widely observed niche conservatism in natural systems. Furthermore, the results show that attempts to understand biotic responses to environmental change need to consider both ecological and evolutionary processes in a realistically diverse setting.     

Niche models tell half the story: spatial context and life‐history traits influence species responses to global change

Aim While niche models are typically used to assess the vulnerability of species to climate change, they have been criticized for their limited assessment of threats other than climate change. We attempt to evaluate this limitation by combining niche models with life‐history models to investigate the relative influence of climate change and a range of fire regimes on the viability of a long‐lived plant population. Specifically, we investigate whether range shift due to climate change is a greater threat to an obligate seeding fire‐prone shrub than altered fire frequency and how these two threatening processes might interact. Location Australian sclerophyll woodland and heathland. Methods The study species is Leucopogon setiger, an obligate seeding fire‐prone shrub. A spatially explicit stochastic matrix model was constructed for this species and linked with a dynamic niche model and fire risk functions representing a suite of average fire return intervals. We compared scenarios with a variety of hypothetical patches, a patch framework based upon current habitat suitability and one with dynamic habitat suitability based on climate change scenarios A1FI and A2. Results Leucopogon setiger was found to be sensitive to fire frequency, with shorter intervals reducing expected minimum abundances (EMAs). Spatial decoupling of fires across the landscape reduced the vulnerability of the species to shortened fire frequencies. Shifting habitat, while reducing EMAs, was less of a threat to the species than frequent fire. Main conclusions Altered fire regime, in particular more frequent fires relative to the historical regime, was predicted to be a strong threat to this species, which may reflect a vulnerability of obligate seeders in general. Range shifts induced by climate change were a secondary threat when habitat reductions were predicted. Incorporating life‐history traits into habitat suitability models by linking species distribution models with population models allowed for the population‐level evaluation of multiple stressors that affect population dynamics and habitat, ultimately providing a greater understanding of the impacts of global change than would be gained by niche models alone. Further investigations of this type could elucidate how particular bioecological factors can affect certain types of species under global change.     

Measuring ecological niche overlap from occurrence and spatial environmental data

Aim Concerns over how global change will influence species distributions, in conjunction with increased emphasis on understanding niche dynamics in evolutionary and community contexts, highlight the growing need for robust methods to quantify niche differences between or within taxa. We propose a statistical framework to describe and compare environmental niches from occurrence and spatial environmental data. Location Europe, North America and South America. Methods The framework applies kernel smoothers to densities of species occurrence in gridded environmental space to calculate metrics of niche overlap and test hypotheses regarding niche conservatism. We use this framework and simulated species with pre‐defined distributions and amounts of niche overlap to evaluate several ordination and species distribution modelling techniques for quantifying niche overlap. We illustrate the approach with data on two well‐studied invasive species. Results We show that niche overlap can be accurately detected with the framework when variables driving the distributions are known. The method is robust to known and previously undocumented biases related to the dependence of species occurrences on the frequency of environmental conditions that occur across geographical space. The use of a kernel smoother makes the process of moving from geographical space to multivariate environmental space independent of both sampling effort and arbitrary choice of resolution in environmental space. However, the use of ordination and species distribution model techniques for selecting, combining and weighting variables on which niche overlap is calculated provide contrasting results. Main conclusions The framework meets the increasing need for robust methods to quantify niche differences. It is appropriate for studying niche differences between species, subspecies or intra‐specific lineages that differ in their geographical distributions. Alternatively, it can be used to measure the degree to which the environmental niche of a species or intra‐specific lineage has changed over time.     

Are species' responses to global change predicted by past niche evolution?

Predicting how and when adaptive evolution might rescue species from global change, and integrating this process into tools of biodiversity forecasting, has now become an urgent task. Here, we explored whether recent population trends of species can be explained by their past rate of niche evolution, which can be inferred from increasingly available phylogenetic and niche data. We examined the assemblage of 409 European bird species for which estimates of demographic trends between 1970 and 2000 are available, along with a species-level phylogeny and data on climatic, habitat and trophic niches. We found that species'' proneness to demographic decline is associated with slow evolution of the habitat niche in the past, in addition to certain current-day life-history and ecological traits. A similar result was found at a higher taxonomic level, where families prone to decline have had a history of slower evolution of climatic and habitat niches. Our results support the view that niche conservatism can prevent some species from coping with environmental change. Thus, linking patterns of past niche evolution and contemporary species dynamics for large species samples may provide insights into how niche evolution may rescue certain lineages in the face of global change.     

