Community assembly of the ferns of Florida

Extending trait dispersion across trophic levels: Predator assemblages act as top-down filters on prey communities

Studies of community assembly typically focus on the effects of abiotic environmental filters and stabilizing competition on functional trait dispersion within single trophic levels. Predation is a well-known driver of community diversity and composition, yet the role of functionally diverse predator communities in filtering prey community traits has received less attention. We examined functionally diverse communities of predators (fishes) and prey (epifaunal crustaceans) in eelgrass (Zostera marina) beds in two northern California estuaries to evaluate the filtering effects of predator traits on community assembly and how filters acting on predators influence their ability to mediate prey community assembly. Fish traits related to bottom orientation were correlated with more clustered epifauna communities, and epifauna were generally overdispersed while fishes were clustered, suggesting prey may be pushed to disparate areas of trait space to avoid capture by benthic sit-and-wait predators. We also found correlations between the trait dispersions of predator and prey communities that strengthened after accounting for the effects of habitat filters on predator dispersion, suggesting that habitat filtering effects on predator species pools may hinder their ability to affect prey community assembly. Our results present compelling observational evidence that specific predator traits have measurable impacts on the community assembly of prey, inviting experimental tests of predator trait means on community assembly and explicit comparisons of how the relative effects of habitat filters and intraguild competition on predators impact their ability to affect prey community assembly. Integrating our understanding of traits at multiple trophic levels can help us better predict the impacts of community composition on food web dynamics as regional species pools shift with climate change and anthropogenic introductions.

PhyloPlus: a Universal Tool for Phylogenetic Interrogation of Metagenomic Communities

Phylogeny is a powerful tool that can be incorporated into quantitative descriptions of community diversity, yet its use has been limited largely due to the difficulty in constructing phylogenies which incorporate the wide genomic diversity of microbial communities. Here, we describe the development of a web portal, PhyloPlus, which enables users to generate customized phylogenies that may be applied to any bacterial or archaeal communities. We demonstrate the power of phylogeny by comparing metrics that employ phylogeny with those that do not when applied to data sets from two metagenomic studies (fermented food, n = 58; human microbiome, n = 60). This example shows how inclusion of all bacterial species identified by taxonomic classifiers (Kraken2 and Kaiju) made the phylogeny perfectly congruent to the corresponding classification outputs. Our phylogeny-based approach also enabled the construction of more constrained null models which (i) shed light into community structure and (ii) minimize potential inflation of type I errors. Construction of such null models allowed for the observation of under-dispersion in 44 (75.86%) food samples, with the metacommunity defined as bacteria that were found in different food matrices. We also observed that closely related species with high abundance and uneven distribution across different sites could potentially exaggerate the dissimilarity between phylogenetically similar communities if they were measured using traditional species-based metrics (P_adj. = 0.003), whereas this effect was mitigated by incorporating phylogeny (P_adj. = 1). In summary, our tool can provide additional insights into microbial communities of interest and facilitate the use of phylogeny-based approaches in metagenomic analyses. IMPORTANCE There has been an explosion of interest in how microbial diversity affects human health, food safety, and environmental functions among many other processes. Accurately measuring the diversity and structure of those communities is central to understanding their effects. Here, we describe the development of a freely available online tool, PhyloPlus, which allows users to generate custom phylogenies that may be applied to any data set, thereby removing a major obstacle to the application of phylogeny to metagenomic data analysis. We demonstrate that the genetic relatedness of the organisms within those communities is a critical feature of their overall diversity, and that using a phylogeny which captures and quantifies this diversity allows for much more accurate descriptions while preventing misleading conclusions based on estimates that ignore evolutionary relationships.

The biogeography of community assembly: latitude and predation drive variation in community trait distribution in a guild of epifaunal crustaceans

While considerable evidence exists of biogeographic patterns in the intensity of species interactions, the influence of these patterns on variation in community structure is less clear. Studying how the distributions of traits in communities vary along global gradients can inform how variation in interactions and other factors contribute to the process of community assembly. Using a model selection approach on measures of trait dispersion in crustaceans associated with eelgrass (Zostera marina) spanning 30° of latitude in two oceans, we found that dispersion strongly increased with increasing predation and decreasing latitude. Ocean and epiphyte load appeared as secondary predictors; Pacific communities were more overdispersed while Atlantic communities were more clustered, and increasing epiphytes were associated with increased clustering. By examining how species interactions and environmental filters influence community structure across biogeographic regions, we demonstrate how both latitudinal variation in species interactions and historical contingency shape these responses. Community trait distributions have implications for ecosystem stability and functioning, and integrating large-scale observations of environmental filters, species interactions and traits can help us predict how communities may respond to environmental change.

