Directional biases in phylogenetic structure quantification: a Mediterranean case study

Distinct Responses of Leaf Traits to Environment and Phylogeny Between Herbaceous and Woody Angiosperm Species in China

Leaf traits play key roles in plant resource acquisition and ecosystem processes; however, whether the effects of environment and phylogeny on leaf traits differ between herbaceous and woody species remains unclear. To address this, in this study, we collected data for five key leaf traits from 1,819 angiosperm species across 530 sites in China. The leaf traits included specific leaf area, leaf dry matter content, leaf area, leaf N concentration, and leaf P concentration, all of which are closely related to trade-offs between resource uptake and leaf construction. We quantified the relative contributions of environment variables and phylogeny to leaf trait variation for all species, as well as for herbaceous and woody species separately. We found that environmental factors explained most of the variation (44.4-65.5%) in leaf traits (compared with 3.9-23.3% for phylogeny). Climate variability and seasonality variables, in particular, mean temperature of the warmest and coldest seasons of a year (MTWM/MTWQ and MTCM/MTCQ) and mean precipitation in the wettest and driest seasons of a year (MPWM/MPWQ and MPDM/MPDQ), were more important drivers of leaf trait variation than mean annual temperature (MAT) and mean annual precipitation (MAP). Furthermore, the responses of leaf traits to environment variables and phylogeny differed between herbaceous and woody species. Our study demonstrated the different effects of environment variables and phylogeny on leaf traits among different plant growth forms, which is expected to advance the understanding of plant adaptive strategies and trait evolution under different environmental conditions.

Identifying the patterns of changes in α- and β-diversity across Dacrydium pectinatum communities in Hainan Island, China

Exploring vegetation distribution spatial patterns facilitates understanding how biodiversity addresses the potential threat of future climate variability, especially for highly diverse and threatened tropical plant communities, but few empirical studies have been performed. Dacrydium pectinatum is a constructive and endangered species in the tropical mountain forests of Hainan Island, China. In this study, sixty-eight 30 m × 30 m permanent plots of D. pectinatum were investigated, and species-based and phylogenetic-based methods were used to analyze the α- and β-diversity pattern variation and its key drivers. Our study showed that species and phylogenetic α-diversity patterns are different on a local scale. However, on a regional scale, the variations in the two α-diversity patterns tend to converge, and they decrease with increasing elevation. The phylogenetic structure changes from overdispersion to convergence with increasing elevation. Soil (SOM, TP, AP), topography (EL, SL), and stand (CD) factors and α-diversity showed close correlations. Species and phylogenetic β-diversity have significant positive correlations with changing environmental distance and geographical distance; however, as a representative form of habitat heterogeneity, elevation distance has a greater impact on β-diversity changes than geographical distance. In conclusion, the α- and β-diversity patterns of the D. pectinatum community are mainly related to habitat filtering, especially in high-elevation areas, and the colonization history of various regions also affects the formation of diversity patterns. Species-based and phylogenetic-based methods robustly demonstrated the key role of the habitat filtering hypothesis in community assembly. We believe that more plant diversity patterns need to be explored to understand the biodiversity formation mechanisms in tropical forests. We also recommend strengthening the construction and management of nature reserves to help address the biodiversity loss crisis in endangered tropical plant communities.

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.

Patterns and drivers of species richness and turnover of neo-endemic and palaeo-endemic vascular plants in a Mediterranean hotspot: the case of Crete, Greece

Background

Exploring species richness and turnover patterns and their drivers can provide new insights into underlying mechanisms shaping community assembly, with significant implications for biodiversity conservation. Here, we explored diversity patterns of non-endemic, neo-endemic and palaeo-endemic vascular plants in Crete, Greece, a Mediterranean hotspot of plant richness and endemism. We evaluated the relationship between α-diversity and environmental (bioclimatic variables, topography), and anthropogenic variables by Generalized Additive Models, after accounting for spatial autocorrelation. Then, we quantified turnover using the novel concept of zeta diversity (the number of shared species by multiple sites), a framework which allows to explore the full spectrum of compositional turnover, the contribution of rare and widespread species to observed patterns and the underlying processes shaping them. Finally, we explored the abiotic and biotic effects, i.e. how well one category of species (non-endemics, palaeo-endemics, neo-endemics) predicts the patterns of the other categories, on zeta diversity by multi-site Generalized Dissimilarity Modelling.

