Phylogenetic signals in the realized climate niches of Chinese grasses (Poaceae)

Explaining relationships between species richness and biogeographical patterns over a broad geographic scale is a central issue of biogeography and macroecology. We document the realized climate niches for grasses in China’s nature reserves and discuss its formation mechanism using grass richness data combined with climatic, physiological, and phylogenetic data. Our results suggest that climate niche structure of grasses is phylogenetically conservative for BEP (Bambusoideae, Ehrhartoideae, and Pooideae) and PACMAD (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, and Danthonioideae) clades along temperature gradients and for Chloridoideae and Panicoideae along precipitation gradients. At the national scale, the divergence patterns of climate niches between two major clades are more distinguishable than between C₃ and C₄ grasses. High rates of climate niche evolution are found in C₄ clades in the subtropical forest region. There appears to be a strong association between elevation gradients and grass diversity: the specific environmental conditions (e.g. energy) and the rapid shifts of climate conditions drive high grass diversification. Evolutionary conservatism of climate niches may be influenced by the specific adaptive ability to changing environmental conditions within NAD-ME/NADP-ME clades. Our results indicate that adaptations to major climate changes may be accomplished by C₄ grass nodes of high climate niche evolutionary rates in China’s nature reserves.     

Seasonal climatic niches diverge in migratory birds

Migratory birds occupy different geographical areas during breeding and non-breeding periods, and thus different factors may determine their range limits depending on each season. One such factor is the spatial climatic component of the niche, which is widely used to model species distributions, yet the temporal component is often neglected and is generally assumed to be constant. We tested the hypothesis that the climatic niche is conserved between breeding and non-breeding areas in 355 bird species migrating through Eurasian–African flyways. For this, we performed niche overlap analyses and compared niche differences between sister or phylogenetically closely related species, as well as linking the differences to migratory distances. For more than 80% of the species, there was no or very little overlap between their breeding and non-breeding climatic niches. For most closely related species, the degree of overlap of their breeding climatic niches was larger than the overlap observed within each species, but not for their wintering climatic niches, suggesting a phylogenetic conservation of breeding climatic niches. Finally, there was a clear negative relationship between migratory distances and climatic niche overlap within each species. Our results confirmed that the climatic niche of most Eurasian–African migratory species differs between both breeding and non-breeding ranges, suggesting distinctive seasonal climatic requirements. Given these results and the geographically uneven effects of climate change, the impact of global change is likely to have different effects in each seasonal range. Hence, both breeding and non-breeding climatic data need to be considered when using species distribution models.     

Phylogenetic conservatism of environmental niches in mammals

Phylogenetic niche conservatism is the pattern where close relatives occupy similar niches, whereas distant relatives are more dissimilar. We suggest that niche conservatism will vary across clades in relation to their characteristics. Specifically, we investigate how conservatism of environmental niches varies among mammals according to their latitude, range size, body size and specialization. We use the Brownian rate parameter, σ(2), to measure the rate of evolution in key variables related to the ecological niche and define the more conserved group as the one with the slower rate of evolution. We find that tropical, small-ranged and specialized mammals have more conserved thermal niches than temperate, large-ranged or generalized mammals. Partitioning niche conservatism into its spatial and phylogenetic components, we find that spatial effects on niche variables are generally greater than phylogenetic effects. This suggests that recent evolution and dispersal have more influence on species' niches than more distant evolutionary events. These results have implications for our understanding of the role of niche conservatism in species richness patterns and for gauging the potential for species to adapt to global change.     

Relating habitat and climatic niches in birds

Predicting species' responses to the combined effects of habitat and climate changes has become a major challenge in ecology and conservation biology. However, the effects of climatic and habitat gradients on species distributions have generally been considered separately. Here, we explore the relationships between the habitat and thermal dimensions of the ecological niche in European common birds. Using data from the French Breeding Bird Survey, a large-scale bird monitoring program, we correlated the habitat and thermal positions and breadths of 74 bird species, controlling for life history traits and phylogeny. We found that cold climate species tend to have niche positions in closed habitats, as expected by the conjunction of the biogeographic history of birds' habitats, and their current continent-scale gradients. We also report a positive correlation between thermal and habitat niche breadths, a pattern consistent with macroecological predictions concerning the processes shaping species' distributions. Our results suggest that the relationships between the climatic and habitat components of the niche have to be taken into account to understand and predict changes in species' distributions.     

