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

Bringing traits back into the equation: A roadmap to understand species redistribution

Ecological and evolutionary theories have proposed that species traits should be important in mediating species responses to contemporary climate change; yet, empirical evidence has so far provided mixed evidence for the role of behavioral, life history, or ecological characteristics in facilitating or hindering species range shifts. As such, the utility of trait-based approaches to predict species redistribution under climate change has been called into question. We develop the perspective, supported by evidence, that trait variation, if used carefully can have high potential utility, but that past analyses have in many cases failed to identify an explanatory value for traits by not fully embracing the complexity of species range shifts. First, we discuss the relevant theory linking species traits to range shift processes at the leading (expansion) and trailing (contraction) edges of species distributions and highlight the need to clarify the mechanistic basis of trait-based approaches. Second, we provide a brief overview of range shift-trait studies and identify new opportunities for trait integration that consider range-specific processes and intraspecific variability. Third, we explore the circumstances under which environmental and biotic context dependencies are likely to affect our ability to identify the contribution of species traits to range shift processes. Finally, we propose that revealing the role of traits in shaping species redistribution may likely require accounting for methodological variation arising from the range shift estimation process as well as addressing existing functional, geographical, and phylogenetic biases. We provide a series of considerations for more effectively integrating traits as well as extrinsic and methodological factors into species redistribution research. Together, these analytical approaches promise stronger mechanistic and predictive understanding that can help society mitigate and adapt to the effects of climate change on biodiversity.

Incorporating eco-evolutionary information into species distribution models provides comprehensive predictions of species range shifts under climate change

As climate changes increasingly influence species distributions, ecosystem functions, and biodiversity, the urgency to understand how species' ranges shift under those changes is great. Species distribution models (SDMs) are vital approaches that can predict species distributions under changing climates. However, SDMs based on the species' current occurrences may underestimate the species' climatic tolerances. Integrating species' realized niches at different periods, also known as multi-temporal calibration, can provide an estimation closer to its fundamental niche. Based on this, we further proposed an integrated framework that combines eco-evolutionary data and SDMs (phylogenetically-informed SDMs) to provide comprehensive predictions of species range shifts under climate change. To evaluate our approach's performance, we applied it to a group of related species, the Chrysanthemum zawadskii species complex (Anthemidae, Asteracee). First, we investigated the niche differentiation between species and intraspecific lineages of the complex and estimated their rates of niche evolution. Next, using both standard SDMs and our phylogenetically-informed SDMs, we generated predictions of suitability areas for all species and lineages and compared the results. Finally, we reconstructed the historical range dynamics for the species of this complex. Our results showed that the species and intraspecific lineages of the complex had varying degrees of niche differentiation and different rates of niche evolution. Lineage-level SDMs can provide more realistic predictions for species with intraspecific differentiation than species-level models can. The phylogenetically-informed SDMs provided more complete environmental envelopes and predicted broader potential distributions for all species than the standard SDMs did. Range dynamics varied among the species that have different rates of niche evolution. Our framework integrating eco-evolutionary data and SDMs contributes to a better understanding of the species' responses to climate change and can help to make more targeted conservation efforts for the target species under climate change, particularly for rare species.

Exploring the Climatic Niche Evolution of the Genus Falco (Aves: Falconidae) in Europe

By integrating species distribution modeling techniques, phylogenetic comparative methods, and climatic data, we analyzed how European falcon climatic niches have changed over evolutionary time in order to understand their tempo and mode of evolution and gain phylogenetic insights related to the ecological context of falcon evolution. For this purpose, we tested the relative contributions of niche conservatism, convergent evolution, and divergent evolution in the evolutionary history of this group of species in Europe. The occupation of climatic niche spaces by falcon species in Europe was not similar, considering that their climatic niche evolution was characterized by heterotachy, especially after ca. 4 Mya. Our results indicate that convergent evolution and niche divergence played an important role in the evolutionary history of these species, with no significant evidence of closely related species retaining their fundamental niche over time (phylogenetic niche conservatism). In most analyses, less closely related falcon species occupied similar climatic environments. We found that speciation in the European genus Falco was influenced by climatic niche differentiation, more prevalent in the last 4 million years, with the main climatic niche shifts occurring between closely related falcon species.

Ecological generalism and physiology mediate fish biogeographic ranges under ocean warming

Climate-driven species redistributions are facilitated by niche modifications that increase a species's chances of establishment in novel communities. It is well understood how range-extending species adjust individual niche traits when entering novel environments, yet whether modification of ecological niche traits collectively alters the pace of range extensions or contractions remains unknown. We quantified habitat niche, abundance, physiological performance and cellular defence/damage of range-extending coral reef fishes and coexisting local temperate fishes along a 2000 km latitudinal gradient. We also assessed their dietary and behavioural niches, and establishment potential, to understand whether ecological generalism facilitates successful range extension of coral reef fishes. The coral reef fish that increased all ecological niches, showed stronger establishment, increased physiological performance and cellular damage, but decreased cellular defence at their cold-range edge, whereas tropical species that showed unmodified ecological niches showed lower establishment. One temperate species showed decreased abundance, habitat niche width and body condition, but increased cellular defence, cellular damage and energy reserves at their warm-trailing range, while other temperate species showed contrasting responses. Therefore, ecological generalists might be more successful than ecological specialists during the initial stages of climate change, with increasing future warming strengthening this pattern by physiologically benefitting tropical generalists but disadvantaging temperate specialists.

The importance of considering the duration of extreme temperatures when investigating responses to climate change

The frequency and duration of heatwaves are increasing because of human activities. To cope with the changes, species with longer generation times may have to rely on plastic responses. The probability that their responses are adaptive is higher if the species have experienced temperature fluctuations also in their evolutionary past. However, experimental studies investigating responses to heatwaves often use exposure times that are significantly shorter than recent heatwaves. We show that this can lead to faulty conclusions and that the duration of higher temperature has to be considered in experimental designs. We recorded the response of threespine stickleback to prolonged duration of higher temperature during the breeding season, using a population that has experienced large fluctuations in temperature in its past and, hence, is expected to endure temperature changes well. We found males to adaptively adjust their reproductive behaviours to short periods of higher temperature, but not to longer periods that extended across two breeding cycles. Males initially increased their reproductive activities-nest building, courtship and parental care-which ensured high reproductive success during the first breeding cycle, but decreased their reproductive activities during the second breeding cycle when exposed to sustained high temperature. This reduced their courtship success and resulted in fewer offspring. Thus, a species expected to cope well with higher temperature suffers fitness reductions when the duration of high temperature is prolonged. The results stress the importance of considering the duration of extreme environmental conditions when investigating the impact that human activities have on species. Responses to short-term exposures cannot be extrapolated to assess responses to longer periods of extreme conditions.

