Phylogenetic Patterns of Colonization and Extinction in Experimentally Assembled Plant Communities

Evolutionary history has provided insights into the assembly and functioning of plant communities, yet patterns of phylogenetic community structure have largely been based on non-dynamic observations of natural communities. We examined phylogenetic patterns of natural colonization, extinction and biomass production in experimentally assembled communities.We used plant community phylogenetic patterns two years after experimental diversity treatments (1, 2, 4, 8 or 32 species) were discontinued. We constructed a 5-gene molecular phylogeny and statistically compared relatedness of species that colonized or went extinct to remaining community members and patterns of aboveground productivity. Phylogenetic relatedness converged as species-poor plots were colonized and speciose plots experienced extinctions, but plots maintained more differences in composition than in phylogenetic diversity. Successful colonists tended to either be closely or distantly related to community residents. Extinctions did not exhibit any strong relatedness patterns. Finally, plots that increased in phylogenetic diversity also increased in community productivity, though this effect was inseparable from legume colonization, since these colonists tended to be phylogenetically distantly related.We found that successful non-legume colonists were typically found where close relatives already existed in the sown community; in contrast, successful legume colonists (on their own long branch in the phylogeny) resulted in plots that were colonized by distant relatives. While extinctions exhibited no pattern with respect to relatedness to sown plotmates, extinction plus colonization resulted in communities that converged to similar phylogenetic diversity values, while maintaining differences in species composition

Characterizations of how species mediate ecosystem properties require more comprehensive functional effect descriptors

The importance of individual species in mediating ecosystem process and functioning is generally accepted, but categorical descriptors that summarize species-specific contributions to ecosystems tend to reference a limited number of biological traits and underestimate the importance of how organisms interact with their environment. Here, we show how three functionally contrasting sediment-dwelling marine invertebrates affect fluid and particle transport - important processes in mediating nutrient cycling - and use high-resolution reconstructions of burrow geometry to determine the extent and nature of biogenic modification. We find that individual functional effect descriptors fall short of being able to adequately characterize how species mediate the stocks and flows of important ecosystem properties and that, in contrary to common practice and understanding, they are not substitutable with one another because they emphasize different aspects of species activity and behavior. When information derived from these metrics is combined with knowledge of how species behave and modify their environment, however, detailed mechanistic information emerges that increases the likelihood that a species functional standing will be appropriately summarized. Our study provides evidence that more comprehensive functional effect descriptors are required if they are to be of value to those tasked with projecting how altered biodiversity will influence future ecosystems

Reply to: “Global Conservation of Phylogenetic Diversity Captures More Than Just Functional Diversity”

Academic biologists have long advocated for conserving phylogenetic diversity (PD), often (but not exclusively) on the basis that PD is a useful proxy for “feature diversity”, defined as the variety of forms and functions represented in set of organisms (see below for an extended discussion of this definition). In a recent paper, we assess the extent to which this proxy (which we coined the “phylogenetic gambit”) holds in three empirical datasets (terrestrial mammals, birds, and tropical marine fishes) when using functional traits and functional diversity (FD) to operationalize feature diversity. Owen et al. offer a criticism of our methods for quantifying feature diversity with FD and disagree with our conclusions. We are grateful that Owen et al. have engaged thoughtfully with our work, but we believe there are more points of agreement than Owen et al. imply

Prioritizing Phylogenetic Diversity Captures Functional Diversity Unreliably

In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have assumed that maximizing phylogenetic diversity (PD) should indirectly capture FD, a hypothesis that we name the “phylogenetic gambit”. Here, we empirically test this gambit using data on ecologically relevant traits from \u3e15,000 vertebrate species. Specifically, we estimate a measure of surrogacy of PD for FD. We find that maximizing PD results in an average gain of 18% of FD relative to random choice. However, this average gain obscures the fact that in over one-third of the comparisons, maximum PD sets contain less FD than randomly chosen sets of species. These results suggest that, while maximizing PD protection can help to protect FD, it represents a risky conservation strategy

Revealing natural relationships among arbuscular mycorrhizal fungi: culture line BEG47 represents Diversispora epigaea, not Glomus versiforme

Background: Understanding the mechanisms underlying biological phenomena, such as evolutionarily conservative trait inheritance, is predicated on knowledge of the natural relationships among organisms. However, despite their enormous ecological significance, many of the ubiquitous soil inhabiting and plant symbiotic arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are incorrectly classified. Methodology/Principal Findings: Here, we focused on a frequently used model AMF registered as culture BEG47. This fungus is a descendent of the ex-type culture-lineage of Glomus epigaeum, which in 1983 was synonymised with Glomus versiforme. It has since then been used as ‘G. versiforme BEG47’. We show by morphological comparisons, based on type material, collected 1860–61, of G. versiforme and on type material and living ex-type cultures of G. epigaeum, that these two AMF species cannot be conspecific, and by molecular phylogenetics that BEG47 is a member of the genus Diversispora. Conclusions: This study highlights that experimental works published during the last >25 years on an AMF named ‘G. versiforme’ or ‘BEG47’ refer to D. epigaea, a species that is actually evolutionarily separated by hundreds of millions of years from all members of the genera in the Glomerales and thus from most other commonly used AMF ‘laboratory strains’. Detailed redescriptions substantiate the renaming of G. epigaeum (BEG47) as D. epigaea, positioning it systematically in the order Diversisporales, thus enabling an evolutionary understanding of genetical, physiological, and ecological traits, relative to those of other AMF. Diversispora epigaea is widely cultured as a laboratory strain of AMF, whereas G. versiforme appears not to have been cultured nor found in the field since its original description

