Phylogenetic niche conservatism: what are the underlying evolutionary and ecological causes?

Ecological diversification preceded geographical expansion during the evolutionary radiation of Cataglyphis desert ants

Biological diversity often arises as organisms adapt to new ecological conditions (i.e., ecological opportunities) or colonize suitable areas (i.e., spatial opportunities). Cases of geographical expansion followed by local ecological divergence are well described; they result in clades comprising ecologically heterogeneous subclades. Here, we show that the desert ant genus Cataglyphis likely originated in open grassland habitats in the Middle East ∼18 million years ago and became a taxon of diverse species specializing in prey of different masses. The genus then colonized the Mediterranean Basin around 9 million years ago. The result was the rapid accumulation of species, and the appearance of local assemblages containing species from different lineages that still displayed ancestral foraging specialties. These findings highlight that, in Cataglyphis, ecological diversification preceded geographical expansion, resulting in a clade composed of ecologically homogeneous subclades.

Climatic niche evolution and niche conservatism of Nymphaea species in Africa, South America, and Australia

BACKGROUND

Interest in the evolution of climatic niches, particularly in understanding the potential adaptive responses of species under climate change, has increased both theoretically and within macroecological studies. These studies have provided valuable insights into how climatic traits of species influence their niche evolution. In this study, we aim to investigate whether niche conservatism plays a role in the species diversification of Nymphaea, a group of aquatic plants with a cosmopolitan distribution that is facing severe habitat loss. We will use climatic models and phylogenetic data for 23 species to reconstruct Nymphaea's niche evolution, measure niche overlap, and assess disparity through time while testing for evolutionary models.

RESULTS

There was a lot of overlap in niches both within and between groups, especially for species that can be found in many places. The breadth and peaks of the niche profile varied depending on the bioclimatic variables, which suggested that the species evolved differently to cope with changes in climate. The analysis also showed that evolutionary changes happened across the phylogeny, with weak to moderate signals. The morphological disparity index (MDI) values indicated that there were disparities within subclades over time but not between or among them. Niche reconstruction and evolution analysis revealed both convergent and divergent evolution among various variables. For example, N. immutabilis, N. atrans, N. violancea, and N. nouchali evolved towards intermediate temperatures for bio2 and bio3 (isothermity) while moving towards extreme temperatures for bio8 and bio9 (wettest and driest average quarterly temperatures).

CONCLUSION

Our study will improve our understanding of how changes in climatic niches are potentially driving the evolution of Nymphaea. It has significant scientific implications for the limits, assemblages, evolution, and diversification of species. This information is crucial for the ongoing efforts of conservation and management, particularly considering the inevitable effects of climate change.

Resource availability and disturbance frequency shape evolution of plant life forms in Neotropical habitats

Organisms use diverse strategies to thrive in varying habitats. While life history theory partly explains these relationships, the combined impact of resource availability and disturbance frequency on life form strategy evolution has received limited attention. We use Chamaecrista species, a legume plant lineage with a high diversity of plant life forms in the Neotropics, and employ ecological niche modeling and comparative phylogenetic methods to examine the correlated evolution of plant life forms and environmental niches. Chamaephytes and phanerophytes have optima in environments characterized by moderate water and nutrient availability coupled with infrequent fire disturbances. By contrast, annual plants thrive in environments with scarce water and nutrients, alongside frequent fire disturbances. Similarly, geophyte species also show increased resistance to frequent fire disturbances, although they thrive in resource-rich environments. Our findings shed light on the evolution of plant strategies along environmental gradients, highlighting that annuals and geophytes respond differently to high incidences of fire disturbances, with one enduring it as seeds in a resource-limited habitat and the other relying on reserves and root resprouting systems in resource-abundant habitats. Furthermore, it deepens our understanding of how organisms evolve associated with their habitats, emphasizing a constraint posed by low-resource and high-disturbance environments.

Divergence time shapes gene reuse during repeated adaptation

When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability.

Temperate woody species across the angiosperm phylogeny acquire tolerance to water deficit stress during the growing season

Understanding the capacity of temperate trees to acclimate to limited soil water has become essential in the face of increasing drought risk due to climate change. We documented seasonal - or phenological - patterns in acclimation to water deficit stress in stems and leaves of tree species spanning the angiosperm phylogeny. Over 3 yr of field observations carried out in two US arboreta, we measured stem vulnerability to embolism (36 individuals of 7 Species) and turgor loss point (119 individuals of 27 species) over the growing season. We also conducted a growth chamber experiment on 20 individuals of one species to assess the mechanistic relationship between soil water restriction and acclimation. In three-quarters of species measured, plants became less vulnerable to embolism and/or loss of turgor over the growing season. We were able to stimulate this acclimatory effect by withholding water in the growth chamber experiment. Temperate angiosperms are capable of acclimation to soil water deficit stress, showing maximum vulnerability to soil water deficits following budbreak and becoming more resilient to damage over the course of the growing season or in response to simulated drought. The species-specific tempo and extent of this acclimatory potential constitutes preadaptive climate change resilience.

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.

Preliminary species diversity and community phylogenetics of wood-inhabiting basidiomycetous fungi in the Dabie Mountains, Central China reveal unexpected richness

Wood-inhabiting fungi have important economic values as well as playing a major ecological role in forest ecosystem cycles. The Dabie Mountains, at the junction of Henan, Hubei, and Anhui Provinces, Central China, provide an ideal climate and favorable niches for the speciation and diversification of various forms of life including fungi. We studied the species diversity and community phylogenetics of wood-inhabiting basidiomycetous fungi that revealed 175 wood-inhabiting basidiomycetous species, of which 20 represented unidentified species, based on morphological and phylogenetic analyses of 575 specimens collected from ten sampling sites. These species belonged to two classes, 11 orders, 42 families, and 106 genera of Basidiomycota, and included 12 edible species, 28 medicinal species, four poisonous species, and seven forest pathogens. Four types of fungal distribution pattern at the genus level were recognized for 65 genera, while another 41 genera could not be placed in any known distribution pattern. The five sampling sites in the eastern part of the Dabie Mountains had significantly higher species diversity and phylogenetic diversity of wood-inhabiting basidiomycetous fungi than those in the western part, and thus deserve priority in terms of conservation. The community of wood-inhabiting basidiomycetous fungi in the Dabie Mountains is generally affected by a combination of habitat filtering and competitive exclusion. This study provides a basis on which to build actions for the comprehensive recognition, utilization, and conservation of wood-inhabiting basidiomycetous fungi in the region.