Bird lineages colonizing urban habitats have diversified at high rates across deep time

AIM

Urbanization exposes species to novel ecological conditions. Some species thrive in urban areas, whereas many others are excluded from these human-made environments. Previous analyses suggest that the ability to cope with rapid environmental change is associated with long-term patterns of diversification, but whether the suite of traits associated with the ability to colonize urban environments is linked to this process remains poorly understood.

LOCATION

World.

TIME PERIOD

Current.

MAJOR TAXA STUDIED

Passerine birds.

METHODS

We applied macroevolutionary models to a large dataset of passerine birds to compare the evolutionary history of urban-tolerant species with that of urban-avoidant species. Specifically, we examined models of state-dependent speciation and extinction to assess the macroevolution of urban tolerance as a binary trait, in addition to models of quantitative trait-dependent diversification based on relative urban abundance. We also ran simulation-based model assessments to explore potential sources of bias.

RESULTS

We provide evidence that historically, species with traits promoting urban colonization have undergone faster diversification than urban-avoidant species, indicating that urbanization favours clades with a historical tendency towards rapid speciation or reduced extinction. In addition, we find that past transitions towards states that currently impede urban colonization by passerines have been more frequent than in the opposite direction. Furthermore, we find a portion of urban-avoidant passerines to be recent and to undergo fast diversification. All highly supported models give this result consistently.

MAIN CONCLUSIONS

Urbanization is mainly associated with the loss of lineages that are inherently more vulnerable to extinction over deep time, whereas cities tend to be colonized by less vulnerable lineages, for which urbanization might be neutral or positive in terms of longer-term diversification. Urban avoidance is associated with high rates of recent diversification for some clades occurring in regions with relatively intact natural ecosystems and low current levels of urbanization.

Anopheles albimanus (Diptera: Culicidae) Ensemble Distribution Modeling: Applications for Malaria Elimination

In the absence of entomological information, tools for predicting Anopheles spp. presence can help evaluate the entomological risk of malaria transmission. Here, we illustrate how species distribution models (SDM) could quantify potential dominant vector species presence in malaria elimination settings. We fitted a 250 m resolution ensemble SDM for Anopheles albimanus Wiedemann. The ensemble SDM included predictions based on seven different algorithms, 110 occurrence records and 70 model projections. SDM covariates included nine environmental variables that were selected based on their importance from an original set of 28 layers that included remotely and spatially interpolated locally measured variables for the land surface of Costa Rica. Goodness of fit for the ensemble SDM was very high, with a minimum AUC of 0.79. We used the resulting ensemble SDM to evaluate differences in habitat suitability (HS) between commercial plantations and surrounding landscapes, finding a higher HS in pineapple and oil palm plantations, suggestive of An. albimanus presence, than in surrounding landscapes. The ensemble SDM suggested a low HS for An. albimanus at the presumed epicenter of malaria transmission during 2018-2019 in Costa Rica, yet this vector was likely present at the two main towns also affected by the epidemic. Our results illustrate how ensemble SDMs in malaria elimination settings can provide information that could help to improve vector surveillance and control.

Fossil-Informed Models Reveal a Boreotropical Origin and Divergent Evolutionary Trajectories in the Walnut Family (Juglandaceae)

Temperate woody plants in the Northern Hemisphere have long been known to exhibit high species richness in East Asia and North America and significantly lower diversity in Europe, but the causes of this pattern remain debated. Here, we quantify the roles of dispersal, niche evolution, and extinction in shaping the geographic diversity of the temperate woody plant family Juglandaceae (walnuts and their relatives). Integrating evidence from molecular, morphological, fossil, and (paleo)environmental data, we find strong support for a Boreotropical origin of the family with contrasting evolutionary trajectories between the temperate subfamily Juglandoideae and the tropical subfamily Engelhardioideae. Juglandoideae rapidly evolved frost tolerance when the global climate shifted to ice-house conditions from the Oligocene, with diversification at high latitudes especially in Europe and Asia during the Miocene. Subsequent range contraction at high latitudes and high levels of extinction in Europe driven by global cooling led to the current regional disparity in species diversity. Engelhardioideae showed temperature conservatism while adapting to increased humidity, tracking tropical climates to low latitudes since the middle Eocene with comparatively little diversification, perhaps due to high competition in the tropical zone. The biogeographic history of Juglandaceae shows that the North Atlantic land bridge and Europe played more critical roles than previously thought in linking the floras of East Asia and North America, and showcases the complex interplay among climate change, niche evolution, dispersal, and extinction that shaped the modern disjunct pattern of species richness in temperate woody plants. [Boreotropical origin; climatic niche evolution; disjunct distribution; dispersal; diversity anomaly; extinction; Juglandaceae.].

Climate-induced range shifts shaped the present and threaten the future genetic variability of a marine brown alga in the Northwest Pacific

Glaciation-induced environmental changes during the last glacial maximum (LGM) have strongly influenced species' distributions and genetic diversity patterns in the northern high latitudes. However, these effects have seldom been assessed on sessile species in the Northwest Pacific. Herein, we chose the brown alga Sargassum thunbergii to test this hypothesis, by comparing present population genetic variability with inferred geographical range shifts from the LGM to the present, estimated with species distribution modelling (SDM). Projections for contrasting scenarios of future climate change were also developed to anticipate genetic diversity losses at regional scales. Results showed that S. thunbergii harbours strikingly rich genetic diversity and multiple divergent lineages in the centre-northern range of its distribution, in contrast with a poorer genetically distinct lineage in the southern range. SDM hindcasted refugial persistence in the southern range during the LGM as well as post-LGM expansion of 18 degrees of latitude northward. Approximate Bayesian computation (ABC) analysis further suggested that the multiple divergent lineages in the centre-northern range limit stem from post-LGM colonization from the southern survived lineage. This suggests divergence due to demographic bottlenecks during range expansion and massive genetic diversity loss during post-LGM contraction in the south. The projected future range of S. thunbergii highlights the threat to unique gene pools that might be lost under global changes.

