Abstract Phylogenetic and species‐based taxonomic descriptions of community structure may provide complementary information about the mechanisms driving community assembly across different environments. Environmental filtering may have similar effects on taxonomic and phylogenetic diversity under the assumption of niche conservatism, whereas competitive exclusion could produce contrasting patterns in these diversity metrics. In grassland restorations, these diversity patterns might then reveal potential assembly mechanisms underlying the impacts of restoration and management conditions on community structure.We compared plant community structure (alpha diversity, composition, and within‐site beta diversity) from both phylogenetic and taxonomic perspectives. Using surveys from 120 tallgrass prairie restorations in four regions of the Midwestern United States, we examined the effects of four potential drivers or environmental gradients: precipitation in the first year of restoration, seed mix richness, time since last prescribed fire, and restoration age, and included soil conditions as a covariate.First‐year precipitation influenced taxonomic community structure, but had weak effects on phylogenetic diversity and composition. Similarly, greater seed mix richness increased taxonomic diversity but did not influence phylogenetic diversity. Taxonomic, but not phylogenetic, diversity generally was lower in older restorations and those with a longer time since the last prescribed fire. These drivers consistently explained more variation in taxonomic than phylogenetic diversity and composition, perhaps in part because species turnover was largely among related species, producing weak impacts on phylogenetic community measures.An impact of precipitation on taxonomic but not phylogenetic diversity suggests that there may not be large differences in drought tolerance among clades that would cause phylogenetic patterns to arise from this environmental filter. Declining taxonomic diversity but not phylogenetic diversity is consistent with competitive exclusion as an assembly mechanism when competition is strongest between related species.Synthesis. This research shows how studying taxonomic and phylogenetic diversity of ecosystem restorations can inform plant community ecology and help natural resource managers better predict the outcomes of restoration actions and management.
more »
« less
Predicting and Prioritising Community Assembly: Learning Outcomes via Experiments
ABSTRACT Community assembly provides the foundation for applications in biodiversity conservation, climate change, invasion, restoration and synthetic ecology. However, predicting and prioritising assembly outcomes remains difficult. We address this challenge via a mechanism‐free approach useful when little data or knowledge exist (LOVE; Learning Outcomes Via Experiments). We carry out assembly experiments (‘actions’, here, random combinations of species additions) potentially in multiple environments, wait, and measure abundance outcomes. We then train a model to predict outcomes of novel actions or prioritise actions that would yield the most desirable outcomes. Across 10 single‐ and multi‐environment datasets, when trained on 89 randomly selected actions,LOVEpredicts outcomes with 0.5%–3.4% mean error, and prioritises actions for maximising richness, maximising abundance, or removing unwanted species, with 94%–99% mean true positive rate and 10%–84% mean true negative rate across tasks.LOVEcomplements existing mechanism‐first approaches for community ecology and may help address numerous applied challenges.
more »
« less
- Award ID(s):
- 1831944
- PAR ID:
- 10548495
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Ecology Letters
- Volume:
- 27
- Issue:
- 10
- ISSN:
- 1461-023X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Integrated community models—an emerging framework in which multiple data sources for multiple species are analyzed simultaneously—offer opportunities to expand inferences beyond the single‐species and single‐data‐source approaches common in ecology. We developed a novel integrated community model that combines distance sampling and single‐visit count data; within the model, information is shared among data sources (via a joint likelihood) and species (via a random‐effects structure) to estimate abundance patterns across a community. Parameters relating to abundance are shared between data sources, and the model can specify either shared or separate observation processes for each data source. Simulations demonstrated that the model provided unbiased estimates of abundance and detection parameters even when detection probabilities varied between the data types. The integrated community model also provided more accurate and more precise parameter estimates than alternative single‐species and single‐data‐source models in many instances. We applied the model to a community of 11 herbivore species in the Masai Mara National Reserve, Kenya, and found considerable interspecific variation in response to local wildlife management practices: Five species showed higher abundances in a region with passive conservation enforcement (median across species: 4.5× higher), three species showed higher abundances in a region with active conservation enforcement (median: 3.9× higher), and the remaining three species showed no abundance differences between the two regions. Furthermore, the community average of abundance was slightly higher in the region with active conservation enforcement but not definitively so (posterior mean: higher by 0.20 animals; 95% credible interval: 1.43 fewer animals, 1.86 more animals). Our integrated community modeling framework has the potential to expand the scope of inference over space, time, and levels of biological organization, but practitioners should carefully evaluate whether model assumptions are met in their systems and whether data integration is valuable for their applications.more » « less