Historical Assembly of Andean Tree Communities

Patterns of species diversity have been associated with changes in climate across latitude and elevation. However, the ecological and evolutionary mechanisms underlying these relationships are still actively debated. Here, we present a complementary view of the well-known tropical niche conservatism (TNC) hypothesis, termed the multiple zones of origin (MZO) hypothesis, to explore mechanisms underlying latitudinal and elevational gradients of phylogenetic diversity in tree communities. The TNC hypothesis posits that most lineages originate in warmer, wetter, and less seasonal environments in the tropics and rarely colonize colder, drier, and more seasonal environments outside of the tropical lowlands, leading to higher phylogenetic diversity at lower latitudes and elevations. In contrast, the MZO hypothesis posits that lineages also originate in temperate environments and readily colonize similar environments in the tropical highlands, leading to lower phylogenetic diversity at lower latitudes and elevations. We tested these phylogenetic predictions using a combination of computer simulations and empirical analyses of tree communities in 245 forest plots located in six countries across the tropical and subtropical Andes. We estimated the phylogenetic diversity for each plot and regressed it against elevation and latitude. Our simulated and empirical results provide strong support for the MZO hypothesis. Phylogenetic diversity among co-occurring tree species increased with both latitude and elevation, suggesting an important influence on the historical dispersal of lineages with temperate origins into the tropical highlands. The mixing of different floras was likely favored by the formation of climatically suitable corridors for plant migration due to the Andean uplift. Accounting for the evolutionary history of plant communities helps to advance our knowledge of the drivers of tree community assembly along complex climatic gradients, and thus their likely responses to modern anthropogenic climate change.

Invasive alien plants are phylogenetically distinct from other alien species across spatial and taxonomic scales in China

Introduction

Phylogenetic relatedness is one of the important factors in the community assembly process. Here, we aimed to understand the large-scale phylogenetic relationship between alien plant species at different stages of the invasion process and how these relationships change in response to the environmental filtering process at multiple spatial scales and different phylogenetic extents.

Methods

We identified the alien species in three invasion stages, namely invasive, naturalized, and introduced, in China. The occurrence records of the species were used to quantify two abundance-based phylogenetic metrics [the net relatedness index (NRI) and the nearest taxon index (NTI)] from a highly resolved phylogenetic tree. The metrics were compared between the three categories of alien species. Generalized linear models were used to test the effect of climate on the phylogenetic pattern. All analyses were conducted at four spatial scales and for three major angiosperm families.

Results

We observed significantly higher NRI and NTI values at finer spatial scales, indicating the formation of more clustered assemblages of phylogenetically closely related species in response to the environmental filtering process. Positive NTI values for the invasive and naturalized aliens suggested that the presence of a close relative in the community may help the successful naturalization and invasion of the introduced alien species. In the two-dimensional phylogenetic space, the invasive species communities significantly differed from the naturalized and introduced species, indicating that established alien species need to be phylogenetically different to become invasive. Positive phylogenetic measures for the invasive aliens across the spatial scales suggested that the presence of invasive aliens could facilitate the establishment of other invasive species. Phylogenetic relatedness was more influenced by temperature than precipitation, especially at a finer spatial scale. With decreased temperature, the invasive species showed a more clustered assemblage, indicating conservatism of their phylogenetic niche. The phylogenetic pattern was different at the family level, although there was a consistent tendency across families to form more clustered assemblages.

Discussion

Overall, our study showed that the community assemblage became more clustered with the progression of the invasion process. The phylogenetic measures varied at spatial and taxonomic scales, thereby highlighting the importance of assessing phylogenetic patterns at different gradients of the community assembly process.

Isotopic niches do not follow the expectations of niche conservatism in the bird genus Cinclodes

Phenotypic traits are expected to be more similar among closely related species than among species that diverged long ago (all else being equal). This pattern, known as phylogenetic niche conservatism, also applies to traits that are important to determine the niche of species. To test this hypothesis on ecological niches, we analysed isotopic data from 254 museum study skins from 12 of the 16 species of the bird genus Cinclodes and measured stable isotope ratios for four different elements: carbon, nitrogen, hydrogen and oxygen. We find that all traits, measured individually, or as a composite measurement, lack any phylogenetic signal, which in turn suggests a high level of lability in ecological niches. We compared these metrics to the measurements of morphological traits in the same genus and found that isotopic niches are uniquely evolutionarily labile compared to other traits. Our results suggest that, in Cinclodes, the realized niche evolves much faster than expected by the constraints of phylogenetic history and poses the question of whether this is a general pattern across the tree of life.

Towards an Understanding of Large-Scale Biodiversity Patterns on Land and in the Sea

This review presents a recent theory named ‘macroecological theory on the arrangement of life’ (METAL). This theory is based on the concept of the ecological niche and shows that the niche-environment (including climate) interaction is fundamental to explain many phenomena observed in nature from the individual to the community level (e.g., phenology, biogeographical shifts, and community arrangement and reorganisation, gradual or abrupt). The application of the theory in climate change biology as well as individual and species ecology has been presented elsewhere. In this review, I show how METAL explains why there are more species at low than high latitudes, why the peak of biodiversity is located at mid-latitudes in the oceanic domain and at the equator in the terrestrial domain, and finally why there are more terrestrial than marine species, despite the fact that biodiversity has emerged in the oceans. I postulate that the arrangement of planetary biodiversity is mathematically constrained, a constraint we previously called ‘the great chessboard of life’, which determines the maximum number of species that may colonise a given region or domain. This theory also makes it possible to reconstruct past biodiversity and understand how biodiversity could be reorganised in the context of anthropogenic climate change.

The origins of climate-diversity relationships and richness patterns in Chinese plants

A major goal of ecology and evolutionary biology is to explain geographic patterns of species richness. Richness is often correlated with climatic variables. However, the processes underlying these climate-diversity relationships remain poorly understood. Two potential hypotheses to explain these relationships involve: (i) faster diversification rates (speciation minus extinction) in high-richness climates and (ii) earlier colonization of high-richness climates, allowing more time for speciation to build up richness. Few studies have tested these hypotheses directly, and most focused on animal clades with limited richness. In this study, we test these hypotheses in Chinese angiosperms, encompassing ~10% of Earth's plant species, using large-scale phylogenetic, climatic, and distributional data including 26,977 species. We find that climatic zones that were colonized earlier have higher species richness. By contrast, relationships between diversification rates and richness of climatic zones are often nonsignificant or negative. Our study reveals that even when richness is strongly correlated with climate, the underlying explanation may still be rooted in phylogenetic history. Thus, climate may not be a competing explanation for richness patterns relative to colonization times and diversification rates. We also show that the timing of colonization can be crucial for explaining richness patterns. Yet, many recent studies have ignored this explanation and instead have focused solely on rates of speciation and diversification as drivers of diversity gradients.