The legacy of Eastern Mediterranean mountain uplifts: rapid disparity of phylogenetic niche conservatism and divergence in mountain vipers

BACKGROUND

The orogeny of the eastern Mediterranean region has substantially affected ecological speciation patterns, particularly of mountain-dwelling species. Mountain vipers of the genus Montivipera are among the paramount examples of Mediterranean neo-endemism, with restricted ranges in the mountains of Anatolia, the Levant, Caucasus, Alborz, and Zagros. Here we explore the phylogenetic and ecological diversification of Montivipera to reconstruct its ecological niche evolution and biogeographic history. Using 177 sequences of three mitochondrial genes, a dated molecular phylogeny of mountain vipers was reconstructed. Based on 320 occurrence points within the entire range of the genus and six climatic variables, ecological niches were modelled and used to infer ancestral niche occupancy. In addition, the biogeographic history and ancestral states of the species were reconstructed across climate gradients.

RESULTS

Dated phylogenetic reconstruction revealed that the ancestor of mountain vipers split into two major clades at around 12.18 Mya followed by multiple vicariance events due to rapid orogeny. Montivipera colonised coastal regions from a mountain-dwelling ancestor. We detected a highly complex ecological niche evolution of mountain vipers to temperature seasonality, a variable that also showed a strong phylogenetic signal and high contribution in niche occupation.

CONCLUSION

Raising mountain belts in the Eastern Mediterranean region and subsequent remarkable changes in temperature seasonality have led to the formation of important centres of diversification and endemism in this biodiversity hotspot. High rates of niche conservatism, low genetic diversity, and segregation of ranges into the endemic distribution negatively influenced the adaptive capacity of mountain vipers. We suggest that these species should be considered as evolutionary significant units and priority species for conservation in Mediterranean mountain ecosystems.

Thermal niches of planktonic foraminifera are static throughout glacial-interglacial climate change

Abiotic niche lability reduces extinction risk by allowing species to adapt to changing environmental conditions in situ. In contrast, species with static niches must keep pace with the velocity of climate change as they track suitable habitat. The rate and frequency of niche lability have been studied on human timescales (months to decades) and geological timescales (millions of years), but lability on intermediate timescales (millennia) remains largely uninvestigated. Here, we quantified abiotic niche lability at 8-ka resolution across the last 700 ka of glacial-interglacial climate fluctuations, using the exceptionally well-known fossil record of planktonic foraminifera coupled with Atmosphere-Ocean Global Climate Model reconstructions of paleoclimate. We tracked foraminiferal niches through time along the univariate axis of mean annual temperature, measured both at the sea surface and at species' depth habitats. Species' temperature preferences were uncoupled from the global temperature regime, undermining a hypothesis of local adaptation to changing environmental conditions. Furthermore, intraspecific niches were equally similar through time, regardless of climate change magnitude on short timescales (8 ka) and across contrasts of glacial and interglacial extremes. Evolutionary trait models fitted to time series of occupied temperature values supported widespread niche stasis above randomly wandering or directional change. Ecotype explained little variation in species-level differences in niche lability after accounting for evolutionary relatedness. Together, these results suggest that warming and ocean acidification over the next hundreds to thousands of years could redistribute and reduce populations of foraminifera and other calcifying plankton, which are primary components of marine food webs and biogeochemical cycles.

Asymmetric Evolvability Leads to Specialization without Trade-Offs

AbstractMany organisms are specialized, and these narrow niches are often explained with trade-offs-the inability for one organism to express maximal performance in two or more environments. However, evidence is lacking that trade-offs are sufficient to explain specialists. Several lines of theoretical inquiry suggest that populations can specialize without explicit trade-offs, as a result of relaxed selection in generalists for their performance in rare environments. Here, I synthesize and extend these approaches, showing that emergent asymmetries in evolvability can push a population toward specialization in the absence of trade-offs and in the presence of substantial ecological costs of specialism. Simulations are used to demonstrate how adaptation to a more common environment interferes with adaptation to a less common but otherwise equal alternative environment and that this interference is greatly exacerbated at low recombination rates. This adaptive process of specialization can effectively trap populations in a suboptimal niche. These modeling results predict that transient differences in evolvability across traits during a single episode of adaptation could have long-term consequences for a population's niche.

Vulnerability to Fishing and Life History Traits Correlate with the Load of Deleterious Mutations in Teleosts

Understanding why some species accumulate more deleterious substitutions than others is an important question relevant in evolutionary biology and conservation sciences. Previous studies conducted in terrestrial taxa suggest that life history traits correlate with the efficiency of purifying selection and accumulation of deleterious mutations. Using a large genome data set of 76 species of teleostean fishes, we show that species with life history traits associated with vulnerability to fishing have an increased rate of deleterious mutation accumulation (measured via dN/dS, i.e., nonsynonymous over synonymous substitution rate). Our results, focusing on a large clade of aquatic species, generalize previous patterns found so far in few clades of terrestrial vertebrates. These results also show that vulnerable species to fishing inherently accumulate more deleterious substitutions than nonthreatened ones, which illustrates the potential links among population genetics, ecology, and fishing policies to prevent species extinction.

