Benjamin Baiser

Decomposing biodiversity data using the Latent Dirichlet Allocation model, a probabilistic multivariate statistical method

We propose a novel multivariate method to analyse biodiversity data based on the Latent Dirichlet Allocation (LDA) model. LDA, a probabilistic model, reduces assemblages to sets of distinct component communities. It produces easily interpretable results, can represent abrupt and gradual changes in composition, accommodates missing data and allows for coherent estimates of uncertainty. We illustrate our method using tree data for the eastern United States and from a tropical successional chronosequence. The model is able to detect pervasive declines in the oak community in Minnesota and Indiana, potentially due to fire suppression, increased growing season precipitation and herbivory. The chronosequence analysis is able to delineate clear successional trends in species composition, while also revealing that site-specific factors significantly impact these successional trajectories. The proposed method provides a means to decompose and track the dynamics of species assemblages along temporal and spatial gradients, including effects of global change and forest disturbances.

Community assembly of the ferns of Florida

PREMISE OF THE STUDY Many ecological and evolutionary processes shape the assembly of organisms into local communities from a regional pool of species. We analyzed phylogenetic and functional diversity to understand community assembly of the ferns of Florida at two spatial scales. METHODS We built a phylogeny for 125 of the 141 species of ferns in Florida using five chloroplast markers. We calculated mean pairwise dissimilarity (MPD) and mean nearest taxon distance (MNTD) from phylogenetic distances and functional trait data for both spatial scales and compared the results to null models to assess significance. KEY RESULTS Our results for over vs. underdispersion in functional and phylogenetic diversity differed depending on spatial scale and metric considered. At the county scale, MPD revealed evidence for phylogenetic overdispersion, while MNTD revealed phylogenetic and functional underdispersion, and at the conservation area scale, MPD revealed phylogenetic and functional underdispersion while MNTD revealed evidence only of functional underdispersion. CONCLUSIONS Our results are consistent with environmental filtering playing a larger role at the smaller, conservation area scale. The smaller spatial units are likely composed of fewer local habitat types that are selecting for closely related species, with the larger-scale units more likely to be composed of multiple habitat types that bring together a larger pool of species from across the phylogeny. Several aspects of fern biology, including their unique physiology and water relations and the importance of the independent gametophyte stage of the life cycle, make ferns highly sensitive to local, microhabitat conditions.

Non-random Patterns of Invasion and Extinction Reduce Phylogenetic Diversity in Island Bird Assemblages

Anthropogenically driven changes in bird communities on oceanic islands exemplify the biotic upheaval experienced by island floras and faunas. While the influence of invasions and extinctions on species richness and beta-diversity of island bird assemblages have been explored, little is known about the impact of these invasions and extinctions on phylogenetic diversity. Here we quantify phylogenetic diversity of island bird assemblages resulting from extinctions alone, invasions alone, and the combination of extinctions and invasions in the historic time period (1500 CE to the current), and compare it to the expected phylogenetic diversity that would result if these processes involved randomly selected island bird species. We assessed phylogenetic diversity and structure at the scale of the island (n =152), the archipelago containing the islands (n=22), and the four oceans containing the archipelagos using three measures. We found that extinction, invasion, and the combination of invasion and extinction generally resulted in lower phylogenetic diversity than expected, regardless of the spatial scale examined. We conclude that extinction and invasion of birds on islands are non-random with respect to phylogeny and that these processes generally leave bird assemblages with lower phylogenetic diversity than we would expect under random invasion or extinction. This article is protected by copyright. All rights reserved.

mangal - making complex ecological network analysis simpler

The study of ecological networks is severely limited by (i) the difficulty to access data, (ii) the lack of a standardized way to link meta-data with interactions, and (iii) the disparity of formats in which ecological networks themselves are represented. To overcome these limitations, we conceived a data specification for ecological networks. We implemented a database respecting this standard, and released a R package (rmangal) allowing users to programmatically access, curate, and deposit data on ecological interactions. In this article, we show how these tools, in conjunctions with other frameworks for the programmatic manipulation of open ecological data, streamlines the analysis process, and improves eplicability and reproducibility of ecological networks studies.

For comparing phylogenetic diversity among communities, go ahead and use synthesis phylogenies