Evaluating niche changes during invasion with seasonal models in Capsella bursa-pastoris

Premise

Researchers often use ecological niche models to predict where species might establish and persist under future or novel climate conditions. However, these predictive methods assume species have stable niches across time and space. Furthermore, ignoring the time of occurrence data can obscure important information about species reproduction and ultimately fitness. Here, we assess compare ecological niche models generated from full-year averages to seasonal models.

Methods

In this study, we generate full-year and monthly ecological niche models for Capsella bursa-pastoris in Europe and North America to see if we can detect changes in the seasonal niche of the species after long-distance dispersal.

Results

We find full-year ecological niche models have low transferability across continents and there are continental differences in the climate conditions that influence the distribution of C. bursa-pastoris. Monthly models have greater predictive accuracy than full-year models in cooler seasons, but no monthly models can predict North American summer occurrences very well.

Conclusions

The relative predictive ability of European monthly models compared to North American monthly models suggests a change in the seasonal timing between the native range to the non-native range. These results highlight the utility of ecological niche models at finer temporal scales in predicting species distributions and unmasking subtle patterns of evolution.     

物种分布模型理论研究进展

利用物种分布模型估计物种的真实和潜在分布区,已成为区域生态学与生物地理学中非常活跃的研究领域。然而,到目前为止,这项技术的理论基础仍然存在不足之处,一些关键的生态过程未能被有效纳入到物种分布模型的理论框架中,从而为解释物种分布模型预测的结果带来了诸多困惑。鉴于此,总结了物种分布模型的理论基础;系统探讨了物种分布模型与物种分布区的关系;特别指出了物种分布模型研究中存在的理论问题;重点阐述了物种分布模型未来的发展方向。研究认为,物种分布模型与生态位理论、源-库理论、种群动态理论、集合种群理论、进化理论等具有重要的联系;正确理解物种分布模型的预测结果与物种分布区的关系,有赖于对影响物种分布的3个主要因素(环境条件、物种相互作用与物种迁移能力)做出定量的分离;目前物种分布模型主要存在的问题是未能将物种的相互作用和物种的迁移能力有效纳入到模型的构建过程中;未来物种分布模型的发展应该加强模型背后理论框架的研究,并进一步加强整合物种相互作用过程、种群动态过程、迁移过程和物种进化过程等内容。研究还认为,从更高的理论层次模拟功能群和群落结构将是未来物种分布模型的重要发展方向。     

Environmental niche conservatism explains the accumulation of species richness in Mediterranean‐hotspot plant genera

The causes of exceptionally high plant diversity in Mediterranean‐climate biodiversity hotspots are not fully understood. We asked whether a mechanism similar to the tropical niche conservatism hypothesis could explain the diversity of four large genera (Protea, Moraea, Banksia, and Hakea) with distributions within and adjacent to the Greater Cape Floristic Region (South Africa) or the Southwest Floristic Region (Australia). Using phylogenetic and spatial data we estimated the environmental niche of each species, and reconstructed the mode and dynamics of niche evolution, and the geographic history, of each genus. For three genera, there were strong positive relationships between the diversity of clades within a region and their inferred length of occupation of that region. Within genera, there was evidence for strong evolutionary constraint on niche axes associated with climatic seasonality and aridity, with different niche optima for hotspot and nonhotspot clades. Evolutionary transitions away from hotspots were associated with increases in niche breadth and elevated rates of niche evolution. Our results point to a process of “hotspot niche conservatism” whereby the accumulation of plant diversity in Mediterranean‐type ecosystems results from longer time for speciation, with dispersal away from hotspots limited by narrow and phylogenetically conserved environmental niches.     