Predicting the past distribution of species climatic niches

Predicting past distributions of species climatic niches, hindcasting, by using climate envelope models (CEMs) is emerging as an exciting research area. CEMs are used to examine veiled evolutionary questions about extinctions, locations of past refugia and migration pathways, or to propose hypotheses concerning the past population structure of species in phylogeographical studies. CEMs are sensitive to theoretical assumptions, to model classes and to projections in non-analogous climates, among other issues. Studies hindcasting the climatic niches of species often make reference to these limitations. However, to obtain strong scientific inferences, we must not only be aware of these potential limitations but we must also overcome them. Here, I review the literature on hindcasting CEMs. I discuss the theoretical assumptions behind niche modelling, i.e. the stability of climatic niches through time and the equilibrium of species with climate. I also summarize a set of 'recommended practices' to improve hindcasting. The studies reviewed: (1) rarely test the theoretical assumptions behind niche modelling such as the stability of species climatic niches through time and the equilibrium of species with climate; (2) they only use one model class (72% of the studies) and one palaeoclimatic reconstruction (62.5%) to calibrate their models; (3) they do not check for the occurrence of non-analogous climates (97%); and (4) they do not use independent data to validate the models (72%). Ignoring the theoretical assumptions behind niche modelling and using inadequate methods for hindcasting CEMs may well entail a cascade of errors and naïve ecological and evolutionary inferences. We should also push integrative research lines linking macroecology, physiology, population biology, palaeontology, evolutionary biology and CEMs for a better understanding of niche dynamics across space and time.     

Risk of extinction increases towards higher elevations across the world's amphibians

Aim

Life in mountains is associated with multiple features that increase the risk of demographic collapses in populations – small geographic ranges, short breeding seasons, specialization to harsh climates – leading to the hypothesis that extinction risk is exacerbated in species inhabiting higher elevations. Here, we implement the first test of this hypothesis across the amphibian tree of life – the tetrapods with the largest proportion of montane species, and nature's most threatened animals.

Location

Global.

Time Period

Present.

Major Taxa Studied

Class Amphibia.

Methods

We collated a dataset spanning 8042 species from across all three amphibian orders (Anura, Caudata and Gymnophiona). We preformed phylogenetic logistic regressions to test the predictions that extinction risk increases with elevation, and whether this effect is caused by factors previously hypothesised to drive high-elevation declines, including restrictions on species' geographic ranges, variation in their life histories and the presence of infectious disease.

Results

Globally, extinction risk increases towards higher elevations. At order-level, this relationship holds for frogs and salamanders. Even when controlling for geographic range size, life histories and infectious disease, extinction risk increases with elevation for amphibians combined and frogs globally, and in the Americas. In contrast, whereas extinction risk is greater among high-elevation Eurasian amphibians, this relationship is explained by larger body sizes and lower fecundity.

Main Conclusions

Our analyses indicate that after considering factors previously thought to explain the increase in extinction risk towards higher elevations (e.g., geographic range size, disease), elevation remains a significant predictor of amphibian extinction risk. Given that the only available tests of this hypothesis in other tetrapods (birds and reptiles) conflict with our findings, we suggest that physiological or life-history features of amphibians may explain this observed phenomenon.     

Quantification of climatic niches in birds: adding the temporal dimension

Quantification of the climatic niche from geographic occurrences is an increasingly important tool for studying species’ relationships to their environment, for example to predict responses to climate change. However, as the geographic distributions of birds are seasonally dynamic, they pose a challenge to carrying out comparable and appropriate quantification of climatic niches. In this review, we first assess how relevant seasonal dynamics are across birds as a whole by compiling a database of migratory behaviour for 10 443 bird species. Second, we examine how studies have quantified climatic niches of birds. Finally, using Australia as a case study, we investigate how well existing distribution datasets represent temporal dynamics by comparing seasonal patterns of species richness obtained from point‐occurrence data with those from range maps and assess the consequences for niche quantification. We provide a consistent classification of migratory behaviour across all birds, and find that a huge variety exists between and within species that should be considered when quantifying climatic niches. Despite this, our review of the literature revealed that seasonal dynamics have often not been accounted for. For future studies, we provide a framework for selecting appropriate occurrence data depending on migratory behaviour and data availability. Our comparison of seasonal species richness patterns obtained from extent‐of‐occurrence range maps and point‐occurrence data suggests that range maps are less able to detect temporal dynamics of bird distributions than point‐occurrence data. We conclude that seasonally explicit range maps combined with climatic data for the corresponding time period can be used to adequately quantify climatic niches for resident birds, but are not adequate to quantify the climatic niches of migratory and nomadic species. Therefore, consistent quantification of climatic niches across all birds requires temporally explicit occurrence points. As such, increasing the availability of occurrence data and methods correcting biases should be a priority.     