Phylogenetic climatic niche conservatism in sandflies (Diptera: Phlebotominae) and their relatives

Phylogenetic niche conservatism is a pattern in which closely related species are more similar than distant relatives in their niche-related traits. Species in the family Psychodidae show notable diversity in climatic niche, and present an opportunity to test for phylogenetic niche conservatism, which is as yet rarely studied in insects. Some species (in the subfamily Phlebotominae) transmit Leishmania parasites, responsible for the disease leishmaniasis, and their geographic range has been systematically characterized. Psychodid genus ranges can be solely tropical, confined to the temperate zones, or span both. We obtained observation site data, and associated climate data, for 234 psychodid species to understand which aspects of climate most closely predict distribution. Temperature and seasonality are strong determinants of species occurrence within the clade. Next, we built a phylogeny of Psychodidae, and found a positive relationship between pairwise genetic distance and climate niche differentiation, which indicates strong niche conservatism. This result is also supported by strong phylogenetic signals of metrics of climate differentiation. Finally, we used ancestral trait reconstruction to infer the tropicality (i.e., proportion of latitudinal range in the tropics minus the proportion of the latitudinal range in temperate areas) of ancestral species, and counted transitions to and from tropicality states. We find that tropical and temperate species produced almost entirely tropical and temperate descendant species, respectively. Taken together, our results imply that climate niches in psychodids are strongly predicted by phylogeny, and represent a formal test of a key prediction of phylogenetic niche conservatism in a clade with implications for human health.

Niche conservatism and evolution of climatic tolerance in the Neotropical orchid genera Sobralia and Brasolia (Orchidaceae)

Sobralia and Brasolia form a large complex of Neotropical Orchidaceae. Although the molecular and morphological studies allowed to increase the rate of work on the modern classification of the taxa, they still require the attention as remaining without complete revision. The niche similarity analysis between representatives of Sobralia and recently segregated from this taxon—genus Brasolia is presented. The ecological tolerance evolution within the group was investigated with molecular clock analysis and phylogeny as the background. The phylogenetic analysis has confirmed the previous results and placed Brasolia representatives in a single clade with Elleanthus and Sobralia core as a separated group. The molecular clock analysis suggests that Sobralia and Brasolia are relatively young groups that evolved between 8.5 and 8 million years ago. Distribution of suitable niches of studied species is generally congruent with the known geographical ranges of particular taxa. The calculated niche overlap did not indicate any correlation between niche overlap and species phylogenetic relationships and remains low for both intra- and intergeneric relationships. The reconstruction of climatic tolerance evolution indicated that the studied species of Brasolia and Sobralia are characterized by generally similar ecological tolerance for most of the analyzed variables.

Niche diversification of Mediterranean and southwestern Asian tortoises

Background

Tortoises of the genus Testudo are widely distributed throughout the Mediterranean region and southwestern Asia. However, the evolutionary mechanisms of diversification in this genus are still poorly understood.

Methods

In this study, we assessed the evolutionary patterns in the climate niches of five species and 11 subspecies of the genus Testudo using ecological niche models and evaluated the niche overlap based on species phylogenetic distances.

Results

The ecological models indicated that most species differ in their climate niches, but show overlap, with gradual transitions at range boundaries. As expected, the ecological divergence among subspecies was lower than that among species. Evaluation of the phylogenetic signal indicated that climate niches have been weakly conserved, but sister species also show high evolutionary divergence.

Ecological and Phenotypic Diversification after A Continental Invasion in Neotropical Freshwater Stingrays

Habitat transitions are key potential explanations for why some lineages have diversified and others have not - from Anolis lizards to Darwin's finches. The ecological ramifications of marine-to-freshwater transitions for fishes suggest evolutionary contingency: some lineages maintain their ancestral niches in novel habitats (niche conservatism), whereas others alter their ecological role. However, few studies have considered phenotypic, ecological, and lineage diversification concurrently to explore this issue. Here, we investigated the macroevolutionary history of the taxonomically and ecologically diverse Neotropical freshwater river rays (subfamily Potamotrygoninae), which invaded and diversified in the Amazon and other South American rivers during the late Oligocene to early Miocene. We generated a time-calibrated, multi-gene phylogeny for Potamotrygoninae and reconstructed evolutionary patterns of diet specialization. We measured functional morphological traits relevant for feeding and used comparative phylogenetic methods to examine how feeding morphology diversified over time. Potamotrygonine trophic and phenotypic diversity are evenly partitioned (non-overlapping) among internal clades for most of their history, until 20-16 mya, when more recent diversification suggests increasing overlap among phenotypes. Specialized piscivores (Heliotrygon and Paratrygon) evolved early in the history of freshwater stingrays, while later trophic specialization (molluscivory, insectivory, and crustacivory) evolved in the genus Potamotrygon. Potamotrygonins demonstrate ecological niche lability in diets and feeding apparatus; however, diversification has mostly been a gradual process through time. We suggest that competition is unlikely to have limited the potamotrygonine invasion and diversification in South America.

Representing plant diversity in land models: An evolutionary approach to make "Functional Types" more functional

Plants are critical mediators of terrestrial mass and energy fluxes, and their structural and functional traits have profound impacts on local and global climate, biogeochemistry, biodiversity, and hydrology. Yet, Earth System Models (ESMs), our most powerful tools for predicting the effects of humans on the coupled biosphere-atmosphere system, simplify the incredible diversity of land plants into a handful of coarse categories of "Plant Functional Types" (PFTs) that often fail to capture ecological dynamics such as biome distributions. The inclusion of more realistic functional diversity is a recognized goal for ESMs, yet there is currently no consistent, widely accepted way to add diversity to models, that is, to determine what new PFTs to add and with what data to constrain their parameters. We review approaches to representing plant diversity in ESMs and draw on recent ecological and evolutionary findings to present an evolution-based functional type approach for further disaggregating functional diversity. Specifically, the prevalence of niche conservatism, or the tendency of closely related taxa to retain similar ecological and functional attributes through evolutionary time, reveals that evolutionary relatedness is a powerful framework for summarizing functional similarities and differences among plant types. We advocate that Plant Functional Types based on dominant evolutionary lineages ("Lineage Functional Types") will provide an ecologically defensible, tractable, and scalable framework for representing plant diversity in next-generation ESMs, with the potential to improve parameterization, process representation, and model benchmarking. We highlight how the importance of evolutionary history for plant function can unify the work of disparate fields to improve predictive modeling of the Earth system.

Phylogenomics and continental biogeographic disjunctions: insight from the Australian starflowers (Calytrix)

PREMISE

Continental-scale disjunctions and associated drivers are core research interests in biogeographic studies. Here, we selected a species-rich Australian plant genus (Calytrix; Myrtaceae) as a case study to investigate these patterns. Species of this endemic Australian starflower genus have a disjunct distribution across the mesic fringes of the continent and are largely absent from the arid center.

METHODS

We used high-throughput sequencing to generate unprecedented resolution and near complete species-level nuclear and plastid phylogenies for Calytrix. BioGeoBEARS and biogeographic stochastic mapping were used to infer ancestral areas, the relative contributions of vicariance and dispersal events, and directionality of dispersal.

RESULTS

Present-day disjunctions in Calytrix are explained by a combination of scenarios: (1) retreat of multiple lineages from the continental center to the more mesic fringes as Australia became progressively more arid, with subsequent extinction in the center as well as (2) origination of ancestral lineages in southwestern Australia (SWA) for species-rich clades. The SWA biodiversity hotspot is a major diversification center and the most common source area of dispersals, with multiple lineages originating in SWA and subsequently spreading to the adjacent arid Eremaean region.