Should we build our own phylogenetic trees based on gene sequence data, or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort, expertise, and cost than subsetting an already available phylogeny (synthesis-based phylogeny). However, we still lack a comparison of how these two approaches to building phylogenetic trees influence common community phylogenetic analyses such as comparing community phylogenetic diversity and estimating trait phylogenetic signal. Here, we generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life [OTL]). We simulated 1,000 communities and 12,000 continuous traits along each purpose-built phylogeny. We then compared the effects of different trees on estimates of phylogenetic diversity (alpha and beta) and phylogenetic signal (Pagel’s λ and Blomberg’s K). Synthesis-based phylogenies generally yielded higher estimates of phylogenetic diversity when compared to purpose-built phylogenies. However, resulting measures of phylogenetic diversity from both types of phylogenies were highly correlated (Spearman’s ρ > 0.8 in most cases). Mean pairwise distance (both alpha and beta) is the index that is most robust to the differences in tree construction that we tested. Measures of phylogenetic diversity based on the OTL showed the highest correlation with measures based on the purpose-built phylogenies. Trait phylogenetic signal estimated with synthesis-based phylogenies, especially from the OTL, were also highly correlated with estimates of Blomberg’s K or close to Pagel’s λ from purpose-built phylogenies when traits were simulated under Brownian Motion. For commonly employed community phylogenetic analyses, our results justify taking advantage of recently developed and continuously improving synthesis trees, especially the Open Tree of Life.Should we build our own phylogenetic trees based on gene sequence data or can we simply use available synthesis phylogenies? This is a fundamental question that any study involving a phylogenetic framework must face at the beginning of the project. Building a phylogeny from gene sequence data (purpose-built phylogeny) requires more effort and expertise than subsetting an already available phylogeny (synthesis-based phylogeny). If phylogenetic diversity estimates based on these two types of phylogenies are highly correlated, using readily available synthesis-based phylogenies is justified for comparing phylogenetic diversity among communities. However, a comparison of how these two approaches to building phylogenetic trees influence the calculation of phylogenetic diversity has not been explicitly tested. We generated three purpose-built phylogenies and their corresponding synthesis-based trees (two from Phylomatic and one from the Open Tree of Life). We then utilized a simulation approach to generate 1000 communities with a fixed number of species per site and compared the effects of different trees on estimates of phylogenetic alpha and beta diversity using Spearman9s rank-based correlation and linear mixed models. Synthesis-based phylogenies generally overestimated phylogenetic diversity when compared to purpose-built ones. However, their resulting measures of phylogenetic diversity were highly correlated (Spearman9s _r_ > 0.8 in most cases). Mean pairwise distance (both alpha and beta version) is the most robust index among the phylogenetic diversity indices we tested. Measures of phylogenetic diversity based on the Open Tree of Life showed the highest correlation with measures based on the purpose-built phylogenies. For comparing phylogenetic diversity among communities, our results justify taking advantage of recently developed and continuously improving synthesis trees such as the Open Tree of Life.

Defaunation and fragmentation erode small mammal diversity dimensions in tropical forests

Forest fragmentation and defaunation are considered the main drivers of biodiversity loss, yet the synergistic effects of landscape changes and biotic interactions on assemblage structure have been poorly investigated. Here, we use an extensive dataset of 283 assemblages and 105 species of small mammals to understand how defaunation of medium and large mammals and forest fragmentation change the community composition and diversity of rodents and marsupials in tropical forests of South America. We used structured equation models to investigate the relationship between small mammal species, functional and phylogenetic diversity with forest size, forest cover and the occurrence of medium and large mammals. The best-fit model showed that defaunation reduced functional diversity, and that species diversity of small mammals increased with forest patch size. Forest cover did not affect functional and phylogenetic diversity. Our results indicate that occurrence of medium and large sized mammals (probably acting as predators, or competitors of small mammals) and forest patch size help to retain species and functional diversity in small mammal communities. Further, the number of species in a small mammal community was critical to the maintenance of phylogenetic diversity, and may have a pronounced influence on the ecological functions played by small mammals. Identifying how phylogenetic and functional diversity change in function of human pressures allows us to better understand the contribution of extant lineages to ecosystem functioning in tropical forests.

Bringing Elton and Grinnell together: a quantitative framework to represent the biogeography of ecological interaction networks

Biogeography has traditionally focused on the spatial distribution and abundance of species. Both are driven by the way species interact with one another, but only recently community ecologists realized the need to document their spatial and temporal variation. Here, we call for an integrated approach, adopting the view that community structure is best represented as a network of ecological interactions, and show how it translates to biogeography questions. We propose that the ecological niche should encompass the effect of the environment on species distribution (the Grinnellian dimension of the niche) and on the ecological interactions among them (the Eltonian dimension). Starting from this concept, we develop a quantitative theory to explain turnover of interactions in space and time – i.e. a novel approach to interaction distribution modeling. We apply this framework to host–parasite interactions across Europe and find that two aspects of the environment (temperature and precipitation) exert a strong imprint on species co-occurrence, but not on species interactions. Even where species co-occur, interaction proves to be stochastic rather than deterministic, adding to variation in realized network structure. We also find that a large majority of host-parasite pairs are never found together, thus precluding any inferences regarding their probability to interact. This first attempt to explain variation of network structure at large spatial scales opens new perspectives at the interface of species distribution modeling and community ecology.

Among‐Species Overlap in Rodent Body Size Distributions Predicts Species Richness Along a Temperature Gradient

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Comparing species–area relationships of native and exotic species

The species–area relationship (SAR) is one of the most general patterns in ecology. Recently, SARs have been employed as tools for comparing the ecology and biogeography of native and exotic species across spatial scales and exploring the influence of invasive species on native biodiversity. Here, we assess published studies to determine if SARs differ between native and exotic assemblages. We conducted a literature search to find studies that estimated the exponent (z) of the power-law SAR for native and exotic species across the same set of locales. We also compiled intercepts (c) of SARs where available. We used linear mixed models to test if z and c differed between native and exotic SARs and if this relationship differed across taxa. Our literature search produced 36 native-exotic pairs from 23 studies with which to compare the exponent of the power-law SAR. Further, SAR intercepts were available for 21 native-exotic pairs. Overall, exotic SAR exponents (z) did not differ from those of natives. However, this pattern did not hold across all taxonomic groups. Plant assemblages, which are best represented in our data (61% of total), mirrored the overall pattern showing no differences in exponents between native and exotic SARs. On the other hand, SAR exponents were greater for both native bird and animal assemblages. The intercepts (c) of native SARs were significantly greater than those of exotics for all taxa combined and for each individual taxonomic grouping. Our results suggest processes driving the increase in species richness with area are similar for native and exotic plant species, but not for animals. Expanding studies that compare SARs of native and exotic species to more taxonomic groups and different types of SARs (e.g., nested, contiguous, non-contiguous) will facilitate a better understanding of how native and exotic species richness scale with area.

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.