Ecophylogenetics: advances and perspectives

Phylogeny structures species' interactions in experimental ecological communities

Species' traits and interactions are products of evolutionary history. Despite the long-standing hypothesis that closely related species possess similar traits, and thus experience stronger competition, measuring the effect of evolutionary history on the ecology of natural communities remains challenging. We propose a novel framework to test whether phylogeny influences patterns of coexistence and abundance of species assemblages. In our approach, phylogenetic trees are used to parameterize species' interactions, which in turn determine the abundance of species in a given assemblage. We use likelihoods to score models parameterized with a given phylogeny, and contrast them with models built using random trees, allowing us to test whether phylogenetic information helps to predict species' abundances. Our statistical framework reveals that interactions are indeed structured by phylogeny in a large set of experimental plant communities. Our results confirm that evolutionary history can help predict, and potentially manage or conserve, the structure and function of complex ecological communities.

Niche convergence and biogeographic history shape elevational tree community assembly in a subtropical mountain forest

Niche convergence or conservatism have been proposed as essential mechanisms underlying elevational plant community assembly in tropical mountain ecosystems. Subtropical mountains, compared to tropical mountains, are likely to be shaped by a mixing of different geographic affinities of species and remain somehow unclear. Here, we used 31 0.1-ha permanent plots distributed in subtropical forests on the eastern and western aspects of the Gaoligong Mountains, southwest China between 1498 m and 3204 m a.sl. to evaluate how niche-based and biogeographic processes shape tree community assembly along elevational gradients. We analyzed the elevational patterns of taxonomic, phylogenetic and functional diversity, as well as of individual traits, and assessed the relative importance of environmental effects on these diversity measures. We then classified tree species as being either tropical affiliated or temperate affiliated and estimated their contribution to the composition of biogeographic affinities. Species richness decreased with elevation, and species composition showed apparent turnover across the aspects and elevations. Most traits exhibited convergent patterns across the entire elevational gradient. Phylogenetic and functional diversity showed opposing patterns, with phylogenetic diversity increasing and functional diversity decreasing with elevation. Soil nutrients, especially phosphorus and nitrogen, appeared to be the main abiotic variables driving the elevational diversity patterns. Communities at lower elevations were occupied by tropical genera, while highlands contained species of tropical and temperate biogeographic affinities. Moreover, the high phylogenetic diversity at high elevations were likely due to differences in evolutionary history between temperate and tropical species. Our results highlight the importance of niche convergence of tropical species and the legacy of biogeographic history on the composition and structure of subtropical mountain forests. Furthermore, limited soil phosphorus caused traits divergence and the partitioning for different forms of phosphorus may explain the high biodiversity found in phosphorus-limited subtropical forests.

Variation in near-surface soil temperature drives plant assemblage differentiation across aspect

Quantifying assemblage variation across environmental gradients provides insight into the ecological and evolutionary mechanisms that differentiate assemblages locally within a larger climate regime. We assessed how vascular plant functional composition and diversity varied across microenvironment to identify ecological differences in assemblages in a mountainous fieldsite in northeastern Utah, USA. Then, we looked at how life-history strategies and information about phylogenetic differences affect the relationship between functional metrics and environment. We found less functionally dispersed assemblages that were shorter and more resource-conservative on south-facing slopes where intra-annual soil temperature was hotter and more variable. In contrast, we found more functionally dispersed assemblages, that were taller and more resource-acquisitive on north-facing slopes where intra-annual temperature was cooler and less variable. Herbaceous and woody perennials drove these trends. Additionally, including information about phylogenetic differences in a dispersion metric indicated that phylogeny accounts for traits we did not measure. At this fieldsite, soil temperature acts as an environmental filter across aspect. If soil temperature increases and becomes more variable, intra-annually, the function of north- versus south-facing assemblages may be at risk for contrasting reasons. On south-facing slopes, assemblages may not have the variance in functional diversity needed to respond to more intense, stressful conditions. Conversely, assemblages on north-facing slopes may not have the resource-conservative strategies needed to persist if temperatures become hotter and more variable intra-annually. Given these results, we advocate for the inclusion of aspect differentiation in studies seeking to understand species and assemblage shifts in response to changing climate conditions.

Macroecological correlates of Darwinian shortfalls across terrestrial vertebrates

Most described species have not been explicitly included in phylogenetic trees-a problem named the Darwinian shortfall-owing to a lack of molecular and/or morphological data, thus hampering the explicit incorporation of evolution into large-scale biodiversity analyses. We investigate potential drivers of the Darwinian shortfall in tetrapods, a group in which at least one-third of described species still lack phylogenetic data, thus necessitating the imputation of their evolutionary relationships in fully sampled phylogenies. We show that the number of preserved specimens in scientific collections is the main driver of phylogenetic knowledge accumulation, highlighting the major role of biological collections in unveiling novel biodiversity data and the importance of continued sampling efforts to reduce knowledge gaps. Additionally, large-bodied and wide-ranged species, as well as terrestrial and aquatic amphibians and reptiles, are phylogenetically better known. Future efforts should prioritize phylogenetic research on organisms that are narrow-ranged, small-bodied and underrepresented in scientific collections, such as fossorial species. Addressing the Darwinian shortfall will be imperative for advancing our understanding of evolutionary drivers shaping biodiversity patterns and implementing comprehensive conservation strategies.