A trait-based approach predicting community assembly and dominance of microbial invasive species

Understanding the mechanisms underlying community assembly helps to define success and susceptibility to biological invasions. Here, we explored phytoplankton community assembly following niche and neutral paradigms and using a trait-based approach. Under the hypothesis that the morphology-based functional groups (MBFG) clusters species with similar niche, we analysed how trait-related differences in fitness influence dominance of an invasive species. This was based on literature review, field data and model simulations. We predict that invading species can be dominant if: 1) do not belong to the local MBFG but use unexploited areas of the niche, or 2) belong to the resident MBFG but exhibit a higher fitness due to a particular combination of traits. The invasive dinoflagellate Ceratium furcoides was used as the model species to evaluate these hypotheses, its morphological (e.g. volume) and physiological (e.g. growth rates) traits were compared with species from the same (V: photosynthetic flagellates) and different (VII: colonial cyanobacteria) MBFG. Fitness was estimated using models parametrized with MBFG rates (R*, ability to draw down phosphate) under different environmental conditions (i.e. flushing). Results contributed to support both hypotheses. First, the alternation of C. furcoides and cyanobacteria dominance was explained by the use of different niches. Secondly, species from MBFG V were dominant under similar environments. Within this group V C. furcoides showed higher fitness under low flushing and high predation, advantage provided by a distinctive combination of traits. The application of trait-based approaches to represent the niche and estimate fitness along environmental gradients was useful to evaluate community assembly and can be used to predict the dominance of microbial species invasions.     

Evolution of thermal performance curves: A meta-analysis of selection experiments

Temperatures are increasing due to global changes, putting biodiversity at risk. Organisms are faced with a limited set of options to cope with this situation: adapt, disperse or die. We here focus on the first possibility, more specifically, on evolutionary adaptations to temperature. Ectotherms are usually characterized by a hump-shaped relationship between fitness and temperature, a non-linear reaction norm that is referred to as thermal performance curve (TPC). To understand and predict impacts of global change, we need to know whether and how such TPCs evolve. Therefore, we performed a systematic literature search and a statistical meta-analysis focusing on experimental evolution and artificial selection studies. This focus allows us to directly quantify relative fitness responses to temperature selection by calculating fitness differences between TPCs from ancestral and derived populations after thermal selection. Out of 7561 publications screened, we found 47 studies corresponding to our search criteria representing taxa across the tree of life, from bacteria, to plants and vertebrates. We show that, independently of species identity, the studies we found report a positive response to temperature selection. Considering entire TPC shapes, adaptation to higher temperatures traded off with fitness at lower temperatures, leading to niche shifts. Effects were generally stronger in unicellular organisms. By contrast, we do not find statistical support for the often discussed “Hotter is better” hypothesis. While our meta-analysis provides evidence for adaptive potential of TPCs across organisms, it also highlights that more experimental work is needed, especially for under-represented taxa, such as plants and non-model systems.     

Global realized niche divergence in the African clawed frog Xenopus laevis

Although of crucial importance for invasion biology and impact assessments of climate change, it remains widely unknown how species cope with and adapt to environmental conditions beyond their currently realized climatic niches (i.e., those climatic conditions existing populations are exposed to). The African clawed frog Xenopus laevis, native to southern Africa, has established numerous invasive populations on multiple continents making it a pertinent model organism to study environmental niche dynamics. In this study, we assess whether the realized niches of the invasive populations in Europe, South, and North America represent subsets of the species’ realized niche in its native distributional range or if niche shifts are traceable. If shifts are traceable, we ask whether the realized niches of invasive populations still contain signatures of the niche of source populations what could indicate local adaptations. Univariate comparisons among bioclimatic conditions at native and invaded ranges revealed the invasive populations to be nested within the variable range of the native population. However, at the same time, invasive populations are well differentiated in multidimensional niche space as quantified via n‐dimensional hypervolumes. The most deviant invasive population are those from Europe. Our results suggest varying degrees of realized niche shifts, which are mainly driven by temperature related variables. The crosswise projection of the hypervolumes that were trained in invaded ranges revealed the south‐western Cape region as likely area of origin for all invasive populations, which is largely congruent with DNA sequence data and suggests a gradual exploration of novel climate space in invasive populations.     