Elevation alters outcome of competition between resident and range-shifting species

Species' geographic range shifts toward higher latitudes and elevations are among the most frequently reported consequences of climate change. However, the role of species interactions in setting range margins remains poorly understood. We used cage experiments in ponds to test competing hypotheses about the role of abiotic and biotic mechanisms for structuring range boundaries of an upslope range-shifting caddisfly Limnephilus picturatus. We found that competition with a ubiquitous species Limnephilus externus significantly decreased L. picturatus survival and emergence at subalpine elevations supporting the notion that species interactions play a critical role in determining upslope range limits. However, without competitors, L. picturatus survival was greater at high-elevation than low-elevation sites. This was contrary to decreases in body mass (a proxy for fecundity) with elevation regardless of the presence of competitors. We ultimately show that species interactions can be important for setting upslope range margins. Yet, our results also highlight the complications in defining what may be abiotically stressful for this species and the importance of considering multiple demographic variables. Understanding how species ranges will respond in a changing climate will require quantifying species interactions and how they are influenced by the abiotic context in which they play out.

Ecological Factors Generally Not Altitude Related Played Main Roles in Driving Potential Adaptive Evolution at Elevational Range Margin Populations of Taiwan Incense Cedar (Calocedrus formosana)

Population diversification can be shaped by a combination of environmental factors as well as geographic isolation interacting with gene flow. We surveyed genetic variation of 243 samples from 12 populations of Calocedrus formosana using amplified fragment length polymorphism (AFLP) and scored a total of 437 AFLP fragments using 11 selective amplification primer pairs. The AFLP variation was used to assess the role of gene flow on the pattern of genetic diversity and to test environments in driving population adaptive evolution. This study found the relatively lower level of genetic diversity and the higher level of population differentiation in C. formosana compared with those estimated in previous studies of conifers including Cunninghamia konishii, Keteleeria davidiana var. formosana, and Taiwania cryptomerioides occurring in Taiwan. BAYESCAN detected 26 F_ST outlier loci that were found to be associated strongly with various environmental variables using multiple univariate logistic regression, latent factor mixed model, and Bayesian logistic regression. We found several environmentally dependent adaptive loci with high frequencies in low- or high-elevation populations, suggesting their involvement in local adaptation. Ecological factors, including relative humidity and sunshine hours, that are generally not altitude related could have been the most important selective drivers for population divergent evolution in C. formosana. The present study provides fundamental information in relation to adaptive evolution and can be useful for assisted migration program of C. formosana in the future conservation of this species.

A complete time-calibrated multi-gene phylogeny of the European butterflies

With the aim of supporting ecological analyses in butterflies, the third most species-rich superfamily of Lepidoptera, this paper presents the first time-calibrated phylogeny of all 496 extant butterfly species in Europe, including 18 very localised endemics for which no public DNA sequences had been available previously. It is based on a concatenated alignment of the mitochondrial gene COI and up to eleven nuclear gene fragments, using Bayesian inferences of phylogeny. To avoid analytical biases that could result from our region-focussed sampling, our European tree was grafted upon a global genus-level backbone butterfly phylogeny for analyses. In addition to a consensus tree, the posterior distribution of trees and the fully concatenated alignment are provided for future analyses. Altogether a complete phylogenetic framework of European butterflies for use by the ecological and evolutionary communities is presented.

Evolutionary diversity in tropical tree communities peaks at intermediate precipitation

Global patterns of species and evolutionary diversity in plants are primarily determined by a temperature gradient, but precipitation gradients may be more important within the tropics, where plant species richness is positively associated with the amount of rainfall. The impact of precipitation on the distribution of evolutionary diversity, however, is largely unexplored. Here we detail how evolutionary diversity varies along precipitation gradients by bringing together a comprehensive database on the composition of angiosperm tree communities across lowland tropical South America (2,025 inventories from wet to arid biomes), and a new, large-scale phylogenetic hypothesis for the genera that occur in these ecosystems. We find a marked reduction in the evolutionary diversity of communities at low precipitation. However, unlike species richness, evolutionary diversity does not continually increase with rainfall. Rather, our results show that the greatest evolutionary diversity is found in intermediate precipitation regimes, and that there is a decline in evolutionary diversity above 1,490 mm of mean annual rainfall. If conservation is to prioritise evolutionary diversity, areas of intermediate precipitation that are found in the South American ‘arc of deforestation’, but which have been neglected in the design of protected area networks in the tropics, merit increased conservation attention.

Diverging phenological responses of Arctic seabirds to an earlier spring

The timing of annual events such as reproduction is a critical component of how free-living organisms respond to ongoing climate change. This may be especially true in the Arctic, which is disproportionally impacted by climate warming. Here, we show that Arctic seabirds responded to climate change by moving the start of their reproduction earlier, coincident with an advancing onset of spring and that their response is phylogenetically and spatially structured. The phylogenetic signal is likely driven by seabird foraging behavior. Surface-feeding species advanced their reproduction in the last 35 years while diving species showed remarkably stable breeding timing. The earlier reproduction for Arctic surface-feeding birds was significant in the Pacific only, where spring advancement was most pronounced. In both the Atlantic and Pacific, seabirds with a long breeding season showed a greater response to the advancement of spring than seabirds with a short breeding season. Our results emphasize that spatial variation, phylogeny, and life history are important considerations in seabird phenological response to climate change and highlight the key role played by the species' foraging behavior.

Physical, ecological and human dimensions of environmental change in Brazil's Pantanal wetland: Synthesis and research agenda

The Pantanal is the world's largest freshwater wetland, located in the geographical centre of South America. It is relatively well conserved, and features unique landscapes, ecosystems, and traditional cultural practices, shaped by the dynamic interaction of climatological, hydrological, geological, ecological, and anthropogenic factors. Its ecological integrity is increasingly threatened by human activities, particularly, in the wider catchment area, for example, deforestation, agricultural intensification, and construction of hydropower plants, with implications for local people's livelihoods. We present a synthesis of current literature on physical, ecological, and human dimensions of environmental change in the wetland, outline key research gaps, and discuss environmental management implications. The literature review suggests that better integration of insights from multiple disciplines is needed and that environmental management could be improved through a better grounding in traditional practices and local perspectives. We conclude with four recommendations: First, future environmental change research should build more strongly on the positive example of a small number of case studies where traditional and local knowledge of the environment was put into a dialogue with scientific knowledge and techniques. Second, we recommend a more explicit consideration of longer temporal scales (>10 years) in environmental change research, making use of oral and written histories, as well as palaeoecological techniques, to understand system responses to different magnitudes of human and climatic pressures, and ultimately, to inform future adaptation activities. Third, we suggest that enhanced stakeholder participation in conceiving and implementing research projects in the Pantanal would strengthen the practical relevance of research in addressing environmental management challenges, livelihood needs, and advocacy processes. Fourth, we call for a more systemic and integrative perspective on environmental education, which encompasses engagement activities between researchers, policy-makers, and citizens, to foster environmental awareness, scientific literacy, and public participation.

