Daniel J. McGlinn

Three keys to the radiation of angiosperms into freezing environments

Early flowering plants are thought to have been woody species restricted to warm habitats. This lineage has since radiated into almost every climate, with manifold growth forms. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species’ traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. Growth habit has long been considered labile, but we find that growth habit was less labile than climate occupancy. Additionally, freezing environments were largely filled by lineages that had already become herbs or, when remaining woody, already had small conduits (that is, the trait evolved before the climate occupancy). By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait). For angiosperms to inhabit novel cold environments they had to gain new structural and functional trait solutions; our results suggest that many of these solutions were probably acquired before their foray into the cold.

The Underpinnings of the Relationship of Species Richness with Space and Time

Various ecological mechanisms influence the forms of species richness relationships (SRRs). These mechanisms can be gathered under five general categories: more individuals, environmental heterogeneity, dispersal limitations, biotic interactions, and multiple species pools. Often only the first two categories are discussed. In contrast, we examine all five and explore how they can influence the form of SRRs. We discuss how various sampling schemes and methods of SRR construction can be used to gain insight about how various processes influence species richness patterns. The field is ripe for probing these effects through more complex simulation models or more sophisticated mathematical approaches. To facilitate deeper understanding, we need to embrace the full spectrum of SRRs and reconsider the assumed common knowledge about the functional form of SRRs. The relationship between species richness and the space or time over which it is sampled has received increasing attention over the past decade, resultin...

Functional distinctiveness of major plant lineages

Summary Plant traits vary widely across species and underpin differences in ecological strategy. Despite centuries of interest, the contributions of different evolutionary lineages to modern-day functional diversity remain poorly quantified. Expanding data bases of plant traits plus rapidly improving phylogenies enable for the first time a data-driven global picture of plant functional diversity across the major clades of higher plants. We mapped five key traits relevant to metabolism, resource competition and reproductive strategy onto a phylogeny across 48324 vascular plant species world-wide, along with climate and biogeographic data. Using a novel metric, we test whether major plant lineages are functionally distinctive. We then highlight the trait–lineage combinations that are most functionally distinctive within the present-day spread of ecological strategies. For some trait–clade combinations, knowing the clade of a species conveys little information to neo- and palaeo-ecologists. In other trait–clade combinations, the clade identity can be highly revealing, especially informative clade–trait combinations include Proteaceae, which is highly distinctive, representing the global slow extreme of the leaf economic spectrum. Magnoliidae and Rosidae contribute large leaf sizes and seed masses and have distinctively warm, wet climatic distributions. Synthesis. This analysis provides a shortlist of the most distinctive trait–lineage combinations along with their geographic and climatic context: a global view of extant functional diversity across the tips of the vascular plant phylogeny.

A global analysis of parenchyma tissue fractions in secondary xylem of seed plants

Summary Parenchyma is an important tissue in secondary xylem of seed plants, with functions ranging from storage to defence and with effects on the physical and mechanical properties of wood. Currently, we lack a large‐scale quantitative analysis of ray parenchyma (RP) and axial parenchyma (AP) tissue fractions. Here, we use data from the literature on AP and RP fractions to investigate the potential relationships of climate and growth form with total ray and axial parenchyma fractions (RAP). We found a 29‐fold variation in RAP fraction, which was more strongly related to temperature than with precipitation. Stem succulents had the highest RAP values (mean ± SD: 70.2 ± 22.0%), followed by lianas (50.1 ± 16.3%), angiosperm trees and shrubs (26.3 ± 12.4%), and conifers (7.6 ± 2.6%). Differences in RAP fraction between temperate and tropical angiosperm trees (21.1 ± 7.9% vs 36.2 ± 13.4%, respectively) are due to differences in the AP fraction, which is typically three times higher in tropical than in temperate trees, but not in RP fraction. Our results illustrate that both temperature and growth form are important drivers of RAP fractions. These findings should help pave the way to better understand the various functions of RAP in plants.

Artifacts and Artifictions in Biodiversity Research

The biodiversity crisis demands that scientists be careful in their application of quantitative methods, because misuse of biodiversity statistics can lead to trivial but real patterns (artifacts) or to false patterns (artifictions). While misuses such as biases in taxonomic ratios, standardization by dividing by area or individuals, and the rarefaction effect have been repeatedly recognized in the literature, they continue to appear regularly in the scientific literature. Here, we illustrate (using data from North American floras and the Tallgrass Prairie Preserve in Oklahoma, USA) examples of how artifacts and artifictions can lead to misinterpretation of biodiversity patterns. We urge biogeographers and ecologists to be vigilant when using biodiversity statistics, to avoid false interpretations.

