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

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

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

Opposing community assembly patterns for dominant and non-dominant plant species in herbaceous ecosystems globally

Biotic and abiotic factors interact with dominant plants—the locally most frequent or with the largest coverage—and nondominant plants differently, partially because dominant plants modify the environment where nondominant plants grow. For instance, if dominant plants compete strongly, they will deplete most resources, forcing nondominant plants into a narrower niche space. Conversely, if dominant plants are constrained by the environment, they might not exhaust available resources but instead may ameliorate environmental stressors that usually limit nondominants. Hence, the nature of interactions among nondominant species could be modified by dominant species. Furthermore, these differences could translate into a disparity in the phylogenetic relatedness among dominants compared to the relatedness among nondominants. By estimating phylogenetic dispersion in 78 grasslands across five continents, we found that dominant species were clustered (e.g., co-dominant grasses), suggesting dominant species are likely organized by environmental filtering, and that nondominant species were either randomly assembled or overdispersed. Traits showed similar trends for those sites (<50%) with sufficient trait data. Furthermore, several lineages scattered in the phylogeny had more nondominant species than expected at random, suggesting that traits common in nondominants are phylogenetically conserved and have evolved multiple times. We also explored environmental drivers of the dominant/nondominant disparity. We found different assembly patterns for dominants and nondominants, consistent with asymmetries in assembly mechanisms. Among the different postulated mechanisms, our results suggest two complementary hypotheses seldom explored: (1) Nondominant species include lineages adapted to thrive in the environment generated by dominant species. (2) Even when dominant species reduce resources to nondominant ones, dominant species could have a stronger positive effect on some nondominants by ameliorating environmental stressors affecting them, than by depleting resources and increasing the environmental stress to those nondominants. These results show that the dominant/nondominant asymmetry has ecological and evolutionary consequences fundamental to understand plant communities.EEA Santa CruzFil: Arnillas, Carlos Alberto. University of Toronto Scarborough. Department of Physical and Environmental Sciences; Canadá.Fil: Borer, Elizabeth T. University of Minnesota; Estados UnidosFil: Seabloom, Eric W. University of Minnesota; Estados UnidosFil: Alberti, Juan. Universidad Nacional de Mar del Plata. Instituto de Investigaciones Marinas y Costeras; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Marinas y Costeras; Argentina.Fil: Baez, Selene. Escuela Politécnica Nacional. Department of Biology; Ecuador.Fil: Bakker, Jonathan D. University of Washington. School of Environmental and Forest Sciences; Estados UnidosFil: Boughton, Elizabeth H. Archbold Biological Station. Venus, Florida; Estados UnidosFil: Buckley, Yvonne M. Trinity College Dublin. School of Natural Sciences, Zoology; IrlandaFil: Bugalho, Miguel Nuno. University of Lisbon. Centre for Applied Ecology Prof. Baeta Neves (CEABN-InBIO). School of Agriculture; Portugal.Fil: Donohue, Ian. Trinity College Dublin. School of Natural Sciences, Zoology; IrlandaFil: Dwyer, John. University of Queensland. School of Biological Sciences; Australia.Fil: Firn, Jennifer. Queensland University of Technology (QUT); Australia.Fil: Peri, Pablo Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina.Fil: Peri, Pablo Luis. Universidad Nacional de la Patagonia Austral; Argentina.Fil: Peri, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Cadotte, Marc W. University of Toronto Scarborough. Department of Biological Sciences; Canadá.Fil: Cadotte, Marc W. University of Toronto. Department of Ecology and Evolutionary Biology; Canadá

Nutrient enrichment increases invertebrate herbivory and pathogen damage in grasslands