Phylogenetic autocorrelation of extinction threat in globally imperilled amphibians

The global extinction crisis demands immediate action to conserve species at risk. However, if entire clades such as superfamilies are at risk due to shared evolutionary history, a shift towards conserving clades rather than individual species may be needed. Using phylogenetic autocorrelation analysis, we demonstrate that multiple kinds of extinction threat clump within the amphibian tree of life. Our study provides insight into how these threats may collectively influence the extinction risk of whole clades, consistent with the supposition that related species, with similar traits, share an intrinsic vulnerability to common kinds of threat. Most strikingly, we find a significant concentration of 'enigmatic' decline and critically endangered status within families of the hyloid frogs. This phylogenetic clumping of risk is also geographically concentrated, with most threats found in Central and South America, and Australia, coinciding with reported outbreaks of chytridiomycosis. We speculate that the phylogenetic clumping of threat represents, in part, shared extinction proneness due to shared evolutionary history. However, even if the phylogenetic clumping of threat were simply a by-product of shared geography, this concordance between phylogenetic and geographical patterns represents a prime opportunity. Where practical, we should implement conservation plans that focus on biogeographical regions where threatened clades occur, thereby improving our ability to conserve species. This approach could outperform the usual triage approach of saving individual species after they have become critically endangered.     

The macroevolution of climatic niches and its role in ant diversification

1. Investigating how climatic niches change over evolutionary timescales is a necessary step to understanding the current distribution of lineages, yet few studies have addressed this issue using comprehensive datasets. In this study, the evolution of ant climatic niches is investigated at a global scale based on bioclimatic data associated with 163 481 ant occurrence records. The resulting dataset was subjected to principal component analysis, and the scores obtained were used to characterise the main axes of ant climatic niche evolution. 2. Principal component axis 1 (PC1) reflected variation in average temperature and seasonality – consistent with typical tropical/temperate gradients – whereas PC2 was associated with varying levels of aridity. Evolution along these two niche axes was markedly different: differences in the amount of explained variance between PC1 (65%) and PC2 (19%) suggest that climatic niche evolution was nearly three times more pronounced along a tropical–temperate climate axis. 3. There was statistically significant phylogenetic signal on PC1, with genera occupying more tropical conditions diversifying at a faster rate, yet neither of these results is significant on PC2. In addition, most of the ancient ant lineages are associated with conditions of low seasonality and high temperatures. 4. These results provide partial support for the tropical conservatism hypothesis as an explanation for geographical patterns of ant species richness.     

Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians

Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with human‐mediated population movements obscuring biogeographic patterns and confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus. Previous phylogenetic studies have identified distinct Chinese giant salamander lineages but were unable to associate these consistently with different landscapes, probably because population structure has been modified by human‐mediated translocations for recent commercial farming. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with Next‐Generation Sequencing methods, using historical museum specimens and late 20th‐century samples, and retrieved partial or near‐complete mitogenomes for 17 individuals. Samples from populations unlikely to have been affected by translocations form three clades from separate regions of China, spatially congruent with isolation by either major river drainages or mountain ranges. Pliocene–Pleistocene divergences for these clades are consistent with topographic modification of southern China associated with uplift of the Qinghai‐Tibet Plateau. General Mixed Yule Coalescent model analysis indicates that these clades represent separate species: Andrias davidianus (Blanchard, 1871) (northern Yangtze/Sichuan), Andrias sligoi (Boulenger, 1924) (Pearl/Nanling), and an undescribed species (Huangshan). Andrias sligoi is possibly the world's largest amphibian. Inclusion of additional reportedly wild samples from areas of known giant salamander exploitation and movement leads to increasing loss of biogeographic signal. Wild Chinese giant salamander populations are now critically depleted or extirpated, and conservation actions should be updated to recognize the existence of multiple species.     

Evolution of climatic niche specialization: a phylogenetic analysis in amphibians

The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change.     

