Riders in the sky (islands): using a mega-phylogenetic approach to understand plant species distribution and coexistence at the altitudinal limits of angiosperm plant life

Geology and climate drive alpine plant compositional variation among peaks in the Cascade Range of Washington

Alpine areas are host to diverse plant communities that support ecosystems through structural and floral resources and persist through specialized adaptations to harsh high-elevation conditions. An ongoing question in these plant communities is whether composition is shaped by stochastic processes (e.g., dispersal limitations) or by deterministic processes (e.g., climate, geology), and if those processes select for common phylogenetic clades across space. This study evaluates the drivers of dissimilarity in alpine vascular plant communities across 32 peaks in the Cascade Mountain Range of Washington State and examines the effects of incorporating phylogenetic relatedness to these conclusions. We documented an average of 54 species per peak and used our overall inventory of 307 taxa to construct a phylogenetic tree for the entire mountain range plant community sampled. We used multivariate techniques to quantify the phylogenetic and taxonomic differences between alpine plant communities and to relate those differences to each peak's climate, geology, and topography. Our models indicate that the age of each peak's parent material formation, precipitation, latitude, and temperature had the largest role in shaping alpine plant communities relative to the baseline effects of distance between peaks and time of sampling. A unique result was a distinct plant community in peaks with ultramafic geologic parent material formed in the Paleozoic Era, which has an extreme geochemistry that we found to form evolutionarily distinct lineages compared to all other peaks. With changing climate conditions and disturbance regimes, understanding facets of alpine plant communities like species turnover, geologic endemism, and responses to precipitation changes are vital to conserving these ecosystems.

Community-level phylogenetic diversity does not differ between rare and common lineages across tallgrass prairies in the northern Great Plains

Niche differentiation has served as one explanation for species coexistence, and phylogenetic relatedness provides a means to approximate how ecologically similar species are to each other. To explore the contribution of rare species to community phylogenetic diversity, we sampled 21 plant communities across the Prairie Coteau ecoregion, an area of high conservation concern. We used breakpoint analysis through the iterative addition of less abundant species to the phylogenetic tree for each community to assess the contribution of rare species to community phylogenetic diversity. We also quantify the phylogenetic signal of abundance using Blomberg's K statistic and calculated the phylogenetic similarity between rare and common species using a phylogenetic beta-diversity metric (D nn). To estimate the phylogenetic structuring of these prairie communities, we calculated two common metrics that capture evolutionary relatedness at different scales (MPD and MNTD). Additionally, we examine the correlation between Faith's PD, MPD, and MNTD and species richness. We found rare species do not generally contribute higher levels of phylogenetic diversity than common species. Eight communities had significant breakpoints, with only four communities having an increasing trend for the rarest species. The phylogenetic signal for abundance was low but significant in only four communities, and communities had lower phylogenetic diversity than expected from the regional species pool. Finally, the strength of the correlation between species richness and phylogenetic diversity was mixed. Our results indicate niche differentiation does not explain the persistence of rare species in tallgrass prairies, as they were more closely related than expected from random, suggesting high functional redundancy between rare and common species. This is promising for the long-term resilience of this ecosystem, but only insofar as enough species remain in the system. With ongoing biodiversity loss, it is essential that we understand the role rare species play in their communities.

Relative Importance of Landscape and Climate Factors to the Species Diversity of Plant Growth Forms along an East Asian Archipelago

Previous studies on island biogeography theory have limitations in that they are mostly focused on total plant species and the landscape factors of the islands. Our study was conducted to overcome these limitations by dividing the plants into five growth forms and analyzing climate and landscape factors on inhabited islands, uninhabited islands, and overall. This was achieved using plant data from 578 islands of an archipelago in South Korea. To test the relationship between the species richness of each growth form and environmental factors, we performed ordinary least squares regressions and multi-model inference tests. The results showed that the island area had the largest influence on species richness of all growth forms in overall and uninhabited islands. Moreover, climate factors, in addition to island area, significantly affected species richness of all growth forms on inhabited islands. However, the effect and of isolation-related landscape factors (i.e., distance from the mainland and structural connectivity) were different among growth forms and island categories. Our study reveals that there are differences in the effects of environmental factors on the growth forms of plants among island categories. This suggests that biodiversity management and conservation strategies should be applied separately to different growth forms and islands.