Results

We found a strong correlation between neo-endemic and palaeo-endemic α-diversity, with climate, topography, and human impact driving species richness. Zeta diversity analysis revealed a sharper decrease of shared palaeo-endemic species, followed by neo-endemics, and then by non-endemics with the number of sites considered to estimate compositional turnover. Perhaps, the narrow distributions of palaeo-endemics as relict species and often habitat specialists, thus persisting locally, and of neo-endemics that may have not reached yet their potential geographical range, resulted in the observed zeta diversity decline pattern. Deterministic processes controlled species turnover of rare non-endemic and neo-endemic species, while deterministic and stochastic processes contributed similarly to palaeo-endemic turnover. However, stochasticity dominates in the case of widespread species in all occasions. The environmental and anthropogenic variables were poor predictors of compositional turnover, especially of widespread species. However, the non-endemic species composition was correlated to rare palaeo-endemics and neo-endemics, highlighting the importance of biotic effects in driving turnover patterns.

Conclusions

It seems that centers of neo-endemism of vascular plants coincide with centers of palaeo-endemism in Crete, but species richness and species turnover are shaped by different drivers.

Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates

Recent availability of biodiversity data resources has enabled an unprecedented ability to estimate phylogenetically based biodiversity metrics over broad scales. Such approaches elucidate ecological and evolutionary processes yielding a biota and help guide conservation efforts. However, the choice of appropriate phylogenetic resources and underlying input data uncertainties may affect interpretation. Here, we address how differences among phylogenetic source trees and levels of phylogenetic uncertainty affect these metrics and test existing hypotheses regarding geographic biodiversity patterns across the diverse vascular plant flora of Florida, US. Ecological niche models for 1,490 Florida species were combined with a "purpose-built" phylogenetic tree (phylogram and chronogram), as well as with trees derived from community resources (Phylomatic and Open Tree of Life). There were only modest differences in phylodiversity metrics given the phylogenetic source tree and taking into account the level of phylogenetic uncertainty; we identify similar areas of conservation interest across Florida regardless of the method used.

Revisiting phylogenetic signal; strong or negligible impacts of polytomies and branch length information?

Background

Inaccurate estimates of phylogenetic signal may mislead interpretations of many ecological and evolutionary processes, and hence understanding where potential sources of uncertainty may lay has become a priority for comparative studies. Importantly, the sensitivity of phylogenetic signal indices and their associated statistical tests to incompletely resolved phylogenies and suboptimal branch-length information has been only partially investigated.

Methods

Here, we use simulations of trait evolution along phylogenetic trees to assess whether incompletely resolved phylogenies (polytomic chronograms) and phylogenies with suboptimal branch-length information (pseudo-chronograms) could produce directional biases in significance tests (p-values) associated with Blomberg et al.’s K and Pagel’s lambda (λ) statistics, two of the most widely used indices to measure and test phylogenetic signal. Specifically, we conducted pairwise comparisons between the p-values resulted from the use of “true” chronograms and their degraded counterparts (i.e. polytomic chronograms and pseudo-chronograms), and computed the frequency with which the null hypothesis of no phylogenetic signal was accepted using “true” chronograms but rejected when using their degraded counterparts (type I bias) and vice versa (type II bias).

Results

We found that the use of polytomic chronograms in combination with Blomberg et al.’s K resulted in both, clearly inflated estimates of phylogenetic signal and moderate levels of type I and II biases. More importantly, pseudo-chronograms led to high rates of type I biases. In contrast, Pagel’s λ was strongly robust to either incompletely resolved phylogenies and suboptimal branch-length information.