Evolutionarily distinct amphibians are disproportionately lost from human-modified ecosystems

Humans continue to alter terrestrial ecosystems, but our understanding of how biodiversity responds is still limited. Anthropogenic habitat conversion has been associated with the loss of evolutionarily distinct bird species at local scales, but whether this evolutionary pattern holds across other clades is unknown. We collate a global dataset on amphibian assemblages in intact forests and nearby human-modified sites to assess whether evolutionary history influences susceptibility to land conversion. We found that evolutionarily distinct amphibian species are disproportionately lost when forested habitats are converted to alternative land-uses. We tested the hypothesis that grassland-associated amphibian lineages have both higher diversification and are pre-adapted to human landscapes, but found only weak evidence supporting this. The loss of evolutionarily distinct amphibians with land conversion suggests that preserving remnant forests will be vital if we aim to preserve the amphibian tree of life in the face of mounting anthropogenic pressures.

Evolution of Ecological Niche Breadth

How ecological niche breadth evolves is central to adaptation and speciation and has been a topic of perennial interest. Niche breadth evolution research has occurred within environmental, ecological, evolutionary, and biogeographical contexts, and although some generalities have emerged, critical knowledge gaps exist. Performance breadth trade-offs, although long invoked, may not be common determinants of niche breadth evolution or limits. Niche breadth can expand or contract from specialist or generalist lineages, and so specialization need not be an evolutionary dead end. Whether niche breadth determines diversification and distribution breadth and how niche breadth is partitioned among individuals and populations within a species are important but particularly understudied topics. Molecular genetic and phylogenetic techniques have greatly expanded understanding of niche breadth evolution, but field studies of how niche breadth evolves are essential for providing mechanistic details and allowing the development of comprehensive theory and improved prediction of biological responses under global change.

Benefits from living together? Clades whose species use similar habitats may persist as a result of eco-evolutionary feedbacks

Contents 66 I. 67 II. 68 III. 69 IV. 70 V. 73 VI. 75 VII. 77 78 References 78 SUMMARY: Recent decades have seen declines of entire plant clades while other clades persist despite changing environments. We suggest that one reason why some clades persist is that species within these clades use similar habitats, because such similarity may increase the degree of co-occurrence of species within clades. Traditionally, co-occurrence among clade members has been suggested to be disadvantageous because of increased competition and enemy pressure. Here, we hypothesize that increased co-occurrence among clade members promotes mutualist exchange, niche expansion or hybridization, thereby helping species avoid population decline from environmental change. We review the literature and analyse published data for hundreds of plant clades (genera) within a well-studied region and find major differences in the degree to which species within clades occupy similar habitats. We tentatively show that, in clades for which species occupy similar habitats, species tend to exhibit increased co-occurrence, mutualism, niche expansion, and hybridization - and rarely decline. Consistently, throughout the geological past, clades whose species occupied similar habitats often persisted through long time-spans. Overall, for many plant species, the occupation of similar habitats among fellow clade members apparently reduced their vulnerability to environmental change. Future research should identify when and how this previously unrecognized eco-evolutionary feedback operates.

Including Fossils in Phylogenetic Climate Reconstructions: A Deep Time Perspective on the Climatic Niche Evolution and Diversification of Spiny Lizards (Sceloporus)

Fossils and other paleontological information can improve phylogenetic comparative method estimates of phenotypic evolution and generate hypotheses related to species diversification. Here, we use fossil information to calibrate ancestral reconstructions of suitable climate for Sceloporus lizards in North America. Integrating data from the fossil record, general circulation models of paleoclimate during the Miocene, climate envelope modeling, and phylogenetic comparative methods provides a geographically and temporally explicit species distribution model of Sceloporus-suitable habitat through time. We provide evidence to support the historic biogeographic hypothesis of Sceloporus diversification in warm North American deserts and suggest a relatively recent Sceloporus invasion into Mexico around 6 Ma. We use a physiological model to map extinction risk. We suggest that the number of hours of restriction to a thermal refuge limited Sceloporus from inhabiting Mexico until the climate cooled enough to provide suitable habitat at approximately 6 Ma. If the future climate returns to the hotter climates of the past, Mexico, the place of highest modern Sceloporus richness, will no longer provide suitable habitats for Sceloporus to survive and reproduce.

Contrasting responses to a climate regime change by sympatric, ice-dependent predators

Background

Models that predict changes in the abundance and distribution of fauna under future climate change scenarios often assume that ecological niche and habitat availability are the major determinants of species’ responses to climate change. However, individual species may have very different capacities to adapt to environmental change, as determined by intrinsic factors such as their dispersal ability, genetic diversity, generation time and rate of evolution. These intrinsic factors are usually excluded from forecasts of species’ abundance and distribution changes. We aimed to determine the importance of these factors by comparing the impact of the most recent climate regime change, the late Pleistocene glacial-interglacial transition, on two sympatric, ice-dependent meso-predators, the emperor penguin (Aptenodytes forsteri) and Weddell seal (Leptonychotes weddellii).

Methods

We reconstructed the population trend of emperor penguins and Weddell seals in East Antarctica over the past 75,000 years using mitochondrial DNA sequences and an extended Bayesian skyline plot method. We also assessed patterns of contemporary population structure and genetic diversity.

Results

Despite their overlapping distributions and shared dependence on sea ice, our genetic data revealed very different responses to climate warming between these species. The emperor penguin population grew rapidly following the glacial-interglacial transition, but the size of the Weddell seal population did not change. The expansion of emperor penguin numbers during the warm Holocene may have been facilitated by their higher dispersal ability and gene flow among colonies, and fine-scale differences in preferred foraging locations.