CONCLUSIONS

Our results suggest that major extinction, as a result of cooling and drying of the Australian continent in the Eocene-Miocene, shaped the present-day biogeography of Calytrix. We hypothesize that this peripheral vicariance pattern, which is similar to the African Rand flora, may explain the disjunctions of many other Australian plant groups. Further studies with densely sampled phylogenies are required to test this hypothesis.

Defining Biologically Meaningful Biomes Through Floristic, Functional, and Phylogenetic Data

While we have largely improved our understanding on what biomes are and their utility in global change ecology, conservation planning, and evolutionary biology is clear, there is no consensus on how biomes should be delimited or mapped. Existing methods emphasize different aspects of biomes, with different strengths and limitations. We introduce a novel approach to biome delimitation and mapping, based upon combining individual regionalizations derived from floristic, functional, and phylogenetic data linked to environmentally trained species distribution models. We define “core Biomes” as areas where independent regionalizations agree and “transition zones” as those whose biome identity is not corroborated by all analyses. We apply this approach to delimiting the neglected Caatinga seasonally dry tropical forest biome in northeast Brazil. We delimit the “core Caatinga” as a smaller and more climatically limited area than previous definitions, and argue it represents a floristically, functionally, and phylogenetically coherent unit within the driest parts of northeast Brazil. “Caatinga transition zones” represent a large and biologically important area, highlighting that ecological and evolutionary processes work across environmental gradients and that biomes are not categorical variables. We discuss the differences among individual regionalizations in an ecological and evolutionary context and the potential limitations and utility of individual and combined biome delimitations. Our integrated ecological and evolutionary definition of the Caatinga and associated transition zones are argued to best describe and map biologically meaningful biomes.

Exploring the role of climatic niche changes in the evolution of the southern South American genus Baripus (Coleoptera: Carabidae): optimization of non-hereditary climatic variables and phylogenetic signal measurement

Baripus is a ground beetle genus endemic to southern South America, currently distributed across grassland and shrub habitats in mountain and lowland regions. The species of this genus are known to have been affected by the Andean orogeny and the climate changes that occurred during this process. In this study, we seek to understand how the orogeny of the Andes may have led to changes in the climatic niches of the species of Baripus over time. We integrated former ecological and historical biogeographic hypotheses, exploring the use of parsimony optimization of phylogenetically structured climate variables and ancestral character state reconstruction methods. We then performed regression analyses of the optimized climatic niche variables within the phylogenetic tree of Baripus. We were able to infer significant climatic niche constraints, and niche changes that provide new insights to the existing knowledge, supporting former ecological and biogeographic hypotheses for this genus. Such trends in climatic niche could be explained by the rain shadow effect caused by the Andean uplift as well as with other climate shifts associated with temperature and precipitation swings that occurred in this region from the Middle Miocene to the Pliocene.

Do mutualistic interactions last longer than antagonistic interactions?

Species interactions are crucial and ubiquitous across organisms. However, it remains unclear how long these interactions last over macroevolutionary timescales, and whether the nature of these interactions (mutualistic versus antagonistic) helps predict how long they persist. Here, we estimated the ages of diverse species interactions, based on phylogenies from 60 studies spanning the Tree of Life. We then tested if mutualistic interactions persist longer than antagonistic interactions. We found that the oldest mutualisms were significantly older than the oldest antagonisms across all organisms, and within plants, fungi, bacteria and protists. Surprisingly, this pattern was reversed in animals, with the oldest mutualisms significantly younger than the oldest antagonisms. We also found that many mutualisms were maintained for hundreds of millions of years (some greater than 1 billion years), providing strong evidence for the long-term stability of mutualisms and for niche conservatism in species interactions.

Ectomycorrhizas and tipping points in forest ecosystems

The resilience of forests is compromised by human-induced environmental influences pushing them towards tipping points and resulting in major shifts in ecosystem state that might be difficult to reverse, are difficult to predict and manage, and can have vast ecological, economic and social consequences. The literature on tipping points has grown rapidly, but almost exclusively based on aquatic and aboveground systems. So far little effort has been made to make links to soil systems, where change is not as drastically apparent, timescales may differ and recovery may be slower. Predicting belowground ecosystem state transitions and recovery, and their impacts on aboveground systems, remains a major scientific, practical and policy challenge. Recently observed major changes in aboveground tree condition across European forests are probably causally linked to ectomycorrhizal (EM) fungal changes belowground. Based on recent breakthroughs in data collection and analysis, we apply tipping point theory to forests, including their belowground component, focusing on EM fungi; link environmental thresholds for EM fungi with nutrient imbalances in forest trees; explore the role of phenotypic plasticity in EM fungal adaptation to, and recovery from, environmental change; and propose major positive feedback mechanisms to understand, address and predict forest ecosystem tipping points.

Herpetological phylogeographic analyses support a Miocene focal point of Himalayan uplift and biological diversification

The Himalaya are among the youngest and highest mountains in the world, but the exact timing of their uplift and origins of their biodiversity are still in debate. The Himalayan region is a relatively small area but with exceptional diversity and endemism. One common hypothesis to explain the rich montane diversity is uplift-driven diversification-that orogeny creates conditions favoring rapid in situ speciation of resident lineages. We test this hypothesis in the Himalayan region using amphibians and reptiles, two environmentally sensitive vertebrate groups. In addition, analysis of diversification of the herpetofauna provides an independent source of information to test competing geological hypotheses of Himalayan orogenesis. We conclude that the origins of the Himalayan herpetofauna date to the early Paleocene, but that diversification of most groups was concentrated in the Miocene. There was an increase in both rates and modes of diversification during the early to middle Miocene, together with regional interchange (dispersal) between the Himalaya and adjacent regions. Our analyses support a recently proposed stepwise geological model of Himalayan uplift beginning in the Paleocene, with a subsequent rapid increase of uplifting during the Miocene, finally giving rise to the intensification of the modern South Asian Monsoon.

Evolution of shade tolerance is associated with attenuation of shade avoidance and reduced phenotypic plasticity in North American milkweeds

PREMISE

Mismatches between light conditions and light-capture strategy can reduce plant performance and prevent colonization of novel habitats. Although light-capture strategies tend to be highly conserved among closely related species, evolutionary transitions from shaded to unshaded habitats (and vice versa) occur in numerous plant lineages.

METHODS

We combined phylogenetic approaches with field and greenhouse experiments to investigate evolutionary constraints on light-capture strategy in North American milkweeds (genus Asclepias) and to determine whether colonization of shaded habitats in this heliophilic clade is associated with reduced plasticity and attenuation of the shade avoidance response.