Conclusions

Our results suggest that pseudo-chronograms can lead to strong overestimation of phylogenetic signal when using Blomberg et al.’s K (i.e. high rates of type I biases), while polytomies may be a minor concern given other sources of uncertainty. In contrast, Pagel’s λ seems strongly robust to either incompletely resolved phylogenies and suboptimal branch-length information. Hence, Pagel’s λ may be a more appropriate alternative over Blomberg et al.’s K to measure and test phylogenetic signal in most ecologically relevant traits when phylogenetic information is incomplete.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0898-y) contains supplementary material, which is available to authorized users.

Climatic and topographical correlates of plant palaeo- and neoendemism in a Mediterranean biodiversity hotspot

BACKGROUND AND AIMS

Understanding the evolutionary and ecological forces contributing to the emergence of biodiversity hotspots is of outstanding importance to elucidate how they may withstand current climate changes. Here we explored patterns of phylogenetic and non-phylogenetic plant endemism in a Mediterranean biodiversity hotspot. We hypothesized that areas with wet and equable climatic conditions would be prone to long-term persistence of endemic lineages (palaeoendemism), whilst areas of recent local speciation (neoendemism) would be more related to harsher environmental conditions and to high topographical relief promoting speciation.

METHODS

We focused on the Baetic-Rifan biodiversity hotspot (southern Iberian Peninsula and northern Morocco) in combination with molecular phylogenetic information and relative phylogenetic endemism (RPE), a recent phylogenetic measure of endemism, allowing us to discern centres of palaeo- from those of neoendemism. Using eco-geographical regions as study units, we explored correlations between both RPE and endemic species richness with precipitation- and temperature-related variables and with elevation range.

KEY RESULTS

Centres of neoendemism were concentrated towards the easternmost part of the hotspot, while centres of palaeoendemism were clustered in the vicinity of the Strait of Gibraltar. The RPE index, indicating more palaeoendemism, was positively correlated with total annual precipitation, while endemic species richness showed a poor correlation. In contrast, elevation range and mean annual temperature were poor predictors of RPE, despite elevation range showing a strong correlation with endemic species richness.

CONCLUSIONS

The Baetic-Rifan biodiversity hotspot shows clearly differentiated centres of neo- and palaeoendemism. Topographical relief may have driven evolutionary diversification of newly evolved species, while water availability seems more critical for the long-term persistence of ancient lineages in refuge areas of smoother topography. Given climatic trends towards increasing aridification, conservation planners should pay particular attention to preserve areas retaining older phylogenetic lineages, as these areas act as 'natural museums' of biodiversity within the Baetic-Rifan biodiversity hotspot.

The building of a biodiversity hotspot across a land-bridge in the Mediterranean

Many of the macroevolutionary processes that have shaped present-day phylogenetic patterns were caused by geological events such as plate tectonics and temporary land-bridges. The study of spatial patterns of phylogenetic diversity can provide insights into these past events. Here we focus on a western Mediterranean biodiversity hotspot located in the southern Iberian Peninsula and northwest Africa, two regions that are separated by the Strait of Gibraltar. We explore the spatial structure of the phylogenetic relationships within and across large-scale plant assemblages. Significant turnover in terminal lineages tends to occur between landmasses, whereas turnover in deep lineages tends to occur within landmasses. Plant assemblages in the western ecoregions of this hotspot tend to be phylogenetically overdispersed but are phylogenetically clustered on its eastern margins. We discuss our results in the light of potential scenarios of niche evolution (or conservatism) and lineage diversification. The significant turnover between landmasses suggests a common scenario of allopatric speciation that could have been facilitated by the intermittent joining of the two continents. This may have constituted an important stimulus for diversification and the emergence of this western Mediterranean biodiversity hotspot.

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

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