Responses of multi-faceted benthic macroinvertebrates alpha and beta diversity to flooding in a highland floodplain

Flooding is an important process in natural fluvial floodplains. How the flood shapes aquatic community diversity in highland floodplains is still poorly understood. The aim of this study was to unravel the multi-faceted responses of benthic macroinvertebrate diversity to flooding and habitat environments in the Baihe River Basin from a taxonomic, phylogenetic, and functional perspective. We examined the alpha and beta diversity patterns of benthic macroinvertebrate communities in the mainstream, tributaries, and oxbow lakes during the normal water and flood periods. The results showed that the traditional alpha taxonomic diversity (TD) varied across habitats, despite minor changes after flood pulse. Alpha phylogenetic diversity (PD) decreased and alpha functional diversity (FD) markedly increased after flooding, with functional traits transiting toward risk avoidance. While all the three facets of beta diversity significantly responded to habitat differences, beta TD and PD shifted in response to flooding. Species turnover prominently increased in beta TD and PD after flood pulse, which contrasted with a weaker response of this process in FD. The explanatory power of significant environmental factors on both alpha and beta diversity was reduced by flooding. Compared with traditional TD, cooperating multi-faceted diversity could better depict the responses of benthic macroinvertebrate communities to flooding. The assessment and conservation of aquatic biodiversity in highland floodplains should take into account the three facets of alpha and beta diversity.

Environmental determinants of phylogenetic diversity in vernal pool habitats

Phylogenetic diversity offers critical insights into the ecological dynamics shaping species composition and ecosystem function, thereby informing conservation strategies. Despite its recognized importance in ecosystem management, the assessment of phylogenetic diversity in endangered habitats, such as vernal pools, remains limited. Vernal pools, characterized by cyclical inundation and unique plant communities, present an ideal system for investigating the interplay between ecological factors and phylogenetic structure. This study aims to characterize the phylogenetic patterns of vernal pools and their associated vegetation zones, addressing questions about taxonomic and phylogenetic community discreteness, the role of flooding as a habitat filter, the influence of invasive species on phylogenetic structure, and the impact of seasonal variation on phylogenetic diversity. I find that zones-of-vegetation exhibit high between zone taxonomic and phylogenetic beta diversity whereas each zone forms a unique cluster, suggesting that zones are taxonomically and phylogenetically discrete units. Regions of high-inundation pressure exhibit phylogenetic clustering, indicating that flooding is a habitat filter in vernal pool habitats. Competition between native species conform to the 'competitive relatedness hypothesis' and, conversely, communities dominated by invasive Eurasian grass species are phylogenetically clustered. In addition, I find that phylogenetic diversity within zones fluctuates across the spring season in response to changing water levels, precipitation, and temperature. By analyzing three pools within the Merced Vernal Pool and Grassland Reserve, this research elucidates the phylogenetic dynamics of vernal pools. The findings underscore the need for tailored conservation strategies that account for the unique ecological characteristics of each vegetation zone within vernal pool habitats.

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.

What Can Evolutionary History Tell Us about the Functioning of Ecological Communities? The ASN Presidential Debate

AbstractIn January 2018, Sharon Strauss, then president of the American Society of Naturalists, organized a debate on the following topic: does evolutionary history inform the current functioning of ecological communities? The debaters-Ives, Lau, Mayfield, and Tobias-presented pro and con arguments, caricatured in standard debating format. Numerous examples show that both recent microevolutionary and longer-term macroevolutionary history are important to the ecological functioning of communities. On the other hand, many other examples illustrate that the evolutionary history of communities or community members does not influence ecological function, or at least not very much. This article aims to provide a provocative discussion of the consistent and conflicting patterns that emerge in the study of contemporary and historical evolutionary influences on community function, as well as to identify questions for further study. It is intended as a thought-provoking exercise to explore this complex field, specifically addressing (1) key assumptions and how they can lead us astray and (2) issues that need additional study. The debaters all agree that evolutionary history can inform us about at least some aspects of community function. The underlying question at the root of the debate, however, is how the fields of ecology and evolution can most profitably collaborate to provide a deeper and broader understanding of ecological communities.

Glacial Influence Affects Modularity in Bacterial Community Structure in Three Deep Andean North-Patagonian Lakes

We analyze the bacteria community composition and the ecological processes structuring these communities in three deep lakes that receive meltwater from the glaciers of Mount Tronador (North-Patagonia, Argentina). Lakes differ in their glacial connectivity and in their turbidity due to glacial particles. Lake Ventisquero Negro is a recently formed proglacial lake and it is still in contact with the glacier. Lakes Mascardi and Frías lost their glacial connectivity during the Pleistocene-Holocene transition. Total dissolved solid concentration has a significant contribution to the environmental gradient determining the segregation of the three lakes. The newly formed lake Ventisquero Negro conformed a particular bacterial community that seemed to be more related to the microorganisms coming from glacier melting than to the other lakes of the basin. The net relatedness index (NRI) showed that the bacterial community of lake Ventisquero Negro is determined by environmental filtering, while in the other lakes, species interaction would be a more important driver. The co-occurrence network analysis showed an increase in modularity and in the number of modules when comparing Lake Ventisquero Negro with the two large glacier-fed lakes suggesting an increase in heterogeneity. At the same time, the presence of modules with phototrophic bacteria (Cyanobium strains) in lakes Frías and Mascardi would reflect the increase of this functional photosynthetic association. Overall, our results showed that the reduction in ice masses in Patagonia will affect downstream large deep Piedmont lakes losing the glacial influence in their bacterial communities.