Plant Sedimentary Ancient DNA From Far East Russia Covering the Last 28,000 Years Reveals Different Assembly Rules in Cold and Warm Climates

Woody plants are expanding into the Arctic in response to the warming climate. The impact on arctic plant communities is not well understood due to the limited knowledge about plant assembly rules. Records of past plant diversity over long time series are rare. Here, we applied sedimentary ancient DNA metabarcoding targeting the P6 loop of the chloroplast trnL gene to a sediment record from Lake Ilirney (central Chukotka, Far Eastern Russia) covering the last 28 thousand years. Our results show that forb-rich steppe-tundra and dwarf-shrub tundra dominated during the cold climate before 14 ka, while deciduous erect-shrub tundra was abundant during the warm period since 14 ka. Larix invasion during the late Holocene substantially lagged behind the likely warmest period between 10 and 6 ka, where the vegetation biomass could be highest. We reveal highest richness during 28–23 ka and a second richness peak during 13–9 ka, with both periods being accompanied by low relative abundance of shrubs. During the cold period before 14 ka, rich plant assemblages were phylogenetically clustered, suggesting low genetic divergence in the assemblages despite the great number of species. This probably originates from environmental filtering along with niche differentiation due to limited resources under harsh environmental conditions. In contrast, during the warmer period after 14 ka, rich plant assemblages were phylogenetically overdispersed. This results from a high number of species which were found to harbor high genetic divergence, likely originating from an erratic recruitment process in the course of warming. Some of our evidence may be of relevance for inferring future arctic plant assembly rules and diversity changes. By analogy to the past, we expect a lagged response of tree invasion. Plant richness might overshoot in the short term; in the long-term, however, the ongoing expansion of deciduous shrubs will eventually result in a phylogenetically more diverse community.

Phylogenetic diversity and community assembly in a naturally fragmented system

We sought to assess effects of fragmentation and quantify the contribution of ecological processes to community assembly by measuring species richness, phylogenetic, and phenotypic diversity of species found in local and regional plant communities. Specifically, our fragmented system is Craters of the Moon National Monument and Preserve, Idaho, USA. CRMO is characterized by vegetated islands, kipukas, that are isolated in a matrix of lava. We used floristic surveys of vascular plants in 19 kipukas to create a local species list to compare traditional dispersion metrics, mean pairwise distance, and mean nearest taxon distance (MPD and MNTD), to a regional species list with phenotypic and phylogenetic data. We combined phylogenetic and functional trait data in a novel machine-learning model selection approach, Community Assembly Model Inference (CAMI), to infer probability associated with different models of community assembly given the data. Finally, we used linear regression to explore whether the geography of kipukas explained estimated support for community assembly models. Using traditional metrics of MPD and MNTD neutral processes received the most support when comparing kipuka species to regional species. Individually no kipukas showed significant support for overdispersion. Rather, five kipukas showed significant support for phylogenetic clustering using MPD and two kipukas using MNTD. Using CAMI, we inferred neutral and filtering models structured the kipuka plant community for our trait of interest. Finally, we found as species richness in kipukas increases, model support for competition decreases and lower elevation kipukas show more support for habitat filtering models. While traditional phylogenetic community approaches suggest neutral assembly dynamics, recently developed approaches utilizing machine learning and model choice revealed joint influences of assembly processes to form the kipuka plant communities. Understanding ecological processes at play in naturally fragmented systems will aid in guiding our understanding of how fragmentation impacts future changes in landscapes.

Alpine lichen diversity in an isolated sky island in the Colorado Plateau, USA-Insight from an integrative biodiversity inventory

