Phylogenetic and functional diversity are theorised to increase invasion resistance. Experimentally testing whether plant communities higher in these components of diversity are less invasible is an important step for guiding restoration designs. To investigate how phylogenetic and functional diversity of vegetation affect invasion resistance in a restoration setting, we used experimental prairie restoration plots. The experiment crossed three levels of phylogenetic diversity with two levels of functional diversity while species richness was held constant. We allowed invaders to colonise plots; these included native species from neighbouring plots and non‐native invasive species from a surrounding old field. We tested if invader biomass was influenced by phylogenetic and functional diversity, and phylogenetic and hierarchical trait distances between invaders and planted species. We binned each invader into three categories: native species from neighbouring experimental plots ( Counter to expectation, both non‐native and native invaders became more abundant in more phylogenetically diverse plots. However, plots with higher abundance of planted Asteraceae, a dominant family of the tallgrass prairie, had lower invader biomass for both native and non‐native invaders. We also found that hierarchical trait differences shaped invasion. The species that became most abundant were non‐native invaders that were taller, and native invaders with low specific leaf area relative to planted species. Site‐specific invaders were not influenced by any plot‐level diversity metrics tested.
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Abstract site‐specific invaders ), native species not part of the experimental species pool (native invaders ) or non‐native species (non‐native invaders ).Synthesis and application : Our results suggest that greater phylogenetic diversity may lower resistance to invasion. This effect may be due to more even but sparser niche packing in high‐diversity plots, associated with greater availability of unsaturated niche space for colonisation. However, trait composition fostered invasion resistance in two ways in our study. First, establishment of native species with strongly dominant traits may confer invasion resistance. Second, species mixes that optimise trait differences between planted vegetation and likely invaders may enhance invasion‐resistance. -
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Abstract The prediction that higher biodiversity leads to denser niche packing and thus higher community resistance to invasion has long been studied, with species richness as the predominant measure of diversity. However, few studies have explored how phylogenetic and functional diversity, which should represent niche space more faithfully than taxonomic diversity, influence community invasibility, especially across longer time frames and over larger spatial extents.
We used a 15‐year, 150‐site grassland dataset to assess relationships between invasive plant abundance and phylogenetic, functional and taxonomic diversity of recipient native plant communities. We analysed the dataset both pooled across all surveys and longitudinally, leveraging time‐series data to compare observed patterns in invasion with those predicted by two community assembly processes: biotic resistance and competitive exclusion. We expected more phylogenetically and functionally diverse communities to exhibit greater resistance to invasion.
With the pooled dataset, we found support for the long‐standing observation that communities with more native species have lower abundance of invasive species, and a more novel finding that more phylogenetically diverse communities had higher abundance of invasive species. We found no influence of aggregate (multivariate) functional diversity on invasion, but assemblages with taller plants, lower variability in plant height and lower seed mass were less invaded. Viewed longitudinally, the phylogenetic diversity relationship was reversed: the most phylogenetically diverse communities were most resistant to invasion. This apparent discrepancy suggests invasion dynamics are influenced by both site attributes and biotic resistance and emphasizes the value in studying invasion across time.
Synthesis . Our results provide insight into the nuances of the diversity–invasibility relationship: invasion dynamics differed for different dimensions of diversity and depending on whether the relationship was evaluated longitudinally. Our findings highlight the limitations of using single time‐point ‘snapshots’ of community composition to infer invasion mechanisms. -
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Abstract An important focus of community ecology, including invasion biology, is to investigate functional trait diversity patterns to disentangle the effects of environmental and biotic interactions. However, a notable limitation is that studies usually rely on a small and easy‐to‐measure set of functional traits, which might not immediately reflect ongoing ecological responses to changing abiotic or biotic conditions, including those that occur at a molecular or physiological level. We explored the potential of using the diversity of expressed genes—functional genomic diversity (FGD)—to understand ecological dynamics of a recent and ongoing alpine invasion. We quantified FGD based on transcriptomic data measured for 26 plant species occurring along adjacent invaded and pristine streambeds. We used an RNA‐seq approach to summarize the overall number of expressed transcripts and their annotations to functional categories, and contrasted this with functional trait diversity (FTD) measured from a suite of characters that have been traditionally considered in plant ecology. We found greater FGD and FTD in the invaded community, independent of differences in species richness. However, the magnitude of functional dispersion was greater from the perspective of FGD than from FTD. Comparing FGD between congeneric alien–native species pairs, we did not find many significant differences in the proportion of genes whose annotations matched functional categories. Still, native species with a greater relative abundance in the invaded community compared with the pristine tended to express a greater fraction of genes at significant levels in the invaded community, suggesting that changes in FGD may relate to shifts in community composition. Comparisons of diversity patterns from the community to the species level offer complementary insights into processes and mechanisms driving invasion dynamics. FGD has the potential to illuminate cryptic changes in ecological diversity, and we foresee promising avenues for future extensions across taxonomic levels and macro‐ecosystems.