Are Mediterranean Island Mountains Hotspots of Taxonomic and Phylogenetic Biodiversity? The Case of the Endemic Flora of the Balearic Islands

The Mediterranean islands are exceptionally rich in endemism, most of which is narrowly distributed. Conservation measures, such as protected areas, have been prioritised, mainly on the basis of species richness and endemism, but phylogenetic information should also be taken into account. In this study, we calculated several taxonomic and phylogenetic metrics at a high resolution for the endemic flora of the Balearic Islands (154 taxa), in order to identify (i) the spatial patterns and environmental factors that explain this endemism, (ii) hotspots of species and phylogenetic endemism, and (iii) gaps in the protected areas. The taxonomic and phylogenetic metrics showed different distribution patterns, but the mountainous areas of Mallorca, and some coastal areas of the Balearic Islands, have the highest values. These values were positively related to elevation, precipitation, temperature, and slope, and negatively related to the distance from the coast, aspect, and the temperature of the wettest quarter. We identified top grid hotspots where all the metrics had the highest values, and we also identified nano-hotspots within these hotspots, in some of the highest peaks of Mallorca, where most of these metrics' maximum values coincided. This approach allowed us to identify some gaps in the conservation priority areas, and to highlight the need to review their boundaries and definition.

A network-based approach to identifying correlations between phylogeny, morphological traits and occurrence of fish species in US river basins

The complex network framework has been successfully used to model interactions between entities in Complex Systems in the Biological Sciences such as Proteomics, Genomics, Neuroscience, and Ecology. Networks of organisms at different spatial scales and in different ecosystems have provided insights into community assembly patterns and emergent properties of ecological systems. In the present work, we investigate two questions pertaining to fish species assembly rules in US river basins, a) if morphologically similar fish species also tend to be phylogenetically closer, and b) to what extent are co-occurring species that are phylogenetically close also morphologically similar? For the first question, we construct a network of Hydrologic Unit Code 8 (HUC8) regions as nodes with interaction strengths (edges) governed by the number of common species. For each of the modules of this network, which are found to be geographically separated, there is differential yet significant evidence that phylogenetic distance predicts morphological distance. For the second question, we construct and analyze nearest neighbor directed networks of species based on their morphological distances and phylogenetic distances. Through module detection on these networks and comparing the module-level mean phylogenetic distance and mean morphological distance with the number of basins of common occurrence of species in modules, we find that both phylogeny and morphology of species have significant roles in governing species co-occurrence, i.e. phylogenetically and morphologically distant species tend to co-exist more. In addition, between the two quantities (morphological distance and phylogentic distance), we find that morphological distance is a stronger determinant of species co-occurrences.

Partitioning and integrating of plant traits and phylogeny in assessing diversity along secondary forest succession in Loess Plateau of China

Assessing plant diversity during community succession based on plant trait and phylogenetic features within a community (alpha scale) and among communities (beta scale) could improve our understanding of community succession mechanism. However, whether changes of community functional diversity at alpha and beta scale are structured by different traits and whether integrating plant traits and phylogeny can enhance the ability in detecting diversity pattern have not been studied in detail. Thirty plots representing different successional stages were established on the Loess Plateau of China and 15 functional traits were measured for all coexisting species. We first analyzed the functional alpha and beta diversity along succession by decomposing species trait into alpha and beta components and then integrated key traits with phylogenetic information to explore their roles in shaping species turnover during community succession. We found that functional alpha diversity increased along successional stages and was structured by morphological traits, while beta diversity decreased during succession and was more structured by stoichiometry traits. Phylogenetic alpha diversity showed congruent pattern with functional alpha diversity because of phylogenetic conservation of trait alpha components (variation within community), while beta diversity showed incongruent pattern due to phylogenetic randomness of trait beta components (variation among communities). Furthermore, only integrating relatively conserved traits (plant height and seed mass) and phylogenetic information can raise the detecting ability in assessing diversity change. Overall, our results reveal the increasing niche differentiation within community and functional convergence among communities with succession process, indicating the importance of matching traits with scale in studying community functional diversity and the asymmetry of traits and phylogeny in reflecting species ecological differences under long-term selection pressures.

Evolutionary history of marginal habitats regulates the diversity of tree communities in the Atlantic Forest

BACKGROUND AND AIMS

The Atlantic Forest biodiversity hotspot is a complex mosaic of habitat types. However, the diversity of the rain forest at the core of this complex has received far more attention than that of its marginal habitats, such as cloud forest, semi-deciduous forest or restinga. Here, we investigate broad-scale angiosperm tree diversity patterns along elevation gradients in the south-east Atlantic Forest and test if the diversity of marginal habitats is shaped from the neighbouring rain forest, as commonly thought.

METHODS

We calculated phylogenetic indices that capture basal [mean pairwise phylogenetic distance (MPD)] and terminal [mean nearest taxon distance (MNTD)] phylogenetic variation, phylogenetic endemism (PE) and taxonomic and phylogenetic beta diversity (BD and PBD) for 2074 angiosperm tree species distributed in 108 circular sites of 10 km diameter across four habitat types i.e. rain forest, cloud forest, semi-deciduous forest and coastal vegetation known as restinga. We then related these metrics to elevation and environmental variables.

KEY RESULTS

Communities in wetter and colder forests show basal phylogenetic overdispersion and short phylogenetic distances towards the tips, respectively. In contrast, communities associated with water deficit and salinity show basal phylogenetic clustering and no phylogenetic structure toward the tips. Unexpectedly, rain forest shows low PE given its species richness, whereas cloud and semi-deciduous forests show unusually high PE. The BD and PBD between most habitat types are driven by the turnover of species and lineages, except for restinga.