-
Abstract Many applications in molecular ecology require the ability to match specific DNA sequences from single‐ or mixed‐species samples with a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding employ PCR and amplicon sequencing to identify taxa based on target sequences, but the target‐specific enrichment capabilities of CRISPR‐Cas systems may offer advantages in some applications. We identified 54,837 CRISPR‐Cas guide RNAs that may be useful for enriching chloroplast DNA across phylogenetically diverse plant species. We tested a subset of 17 guide RNAs in vitro to enrich plant DNA strands ranging in size from diagnostic DNA barcodes of 1,428 bp to entire chloroplast genomes of 121,284 bp. We used an Oxford Nanopore sequencer to evaluate sequencing success based on both single‐ and mixed‐species samples, which yielded mean chloroplast sequence lengths of 2,530–11,367 bp, depending on the experiment. In comparison to mixed‐species experiments, single‐species experiments yielded more on‐target sequence reads and greater mean pairwise identity between contigs and the plant species' reference genomes. But nevertheless, these mixed‐species experiments yielded sufficient data to provide ≥48‐fold increase in sequence length and better estimates of relative abundance for a commercially prepared mixture of plant species compared to DNA metabarcoding based on the chloroplasttrnL‐P6 marker. Prior work developed CRISPR‐based enrichment protocols for long‐read sequencing and our experiments pioneered its use for plant DNA barcoding and chloroplast assemblies that may have advantages over workflows that require PCR and short‐read sequencing. Future work would benefit from continuing to develop in vitro and in silico methods for CRISPR‐based analyses of mixed‐species samples, especially when the appropriate reference genomes for contig assembly cannot be known a priori.more » « less
-
The finding that adaptive evolution can often be substantial enough to alter ecological dynamics challenges traditional views of community ecology that ignore evolution. Here, we propose that evolution might commonly alter both local and regional processes of community assembly. We show how adaptation can substantially affect community assembly and that these effects depend on regional (metacommunity) factors, including environmental heterogeneity and its spatial structure. In particular, early colonists can often arrive from a nearby community, adapt to local conditions, and subsequently alter the establishment or abundance of late-arriving species, often producing an evolutionary priority effect. We also discuss how interaction type and relative rates of colonization, evolution, and community interactions determine divergent community outcomes. We describe new conceptual approaches that provide insights into these dynamics and statistical methods that can better evaluate their importance. Overall, we demonstrate that accounting for adaptation during community assembly opens up novel ways for making progress on fundamental questions in community ecology.more » « less
-
Abstract Understanding patterns of diversity is central to ecology and conservation, yet estimates of diversity are often biased by imperfect detection. In recent years, multi‐species occupancy models (MSOM) have been developed as a statistical tool to account for species‐specific heterogeneity in detection while estimating true measures of diversity. Although the power of these models has been tested in various ways, their ability to estimate gamma diversity—or true community size,Nis a largely unrecognized feature that needs rigorous evaluation.We use both simulations and an empirical dataset to evaluate the bias, precision, accuracy and coverage of estimates ofNfrom MSOM compared to the widely applied iChao2 non‐parametric estimator. We simulated 5,600 datasets across seven scenarios of varying average occupancy and detectability covariates, as well as varying numbers of sites, replicates and true community size. Additionally, we use a real dataset of surveys over 9 years (where species accumulation reached an asymptote, indicating trueN), to estimateNfrom each annual survey.Simulations showed that both MSOM and iChao2 estimators are generally accurate (i.e. unbiased and precise) except under unideal scenarios where mean species occupancy is low. In such scenarios, MSOM frequently overestimatedN. Across all scenarios, MSOM estimates were less certain than iChao2, but this led to over‐confident iChao2 estimates that showed poor coverage. Results from the real dataset largely confirmed the simulation findings, with MSOM estimates showing greater accuracy and coverage than iChao2.Community ecologists have a wide choice of analytical methods, and both iChao2 and MSOM estimates ofNare substantially preferable to raw species counts. The simplicity of non‐parametric estimators has obvious advantages, but our results show that in many cases, MSOM may provide superior estimates that also account more accurately for uncertainty. Both methods can show strong bias when average occupancy is very low, and practitioners should show caution when using estimates derived from either method under such conditions.more » « less
An official website of the United States government