Life in the canopy: community trait assessments reveal substantial functional diversity among fern epiphytes

The expansion of angiosperm-dominated forests in the Cretaceous and early Cenozoic had a profound effect on terrestrial biota by creating novel ecological niches. The majority of modern fern lineages are hypothesized to have arisen in response to this expansion, particularly fern epiphytes that radiated into the canopy. Recent evidence, however, suggests that epiphytism does not correlate with increased diversification rates in ferns, calling into question the role of the canopy habitat in fern evolution. To understand the role of the canopy in structuring fern community diversity, we investigated functional traits of fern sporophytes and gametophytes across a broad phylogenetic sampling on the island of Moorea, French Polynesia, including > 120 species and representatives of multiple epiphytic radiations. While epiphytes showed convergence in small size and a higher frequency of noncordate gametophytes, they showed greater functional diversity at the community level relative to terrestrial ferns. These results suggest previously overlooked functional diversity among fern epiphytes, and raise the hypothesis that while the angiosperm canopy acted as a complex filter that restricted plant size, it also facilitated diversification into finely partitioned niches. Characterizing these niche axes and adaptations of epiphytic ferns occupying them should be a priority for future pteridological research.

Taxonomic, Phylogenetic, and Functional Diversity of Ferns at Three Differently Disturbed Sites in Longnan County, China

Human disturbances are greatly threatening to the biodiversity of vascular plants. Compared to seed plants, the diversity patterns of ferns have been poorly studied along disturbance gradients, including aspects of their taxonomic, phylogenetic, and functional diversity. Longnan County, a biodiversity hotspot in the subtropical zone in South China, was selected to obtain a more thorough picture of the fern–disturbance relationship, in particular, the taxonomic, phylogenetic, and functional diversity of ferns at different levels of disturbance. In 90 sample plots of 5 × 5 m2 along roadsides at three sites, we recorded a total of 20 families, 50 genera, and 99 species of ferns, as well as 9759 individual ferns. The sample coverage curve indicated that the sampling effort was sufficient for biodiversity analysis. In general, the taxonomic, phylogenetic, and functional diversity measured by Hill numbers of order q = 0–3 indicated that the fern diversity in Longnan County was largely influenced by the level of human disturbance, which supports the ‘increasing disturbance hypothesis’. Many functional traits of ferns at the most disturbed site were adaptive to the disturbance. There were also some indicators of fern species responding to the different disturbance levels. Hence, ferns may be considered as a good indicator group for environmental stress.

Community phylogeny of the globally critically imperiled pine rockland ecosystem

PREMISE OF THE STUDY

Community phylogenetic methods incorporate information on evolutionary relationships into studies of organismal assemblages. We used a community phylogenetic framework to investigate relationships and biogeographic affinities and to calculate phylogenetic signal of endemism and invasiveness for the flora of the pine rocklands-a globally critically imperiled ecosystem with a significant portion of its distribution in South Florida, United States.

METHODS

We reconstructed phylogenetic relationships of 538 vascular plant taxa, which represent 92.28% of the vascular flora of the pine rocklands. We estimated phylogenetic signal for endemism and invasiveness using phylogenetic generalized linear mixed models. We determined the native range for each species in the data set and calculated the total number of species sourced from each region and all possible combinations of these regions.

KEY RESULTS

The pine rockland flora includes representatives of all major vascular plant lineages, and most species have native ranges in the New World. There was strong phylogenetic signal for endemism, but not for invasiveness.

CONCLUSIONS

Community phylogenetics has high potential value for conservation planning, particularly for fragmented and endangered ecosystems like the pine rockland. Strong phylogenetic signal for endemic species in our data set, which also tend to be threatened or endangered, can help to identify species at risk, as well as fragments where those species occur, highlighting conservation priorities. Our results indicate, at least in the pine rockland ecosystem, no phylogenetic signal for invasive species, and thus other information must be used to predict the potential for invasiveness.

Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing

PREMISE OF THE STUDY

Phenotypic data sets are necessary to elucidate the genealogy of life, but assembling phenotypic data for taxa across the tree of life can be technically challenging and prohibitively time consuming. We describe a semi-automated protocol to facilitate and expedite the assembly of phenotypic character matrices of plants from formal taxonomic descriptions. This pipeline uses new natural language processing (NLP) techniques and a glossary of over 9000 botanical terms.

METHODS AND RESULTS

Our protocol includes the Explorer of Taxon Concepts (ETC), an online application that assembles taxon-by-character matrices from taxonomic descriptions, and MatrixConverter, a Java application that enables users to evaluate and discretize the characters extracted by ETC. We demonstrate this protocol using descriptions from Araucariaceae.

CONCLUSIONS

The NLP pipeline unlocks the phenotypic data found in taxonomic descriptions and makes them usable for evolutionary analyses.