CONCLUSIONS

Our results contradict the idea that all marginal habitat types of the Atlantic Forest are sub-sets of the rain forest. We show that marginal habitat types have different evolutionary histories and may act as 'equilibrium zones for biodiversity' in the Atlantic Forest, generating new species or conserving others. Overall, our results add evolutionary insights that reinforce the urgency of encompassing all habitat types in the Atlantic Forest concept.

Deterministic Assembly Processes Strengthen the Effects of β-Diversity on Community Biomass of Marine Bacterioplankton

The presence of more species in the community of a sampling site (α diversity) typically increases ecosystem functions via nonrandom processes like resource partitioning. When considering multiple communities, we hypothesize that higher compositional difference (β diversity) increases overall functions of these communities. Further, we hypothesize that the β diversity effect is more positive when β diversity is increased by nonrandom assembly processes. To test these hypotheses, we collected bacterioplankton along a transect of 6 sampling sites in the southern East China Sea in 14 cruises. For any pairs of the 6 sites within a cruise, we calculated the Bray-Curtis index to represent β diversity and summed bacterial biomass as a proxy to indicate the overall function of the two communities. We then calculated deviation of observed mean pairwise phylogenetic similarities among species in two communities from random to represent the influences of nonrandom processes. The bacterial β diversity was found to positively affect the summed bacterial biomass; however, the effect varied among cruises. Cross-cruise comparison indicated that the β diversity effect increased with the nonrandom processes selecting for phylogenetically dissimilar species. This study extends biodiversity-ecosystem functioning research to the scale of multiple sites and enriches the framework by considering community assembly processes. IMPORTANCE The implications of our analyses are twofold. First, we emphasize the importance of studying β diversity. We expanded the current biodiversity-ecosystem functioning framework from single to multiple sampling sites and investigated the influences of species compositional differences among sites on the overall functioning of these sites. Since natural ecological communities never exist alone, our analyses allow us to more holistically perceive the role of biodiversity in natural ecosystems. Second, we took community assembly processes into account to attain a more mechanistic understanding of the impacts of biodiversity on ecosystem functioning.

Decomposing niche components reveals simultaneous effects of opposite deterministic processes structuring alpine small mammal assembly

Introduction

Species distribution in alpine areas is constrained by multiple abiotic and biotic stressors. This leads to discrepant assembly patterns between different locations and study objects as opposite niche-based processes—limiting similarity and habitat filtering—simultaneously structure communities, masking overall patterns. We aimed to address how these processes structure small mammal communities in the alpine tree line transition zone, one of the most distinct vegetation transitions between alpine and montane habitats.

Methods

We compiled a dataset of species checklist, phylogeny, and functional traits from field collection and published sources spanning 18 mountains in southwest China. We first examined hypothetical niche-based processes with frequently used phylogenetic and trait approaches using this dataset. The species traits were decomposed into different niche components to explore the respective effects of specific stressors. Indices representing evolutionary history, trait space, and pairwise species distance were estimated and compared with null model expectations. Linear mixed-effect models were used to assess the association patterns between diversity indices and elevation.

Results

The results indicated that phylogenetic and functional richness were positively correlated with species richness. In contrast, distance-based indices were either negatively or weakly positively correlated with species richness. Null model analyses suggested no evidence of non-random phylogenetic or overall trait patterns. However, the resource acquisition niche tended to be more overdispersed (positive slopes), while the habitat affinity niche tended to be more clustered (negative slopes) beyond the high elevation tree line.

Discussion

These findings show that opposite niche-based processes simultaneously structure small mammal communities in alpine areas. Overall, the present study provides vital insights into the complexity of assembly processes in these habitats. It also highlights the importance of relating relevant traits to distinguish the influences of specific abiotic and biotic stressors.

Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations

Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.

The community ecology perspective of omics data

The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.

Factors underlying bird community assembly in anthropogenic habitats depend on the biome

Production activities drive the replacement of original habitats with artificial ones, leading to new bird assemblages. In this study, we assessed if anthropogenic habitats acted as environmental filters causing functional redundancy or as promoters of functional divergence, depending on the biome. We also investigated if functional patterns derived from phylogenetic convergence or clustering. For this purpose, we computed the standardized effect sizes (SES) for avian functional and phylogenetic diversity using null models and compared the SES values among tree plantations, urban settlements (US), cattle pastures (CP), crop fields (CF) and natural habitats from two biomes: grassland and forest. We used generalized least squares models to test if functional and phylogenetic SES indicated functional redundancy or divergence, and phylogenetic convergence or clustering. We found functional redundancy in grassland and functional divergence in forest associated with environmental filtering and competitive exclusion, respectively. In grassland, functional structure was not associated with a clear phylogenetic pattern, while in forest functional divergence was caused by evolutionary convergence in CF and CP and conservation in US. The prevalences of functional redundancy and functional divergence patterns and their associated predominant mechanism of community assembly were found to depend on the biome and the regional species pool.