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Premise Large‐scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA‐seq data from diverse plant communities.
Methods We generated >650 Gbp of RNA‐seq for 24 vascular plant species representing 12 genera and nine families at the Harvard Forest NEON site. Each species was sampled twice in 2016 (July and August). We assessed transcriptome quality and content with TransRate, BUSCO, and Gene Ontology annotations.
Results Only modest differences in assembly quality were observed across multiple
k ‐mers. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated transcripts between diploid and polyploid transcriptomes.Discussion We provide new RNA‐seq data sets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high‐quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers opportunities for large‐scale studies at the intersection of ecology and genomics.
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Premise TagSeq is a cost‐effective approach for gene expression studies requiring a large number of samples. To date, TagSeq studies in plants have been limited to those with a high‐quality reference genome. We tested the suitability of reference transcriptomes for TagSeq in non‐model plants, as part of a study of natural gene expression variation at the Santa Rita Experimental Range National Ecological Observatory Network (NEON) core site.
Methods Tissue for TagSeq was sampled from multiple individuals of four species (
Bouteloua aristidoides andEragrostis lehmanniana [Poaceae],Tidestromia lanuginosa [Amaranthaceae], andParkinsonia florida [Fabaceae]) at two locations on three dates (56 samples total). One sample per species was used to create a reference transcriptome via standard RNA‐seq. TagSeq performance was assessed by recovery of reference loci, specificity of tag alignments, and variation among samples.Results A high fraction of tags aligned to each reference and mapped uniquely. Expression patterns were quantifiable for tens of thousands of loci, which revealed consistent spatial differentiation in expression for all species.
Discussion TagSeq using de novo reference transcriptomes was an effective approach to quantifying gene expression in this study. Tags were highly locus specific and generated biologically informative profiles for four non‐model plant species.
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Abstract Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid species differentiated faster than those of related diploids. We found that polyploids are often more climatically differentiated from their diploid parents than the diploids are from each other. Consistent with this pattern, we estimated that polyploid species generally have higher rates of multivariate niche differentiation than their diploid relatives. In contrast to recent analyses, our results confirm that ecological niche differentiation is an important component of polyploid speciation and that niche differentiation is often significantly faster in polyploids.
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Premise At the intersection of ecology and evolutionary biology, community phylogenetics can provide insights into overarching biodiversity patterns, particularly in remote and understudied ecosystems. To understand community assembly of the high alpine flora in the Sawtooth National Forest,
USA , we analyzed phylogenetic structure within and between nine summit communities.Methods We used high‐throughput sequencing to supplement existing data and infer a nearly completely sampled community phylogeny of the alpine vascular flora. We calculated mean nearest taxon distance (
MNTD ) and mean pairwise distance (MPD ) to quantify phylogenetic divergence within summits, and assessed whether maximum elevation explains phylogenetic structure. To evaluate similarities between summits, we quantified phylogenetic turnover, taking into consideration microhabitats (talus vs. meadows).Results We found different patterns of community phylogenetic structure within the six most species‐rich orders, but across all vascular plants phylogenetic structure was largely not different from random. There was a significant negative correlation between elevation and tree‐wide phylogenetic diversity (
MPD ) within summits: overdispersion degraded as elevation increased. Between summits, we found high phylogenetic turnover driven by greater niche heterogeneity on summits with alpine meadows.Conclusions Our results provide further evidence that stochastic processes may also play an important role in the assembly of vascular plant communities in high alpine habitats at regional scales. However, order‐specific patterns suggest that adaptations are still important for assembly of specific sectors of the plant tree of life. Further studies quantifying functional diversity will be important in disentangling the interplay of eco‐evolutionary processes that likely shape broad community phylogenetic patterns in extreme environments.