RESULTS

Colonization of shaded habitats has occurred at least 10 times in this genus, including at least once in each major North American clade. Evolutionary transitions between habitats exhibit strong directional bias, with shifts from full-sun to shaded habitats occurring at least three times as often as the opposite transition. In field and greenhouse experiments, sun species responded to shade by increasing internode length, height, and specific leaf area, consistent with the shade avoidance response; paired shade species exhibited reduced plasticity overall, and only one trait (specific leaf area) responded to experimental shade.

CONCLUSIONS

Our results suggest that milkweeds colonized shaded environments multiple times using a light-capture strategy distinct from the ancestral (putatively shade avoidant) strategy, including a general attenuation of plasticity in response to variable light conditions. This pattern bolsters the notion that shade avoidance and tolerance represent divergent evolutionary strategies for maximizing performance under qualitatively different types of shade.

Macroecological diversification and convergence in a clade of keystone symbionts

Lichens are classic models of symbiosis, and one of the most frequent nutritional modes among fungi. The ecologically and geographically widespread lichen-forming algal (LFA) genus Trebouxia is one of the best-studied groups of LFA and associates with over 7000 fungal species. Despite its importance, little is known about its diversification. We synthesized twenty years of publicly available data by characterizing the ecological preferences of this group and testing for time-variant shifts in climatic regimes over a distribution of trees. We found evidence for limited shifts among regimes, but that disparate lineages convergently evolved similar ecological tolerances. Early Trebouxia lineages were largely forest specialists or habitat generalists that occupied a regime whose extant members occur in moderate climates. Trebouxia then convergently diversified in non-forested habitats and expanded into regimes whose modern representatives occupy wet-warm and cool-dry climates. We rejected models in which climatic diversification slowed through time, suggesting climatic diversification is inconsistent with that expected under an adaptive radiation. In addition, we found that climatic and vegetative regime shifts broadly coincided with the evolution of biomes and associated or similar taxa. Together, our work illustrates how this keystone symbiont from an iconic symbiosis evolved to occupy diverse habitats across the globe.

Plastome-based phylogeny improves community phylogenetics of subtropical forests in China

Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.

Seed dispersers shape the pulp nutrients of fleshy-fruited plants

The dispersal-syndrome hypothesis posits that fruit traits are a product of selection by frugivores. Although criticized as adaptationist, recent studies have suggested that traits such as fruit or seed size, colour and odour exhibit signatures that imply selection by animal mutualists. These traits imply nutritional rewards (e.g. lipid, carbohydrate), attracting frugivores; however, this remains incompletely resolved. Here, we investigated whether fruit nutrients (lipid, sugar, protein, vitamin C, water content) moderate the co-adaptation of key disperser-group mutualisms. Multivariate techniques revealed that fruit nutrients assembled non-randomly and grouped according to key dispersal modes. Bird-dispersed fruits were richer in lipids than mammal-dispersed fruits. Mixed-dispersed fruits had significantly higher vitamin C than did mammal- or bird-dispersed fruits separately. Sugar and water content were consistently high irrespective of dispersal modes, suggesting that these traits appeal to both avian and mammalian frugivores to match high-energy requirements. Similarly, protein content was low irrespective of dispersal modes, corroborating that birds and mammals avoid protein-rich fruits, which are often associated with toxic levels of nitrogenous secondary compounds. Our results provide substantial over-arching evidence that seed disperser assemblages co-exert fundamental selection pressures on fruit nutrient trait adaptation, with broad implications for structuring fruit-frugivore mutualism and maintaining fruit trait diversity.

Does a trade-off between growth plasticity and resource conservatism mediate post-fire shrubland responses to rainfall seasonality?

Growth plasticity may allow fire-prone species to maximize their recovery rates during temporary, sporadic periods of rainfall availability in the post-fire environment. However, moisture-driven growth plasticity could be maladaptive in nutrient-limited environments that require tighter control of growth and resource use. We investigated whether a trade-off between plasticity and conservatism mediates growth responses to altered rainfall seasonality in neighbouring shrubland communities that occupy different soils. We monitored post-fire vegetation regrowth in two structurally similar, Mediterranean-type shrublands for 3 years. We investigated the effects of experimentally altered rainfall seasonality on post-fire species' growth rates. We found that moisture-driven growth plasticity was higher among species occupying the fertile soils of the renosterveld site relative to those occupying the nutrient-poor soils of the fynbos site. This resulted in higher overall responsiveness of post-fire recovery patterns in renosterveld to experimental shifts in rainfall seasonality. In post-fire shrubland communities, the trade-off between moisture-dependent growth plasticity and resource conservatism could be mediated by soil nutrient availability. Therefore, edaphic differences between structurally similar shrublands could lead to differences in their sensitivity to post-fire rainfall seasonality.

Phylogenetic relatedness of woody angiosperm assemblages and its environmental determinants along a subtropical elevational gradient in China

The species composition of plant communities is determined by a number of factors, including current environmental conditions as well as biogeographical and evolutionary history. Despite evidence that plant diversity decreases and species relatedness increases along latitudinal and environmental gradients (e.g., low temperatures), it remains unclear whether these same patterns occur along elevational gradients, especially in the subtropical mountainous areas harboring rich biodiversity. In this study, we explored the pattern of phylogenetic relatedness of woody angiosperm assemblages and examined the effects of temperature variables on the phylogenetic relatedness among angiosperm woody plants using generalized linear model in subtropical forest communities along a broad elevational gradient in the Dulong Valley of Yunnan Province, China. Our results showed that woody angiosperm species in local forest plots tend to be more phylogenetically related at higher elevations and in areas with lower temperatures. Additionally, winter average temperature, rather than mean annual temperature, is a major predictor of the pattern of increasing phylogenetic relatedness with increasing elevation. This finding is consistent with the prediction of 'Tropical Niche Conservatism' hypothesis, which highlights the role of niche constraints in driving phylogenetic community assembly along an elevational gradient.

Bridging Rare and Abundant Bacteria with Ecosystem Multifunctionality in Salinized Agricultural Soils: from Community Diversity to Environmental Adaptation

Bacterial diversity and ecosystem multifunctionality (EMF) vary along environmental gradients. However, little is known about interconnections between EMF and taxonomic and phylogenetic diversities of rare and abundant bacteria. Using MiSeq sequencing and multiple statistical analyses, we evaluated the maintenance of taxonomic and phylogenetic diversities of rare and abundant bacteria and their contributions to EMF in salinized agricultural soils (0.09 to 19.91 dS/m). Rare bacteria exhibited closer phylogenetic clustering and broader environmental breadths than abundant ones, while abundant bacteria showed higher functional redundancies and stronger phylogenetic signals of ecological preferences than rare ones. Variable selection (86.7%) dominated rare bacterial community assembly, and dispersal limitation (54.7%) and variable selection (24.5%) determined abundant bacterial community assembly. Salinity played a decisive role in mediating the balance between stochastic and deterministic processes and showed significant effects on functions and diversities of both rare and abundant bacteria. Rare bacterial taxonomic α-diversity and abundant bacterial phylogenetic α-diversity contributed significantly to EMF, while abundant bacterial taxonomic α-diversity and rare bacterial phylogenetic α-diversity did not. Additionally, abundant rather than rare bacterial community function had a significant effect on soil EMF. These findings extend our knowledge of environmental adaptation of rare and abundant bacteria and highlight different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF.IMPORTANCE Soil salinization is a worldwide environmental problem and threatens plant productivity and microbial diversity. Understanding the generation and maintenance of microbial diversity is essential to estimate soil tillage potential via investigating ecosystem multifunctionality. Our sequence-based data showed differences in environmental adaptations of rare and abundant bacteria at taxonomic and phylogenetic levels, which led to different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF. Studying the diversity of rare and abundant bacteria and their contributions to EMF in salinized soils is critical for guiding soil restoration.