A comparison of gene organisations and phylogenetic relationships of all 22 squamate species listed in South Korea using complete mitochondrial DNA

Studies using complete mitochondrial genome data have the potential to increase our understanding on gene organisations and evolutionary species relationships. In this study, we compared complete mitochondrial genomes between all 22 squamate species listed in South Korea. In addition, we constructed Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic trees using 13 mitochondrial protein-coding genes. The mitochondrial genes for all six species in the suborder Sauria followed the same organisation as the sequenced Testudines (turtle) outgroup. In contrast, 16 snake species in the suborder Serpentes contained some gene organisational variations. For example, all snake species contained a second control region (CR2), while three species in the family Viperidae had a translocated tRNA-Pro gene region. In addition, the snake species, Elapheschrenckii, carried a tRNA-Pro pseudogene. We were also able to identify a translocation of a tRNA-Asn gene within the five tRNA (WANCY gene region) gene clusters for two true sea snake species in the subfamily Hydrophiinae. Our BI phylogenetic tree was also well fitted against currently known Korean squamate phylogenetic trees, where each family and genus unit forms monophyletic clades and the suborder Sauria is paraphyletic to the suborder Serpentes. Our results may form the basis for future northeast Asian squamate phylogenetic studies.

Loss of lateral hydrological connectivity impacts multiple facets of molluscan biodiversity in floodplain lakes

Lateral hydrological connectivity (LHC) is a key process in maintaining aquatic biodiversity in river floodplain ecosystems. However, the effects of LHC loss on aquatic biodiversity are rarely studied. Here, we evaluated, for the first time, the responses of multiple facets (i.e., taxonomic, functional and phylogenetic) of alpha and beta diversity of freshwater molluscs to the LHC loss in 23 floodplain lakes in the Yangtze River Basin in China. Our results showed that taxonomic and functional alpha diversities were all significantly higher in connected lakes (CLs) than in disconnected lakes (DLs), whereas phylogenetic alpha diversity (Δ⁺) was lower in CLs than in DLs. For beta diversity facets, taxonomic (Tβ_sor) and phylogenetic (Pβ_sor) dissimilarities were slightly more contributed by the turnover component or equally contributed by the turnover and nestedness-resultant components both in CLs and DLs. Instead, functional beta diversity (Fβ_sor), generally showing much lower values than Tβ_sor and Pβ_sor, was mainly contributed by the nestedness-resultant component (76.6-84.0%), especially in DLs. We found that only functional dissimilarities were significantly higher in DLs than CLs, indicating a high level of functional diversity loss without replacement of species possessing traits sensitive to hydrological disconnection (i.e., large body size, lamellibranch body form, filter feeding, ovoviviparity and burrowing habits). In general, lake area, hydrological connectivity, aquatic vegetation coverage and nutrient levels (TN and TP) played important roles in structuring variation in molluscan alpha and beta diversities, although the three diversity facets responded to different environmental factors. Our results suggest that loss of connectivity to the mainstem river has negative impacts on molluscan assemblages in floodplain lakes. More importantly, as taxonomic, functional and phylogenetic diversities responded somewhat differently to the loss of hydrological connectivity, all of these biodiversity facets should be better incorporated into aquatic biodiversity assessment and conservation programs in large river floodplains.

Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional-scale disturbance

Much attention is paid in conservation planning to the concept of a species, to ensure comparability across studies and regions when classifying taxa against criteria of endangerment and setting priorities for action. However, various jurisdictions now allow taxonomic ranks below the level of species and nontaxonomic intraspecific divisions to be factored into conservation planning—subspecies, key populations, evolutionarily significant units, or designatable units. Understanding patterns of genetic diversity and its distribution across the landscape is a key component in the identification of species boundaries and determination of substantial geographic structure within species. A total of 12,532 reliable polymorphic SNP loci were generated from 63 populations (286 individuals) covering the distribution of the Australian eastern three‐lined skink, Bassiana duperreyi, to assess genetic population structure in the form of diagnosable lineages and their distribution across the landscape, with particular reference to the recent catastrophic bushfires of eastern Australia. Five well‐supported diagnosable operational taxonomic units (OTUs) existed within B. duperreyi. Low levels of divergence of B. duperreyi between mainland Australia and Tasmania (no fixed allelic differences) support the notion of episodic exchange of alleles across Bass Strait (ca 60 m, 25 Kya) during periods of low sea level during the Upper Pleistocene rather than the much longer period of isolation (1.7 My) indicated by earlier studies using mitochondrial sequence variation. Our study provides foundational work for the detailed taxonomic re‐evaluation of this species complex and the need for biodiversity assessment to include an examination of cryptic species and/or cryptic diversity below the level of species. Such information on lineage diversity within species and its distribution in the context of disturbance at a regional scale can be factored into conservation planning regardless of whether a decision is made to formally diagnose new species taxonomically and nomenclaturally.

Climatic niche breadths of the Atlantic Forest snakes do not increase with increasing latitude

The climatic niche is a central concept for understanding species distribution, with current and past climate interpreted as strong drivers of present and historical-geographical ranges. Our aim is to understand whether Atlantic Forest snakes follow the general geographical pattern of increasing species climatic niche breadths with increasing latitude. We also tested if there is a tradeoff between temperature and precipitation niche breadths of species in order to understand if species with larger breadths of one niche dimension have stronger dispersal constraints by the other due to narrower niche breadths. Niche breadths were calculated by the subtraction of maximal and minimal values of temperature and precipitation across species ranges. We implemented Phylogenetic Generalized Least Squares to measure the relationship between temperature and precipitation niche breadths and latitude. We also tested phylogenetic signals by Lambda statistics to analyze the degree of phylogenetic niche conservatism to both niche dimensions. Temperature niche breadths were not related to latitude. Precipitation niche breadths decreased with increasing latitude and presented a high phylogenetic signal, that is, significant phylogenetic niche conservatism. We rejected the tradeoff hypotheses of temperature and precipitation niche breadths. Our results also indicate that precipitation should be an important ecological constraint affecting the geographical distribution of snake lineages across the South American Atlantic Forest. We then provide a general view of how phylogenetic niche conservatism could impact the patterns of latitudinal variation of climatic niches across this biodiversity hotspot.