Conclusions

The vastly different climate change responses of two sympatric ice-dependent predators suggests that differing adaptive capacities and/or fine-scale niche differences can play a major role in species’ climate change responses, and that adaptive capacity should be considered alongside niche and distribution in future species forecasts.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0630-3) contains supplementary material, which is available to authorized users.

Quantifying dilution and amplification in a community of hosts for tick-borne pathogens

Recent controversy over whether biodiversity reduces disease risk (dilution effect) has focused on the ecology of Lyme disease, a tick-borne zoonosis. A criticism of the dilution effect is that increasing host species richness might amplify disease risk, assuming that total host abundance, and therefore feeding opportunities for ticks, increase with species richness. In contrast, a dilution effect is expected when poor quality hosts for ticks and pathogens (dilution hosts) divert tick blood meals away from competent hosts. Even if host densities are additive, the relationship between host density and tick encounters can be nonlinear if the number of ticks that encounter a host is a saturating function of host density, which occurs if ticks aggregate on the remaining hosts rather than failing to find a host before death. Both dilution and amplification are theoretical possibilities, and assessing which is more prevalent required detailed analyses of empirical systems. We used field data to explore the degree of tick redistribution onto fewer individuals with variation in intraspecific host density and novel data-driven models for tick dynamics to determine how changes in vertebrate community composition influence the density of nymphs infected with the Lyme bacterium. To be conservative, we allowed total host density to increase additively with species richness. Our long-term field studies found that larval and nymphal ticks redistribute onto fewer individuals as host densities decline, that a large proportion of nymphs and adults find hosts, and that mice and chipmunks feed a large proportion of nymphs. White-footed mice, eastern chipmunks, short-tailed shrews, and masked shrews were important amplification hosts that greatly increased the density of infected nymphs. Gray squirrels and Virginia opossums were important dilution hosts. Removing these two species increased the maximum number of larvae attached to amplification hosts by 57%. Raccoons and birds were minor dilution hosts under some conditions. Even under the assumption of additive community assembly, some species are likely to reduce the density of infected nymphs as diversity increases. If the assumption of additivity is relaxed, then species that reduce the density of small mammals through predation or competition might substantially reduce disease risk.

Does the legacy of historical biogeography shape current invasiveness in pines?

Why are some introduced species more successful at establishing and spreading than others? Until now, characteristics of extant species have been intensively investigated to answer this question. We propose to gain new insights on species invasiveness by exploring the long-term biogeographic and evolutionary history of lineages. We exemplify our approach using one of the best-studied invasive plant genera, Pinus. We notably estimated the historical biogeography of pines and the rates of trait evolution in pines. These estimates were analysed with regard to species invasiveness status. The results revealed that currently invasive species belong to lineages that were particularly successful at colonizing new regions in the past. We also showed that highly mobile lineages had faster rates of niche evolution, but that these rates are poor proxies for species adaptive potential in invaded regions (estimated by niche shift among native and invaded regions). In summary, working at the interface of ecology, historical biogeography and evolutionary history offers stimulating perspectives to improve our understanding of the drivers of invasion success.

Why evolution matters for species conservation: perspectives from three case studies of plant metapopulations

We advocate the advantage of an evolutionary approach to conservation biology that considers evolutionary history at various levels of biological organization. We review work on three separate plant taxa, spanning from one to multiple decades, illustrating extremes in metapopulation functioning. We show how the rare endemics Centaurea corymbosa (Clape Massif, France) and Brassica insularis in Corsica (France) may be caught in an evolutionary trap: disruption of metapopulation functioning due to lack of colonization of new sites may have counterselected traits such as dispersal ability or self‐compatibility, making these species particularly vulnerable to any disturbance. The third case study concerns the evolution of life history strategies in the highly diverse genus Leucadendron of the South African fynbos. There, fire disturbance and the recolonization phase after fires are so integral to the functioning of populations that recruitment of new individuals is conditioned by fire. We show how past adaptation to different fire regimes and climatic constraints make species with different life history syndromes more or less vulnerable to global changes. These different case studies suggest that management strategies should promote evolutionary potential and evolutionary processes to better protect extant biodiversity and biodiversification.

Phylodiversity to inform conservation policy: An Australian example

Phylodiversity measures summarise the phylogenetic diversity patterns of groups of organisms. By using branches of the tree of life, rather than its tips (e.g., species), phylodiversity measures provide important additional information about biodiversity that can improve conservation policy and outcomes. As a biodiverse nation with a strong legislative and policy framework, Australia provides an opportunity to use phylogenetic information to inform conservation decision-making. We explored the application of phylodiversity measures across Australia with a focus on two highly biodiverse regions, the south west of Western Australia (SWWA) and the South East Queensland bioregion (SEQ). We analysed seven diverse groups of organisms spanning five separate phyla on the evolutionary tree of life, the plant genera Acacia and Daviesia, mammals, hylid frogs, myobatrachid frogs, passerine birds, and camaenid land snails. We measured species richness, weighted species endemism (WE) and two phylodiversity measures, phylogenetic diversity (PD) and phylogenetic endemism (PE), as well as their respective complementarity scores (a measure of gains and losses) at 20 km resolution. Higher PD was identified within SEQ for all fauna groups, whereas more PD was found in SWWA for both plant groups. PD and PD complementarity were strongly correlated with species richness and species complementarity for most groups but less so for plants. PD and PE were found to complement traditional species-based measures for all groups studied: PD and PE follow similar spatial patterns to richness and WE, but highlighted different areas that would not be identified by conventional species-based biodiversity analyses alone. The application of phylodiversity measures, particularly the novel weighted complementary measures considered here, in conservation can enhance protection of the evolutionary history that contributes to present day biodiversity values of areas. Phylogenetic measures in conservation can include important elements of biodiversity in conservation planning, such as evolutionary potential and feature diversity that will improve decision-making and lead to better biodiversity conservation outcomes.

Biological, ecological, conservation and legal information for all species and subspecies of Australian bird

We introduce a dataset of biological, ecological, conservation and legal information for every species and subspecies of Australian bird, 2056 taxa or populations in total. Version 1 contains 230 fields grouped under the following headings: Taxonomy & nomenclature, Phylogeny, Australian population status, Conservation status, Legal status, Distribution, Morphology, Habitat, Food, Behaviour, Breeding, Mobility and Climate metrics. It is envisaged that the dataset will be updated periodically with new data for existing fields and the addition of new fields. The dataset has already had, and will continue to have applications in Australian and international ornithology, especially those that require standard information for a large number of taxa.

