Directional biases in phylogenetic structure quantification: a Mediterranean case study

Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, using a large plant community and elevational dataset, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure; and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well-resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly differ depending on phylogenetic tree shape

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

Appendix 1. (extra analyses). (ZIP 4769 kb

A generalized framework to expand incomplete phylogenies using non-molecular phylogenetic information

Aim: The increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the world's biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come. This prospect has urged the development of software to expand phylogenies based on non-molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms. Innovation: Here, we present a completely generalized and flexible framework to expand incomplete phylogenies. The framework is implemented in the R package “randtip”, a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information. Although randtip can generate fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the “blind” expansion of phylogenies using “quick-and-dirty” approaches often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step-by-step tutorial that was designed to provide guidelines to non-specialist users. Main Conclusions: Phylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete phylogenies and thereby account for phylogenetic uncertainty in quantitative analysesMinistry of Science and Innovation of Spain, Grant/Award Number: CGL2017- 86926-P; Regional Government of Madrid, Spain, Grant/Award Number: CM/ JIN/2019-00

Phylogenetic patterns of extinction risk in the endemic flora of a Mediterranean hotspot as a guiding tool for preemptive conservation actions

Climate change is a major driver of biodiversity decline with pervasive effects in biodiversity hotspots, where many endemic and threatened species thrive. However, the biological drivers of extinction susceptibility remain largely elusive, which hampers the implementation of effective conservation policies. Here, we advocate for the use of phylogenies as a complementary tool to inform policy makers. If we assume that the traits that determine extinction susceptibility are somewhat evolutionarily conserved, identifying the clades that accumulate a disproportionate amount of threatened species may help to mitigate potential increases in extinction risk among currently unthreatened species in these clades, even if the underlying biological drivers are unknown. We focused on the complete endemic angiosperm flora of a Mediterranean hotpot (Iberian Peninsula) to examine phylogenetic patterns in extinction risk expressed as IUCN categories (Least Concern “LC”, Near Threatened “NT”, Vulnerable “VU”, Endangered “EN” and Critically Endangered “CR”) using alpha and beta diversity metrics, comparative methods and a “hot node” approach. Phylogenetic diversity was significantly low for EN species and marginally significant for NT and CR, while LC and VU categories showed random pattern. Phylogenetic beta diversity (PBD) between IUCN categories was intermediate (0.40 – 0.61) and predominantly due to the “true” turnover component of PBD. Phylogenetic turnover was significantly low between NT – VU and VU – EN, suggesting that closely related species tend to show different threat status. In contrast, the comparisons involving the CR category sit toward the higher tail of the distribution, indicating a somewhat higher degree of clade specificity for CR species. In line with these patterns, phylogenetic signal in extinction risk was rather low (lambda = 0.23). Several of the “hot” clades that accumulated a significantly high number of species with the same threat status were specific to certain IUCN categories, yet few of them were observed across the categories. Most notably, the Caryophyllales stood out as the main threat-accumulating lineage, particularly within the Plumbaginaceae. All in all, our results indicate that few phylogenetic clades concentrate a great fraction of the extinction-risk gradient in the endemic flora of the western Mediterranean, and monitoring programs should pay particular attention to these extinction-prone lineagesThis paper contributes to the project REMEDINAL TE (P2018/EMT-4338) from the Regional Government of the Community of Madri

Biogeographic deconstruction of phylogenetic and functional diversity provides insights into the formation of regional assemblages