Ecological opportunity and adaptive radiations reveal eco-evolutionary perspectives on community structure in competitive communities

It is well known that ecological and evolutionary processes act in concert while shaping biological communities. Diversification can, for example, arise through ecological opportunity and adaptive radiations and competition play an essential role in such diversification. Eco-evolutionary components of competition are thus important for our understanding of community assembly. Such understanding in turn facilitates interpretation of trait- and phylogenetic community patterns in the light of the processes that shape them. Here, I investigate the link between competition, diversification, and trait- and phylogenetic- community patterns using a trait-based model of adaptive radiations. I evaluate the paradigm that competition is an ecological process that drives large trait- and phylogenetic community distances through limiting similarity. Contrary to the common view, I identify low or in some cases counterintuitive relationships between competition and mean phylogenetic distances due to diversification late in evolutionary time and peripheral parts of niche space when competition is weak. Community patterns as a function of competition also change as diversification progresses as the relationship between competition and trait similarity among species can flip from positive to negative with time. The results thus provide novel perspectives on community assembly and emphasize the importance of acknowledging eco-evolutionary processes when interpreting community data.

High functional diversity in deep-sea fish communities and increasing intraspecific trait variation with increasing latitude

Variation in both inter- and intraspecific traits affects community dynamics, yet we know little regarding the relative importance of external environmental filters versus internal biotic interactions that shape the functional space of communities along broad-scale environmental gradients, such as latitude, elevation, or depth. We examined changes in several key aspects of functional alpha diversity for marine fishes along depth and latitude gradients by quantifying intra- and interspecific richness, dispersion, and regularity in functional trait space. We derived eight functional traits related to food acquisition and locomotion and calculated seven complementary indices of functional diversity for 144 species of marine ray-finned fishes along large-scale depth (50-1200 m) and latitudinal gradients (29°-51° S) in New Zealand waters. Traits were derived from morphological measurements taken directly from footage obtained using Baited Remote Underwater Stereo-Video systems and museum specimens. We partitioned functional variation into intra- and interspecific components for the first time using a PERMANOVA approach. We also implemented two tree-based diversity metrics in a functional distance-based context for the first time: namely, the variance in pairwise functional distance and the variance in nearest neighbor distance. Functional alpha diversity increased with increasing depth and decreased with increasing latitude. More specifically, the dispersion and mean nearest neighbor distances among species in trait space and intraspecific trait variability all increased with depth, whereas functional hypervolume (richness) was stable across depth. In contrast, functional hypervolume, dispersion, and regularity indices all decreased with increasing latitude; however, intraspecific trait variation increased with latitude, suggesting that intraspecific trait variability becomes increasingly important at higher latitudes. These results suggest that competition within and among species are key processes shaping functional multidimensional space for fishes in the deep sea. Increasing morphological dissimilarity with increasing depth may facilitate niche partitioning to promote coexistence, whereas abiotic filtering may be the dominant process structuring communities with increasing latitude.

Spatial Scale Dependence of Ecological Factors That Regulate Functional and Phylogenetic Assembly in a Mediterranean High Mountain Grassland

Understanding how functional and phylogenetic patterns vary among scales and along ecological gradients within a given species pool is critical for inferring community assembly processes. However, we lack a clear understanding of these patterns in stressful habitats such as Mediterranean high mountains where ongoing global warming is expected to affect species fitness and species interactions, and subsequently species turnover. In this study, we investigated 39 grasslands with the same type of plant community and very little species turnover across an elevation gradient above the treeline at Sierra de Guadarrama National Park in central Spain. In particular, we assessed functional and phylogenetic patterns, including functional heterogeneity, using a multi-scale approach (cells, subplots, and plots) and determined the relevance of key ecological factors (i.e., elevation, potential solar radiation, pH, soil organic carbon, species richness, and functional heterogeneity) that affect functional and phylogenetic patterns at each spatial scale. Overall, at the plot scale, coexisting species tended to be more functionally and phylogenetically similar. By contrast, at the subplot and cell scales, species tended to be more functionally different but phylogenetically similar. Functional heterogeneity at the cell scale was comparable to the variation across plots along the gradient. The relevance of ecological factors that regulate diversity patterns varied among spatial scales. An increase in elevation resulted in functional clustering at larger scales and phylogenetic overdispersion at a smaller scale. The soil pH and organic carbon levels exhibited complex functional patterns, especially at small spatial scales, where an increase in pH led to clustering patterns for the traits related to the leaf economic spectrum (i.e., foliar thickness, specific leaf area, and leaf dry matter content). Our findings confirm the presence of primary environmental filters (coldness and summer drought at our study sites) that constrain the regional species pool, suggesting the presence of additional assembly mechanisms that act at the smallest scale (e.g., micro-environmental gradients and/or species interactions). Functional and phylogenetic relatedness should be determined using a multi-scale approach to help interpret community assembly processes and understand the initial community responses to environmental changes, including ongoing global warming.

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.