Linking environmental filtering and disequilibrium to biogeography with a community climate framework

We present a framework to measure the strength of environmental filtering and disequilibrium of the species composition of a local community across time, relative to past, current, and future climates. We demonstrate the framework by measuring the impact of climate change on New World forests, integrating data for climate niches of more than 14000 species, community composition of 471 New World forest plots, and observed climate across the most recent glacial-interglacial interval. We show that a majority of communities have species compositions that are strongly filtered and are more in equilibrium with current climate than random samples from the regional pool. Variation in the level of current community disequilibrium can be predicted from Last Glacial Maximum climate and will increase with near-future climate change.

Convergence, divergence, and parallelism in marine biodiversity trends: Integrating present-day and fossil data

Paleontological data provide essential insights into the processes shaping the spatial distribution of present-day biodiversity. Here, we combine biogeographic data with the fossil record to investigate the roles of parallelism (similar diversities reached via changes from similar starting points), convergence (similar diversities reached from different starting points), and divergence in shaping the present-day latitudinal diversity gradients of marine bivalves along the two North American coasts. Although both faunas show the expected overall poleward decline in species richness, the trends differ between the coasts, and the discrepancies are not explained simply by present-day temperature differences. Instead, the fossil record indicates that both coasts have declined in overall diversity over the past 3 My, but the western Atlantic fauna suffered more severe Pliocene-Pleistocene extinction than did the eastern Pacific. Tropical western Atlantic diversity remains lower than the eastern Pacific, but warm temperate western Atlantic diversity recovered to exceed that of the temperate eastern Pacific, either through immigration or in situ origination. At the clade level, bivalve families shared by the two coasts followed a variety of paths toward today's diversities. The drivers of these lineage-level differences remain unclear, but species with broad geographic ranges during the Pliocene were more likely than geographically restricted species to persist in the temperate zone, suggesting that past differences in geographic range sizes among clades may underlie between-coast contrasts. More detailed comparative work on regional extinction intensities and selectivities, and subsequent recoveries (by in situ speciation or immigration), is needed to better understand present-day diversity patterns and model future changes.

Phylogeny and niche conservatism in North and Central American triatomine bugs (Hemiptera: Reduviidae: Triatominae), vectors of Chagas' disease

The niche conservatism hypothesis states that related species diverge in niche characteristics at lower rates than expected, given their lineage divergence. Here we analyze whether niche conservatism is a common pattern among vector species (Hemiptera: Reduviidae: Triatominae) of Trypanosoma cruzi that inhabit North and Central America, a highly heterogeneous landmass in terms of environmental gradients. Mitochondrial and nuclear loci were used in a multi-locus phylogenetic framework to reconstruct phylogenetic relationships among species and estimate time of divergence of selected clades to draw biogeographic inferences. Then, we estimated similarity between the ecological niche of sister species and tested the niche conservatism hypothesis using our best estimate of phylogeny. Triatoma is not monophyletic. A primary clade with all North and Central American (NCA) triatomine species from the genera Triatoma, Dipetalogaster, and Panstrongylus, was consistently recovered. Nearctic species within the NCA clade (T. p. protracta, T. r. rubida) diverged during the Pliocene, whereas the Neotropical species (T. phyllosoma, T. longipennis, T. dimidiata complex) are estimated to have diverged more recently, during the Pleistocene. The hypothesis of niche conservatism could not be rejected for any of six sister species pairs. Niche similarity between sister species best fits a retention model. While this framework is used here to infer niche evolution, it has a direct impact on spatial vector dynamics driven by human population movements, expansion of transportation networks and climate change scenarios.

One tree to link them all: a phylogenetic dataset for the European tetrapoda

Since the ever-increasing availability of phylogenetic informative data, the last decade has seen an upsurge of ecological studies incorporating information on evolutionary relationships among species. However, detailed species-level phylogenies are still lacking for many large groups and regions, which are necessary for comprehensive large-scale eco-phylogenetic analyses. Here, we provide a dataset of 100 dated phylogenetic trees for all European tetrapods based on a mixture of supermatrix and supertree approaches. Phylogenetic inference was performed separately for each of the main Tetrapoda groups of Europe except mammals (i.e. amphibians, birds, squamates and turtles) by means of maximum likelihood (ML) analyses of supermatrix applying a tree constraint at the family (amphibians and squamates) or order (birds and turtles) levels based on consensus knowledge. For each group, we inferred 100 ML trees to be able to provide a phylogenetic dataset that accounts for phylogenetic uncertainty, and assessed node support with bootstrap analyses. Each tree was dated using penalized-likelihood and fossil calibration. The trees obtained were well-supported by existing knowledge and previous phylogenetic studies. For mammals, we modified the most complete supertree dataset available on the literature to include a recent update of the Carnivora clade. As a final step, we merged the phylogenetic trees of all groups to obtain a set of 100 phylogenetic trees for all European Tetrapoda species for which data was available (91%). We provide this phylogenetic dataset (100 chronograms) for the purpose of comparative analyses, macro-ecological or community ecology studies aiming to incorporate phylogenetic information while accounting for phylogenetic uncertainty.

Climate-driven range shifts explain the distribution of extant gene pools and predict future loss of unique lineages in a marine brown alga

The climate-driven dynamics of species ranges is a critical research question in evolutionary ecology. We ask whether present intraspecific diversity is determined by the imprint of past climate. This is an ongoing debate requiring interdisciplinary examination of population genetic pools and persistence patterns across global ranges. Previously, contrasting inferences and predictions have resulted from distinct genomic coverage and/or geographical information. We aim to describe and explain the causes of geographical contrasts in genetic diversity and their consequences for the future baseline of the global genetic pool, by comparing present geographical distribution of genetic diversity and differentiation with predictive species distribution modelling (SDM) during past extremes, present time and future climate scenarios for a brown alga, Fucus vesiculosus. SDM showed that both atmospheric and oceanic variables shape the global distribution of intertidal species, revealing regions of persistence, extinction and expansion during glacial and postglacial periods. These explained the distribution and structure of present genetic diversity, consisting of differentiated genetic pools with maximal diversity in areas of long-term persistence. Most of the present species range comprises postglacial expansion zones and, in contrast to highly dispersive marine organisms, expansions involved only local fronts, leaving distinct genetic pools at rear edges. Besides unravelling a complex phylogeographical history and showing congruence between genetic diversity and persistent distribution zones, supporting the hypothesis of niche conservatism, range shifts and loss of unique genetic diversity at the rear edge were predicted for future climate scenarios, impoverishing the global gene pool.