Historical biogeography of Pomaderris (Rhamnaceae): Continental vicariance in Australia and repeated independent dispersals to New Zealand

AIM

Gondwanan biogeographic patterns include a combination of old vicariance events following the breakup of the supercontinent, and more recent long-distance dispersals across the southern landmasses. Floristic relationships between Australia and New Zealand have mostly been attributed to recent dispersal events rather than vicariance. We assessed the biogeographic history of Pomaderris (Rhamnaceae), which occurs in both Australia and New Zealand, by constructing a time-calibrated molecular phylogeny to infer (1) phylogenetic relationships and (2) the relative contributions of vicariance and dispersal events in the biogeographic history of the genus.

LOCATION

Australia and New Zealand.

METHODS

Using hybrid capture and high throughput sequencing, we generated nuclear and plastid data sets to estimate phylogenetic relationships and fossil calibrated divergence time estimates for Pomaderris. BioGeoBEARS and biogeographical stochastic mapping (BSM) were used to assess the ancestral area of the genus and the relative contributions of vicariance vs dispersal, and the directionality of dispersal events.

RESULTS

Our analyses indicate that Pomaderris originated in the Oligocene and had a widespread Australian distribution. Vicariance of western and eastern Australian clades coincides with the uplift of the Nullarbor Plain c. 14 Ma, followed by subsequent in-situ and within-biome diversification with little exchange across regions. A rapid radiation of southeastern Australian taxa beginning c. 10 Ma was the source for at least six independent long-distance dispersal events to New Zealand during the Pliocene-Pleistocene.

MAIN CONCLUSIONS

Our study demonstrates the importance of dispersal in explaining not only the current cross-Tasman distributions of Pomaderris, but for the New Zealand flora more broadly. The pattern of multiple independent long-distance dispersal events for Pomaderris, without significant radiation within New Zealand, is congruent with other lowland plant groups, suggesting that this biome has a different evolutionary history compared with the younger alpine flora of New Zealand, which exhibits extensive radiations often following single long distance dispersal events.

Impacts of growth form and phylogenetic relatedness on seed germination: A large-scale analysis of a subtropical regional flora

Plant regeneration strategy plays a critical role in species survival and can be used as a proxy for the evolutionary response of species to climate change. However, information on the effects of key plant traits and phylogenetic relatedness on seed germination is limited at large regional scales that vary in climate. To test the hypotheses that phylogenetic niche conservatism plays a critical force in shaping seed ecophysiological traits across species, and also drives their response to climatic fluctuation, we conducted a controlled experiment on seed germination and determined the percentage and rate of germination for 249 species in subtropical China under two temperature regimes (i.e., daily 25°C; daily alternating 25/15°C for each 12 hr). Germination was low with a skewed distribution (mean = 38.9% at 25°C, and 43.3% at 25/15°C). One fifth of the species had low (<10%) and slow (4-30 days) germination, and only a few (8%) species had a high (>80%) and rapid (1.2-6.6 days) germination. All studied plant traits (including germination responses) showed a significant phylogenetic signal, with an exception of seed germination percentage under the alternating temperature scenario. Generalized linear models (GLMs) and phylogenetic generalized estimation equations (GEEs) demonstrated that growth form and seed dispersal mode were strong drivers of germination. Our experimental study highlights that integrating plant key traits and phylogeny is critical to predicting seed germination response to future climate change.

Out of the OCBILs: new hypotheses for the evolution, ecology and conservation of the eucalypts

OCBIL theory is a multi-hypothesis formulation aimed towards an understanding of the evolution, ecology and conservation of biological and cultural diversity on old, climatically buffered, infertile landscapes (OCBILs). OCBILs have been in existence contemporaneously with rainforest since Gondwanan times. Such landscapes are common in areas of eucalypt species richness embraced by Australia’s two Global Biodiversity Hotspots, the Southwest Australian Floristic Region and the Forests of East Australia. Here, I summarize evidence pertaining to the eucalypts in the context of a recent reformulation of OCBIL theory into 12 evolutionary, ecological and cultural hypotheses and ten conservation management hypotheses. A compelling argument emerges for a new interpretation of the eucalypts evolving out of the OCBILs, rather than out of the rainforests as traditionally interpreted. This calls for a significant reinterpretation of best conservation management of the eucalypts. For example, traditional ideas on application of fire in eucalypt communities regarded as well adapted to this disturbance need to give way to a more nuanced and cautious view. This review of eucalypts seen as evolving out of the OCBILs helps in understanding the group from several new perspectives. Interpretation of other sedentary plant and animal groups as out of the OCBILs is commended for further study.

Does Cathaya argyrophylla, an ancient and threatened Pinaceae species endemic to China, show eco-physiological outliers to its Pinaceae relatives?

Cathaya argyrophylla is an ancient and threatened Pinaceae species endemic to China, but its eco-physiological traits are rarely reported. We hypothesized that Cathaya showed eco-physiological outliers to its Pinaceae relatives, which lead to its current endangered status. Here we collected the photosynthetic capacity (P _n, maximum photosynthesis rate) and branchlet hydraulic safety (P ₅₀, the water potential at which a 50% loss in conductivity occurs) of Pinaceae species globally, including our measurements on Cathaya. We applied the phylogenetic comparative methods to investigate: (i) the phylogenetic signal of the two key traits across Pinaceae species, and (ii) the trait-climate relationships and the photosynthesis-cavitation resistance relationship across Pinaceae species. We applied the polygenetic quantile regression (PQR) method to assess whether Cathaya showed eco-physiological outliers to its Pinaceae relatives in terms of cavitation resistance and photosynthetic capacity. It was found that P ₅₀, and to a less extent, P _n, had a strong phylogenetic signal consistent with niche conservation among Pinaceae species. Hydraulic safety largely determined non-threatened Pinaceae species' distribution across moisture gradients at the global scale. There was also an adaptive trade-off relationship between P _n and P ₅₀. Cathaya is a high cavitation resistant, low photosynthetic capacity species. It showed eco-physiological outliers to its Pinaceae relatives because it had lower P ₅₀ and P _n below the 10% quantile boundaries along moisture and/or temperature gradients; also, it was above the 90% quantile boundary of the P _n and P ₅₀ relationship across non-endangered Pinaceae species. The PQR output demonstrated that in the subtropical area of China characterized by abundant rainfall, Cathaya has extra high hydraulic safety, suggesting inefficiency of carbon economy associated with either competition or other life history strategies, which lead to its current endangered status.