Localized environmental heterogeneity drives the population differentiation of two endangered and endemic Opisthopappus Shih species

BACKGROUND

Climate heterogeneity not only indirectly shapes the genetic structures of plant populations, but also drives adaptive divergence by impacting demographic dynamics. The variable localized climates and topographic complexity of the Taihang Mountains make them a major natural boundary in Northern China that influences the divergence of organisms distributed across this region. Opisthopappus is an endemic genus of the Taihang Mountains that includes only two spatially partitioned species Opisthopappus longilobus and Opisthopappus taihangensis. For this study, the mechanisms behind the genetic variations in Opisthopappus populations were investigated.

RESULTS

Using SNP and InDel data coupled with geographic and climatic information, significant genetic differentiation was found to exist either between Opisthopappus populations or two species. All studied populations were divided into two genetic groups with the differentiation of haplotypes between the groups. At approximately 17.44 Ma of the early Miocene, O. taihangensis differentiated from O. longilobus under differing precipitation regimes due to the intensification of the Asian monsoon. Subsequently, intraspecific divergence might be induced by the dramatic climatic transformation from the mid- to late Miocene. During the Pleistocene period, the rapid uplift of the Taihang Mountains coupled with violent climatic oscillations would further promote the diversity of the two species. Following the development of the Taihang Mountains, its complex topography created geographical and ecological heterogeneity, which could lead to spatiotemporal isolation between the Opisthopappus populations. Thus the adaptive divergence might occur within these intraspecific populations in the localized heterogeneous environment of the Taihang Mountains.

CONCLUSIONS

The localized environmental events through the integration of small-scale spatial effects impacted the demographic history and differentiation mechanism of Opisthopappus species in the Taihang Mountains. The results provide useful information for us to understand the ecology and evolution of organisms in the mountainous environment from population and species perspective.

Phylogenetic structure of understorey annual and perennial plant species reveals opposing responses to aridity in a Mediterranean biodiversity hotspot

Aridity is a critical driver of the diversity and composition of plant communities. However, how aridity influences the phylogenetic structure of functional groups (i.e. annual and perennial species) is far less understood than its effects on species richness. As perennials have to endure stressful conditions during the summer drought, as opposed to annuals that avoid it, they may be subjected to stronger environmental filtering. In contrast, annuals may be more susceptible to interannual climatic variability. Here we studied the phylogenetic structure of the annual and perennial components of understorey plant communities, along a regional aridity gradient in Mediterranean drylands. Specifically, we asked: (1) How do species richness (S) and phylogenetic structure (PS) of annuals and perennials in plant communities respond to aridity? (2) What is the contribution of other climatic and topo-edaphic variables in predicting S and PS for both components? (3) How does the taxonomic and phylogenetic turnover of annuals and perennials vary with spatial and environmental distances? We assessed annuals' and perennials' species richness, the phylogenetic structure at deep and shallow phylogenetic levels, and taxonomic and phylogenetic turnover along spatial and environmental distances. We found no relationship between annuals' richness and aridity, whereas perennials' richness showed a unimodal pattern. The phylogenetic structure of annuals and perennials showed contrasting responses to aridity and negatively correlated with topo-edaphic variables. We found phylogenetic clustering at intermediate-to-higher aridity levels for annuals, and at lower aridity levels for perennials. Both taxonomic and phylogenetic turnover in annuals and perennials correlated with the environmental distance rather than with spatial distance between communities, suggesting adaptation to local factors. Overall, our results show a decoupling in the response of the phylogenetic structure of annual and perennial components of plant communities to aridity in Mediterranean drylands. Our findings have significant implications for land management strategies under climate change.

Intraspecific diversity loss in a predator species alters prey community structure and ecosystem functions

Loss in intraspecific diversity can alter ecosystem functions, but the underlying mechanisms are still elusive, and intraspecific biodiversity-ecosystem function (iBEF) relationships have been restrained to primary producers. Here, we manipulated genetic and functional richness of a fish consumer (Phoxinus phoxinus) to test whether iBEF relationships exist in consumer species and whether they are more likely sustained by genetic or functional richness. We found that both genotypic and functional richness affected ecosystem functioning, either independently or interactively. Loss in genotypic richness reduced benthic invertebrate diversity consistently across functional richness treatments, whereas it reduced zooplankton diversity only when functional richness was high. Finally, losses in genotypic and functional richness altered functions (decomposition) through trophic cascades. We concluded that iBEF relationships lead to substantial top-down effects on entire food chains. The loss of genotypic richness impacted ecological properties as much as the loss of functional richness, probably because it sustains "cryptic" functional diversity.

Ecophylogenetics redux

Species' evolutionary histories shape their present-day ecologies, but the integration of phylogenetic approaches in ecology has had a contentious history. The field of ecophylogenetics promised to reveal the process of community assembly from simple indices of phylogenetic pairwise distances - communities shaped by environmental filtering were composed of closely related species, whereas communities shaped by competition were composed of less closely related species. However, the mapping of ecology onto phylogeny proved to be not so straightforward, and the field remains mired in controversy. Nonetheless, ecophylogenetic methods provided important advances across ecology. For example the phylogenetic distances between species is a strong predictor of pest and pathogen sharing, and can thus inform models of species invasion, coexistence and the disease dilution/amplification effect of biodiversity. The phylogenetic structure of communities may also provide information on niche space occupancy, helping interpret patterns of facilitation, succession and ecosystem functioning - with relevance for conservation and restoration - and the dynamics among species within foodwebs and metacommunities. I suggest leveraging advances in our understanding of the process of evolution on phylogenetic trees would allow the field to progress further, while maintaining the essence of the original vision that proved so seductive.