CLIMBER: Climatic niche characteristics of the butterflies in Europe

Detailed information on species’ ecological niche characteristics that can be related to declines and extinctions is indispensable for a better understanding of the relationship between the occurrence and performance of wild species and their environment and, moreover, for an improved assessment of the impacts of global change. Knowledge on species characteristics such as habitat requirements is already available in the ecological literature for butterflies, but information about their climatic requirements is still lacking. Here we present a unique dataset on the climatic niche characteristics of 397 European butterflies representing 91% of the European species (see Appendix). These characteristics were obtained by combining detailed information on butterfly distributions in Europe (which also led to the ‘Distribution Atlas of Butterflies in Europe’) and the corresponding climatic conditions. The presented dataset comprises information for the position and breadth of the following climatic niche characteristics: mean annual temperature, range in annual temperature, growing degree days, annual precipitation sum, range in annual precipitation and soil water content. The climatic niche position is indicated by the median and mean value for each climate variable across a species’ range, accompanied by the 95% confidence interval for the mean and the number of grid cells used for calculations. Climatic niche breadth is indicated by the standard deviation and the minimum and maximum values for each climatic variable across a species’ range. Database compilation was based on high quality standards and the data are ready to use for a broad range of applications.

It is already evident that the information provided in this dataset is of great relevance for basic and applied ecology. Based on the species temperature index (STI, i.e. the mean temperature value per species), the community temperature index (CTI, i.e. the average STI value across the species in a community) was recently adopted as an indicator of climate change impact on biodiversity by the pan-European framework supporting the Convention on Biological Diversity (Streamlining European Biodiversity Indicators 2010) and has already been used in several scientific publications. The application potential of this database ranges from theoretical aspects such as assessments of past niche evolution or analyses of trait interdependencies to the very applied aspects of measuring, monitoring and projecting historical, ongoing and potential future responses to climate change using butterflies as an indicator.

Darwinian shortfalls in biodiversity conservation

If we were to describe all the species on Earth and determine their distributions, we would solve the popularly termed 'Linnean' and 'Wallacean' shortfalls in biodiversity conservation. Even so, we would still be hindered by a 'Darwinian shortfall', that is, the lack of relevant phylogenetic information for most organisms. Overall, there are too few comprehensive phylogenies, large uncertainties in the estimation of divergence times, and, most critically, unknown evolutionary models linking phylogenies to relevant ecological traits and life history variation. Here, we discuss these issues and offer suggestions for further research to support evolutionary-based conservation planning.

Niche breadth predicts geographical range size: a general ecological pattern

The range of resources that a species uses (i.e. its niche breadth) might determine the geographical area it can occupy, but consensus on whether a niche breadth-range size relationship generally exists among species has been slow to emerge. The validity of this hypothesis is a key question in ecology in that it proposes a mechanism for commonness and rarity, and if true, may help predict species' vulnerability to extinction. We identified 64 studies that measured niche breadth and range size, and we used a meta-analytic approach to test for the presence of a niche breadth-range size relationship. We found a significant positive relationship between range size and environmental tolerance breadth (z = 0.49), habitat breadth (z = 0.45), and diet breadth (z = 0.28). The overall positive effect persisted even when incorporating sampling effects. Despite significant variability in the strength of the relationship among studies, the general positive relationship suggests that specialist species might be disproportionately vulnerable to habitat loss and climate change due to synergistic effects of a narrow niche and small range size. An understanding of the ecological and evolutionary mechanisms that drive and cause deviations from this niche breadth-range size pattern is an important future research goal.

Evolutionary rescue: an emerging focus at the intersection between ecology and evolution

There is concern that the rate of environmental change is now exceeding the capacity of many populations to adapt. Mitigation of biodiversity loss requires science that integrates both ecological and evolutionary responses of populations and communities to rapid environmental change, and can identify the conditions that allow the recovery of declining populations. This special issue focuses on evolutionary rescue (ER), the idea that evolution might occur sufficiently fast to arrest population decline and allow population recovery before extinction ensues. ER emphasizes a shift to a perspective on evolutionary dynamics that focuses on short time-scales, genetic variants of large effects and absolute rather than relative fitness. The contributions in this issue reflect the state of field; the articles address the latest conceptual developments, and report novel theoretical and experimental results. The examples in this issue demonstrate that this burgeoning area of research can inform problems of direct practical concern, such as the conservation of biodiversity, adaptation to climate change and the emergence of infectious disease. The continued development of research on ER will be necessary if we are to understand the extent to which anthropogenic global change will reduce the Earth's biodiversity.

Evolutionary rescue in vertebrates: evidence, applications and uncertainty

The current rapid rate of human-driven environmental change presents wild populations with novel conditions and stresses. Theory and experimental evidence for evolutionary rescue present a promising case for species facing environmental change persisting via adaptation. Here, we assess the potential for evolutionary rescue in wild vertebrates. Available information on evolutionary rescue was rare and restricted to abundant and highly fecund species that faced severe intentional anthropogenic selective pressures. However, examples from adaptive tracking in common species and genetic rescues in species of conservation concern provide convincing evidence in favour of the mechanisms of evolutionary rescue. We conclude that low population size, long generation times and limited genetic variability will result in evolutionary rescue occurring rarely for endangered species without intervention. Owing to the risks presented by current environmental change and the possibility of evolutionary rescue in nature, we suggest means to study evolutionary rescue by mapping genotype → phenotype → demography → fitness relationships, and priorities for applying evolutionary rescue to wild populations.

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.