Phylogenetic diversity does not capture body size variation at risk in the world's mammals

Mammals contribute to important ecosystem processes and services, but many mammalian species are threatened with extinction. We compare how global patterns in three measures of mammalian diversity—species richness, phylogenetic diversity (PD) and body mass variance (BMV)—would change if all currently threatened species were lost. Given that many facets of species'' ecology and life history scale predictably with body mass, the BMV in a region roughly reflects the diversity of species'' roles within ecosystems and so is a simple proxy for functional diversity (FD). PD is also often considered to be a proxy for FD, but our results suggest that BMV losses within ecoregions would be much more severe than losses of PD or species richness, and that its congruence with the latter two measures is low. Because of the disproportionate loss of large mammals, 65 per cent of ecoregions would lose significantly more BMV than under random extinction, while only 11 per cent would lose significantly more PD. Ecosystem consequences of these selective losses may be profound, especially throughout the tropics, but are not captured by PD. This low surrogacy stresses a need for conservation prioritization based on threatened trait diversity, and for conservation efforts to take an ecosystem perspective.     

Contrasting road effect signals in reproduction of long- versus short-lived amphibians

Despite an increasing understanding of the effects of roadways on amphibian populations, no studies have examined road effects on demographic traits other than survival. We predicted that road mortality could exert a disproportionate effect on fecundity in long-lived species due to shifts in population age structures to younger individuals of smaller size that produce commensurately smaller egg masses. To test this hypothesis, we assessed egg mass sizes of a long-lived amphibian (spotted salamander, Ambystoma maculatum) and short-lived one (wood frog, Rana sylvatica) in wetlands near and far from highways. Egg mass sizes of A. maculatum were smaller in wetlands near highways. In contrast, those of R. sylvatica were similar among wetlands regardless of the distance from highways. We conclude that paved highways with moderate traffic volume may be having important effects on populations of long-lived amphibians through mortality-mediated depression of reproduction.     

Phylogenetic implications of the morphology of the braincase of caecilian amphibians (Gymnophiona)

Caecilian morphology is strongly modified in association with their fossorial mode of life. Currently phylogenetic analyses of characters drawn from the morphology of caecilians lack resolution, as well as complementarity, with results of phylogenetic analyses that employ molecular data. Stemming from the hypothesis derived from the mammal literature that the braincase has the greatest potential (in comparison to other cranial units) to yield phylogenetic information, the braincase and intimately associated stapes of 27 species (23 genera) of extant caecilians were examined using images assembled via microcomputed tomography. Thirty‐four new morphological characters pertaining to the braincase and stapes were identified and tested for congruence with previously recognized morphological characters. The results reveal that when added to previous character matrices, characters of the braincase and stapes resolve generic‐level relationships in a way that is largely congruent with the results of molecular analyses. Analysis of a combined data set of molecular and morphological data provides a framework for conducting ancestral character state reconstructions, which resulted in the identification of 95 new synapomorphies for various clades and taxa, 27 of which appear to be unique for the taxa that possess them. Together these data demonstrate the utility of the application of characters of the braincase and stapes for resolving phylogenetic relationships for a group whose morphology is largely confounded by functional modifications. In addition this study provides evidence of the utility of the braincase in resolving problematic morphology‐based phylogeny outside of Amniota, in an amphibian group. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 160–201.     

Phylogenetic relationships and climatic adaptations in the Drosophila takahashii and montium species subgroups

We analyze phylogenetic relationships among temperate, subtropical highland, and subtropical lowland species of the Drosophila takahashii and montium species subgroups based on sequence data of COI and Gpdh genes and discuss the evolution of temperate species in these subgroups with reference to their climatic adaptations. In the takahashii subgroup, D. lutescens (the temperate species) branched off first in the tree based on the combined data set, but D. prostipennis (the subtropical highland species) branched off first in the trees based on single genes. Thus, phylogenetic relationships in this subgroup are still ambiguous. In the montium subgroup, the cool-temperate species are phylogenetically close to the warm-temperate species, and these cool- and warm-temperate species form a cluster with the subtropical highland species. This suggests that perhaps the cool-temperate species derived from the warm-temperate species and the warm-temperate species derived from the subtropical highland species. In comparison with the subtropical lowland species, the subtropical highland species may be better able to colonize temperate areas since, as in the temperate species, they have an ability to develop their ovaries at moderately low temperature. However, the subtropical highland species, as well as the subtropical lowland species, were much less cold tolerant than the temperate species. Therefore, considerable genetic reformation would be required for both the subtropical highland and the subtropical lowland species to adapt to temperate climates.