The role of ecological niche evolution on diversification patterns of birds distinctly distributed between the Amazonia and Atlantic rainforests

The Amazonian and Atlantic Forest share several organisms that are currently isolated but were continuously distributed during the Quaternary period. As both biomes are under different climatic regimes, paleoclimatic events may have modulated species' niches due to a lack of gene flow and imposing divergent selection pressure. Here, we assessed patterns of ecological niche overlap in 37 species of birds with disjunct ranges between the Amazonian and Brazilian Atlantic Forests. We performed niche overlap analysis and ecological niche modeling using four machine-learning algorithms to evaluate whether species' ecological niches evolved or remained conserved after the past South American biogeographic events. We found a low niche overlap among the same species populations in the two biomes. However, niche similarity tests showed that, for half of the species, the overlap was higher than the ones generated by our null models. These results lead us to conclude that niche conservatism was not enough to avoid ecological differentiation among species even though detected in many species. In sum, our results support the role of climatic changes in late-Pleistocene—that isolated Amazon and the Atlantic Forest—as a driving force of ecological differences among the same species populations and potential mechanism of current diversification in both regions.

Root colonization and arbuscular mycorrhizal fungal community composition in a genetically modified maize, its non-modified isoline, and a landrace

The use of genetically modified (GM) plants has increased in recent decades, but there are uncertainties about their effects on soil microbial communities. Aiming to quantify root colonization and characterize arbuscular mycorrhizal fungi (AMF) communities associated with roots and rhizosphere soil of different maize genotypes, a field trial was carried out in Southern Brazil with three maize genotypes as follows: a GM hybrid (DKB 240 VTPRO), its non-modified isoline (DKB 240), and a landrace (Pixurum). Soil samples were collected to evaluate the occurrence of AMF during the growth of corn genotypes at sowing and V3 (vegetative), R1 (flowering), and R3 (grain formation) stages of the crop. The occurrence of AMF was determined by the morphological identification of spores, and by analyzing AMF community composition in soil and roots of maize, using PCR-DGGE. The GM genotype of maize promoted lower mycorrhizal colonization in the vegetative stage and had lower sporulation at grain development than the conventional hybrid and the landrace maize. Twenty AMF morphotypes were identified and 13 were associated with all maize genotypes. The genera Acaulospora, Glomus, and Dentiscutata had the largest numbers of species. There were no differences in AMF community composition due to maize genotypes or genetic modification, but crop phenological stages affected AMF communities associated with maize roots.

The Snowmelt Niche Differentiates Three Microbial Life Strategies That Influence Soil Nitrogen Availability During and After Winter

Soil microbial biomass can reach its annual maximum pool size beneath the winter snowpack and is known to decline abruptly following snowmelt in seasonally snow-covered ecosystems. Observed differences in winter versus summer microbial taxonomic composition also suggests that phylogenetically conserved traits may permit winter- versus summer-adapted microorganisms to occupy distinct niches. In this study, we sought to identify archaea, bacteria, and fungi that are associated with the soil microbial bloom overwinter and the subsequent biomass collapse following snowmelt at a high-altitude watershed in central Colorado, United States. Archaea, bacteria, and fungi were categorized into three life strategies (Winter-Adapted, Snowmelt-Specialist, Spring-Adapted) based upon changes in abundance during winter, the snowmelt period, and after snowmelt in spring. We calculated indices of phylogenetic relatedness (archaea and bacteria) or assigned functional attributes (fungi) to organisms within life strategies to infer whether phylogenetically conserved traits differentiate Winter-Adapted, Snowmelt-Specialist, and Spring-Adapted groups. We observed that the soil microbial bloom was correlated in time with a pulse of snowmelt infiltration, which commenced 65 days prior to soils becoming snow-free. A pulse of nitrogen (N, as nitrate) occurred after snowmelt, along with a collapse in the microbial biomass pool size, and an increased abundance of nitrifying archaea and bacteria (e.g., Thaumarchaeota, Nitrospirae). Winter- and Spring-Adapted archaea and bacteria were phylogenetically clustered, suggesting that phylogenetically conserved traits allow Winter- and Spring-Adapted archaea and bacteria to occupy distinct niches. In contrast, Snowmelt-Specialist archaea and bacteria were phylogenetically overdispersed, suggesting that the key mechanism(s) of the microbial biomass crash are likely to be density-dependent (e.g., trophic interactions, competitive exclusion) and affect organisms across a broad phylogenetic spectrum. Saprotrophic fungi were the dominant functional group across fungal life strategies, however, ectomycorrhizal fungi experienced a large increase in abundance in spring. If well-coupled plant-mycorrhizal phenology currently buffers ecosystem N losses in spring, then changes in snowmelt timing may alter ecosystem N retention potential. Overall, we observed that snowmelt separates three distinct soil niches that are occupied by ecologically distinct groups of microorganisms. This ecological differentiation is of biogeochemical importance, particularly with respect to the mobilization of nitrogen during winter, before and after snowmelt.

Phylogenetic niche conservatism and plant diversification in South American subtropical grasslands along multiple climatic dimensions

Phylogenetic niche conservatism can be investigated at multiple scales on an explicit geographical context. Haplotype-based comparative analyses of lineages occupying the same region, and thus subjected to similar environmental factors, allow decoupling shared evolutionary and ecological patterns, as well as multiple dimensions of adaptive diversification. Here we aimed to assess the role of environmental drivers on diversification of subtropical grassland, based on haplotypic diversity of two plant genera. We sampled two closely related and co-distributed grassland plant genera, Petunia and Calibrachoa, across their entire distribution area. Eigenvectors extracted from pairwise distances based on chloroplast DNA haplotypes were used to fit Phylogenetic Signal-Representation (PSR) curves to estimate evolutionary patterns in 19 bioclimatic variables and altitude. The PSR curves showed that altitude, precipitation, and temperature variables changed at different rates with haplotype differentiation. Altitude and temperature traits evolved under conditions closer to a neutral dynamics, whereas precipitation traits differentiated following more complex models. Our results indicated that the diversification in the two genera was more limited by precipitation conditions. Based on these novel findings, we suggest that future studies should test the possible impact of precipitation variables on the process of ecological differentiation in these genera.