Taxonomic and phylogenetic beta diversity of cricetid rodents in Oaxaca, southern Mexico

Understanding the ecological and historical causes and processes that shape biodiversity distribution patterns remains a challenging and fundamental task in biogeography, ecology, and evolution. To address this issue, taxonomic and phylogenetic β diversity can help us to assess the importance of ecological and historical factors that structure these biotic patterns. To make inferences about the processes underlying current spatial patterns in communities of Cricetidae across the state of Oaxaca, Mexico, their taxonomic and phylogenetic β diversity were assessed jointly. Our aims were: 1) to examine taxonomic and phylogenetic β diversity and their turnover and nestedness components among physiographic subprovinces; 2) to test for statistical significance of observed phylogenetic β diversity against the expected values of a null model; and 3) to evaluate if these metrics were correlated with geographical distance. We obtained the species composition for 12 subprovinces based on distribution models for 49 cricetid species present in Oaxaca, then carried out a maximum likelihood analysis to estimate their phylogenetic relationships. Our results show that the taxonomic and phylogenetic dissimilarities mainly were explained by the turnover component of species and lineages. In almost all pairwise comparisons, the null model approach revealed random patterns for phylogenetic β diversity values and its components. Mantel correlation models showed that the values of total taxonomic and phylogenetic diversity and their components are correlated with the geographical distances between subprovinces. Our results suggest that both taxonomic and phylogenetic β diversity are explained by the interplay between biogeographical history from southern Mexico, and the recent speciation processes in cricetid rodents. Given that speciation processes are allopatric for most cricetid taxa, the high values of spatial turnover can be explained by the small ranges of species, coupled with current abiotic conditions that act as filters, promoting specialization of species on particular conditions. Our results show the importance of the phylogenetic approach to unravel the multidimensional spatial patterns of biodiversity.

Effects of two measures of riparian plant biodiversity on litter decomposition and associated processes in stream microcosms

Plant litter decomposition is a key ecosystem process that can be altered by global changes such as biodiversity loss. These effects can be particularly important in detritus-based ecosystems, such as headwater streams, which are mainly fuelled by allochthonous plant litter inputs. However, experiments examining effects of plant diversity on litter decomposition in streams have not reached consensus about which measures of biodiversity are more relevant. We explored the influence of two of these measures, plant species richness (SR; monocultures vs. 3-species mixtures) and phylogenetic distance (PD; species belonging to the same family vs. different families), on leaf litter decomposition and associated processes and variables (nutrient dynamics, fungal biomass and detritivore growth), in a stream microcosm experiment using litter from 9 tree species belonging to 3 families. We found a negative effect of SR on decomposition (which contradicted the results of previous experiments) but a positive effect on fungal biomass. While PD did not affect decomposition, both SR and PD altered nutrient dynamics: there was greater litter and detritivore N loss in low-PD mixtures, and greater litter P loss and detritivore P gain in monocultures. This suggested that the number of species in mixtures and the similarity of their traits both modulated nutrient availability and utilization by detritivores. Moreover, the greater fungal biomass with higher SR could imply positive effects on detritivores in the longer term. Our results provide new insights of the functional repercussions of biodiversity loss by going beyond the often-explored relationship between SR and decomposition, and reveal an influence of plant species phylogenetic relatedness on nutrient cycling that merits further investigation.

Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research

Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.

Freshwater phytoplankton diversity: models, drivers and implications for ecosystem properties

Our understanding on phytoplankton diversity has largely been progressing since the publication of Hutchinson on the paradox of the plankton. In this paper, we summarise some major steps in phytoplankton ecology in the context of mechanisms underlying phytoplankton diversity. Here, we provide a framework for phytoplankton community assembly and an overview of measures on taxonomic and functional diversity. We show how ecological theories on species competition together with modelling approaches and laboratory experiments helped understand species coexistence and maintenance of diversity in phytoplankton. The non-equilibrium nature of phytoplankton and the role of disturbances in shaping diversity are also discussed. Furthermore, we discuss the role of water body size, productivity of habitats and temperature on phytoplankton species richness, and how diversity may affect the functioning of lake ecosystems. At last, we give an insight into molecular tools that have emerged in the last decades and argue how it has broadened our perspective on microbial diversity. Besides historical backgrounds, some critical comments have also been made.

The mechanisms generating community phylogenetic patterns change with spatial scale

Studies that test community assembly hypotheses in observational communities frequently evaluate patterns for plots or entire communities, yet studies that examine assembly patterns across spatial scales show that they are greatly influenced by scale. Here, we test the spatial dependency of patterns of relatedness and plant height for all individual herbaceous plants along five 40-m old-field transects (Southern Ontario, Canada). We identified each individual plant and measured its distance along the transect and its height, and we constructed a molecular phylogeny for all observed species. To uncover the scale at which community phylogenetic and trait similarities shift, we used partial Mantel correlograms and distance-based Moran Eigenvector Maps (dbMEMs). We found that communities shift from significantly overdispersed at relatively smaller scales (i.e., < 15 m) to spatially clustered at larger scales, showing that assembly mechanism influence depends on scale of observation. This pattern was observed for both phylogeny and height, but was the strongest when considering phylogeny only. These results reveal the importance of spatial scale when examining community phylogenetic or trait patterns, where finding support for one assembly mechanism at a single scale does not necessarily mean that other mechanisms are also not important for structuring community composition and diversity.