Evolutionary history and environmental filtering shape the phylogenetic and functional structure of regional assemblages. However, detecting the footprint of such eco-evolutionary drivers is challenging because these may often counter each other's signature. Here, we examined whether a biogeographic deconstruction approach of phylogenetic (PD) and functional diversity (FD) patterns may help in identifying eco-evolutionary signals in extant regional assemblages. As model system, we used forest understorey angiosperms found in three regions of Italy (Alpine, Mediterranean, Continental). We quantified PD and FD of all species inhabiting the three regions (regional assemblages). Then, we computed PD and FD for the subsets of species restricted to each region (biogeographic elements), also examining diversity patterns of species found across the three regions (widespread element). We used aboveground and belowground traits capturing major plant functions to calculate FD. Additionally, we assessed FD patterns decoupled from phylogeny. We found that species restricted to climatically harsh regions (Alpine and Mediterranean elements) were phylogenetically and functionally clustered, whereas widespread species were characterised by overdispersion. Species confined to the climatically intermediate (Continental) region were randomly sorted. By including all species occurring within a region, the patterns found for the region-restricted species blurred. Phylogenetically decoupled FD patterns were qualitatively similar to non-decoupled ones with the exception of the Alpine element, where we detected a clear signature of functional differentiation between closely related species. This suggests that recent speciation events contributed to shaping the Alpine flora. Compared to the belowground compartment, aboveground traits showed a more coherent pattern with that of all-trait FD – likely because most biomass is allocated aboveground in forest understoreys. This biogeographic deconstruction study illustrates which type of eco-evolutionary insights can be gained by implementing multifaceted and integrated approaches at the macroecological scal

Biogeographic deconstruction of phylogenetic and functional diversity provides insights into the formation of regional assemblages

Evolutionary history and environmental filtering shape the phylogenetic and functional structure of regional assemblages. However, detecting the footprint of such eco-evolutionary drivers is challenging because these may often counter each other's signature. Here, we examined whether a biogeographic deconstruction approach of phylogenetic (PD) and functional diversity (FD) patterns may help in identifying eco-evolutionary signals in extant regional assemblages. As model system, we used forest understorey angiosperms found in three regions of Italy (Alpine, Mediterranean, Continental). We quantified PD and FD of all species inhabiting the three regions (regional assemblages). Then, we computed PD and FD for the subsets of species restricted to each region (biogeographic elements), also examining diversity patterns of species found across the three regions (widespread element). We used aboveground and belowground traits capturing major plant functions to calculate FD. Additionally, we assessed FD patterns decoupled from phylogeny. We found that species restricted to climatically harsh regions (Alpine and Mediterranean elements) were phylogenetically and functionally clustered, whereas widespread species were characterised by overdispersion. Species confined to the climatically intermediate (Continental) region were randomly sorted. By including all species occurring within a region, the patterns found for the region-restricted species blurred. Phylogenetically decoupled FD patterns were qualitatively similar to non-decoupled ones with the exception of the Alpine element, where we detected a clear signature of functional differentiation between closely related species. This suggests that recent speciation events contributed to shaping the Alpine flora. Compared to the belowground compartment, aboveground traits showed a more coherent pattern with that of all-trait FD – likely because most biomass is allocated aboveground in forest understoreys. This biogeographic deconstruction study illustrates which type of eco-evolutionary insights can be gained by implementing multifaceted and integrated approaches at the macroecological scal

Conserving avian evolutionary history can effectively safeguard future benefits for people

Phylogenetic diversity (PD)—the evolutionary history of a set of species—is conceptually linked to the maintenance of yet-to-be-discovered benefits from biodiversity or “option value.” We used global phylogenetic and utilization data for birds to test the PD option value link, under the assumption that the performance of sets of PD-maximizing species at capturing known benefits is analogous to selecting the same species at a point in human history before these benefits were realized. PD performed better than random at capturing utilized bird species across 60% of tests, with performance linked to the phylogenetic dispersion and prevalence of each utilization category. Prioritizing threatened species for conservation by the PD they encapsulate performs comparably to prioritizing by their functional distinctiveness. However, species selected by each metric show low overlap, indicating that we should conserve both components of biodiversity to effectively conserve a variety of uses. Our findings provide empirical support for the link between evolutionary history and benefits for future generationsWe thank S. Butchart for valuable feedback on an earlier draft of this manuscript. R.G. was funded by the Natural Environment Research Council Science and Solutions for a Changing Planet Doctoral Training Programme (grant number NE/L002515/ 1), the CASE component of which was funded by the Zoological Society of Londo