A strong test of the maximum entropy theory of ecology.

The maximum entropy theory of ecology (METE) is a unified theory of biodiversity that predicts a large number of macroecological patterns using information on only species richness, total abundance, and total metabolic rate of the community. We evaluated four major predictions of METE simultaneously at an unprecedented scale using data from 60 globally distributed forest communities including more than 300,000 individuals and nearly 2,000 species. METE successfully captured 96% and 89% of the variation in the rank distribution of species abundance and individual size but performed poorly when characterizing the size-density relationship and intraspecific distribution of individual size. Specifically, METE predicted a negative correlation between size and species abundance, which is weak in natural communities. By evaluating multiple predictions with large quantities of data, our study not only identifies a mismatch between abundance and body size in METE but also demonstrates the importance of conducting strong tests of ecological theories.

Modeling the sampling effect in the species–time–area relationship

Recent empirical work in numerous systems has demonstrated the interdependence of spatial and temporal accumulation of species in the species-time-area relationship (STAR). The purpose of this study was to develop a process-based stochastic model for the STAR that assumes species neutrality and to compare the models expectations to data collected on plant species in a tallgrass prairie. We varied two important aspects of the neutral species assemblage: evenness in the species pool and individual replacement rate (R). When R is larger than approximately 0.5 and evenness is intermediate to high, the neutral STAR generates patterns qualitatively similar to the empirical STAR. Our model also indicates that space and time were not symmetrical in their effects on species accumulation, except in the special case of R = 1.0. We observed both positive and negative time-by-area interactions in the sampling model, which indicates that nonzero interactions are not necessarily evidence of ecological processes. Furthermore, as accumulated richness approaches the size of the species pool, the time-by-area interaction becomes increasingly negative in our model. This suggests that negative time-by-area interactions should be expected a priori in empirical systems if rates of species accumulation decrease due to increasing rarity of unique species. Given the wide range of STARs that the sampling model generated, the difficulty in estimating key parameters, and the complexity of assessing the relative abundance distribution and scale of the species pool, we cannot refute the sampling effect, and we suggest caution in accepting ecologically oriented explanations of empirical STARs.

Mutualism Persistence and Abandonment during the Evolution of the Mycorrhizal Symbiosis

Mutualistic symbioses with mycorrhizal fungi are widespread in plants. The majority of plant species associate with arbuscular mycorrhizal (AM) fungi. By contrast, the minority associate with ectomycorrhizal (EM) fungi, have abandoned the symbiosis and are nonmycorrhizal (NM), or engage in an intermediate, weakly AM symbiosis (AMNM). To understand the processes that maintain the mycorrhizal symbiosis or cause its loss, we reconstructed its evolution using a ∼3,000-species seed plant phylogeny integrated with mycorrhizal state information. Reconstruction indicated that the common ancestor of seed plants most likely associated with AM fungi and that the EM, NM, and AMNM states descended from the AM state. Direct transitions from the AM state to the EM and NM states were infrequent and generally irreversible, implying that natural selection or genetic constraint could promote stasis once a particular state evolved. However, the evolution of the NM state was more frequent via an indirect pathway through the AMNM state, suggesting that weakening of the AM symbiosis is a necessary precursor to mutualism abandonment. Nevertheless, reversions from the AMNM state back to the AM state were an order of magnitude more likely than transitions to the NM state, suggesting that natural selection favors the AM symbiosis over mutualism abandonment.

Scale dependence in species turnover reflects variance in species occupancy

Patterns of species turnover may reflect the processes driving community dynamics across scales. While the majority of studies on species turnover have examined pairwise comparison metrics (e.g., the average Jaccard dissimilarity), it has been proposed that the species-area relationship (SAR) also offers insight into patterns of species turnover because these two patterns may be analytically linked. However, these previous links only apply in a special case where turnover is scale invariant, and we demonstrate across three different plant communities that over 90% of the pairwise turnover values are larger than expected based on scale-invariant predictions from the SAR. Furthermore, the degree of scale dependence in turnover was negatively related to the degree of variance in the occupancy frequency distribution (OFD). These findings suggest that species turnover diverges from scale invariance, and as such pairwise turnover and the slope of the SAR are not redundant. Furthermore, models developed to explain the OFD should be linked with those developed to explain species turnover to achieve a more unified understanding of community structure.

Sustainable computational science: the ReScience initiative

Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. James Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. The actual scholarship is the full software environment, code, and data that produced the result. This implies new workflows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically different from other traditional scientific journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and software tests.