Biodiversity change under adaptive community dynamics

Compositional change is a ubiquitous response of ecological communities to environmental drivers of global change, but is often regarded as evidence of declining “biotic integrity” relative to historical baselines. Adaptive compositional change, however, is a foundational idea in evolutionary biology, whereby changes in gene frequencies within species boost population-level fitness, allowing populations to persist as the environment changes. Here, we present an analogous idea for ecological communities based on core concepts of fitness and selection. Changes in community composition (i.e., frequencies of genetic differences among species) in response to environmental change should normally increase the average fitnessof community members. We refer to compositional changes that improve the functional match, or “fit,” between organisms' traits and their environment as adaptive community dynamics. Environmental change (e.g., land-use change) commonly reduces the fit between antecedent communities and new environments. Subsequent change in community composition in response to environmental changes, however, should normally increase community-level fit, as the success of at least some constituent species increases. We argue that adaptive community dynamics are likely to improve or maintain ecosystem function (e.g., by maintaining productivity). Adaptive community responses may simultaneously produce some changes that are considered societally desirable (e.g., increased carbon storage) and others that are undesirable (e.g., declines of certain species), just as evolutionary responses within species may be deemed desirable (e.g., evolutionary rescue of an endangered species) or undesirable (e.g., enhanced virulence of an agricultural pest). When assessing possible management interventions, it is important to distinguish between drivers of environmental change (e.g., undesired climate warming) and adaptive community responses, which may generate some desirable outcomes. Efforts to facilitate, accept, or resist ecological change require separate consideration of drivers and responses, and may highlight the need to reconsider preferences for historical baseline communities over communities that are better adapted to the new conditions.     

No species is an island: testing the effects of biotic interactions on models of avian niche occupation

Traditionally, the niche of a species is described as a hypothetical 3D space, constituted by well‐known biotic interactions (e.g. predation, competition, trophic relationships, resource–consumer interactions, etc.) and various abiotic environmental factors. Species distribution models (SDMs), also called “niche models” and often used to predict wildlife distribution at landscape scale, are typically constructed using abiotic factors with biotic interactions generally been ignored. Here, we compared the goodness of fit of SDMs for red‐backed shrike Lanius collurio in farmlands of Western Poland, using both the classical approach (modeled only on environmental variables) and the approach which included also other potentially associated bird species. The potential associations among species were derived from the relevant ecological literature and by a correlation matrix of occurrences. Our findings highlight the importance of including heterospecific interactions in improving our understanding of niche occupation for bird species. We suggest that suite of measures currently used to quantify realized species niches could be improved by also considering the occurrence of certain associated species. Then, an hypothetical “species 1” can use the occurrence of a successfully established individual of “species 2” as indicator or “trace” of the location of available suitable habitat to breed. We hypothesize this kind of biotic interaction as the “heterospecific trace effect” (HTE): an interaction based on the availability and use of “public information” provided by individuals from different species. Finally, we discuss about the incomes of biotic interactions for enhancing the predictive capacities on species distribution models.     

Climatic‐niche evolution with key morphological innovations across clades within Scutiger boulengeri (Anura: Megophryidae)

The studies of climatic‐niche shifts over evolutionary time accompanied by key morphological innovations have attracted the interest of many researchers recently. We applied ecological niche models (ENMs), ordination method (environment principal component analyses; PCA‐env), combined phylogenetic comparative methods (PCMs), and phylogenetic generalized least squares (PGLS) regression methods to analyze the realized niche dynamics and correspondingly key morphological innovations across clades within Scutiger boulengeri throughout their distributions in Qinghai–Tibet Plateau (QTP) margins of China. Our results show there are six clades in S. boulengeri and obvious niche divergences caused by niche expansion in three clades. Moreover, in our system, niche expansion is more popular than niche unfilling into novel environmental conditions. Annual mean temperature, annual precipitation, and precipitation of driest month may contribute to such a shift. In addition, we identified several key climatic factors and morphological traits that tend to be associated with niche expansion in S. boulengeri clades correspondingly. We found phenotypic plasticity [i.e., length of lower arm and hand (LAHL), hind‐limb length (HLL), and foot length (FL)] and evolutionary changes [i.e., snout–vent length (SVL)] may together contribute to niche expansion toward adapting novel niche, which provides us a potential pattern of how a colonizing toad might seed a novel habitat to begin the process of speciation and finally adaptive radiation. For these reasons, persistent phylogeographic divisions and accompanying divergences in niche occupancy and morphological adaption suggest that for future studies, distinct genetic structure and morphological changes corresponding to each genetic clade should be included in modeling niche evolution dynamics, but not just constructed at the species level.     