Climatic-niche evolution follows similar rules in plants and animals

Climatic niches are essential in determining where species can occur and how they will respond to climate change. However, it remains unclear if climatic-niche evolution is similar in plants and animals or is intrinsically different. For example, previous authors have proposed that plants have broader environmental tolerances than animals but are more sensitive to climate change. Here, we test ten predictions about climatic-niche evolution in plants and animals, using phylogenetic and climatic data for 19 plant clades and 17 vertebrate clades (2,087 species total). Surprisingly, we find that for all ten predictions, plants and animals show similar patterns. For example, in both groups, climatic niches change at similar mean rates and species have similar mean niche breadths, and niche breadths show similar relationships with latitude across groups. Our results suggest that there are general 'rules' of climatic-niche evolution that span plants and animals, despite the fundamental differences in their biology. These results may help to explain why plants and animals have similar responses to climate change and why they often have shared species richness patterns, biogeographic regions, biomes and biodiversity hotspots.

Increasing the phylogenetic coverage for understanding broad-scale diversity gradients

Despite decades of scientific effort, there is still no consensus on the determinants of broad-scale gradients of animal diversity. We argue that general drivers of diversity are unlikely to be found among the narrowly defined taxa which are typically analyzed in studies of broad-scale diversity gradients because ecological niches evolve largely conservatively. This causes constraints in the use of available niche space leading to systematic differences in diversity gradients among taxa. We instead advocate studies of phylogenetically diverse animal communities along broad environmental gradients. Such multi-taxa communities are less constrained in resource use and diversification and may be better targets for testing major classical hypotheses on diversity gradients. Besides increasing the spatial scale in analyses, expanding the phylogenetic coverage may be a second way to achieve higher levels of generality in studies of broad-scale diversity gradients.

Plant Phylogeny and Growth Form as Drivers of the Altitudinal Variation in Woody Leaf Vein Traits

Variation in leaf veins along environmental gradients reflects an important adaptive strategy of plants to the external habitats, because of their crucial roles in maintaining leaf water status and photosynthetic capacity. However, most studies concentrate on a few species and their vein variation across horizontal spatial scale, we know little about how vein traits shift along the vertical scale, e.g., elevational gradient along a mountain, and how such patterns are shaped by plant types and environmental factors. Here, we aimed to investigate the variation in leaf vein traits (i.e., vein density, VD; vein thickness, VT; and vein volume per unit leaf area, VV) of 93 woody species distributed along an elevational gradient (1,374-3,375 m) in a temperate mountain in China. Our results showed that altitude-related trends differed between growth forms. Tree plants from higher altitudes had lower VD but higher VT and VV than those from lower altitude; however, the opposite tend was observed in VD of shrubs, and no significant altitudinal changes in their VT or VV. Plant phylogenetic information at the clade level rather than climate explained most of variation in three leaf vein traits (17.1-86.6% vs. <0.011-6.3% explained variance), supporting the phylogenetic conservatism hypothesis for leaf vein traits. Moreover, the phylogenetic effects on vein traits differed between trees and shrubs, with the vein traits of trees being relatively more conserved. Together, our study provides new picture of leaf vein variation along the altitude, and highlights the importance of taking plant phylogeny into consideration when discussing trait variation from an ecological to a biogeographic scale.

Passive rewilding may (also) restore phylogenetically rich and functionally resilient forest plant communities

Passive rewilding is increasingly seen as a promising tool to counterbalance biodiversity losses and recover native forest ecosystems. One key question, crucial to understanding assembly processes and conservation issues underlying land-use change, is the extent to which functional and phylogenetic diversity may recover in spontaneous recent woodlands. Here, we compared understorey plant communities of recent woodlands (which result from afforestation on agricultural lands during the 20th century) with those of ancient forests (uninterrupted for several centuries) in a hotspot of farmland abandonment in western Europe. We combined taxonomic, functional, and phylogenetic diversity metrics to detect potential differences in community composition, structure (richness, divergence), conservation importance (functional originality and specialization, evolutionary distinctiveness) and resilience (functional redundancy, response diversity). The recent and ancient forests harbored clearly distinct compositions, especially regarding the taxonomic and phylogenetic facets. Recent woodlands had higher taxonomic, functional and phylogenetic richness and a higher evolutionary distinctiveness, whereas functional divergence and phylogenetic divergence were higher in ancient forests. On another hand, we did not find any significant differences in functional specialization, originality, redundancy, or response diversity between recent and ancient forests. Our study constitutes one of the first empirical pieces of evidence that recent woodlands may spontaneously regain plant communities phylogenetically rich and functionally resilient, at least as much as those of ancient relict forests. As passive rewilding is the cheapest restoration method, we suggest that it should be a very useful tool to restore and conserve native forest biodiversity and functions, especially when forest areas are restricted and fragmented.

Climate and evolutionary history define the phylogenetic diversity of vegetation types in the central region of South America

In South America the biogeographic history has produced different biomes with different vegetation types and distinct floras. As these vegetation types may diverge in evolutionary histories, we analysed how alpha and beta phylogenetic diversity vary across them and determine the main drivers of variation in phylogenetic diversity. To this end, we compiled a list of 205 sites and 1222 tree species spread over four biomes and eight vegetation types in central South America. For each site we evaluated six measures of evolutionary alpha diversity (species richness, phylogenetic diversity sensu stricto and the standardized effect size of phylogenetic diversity, mean phylogenetic distance and mean nearest taxon distance) and beta diversity (phylogenetic Sorensen's similarity). We checked the influence of spatial and environmental variables using generalized least squares models. The greatest phylogenetic differentiation was found between west and east of central South America, mainly between the Chaco communities and the other vegetation types, suggesting that species found in this biome come from different lineages, comparing with the others vegetation types. Our results also showed a clustered phylogenetic structure for the Dry Chaco woodlands, which may be associated with harsh environmental conditions. In addition to historical process, climatic conditions are the main drivers shaping phylogenetic patterns among the distinct vegetation types. Understanding patterns of phylogenetic diversity and distribution can greatly improve conservation planning and management since it allows the conservation of unique biome characteristics.

Realistic scenarios of missing taxa in phylogenetic comparative methods and their effects on model selection and parameter estimation

Model-based analyses of continuous trait evolution enable rich evolutionary insight. These analyses require a phylogenetic tree and a vector of trait values for the tree's terminal taxa, but rarely do a tree and dataset include all taxa within a clade. Because the probability that a taxon is included in a dataset depends on ecological traits that have phylogenetic signal, missing taxa in real datasets should be expected to be phylogenetically clumped or correlated to the modelled trait. I examined whether those types of missing taxa represent a problem for model selection and parameter estimation. I simulated univariate traits under a suite of Brownian Motion and Ornstein-Uhlenbeck models, and assessed the performance of model selection and parameter estimation under absent, random, clumped or correlated missing taxa. I found that those analyses perform well under almost all scenarios, including situations with very sparsely sampled phylogenies. The only notable biases I detected were in parameter estimation under a very high percentage (90%) of correlated missing taxa. My results offer a degree of reassurance for studies of continuous trait evolution with missing taxa, but the problem of missing taxa in phylogenetic comparative methods still demands much further investigation. The framework I have described here might provide a starting point for future work.