Phylogenetic Diversity of Urban Floras in the Central Urals

Modern cities harbor a high diversity of plants, and urban floras are significantly different from non-urban floras especially when considering the proportion of alien species found in cities. However, it is not clear whether urban areas disproportionately select for species from relatively few evolutionary lineages or provide opportunities for species across the full spectrum of plant lineages. Here, we examined the taxonomic and phylogenetic diversity of the floras in four cities (Yekaterinburg, Kamensk-Uralsky, Krasnoufimsk, and Turinsk) in the understudied region of Central Urals (Russian Federation). We classified native species into indigenous and apophytic species, namely, those that are sensitive to anthropogenic disturbance and those that have expanded their range with human activity, respectively. Alien species were classified into archaeophytes and neophytes according to when they were introduced (i.e., before or after than 1800). Phylogenetic diversity was quantified using Faith’s index to reflect total evolutionary history in urban areas and mean phylogenetic distance (MPD) to reflect species dissimilarity. Phylogenetic diversity of native species was higher than that for alien species, and the standardized effect size (SES) of MPD for natives was positive, reflecting their general dissimilarity from one another, while it was very negative for aliens, showing that they were phylogenetically clustered. However, among natives, apophytes were significantly clustered, while indigenous species were overdispersed. For the aliens, MPD was higher for archaeophytes compared to neophytes, though both groups were significantly clustered. These results show that urbanization leads to a non-random selection of plants. Apophytes and alien plants were composed of closely related species, reflecting similar ecological traits and are likely to be pre-adapted to the environmentally altered and highly disturbed urban environment. © Copyright © 2021 Tretyakova, Yakimov, Kondratkov, Grudanov and Cadotte.Funding for this collaboration was provided to MC by the Connaught Global Challenges Award, the Office of the Vice-President International, the School of Graduate Studies at the University of Toronto, the Office of the Vice-Principal Research at the University of Toronto Scarborough, and funding from the Natural Sciences and Engineering Research Council of Canada (#386151). This work was supported in part by the Program for Improving the Competitiveness of the Ural Federal University (the decree no. 211 of the Government of the Russian Federation, contract no. 02.A03.21.0006) and by the Russian Foundation for Basic Research (project no. 19-04-01084)

On the Relationship Between Phylogenetic Diversity and Trait Diversity

Niche differences are key to understanding the distribution and structure of biodiversity. To examine niche differences, we must first characterize how species occupy niche space, and two approaches are commonly used in the ecological literature. The first uses species traits to estimate multivariate trait space (so‐called functional trait diversity, FD); the second quantifies the amount of time or evolutionary history captured by a group of species (phylogenetic diversity, PD). It is often—but controversially—assumed that these putative measures of niche space are at a minimum correlated and perhaps redundant, since more evolutionary time allows for greater accumulation of trait changes. This theoretical expectation remains surprisingly poorly evaluated, particularly in the context of multivariate measures of trait diversity. We evaluated the relationship between phylogenetic diversity and trait diversity using analytical and simulation‐based methods across common models of trait evolution. We show that PD correlates with FD increasingly strongly as more traits are included in the FD measure. Our results indicate that phylogenetic diversity can be a useful surrogate for high‐dimensional trait diversity, but we also show that the correlation weakens when the underlying process of trait evolution includes variation in rate and optima

Diversity and community biomass depend on dispersal and disturbance in microalgal communities

The evidence for species diversity effects on ecosystem functions is mainly based on studies not explicitly addressing local or regional processes regulating coexistence or the importance of community structure in terms of species evenness. In experimental communities of marine benthic microalgae, we altered the successional stages and thus the strength of local species interactions by manipulating rates of dispersal and disturbance. The treatments altered realized species richness, evenness and community biomass. For species richness, dispersal mattered only at high disturbance rates; when opening new space, dispersal led to maximized richness at intermediate dispersal rates. Evenness, in contrast, decreased with dispersal at low or no disturbance, i.e. at late successional stages. Community biomass showed a nonlinear hump-shaped response to increasing dispersal at all disturbance levels.We found a positive correlation between richness and biomass at early succession, and a strong negative correlation between evenness and biomass at late succession. In early succession both community biomass and richness depend directly on dispersal from the regional pool, whereas the late successional pattern shows that if interactions allow the most productive species to become dominant, diverting resources from this species (i.e. higher evenness) reduces production. Our study emphasizes the difference in biodiversity–function relationships over time, as different mechanisms contribute to the regulation of richness and evenness in early and late successional stages