Vanishing islands in the sky? A comparison of correlation- and mechanism-based forecasts of range dynamics for montane salamanders under climate change

Forecasting the effects of climate change on species and populations is a fundamental goal of conservation biology, especially for montane endemics which seemingly are under the greatest threat of extinction given their association with cool, high elevation habitats. Species distribution models (also known as niche models) predict where on the landscape there is suitable habitat for a species of interest. Correlative niche modeling, the most commonly employed approach to predict species' distributions, relies on correlations between species' localities and current environmental data. This type of model could spuriously forecast less future suitable habitat because species' current distributions may not adequately represent their thermal tolerance, and future climate conditions may not be analogous to current conditions. We compared the predicted distributions for three montane species of Plethodon salamanders in the southern Appalachian Mountains of North America using a correlative modeling approach and a mechanistic model. The mechanistic model incorporates species-specific physiology, morphology and behavior to predict an annual energy budget on the landscape. Both modeling approaches performed well at predicting the species' current distributions and predicted that all species could persist in habitats at higher elevation through 2085. The mechanistic model predicted more future suitable habitat than the correlative model. We attribute these differences to the mechanistic approach being able to model shifts in key range-limiting biological processes (changes in surface activity time and energy costs) that the correlative approach cannot. Choice of global circulation model (GCM) contributed significantly to distribution predictions, with a tenfold difference in future suitability based on GCM, indicating that GCM variability should be either directly included in models of species distributions or, indirectly, through the use of multi-model ensemble averages. Our results indicate that correlative models are over-predicting habitat loss for montane species, suggesting a critical need to incorporate mechanisms into forecasts of species' range dynamics.     

The role of phenotypic plasticity in shaping ecological networks

Plasticity-mediated changes in interaction dynamics and structure may scale up and affect the ecological network in which the plastic species are embedded. Despite their potential relevance for understanding the effects of plasticity on ecological communities, these effects have seldom been analysed. We argue here that, by boosting the magnitude of intra-individual phenotypic variation, plasticity may have three possible direct effects on the interactions that the plastic species maintains with other species in the community: may expand the interaction niche, may cause a shift from one interaction niche to another or may even cause the colonization of a new niche. The combined action of these three factors can scale to the community level and eventually expresses itself as a modification in the topology and functionality of the entire ecological network. We propose that this causal pathway can be more widespread than previously thought and may explain how interaction niches evolve quickly in response to rapid changes in environmental conditions. The implication of this idea is not solely eco-evolutionary but may also help to understand how ecological interactions rewire and evolve in response to global change.     

Population demography influences climatic niche evolution: evidence from diploid American Hordeum species (Poaceae)

In this study, we explore the interplay of population demography with the evolution of ecological niches during or after speciation in Hordeum. While large populations maintain a high level of standing genetic diversity, gene flow and recombination buffers against fast alterations in ecological adaptation. Small populations harbour lower allele diversity but can more easily shift to new niches if they initially survive under changed conditions. Thus, large populations should be more conservative regarding niche changes in comparison to small populations. We used environmental niche modelling together with phylogenetic, phylogeographic and population genetic analyses to infer the correlation of population demography with changes in ecological niche dimensions in 12 diploid Hordeum species from the New World, forming four monophyletic groups. Our analyses found both shifts and conservatism in distinct niche dimensions within and among clades. Speciation due to vicariance resulted in three species with no pronounced climate niche differences, while species originating due to long‐distance dispersals or otherwise encountering genetic bottlenecks mostly revealed climate niche shifts. Niche convergence among clades indicates a niche‐filling pattern during the last 2 million years in South American Hordeum. We provide evidence that species, which did not encounter population reductions mainly showed ecoclimatic niche conservatism, while major niche shifts occurred in species which have undergone population bottlenecks. Our data allow the conclusion that population demography influences adaptation and niche shifts or conservatism in South American Hordeum species.     

Operationalizing niche construction theory with stone tools

One of the greatest difficulties with evolutionary approaches in the study of stone tools (lithics) has been finding a mechanism for tying culture and biology in a way that preserves human agency and operates at scales that are visible in the archaeological record. The concept of niche construction, whereby organisms actively construct their environments and change the conditions for selection, could provide a solution to this problem. In this review, we evaluate the utility of niche construction theory (NCT) for stone tool archaeology. We apply NCT to lithics both as part of the “extended phenotype” and as residuals or precipitates of other niche‐constructing activities, suggesting ways in which archaeologists can employ niche construction feedbacks to generate testable hypotheses about stone tool use. Finally, we conclude that, as far as its applicability to lithic archaeology, NCT compares favorably to other prominent evolutionary approaches, such as human behavioral ecology and dual‐inheritance theory.