Lichens are major components of high altitude/latitude ecosystems. However, accurately characterizing their biodiversity is challenging because these regions and habitats are often underexplored, there are numerous poorly known taxonomic groups, and morphological variation in extreme environments can yield conflicting interpretations. Using an iterative taxonomic approach based on over 800 specimens and incorporating both traditional morphology-based identifications and information from the standard fungal DNA barcoding marker, we compiled a voucher-based inventory of biodiversity of lichen-forming fungi in a geographically limited and vulnerable alpine community in an isolated sky island in the Colorado Plateau, USA-the La Sal Mountains. We used the newly proposed Assemble Species by Automatic Partitioning (ASAP) approach to empirically delimit candidate species-level lineages from family-level multiple sequence alignments. Specimens comprising DNA-based candidate species were evaluated using traditional taxonomically diagnostic phenotypic characters to identify specimens to integrative species hypotheses and link these, where possible, to currently described species. Despite the limited alpine habitat (ca. 3,250 ha), we document the most diverse alpine lichen community known to date from the southern Rocky Mountains, with up to 240 candidate species/species-level lineages of lichen-forming fungi. 139 species were inferred using integrative taxonomy, plus an additional 52 candidate species within 29 different putative species complexes. Over 68% of sequences could not be assigned to species-level rank with statistical confidence, corroborating the limited utility of current sequence repositories for species-level DNA barcoding of lichen-forming fungi. By integrating vouchered specimens, DNA sequence data, and photographic documentation, we provide an important baseline of lichen-forming fungal diversity for the limited alpine habitat in the Colorado Plateau. These data provide an important resource for subsequent research in the ecology and evolution of lichens alpine habitats, including DNA barcodes for most putative species/species-level lineages occurring in the La Sal Mountains, and vouchered collections representing any potentially undescribed species that can be used for future taxonomic studies.

Discovery of cryptic plant diversity on the rooftops of the Alps

High elevation temperate mountains have long been considered species poor owing to high extinction or low speciation rates during the Pleistocene. We performed a phylogenetic and population genomic investigation of an emblematic high-elevation plant clade (Androsace sect. Aretia, 31 currently recognized species), based on plant surveys conducted during alpinism expeditions. We inferred that this clade originated in the Miocene and continued diversifying through Pleistocene glaciations, and discovered three novel species of Androsace dwelling on different bedrock types on the rooftops of the Alps. This highlights that temperate high mountains have been cradles of plant diversity even during the Pleistocene, with in-situ speciation driven by the combined action of geography and geology. Our findings have an unexpected historical relevance: H.-B. de Saussure likely observed one of these species during his 1788 expedition to the Mont Blanc and we describe it here, over two hundred years after its first sighting.

Evolutionary assembly of flowering plants into sky islands

Alpine floras (plants in the vegetation belts above the climatic treelines) experience cold climates, particularly in temperate mountains during winter, but they are generally species-rich. Yet, biogeographers have not determined whether these floras represent evolutionarily independent but convergent assemblages drawn from their regional floras, or whether they originated from particular clades pre-adapted to harsh conditions. Here, we analyse the evolutionary relationships of angiosperm (flowering plant) species in 63 alpine floras worldwide (~7,000 species) in comparison with their regional floras (~94,000 species) and with the entire global flora. We find that each of the alpine floras represents an assemblage of more closely related species than their respective regional floras. The degree of phylogenetic clustering of species in alpine floras in tropical mountains exceeds that in temperate mountains. However, in relation to the global flora, temperate alpine floras are phylogenetically closely related subsets of floras that colonized cold temperate areas during interglacial periods. We conclude that alpine floras include a few dominant families that have evolved tolerance to low temperature, and that evolutionary niche conservatism explains their phylogenetic clustering, compared with species in their regional species pools.

For common community phylogenetic analyses, 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, was 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.

Increasing phylogenetic stochasticity at high elevations on summits across a remote North American wilderness

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.

Drivers of Phylogenetic Assemblage Structure of the Furnariides, a Widespread Clade of Lowland Neotropical Birds

Species co-occurrence in local assemblages is shaped by distinct processes at different spatial and temporal scales. Here we focus on historical explanations and examine the phylogenetic structure of local assemblages of the Furnariides clade (Aves: Passeriformes), assessing the influence of diversification rates on the assembly and species co-occurrence within those assemblages. Using 120 local assemblages across Bolivia and Argentina and a nearly complete phylogeny for the clade, we analyzed assemblage phylogenetic structure, applying a recently developed model (DAMOCLES, or dynamic assembly model of colonization, local extinction, and speciation) accounting for the historical processes of speciation, colonization, and local extinction. We also evaluated how diversification rates determine species co-occurrence. We found that the assembly of Furnariides assemblages can be explained largely by speciation, colonization, and local extinction without invoking current local species interactions. Phylogenetic structure of open habitat assemblages mainly showed clustering, characterized by faster rates of colonization and local extinction than in forest habitats, whereas forest habitat assemblages were congruent with the model's equal rates expectation, thus highlighting the influence of habitat preferences on assembly and co-occurrence patterns. Our results suggest that historical processes are sufficient to explain local assemblage phylogenetic structure, while there is little evidence for species ecological interactions in avian assemblage diversity and composition.