Searching for predictors of the variability of impacts caused by non-native trees on regulating ecosystem services worldwide

Humans have introduced non-native trees (NNT) all over the world to take advantage of the plethora of benefits they provide. However, depending on the context, NNT may present a diverse range of effects on ecosystem services (ES), from benefits to drawbacks, which may hinder the development of policies for these species. Unfortunately, the attempts so far to understand the impacts of NNT on ES only explained a low proportion of their variation. Here we analyze the variation in impacts of NNT on regulating ecosystem services (RES) by using a global database, which covers the effect size of multiple NNT species on six RES (climate regulation, soil erosion regulation, soil fertility, soil formation, hydrological cycle regulation, and fire protection). We used a wide range of predictors to account for the context-dependency of impacts distributed in five groups: the RES type, functional traits of both the NNT and the dominant NT of the recipient ecosystem, phylogenetic and functional distances between NNT and NT, climatic context, and human population characteristics. Using boosted regression trees and regression trees, we found that the most influential predictors of NNT impacts on RES were annual mean temperatures and precipitation seasonality, followed by the type of RES, human population density, and NNT height. In regions with warm temperatures and low seasonality, NNT tended to increase RES. NNT impacts were greater in densely populated regions. Smaller NNT exerted greater positive impacts on climate regulation and soil erosion regulation in tropical regions than in other climates. We highlight that benign climates and high population density exacerbate the effects of NNT on RES, and that soil fertility is the most consistently affected RES. Knowledge of the factors that modulate NNT impacts can help to predict their potential effects on RES in different parts of the world and at various environmental setting

Maximum levels of global phylogenetic diversity efficiently capture plant services for humankind

The divergent nature of evolution suggests that securing the human benefits that are directly provided by biodiversity may require counting on disparate lineages of the Tree of Life. However, quantitative evidence supporting this claim is still tenuous. Here, we draw on a global review of plant-use records demonstrating that maximum levels of phylogenetic diversity capture significantly greater numbers of plant-use records than random selection of taxa. Our study establishes an empirical foundation that links evolutionary history to human wellbeing, and it will serve as a discussion baseline to promote better-grounded accounts of the services that are directly provided by biodiversity.Comunidad de MadridUniversidad de AlcaláConsejería de Ciencia, Universidades e Innovació

A global database of plant services for humankind

Humanity faces the challenge of conserving the attributes of biodiversity that may be essential to secure human wellbeing. Among all the organisms that are beneficial to humans, plants stand out as the most important providers of natural resources. Therefore, identifying plant uses is critical to preserve the beneficial potential of biodiversity and to promote basic and applied research on the relationship between plants and humans. However, much of this information is often uncritical, contradictory, of dubious value or simply not readily accessible to the great majority of scientists and policy makers. Here, we compiled a genuslevel dataset of plant-use records for all accepted vascular plant taxa (13489 genera) using the information gathered in the 4th Edition of Mabberley’s plant-book, the most comprehensive global review of plant classification and their uses published to date. From 1974 to 2017 all the information was systematically gathered, evaluated, and synthesized by David Mabberley, who reviewed over 1000 botanical sources including modern Floras, monographs, periodicals, handbooks, and authoritative websites. Plant uses were arranged across 28 standard categories of use following the Economic Botany Data Collection Standard guidelines, which resulted in a binary classification of 9478 plant-use records pertaining human and animal nutrition, materials, fuels, medicine, poisons, social and environmental uses. Of all the taxa included in the dataset, 33% were assigned to at least one category of use, the most common being “ornamental” (26%), “medicine” (16%), “human food” (13%) and “timber” (8%). In addition to a readily available binary matrix for quantitative analyses, we provide a control text matrix that links the former to the description of the uses in Mabberley’s plant-book. We hope this dataset will serve to establish synergies between scientists and policy makers interested in plant-human interactions and to move towards the complete compilation and classification of the nature’s contributions to people upon which the wellbeing of future generations may depen