1- Plant damage by invertebrate herbivores and pathogens influences the dynamics of grassland ecosystems, but anthropogenic changes in nitrogen and phosphorus availability can modify these relationships. 2- Using a globally distributed experiment, we describe leaf damage on 153 plant taxa from 27 grasslands worldwide, under ambient conditions and with experimentally elevated nitrogen and phosphorus. 3- Invertebrate damage significantly increased with nitrogen addition, especially in grasses and non-leguminous forbs. Pathogen damage increased with nitrogen in grasses and legumes but not forbs. Effects of phosphorus were generally weaker. Damage was higher in grasslands with more precipitation, but climatic conditions did not change effects of nutrients on leaf damage. On average, invertebrate damage was relatively higher on legumes and pathogen damage was relatively higher on grasses. Community-weighted mean damage reflected these functional group patterns, with no effects of N on community-weighted pathogen damage (due to opposing responses of grasses and forbs) but stronger effects of N on community-weighted invertebrate damage (due to consistent responses of grasses and forbs). 4- Synthesis. As human-induced inputs of nitrogen and phosphorus continue to increase, understanding their impacts on invertebrate and pathogen damage becomes increasingly important. Our results demonstrate that eutrophication frequently increases plant damage and that damage increases with precipitation across a wide array of grasslands. Invertebrate and pathogen damage in grasslands is likely to increase in the future, with potential consequences for plant, invertebrate and pathogen communities, as well as the transfer of energy and nutrients across trophic levels.EEA Santa CruzFil: Ebeling, Anne. University of Jena. Institute of Ecology and Evolution; AlemaniaFil: Strauss, Alex T. University of Minnesota. Department of Ecology, Evolution, and Behavior; Estados UnidosFil: Strauss, Alex T. University of Georgia. Odum School of Ecology; Estados UnidosFil: Adler, Peter B. Utah State University. Department of Wildland Resources and the Ecology Center; Estados UnidosFil: Arnillas, Carlos Alberto. University of Toronto —Scarborough. Department of Physical and Environmental Sciences; CanadáFil: Barrio, Isabel C. Agricultural University of Iceland. Faculty of Environmental and Forest Sciences; IslandiaFil: Biederman, Lori A. Iowa State University. Department of Ecology, Evolution, and Organismal Biology; Estados UnidosFil. Borer, Elizabeth T. University of Minnesota. Department of Ecology, Evolution, and Behavior; Estados UnidosFil: Bugalho, Miguel N. University of Lisbon. Centre for Applied Ecology (CEABN-InBIO). School of Agriculture; Portugal.Fil: Caldeira, Maria C. University of Lisbon. Forest Research Centre. School of Agriculture; Portugal.Fil: Cadotte, Marc W. University of Toronto Scarborough. Department of Biological Sciences; CanadáFil: Peri, Pablo Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina.Fil: Peri, Pablo Luis. Universidad Nacional de la Patagonia Austral; Argentina.Fil: Peri, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Blumenthal, Dana M. USDA-ARS, Rangeland Resources & Systems Research Unit; Estados Unido

Rarity, Species Richness, and the Threat of Extinction—Are Plants the Same as Animals?

Assessment of conservation status is done both for areas or habitats and for species (or taxa). IUCN Red List categories have been the principal method of categorising species in terms of extinction risk, and have been shown to be robust and helpful in the groups for which they have been developed. A recent study highlights properties associated with extinction risk in flowering plants, focusing on the species-rich hot spot of the Cape region of South Africa, and concludes that merely following methods derived from studies of vertebrates may not provide the best estimates of extinction risk for plants. Biology, geography, and history all are important factors in risk, and the study poses many questions about how we categorise and assess species for conservation priorities

Life cycle assessment of Polychlorinated Biphenyl contaminated soil remediation processes

Goal and scope. A life-cycle assessment (LCA) was performed to evaluate the environmental impacts of the remediation of industrial soils contaminated by polychlorobiphenyl (PCB). Two new bioremediation treatment options were compared with the usual incineration process. In this attributional LCA, only secondary impacts were considered. The contaminated soil used for the experiments contained 200 mg of PCB per kg. Methods. Three off-site treatments scenarios were studied: 1) bioremediation with mechanical aeration, 2) bioremediation with electric aeration and 3) incineration with natural gas. Bioremediation processes were designed from lab-scale, scale-up and pilot experiments. The incineration technique was inspired by a French plant. A semi-quantitative uncertainty analysis was performed on the data. Environmental impacts were evaluated with the CML 2001 method using the Simapro software program. Results and discussion. In most compared categories, the bioremediation processes are favorable. Of the bioremediation options, the lowest environmental footprint was observed for electric aeration. The uncertainty analysis supported the results that compared incineration and bioremediation but decreased the difference between the options of aeration. The distance of transportation was one of the most sensitive parameters, especially for bioremediation. At equal distances between the polluted sites and the treatment plant, bioremediation had fewer impacts than incineration in eight out of thirteen categories. Conclusions. The use of natural gas for the incineration process generated the most impacts. Irrespective of the aeration option, bioremediation was better than incineration. Recommendations. The time of treatment should be taken into account. More precise and detailed data are required for the incineration scenario. More parameters of biological treatments should be measured. LCA results should be completed using ecological and health risk assessment and an acceptability evaluation