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Figure S44 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Figure S44. Phyloregionalization per continent using the genus-level Mimosoid phylogeny (rather than the metachronogram). Caption otherwise as for Figure 3.

Figure S41 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Figure S41. Phyloregionalization of the global tropics using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.

Figure S39 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Figure S39. Phyloregionalization of Asia using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.

Figure S32 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Figure S32 (lef). Internode certainty values based on the 821 single-copy gene trees mapped onto the single-copy genes ASTRAL species tree (Figure S14). For each node, the upper number shows the quartet-based Extended Quadripartition Internode Certainty (EQP-IC) score calculated with QuartetScores, and the lower number shows the bipartition-based Internode Certainty All score calculated with PhyParts, both rounded down to two digits. Boxes are coloured based on unrounded values: green for values ≥ 0.5, yellow for values ≥ 0 and <0.5, and red for values <0. Branch lengths are set equal for easier visualisation. Inset depicts a correlation plot between the two measures.

Figure S33 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Figure S33 (right).'esults of ASTRAL's polytomy test based on the 821 single-copy gene trees mapped onto the single-copy genes ASTRAL species tree (Figure S14). Node numbers are tests of the null hypothesis that a branch should be replaced by a polytomy. Only node numbers> 0.05 are shown. Branch lengths are set equal for easier visualisation.

Figure S31 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Figure S31. Gene tree incongruence mapped onto the time-calibrated version of the phylogenomic backbone of Caesalpinioideae. Each branch is coloured to reflect the ratio of total supporting versus total conflicting gene trees as determined by PhyParts. Clades named by Koenen et al. (24) are labelled. Two recent radiations in Madagascar, one in the Dichrostachys clade and one in Albizia, are highlighted.

Figure S36 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Figure S36. Phyloregionalization of North America using the metachronogram. Subfigures show clustering results with two to eight phyloregions, as well as the results of phyloregionalization analyses using the geographic residuals of phylogenetic turnover, and ancient phylogenetic turnover with a cut-off of 5, 10, and 20 million years.

Figure S14 in Supplementary Materials for Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Figure S14. Phylogeny of Caesalpinioideae. ASTRAL species tree based on the 821 single-copy gene trees. Local posterior probability support values are only shown for nodes with a local posterior probability <1. Branch lengths are expressed in coalescent units. Terminal branches were assigned an arbitrary uniform length for visual clarity.

Fig. 2 in Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Fig. 2. Drivers of phylogenetic turnover of Mimosoid legumes across the global lowland tropics. Bars show relative fractions of phylogenetic turnover explained by predictors (rescaled to add up to one). Numbers above bars are absolute explained percentages of turnover (tables S12 and S20). (A) Phylogenetic turnover explained by climatic distance (maroon), geographic distance (blue), or their interaction (cream). Turnover is assessed across four depths in the phylogeny: with the full metachronogram (age cutoff of 0) and with all clades younger than 5, 10, and 20 Ma collapsed. Note that it was not possible to fit a model to the phylogeny collapsed at 20 Ma for the pantropical and Australian models. (B) Phylogenetic turnover explained by MAP (green) and/or annual mean temperature (orange). Turnover is expressed as phylogenetic turnover not explained by geographic distance ("geographic residuals"). (C) Geographic residuals of phylogenetic turnover explained by MAP (green) and/or precipitation seasonality (gray; left) or dry season length (DSL) (i.e., the number of consecutive months with precipitation <100 mm/month; yellow; right). See fig. S45 for results obtained with an alternative, genus-level Mimosoid phylogeny. P, MAP; T, annual mean temperature; Pseas, precipitation seasonality.

Fig. 1 in Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Fig. 1. Mimosoid evolution and diversity across precipitation gradients. (A) Phylogeny of Mimosoid legumes showing the evolution of precipitation niches and transcontinental dispersal events through time. Branch colors correspond to mean annual precipitation (MAP) estimates [see (C) for scale]. Pie charts at tips and nodes of named clades [sensu (24)] represent observed and estimated spatial distributions [based on area definitions in (D)]. Ancestral niches and areas were estimated using a complete metachronogram for Caesalpinioideae, including non-Mimosoid Caesalpinioideae taxa, but only the Mimosoid clade is shown here. Green circles on branches indicate shifts between precipitation categories [following (17)] that encompass a difference of at least 250-mm MAP; red triangles indicate postulated transcontinental dispersals according to the best-supported model. The six most species-rich genera are labeled. (B) Fractions of niche shifts and transcontinental dispersal events, averaged across multiple optimizations, relative to total phylogenetic splits plotted through time for 5-Ma bins. (E) Mimosoid growth form diversity across the tropical precipitation gradient, from deserts with <50-mm MAP (left) through savannas to rain forests with>5000-mm MAP (right). See the Supplementary Results for species names and photographers. See fig. S51 for more information.

opencc-by-4.0Oct 2022View details →

Supplement: Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities

Background Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. Results We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. Conclusions Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry.

opencc-zeroMay 2023View details →

Patterns of species richness and turnover in endemic amphibians of the Guineo-Congolian rainforest

Aim: The African Guineo-Congolian (GC) region is a global biodiversity hotspot with high species endemism, bioclimatic heterogeneity, complex landscape features, and multiple biogeographic barriers. Bioclimatic and geographic variables influence global patterns of species richness and endemism, but their relative importance varies across taxa and regions and is poorly understood for many faunas. We characterized patterns of richness and turnover in endemic amphibians of the GC biodiversity hotspot and evaluated the relative roles of geographic distance and bioclimatic variables in predicting turnover. Location: West and Central Africa. Major taxa studied: Amphibians Methods: We compiled species-occurrence records via field sampling, online databases, and taxonomic literature. Our study used 1205 unique georeferenced records of 222 amphibian species endemic to the GC region. Patterns of species richness were mapped onto a grid with a spatial resolution of 0.5° × 0.5°. We estimated weighted endemism and tested whether endemism was higher than the expected species richness (randomization test). We quantified species turnover using generalized dissimilarity modelling to evaluate the processes underlying observed patterns of species richness in GC endemic amphibians. We explored bioregionalization using agglomerative hierarchical clustering based on the unweighted pair group method with arithmetic averages. Results: We identified six areas within the lower GC region – forests in Southern Nigeria, Cameroon, Equatorial Guinea, Gabon, Republic of Congo, and Democratic Republic of Congo – as having high species richness of endemic amphibians. The randomization test returned four major areas of significant weighted endemism: Nigeria-Cameroon mountains, forest regions of the Democratic Republic of Congo, Cote d'Ivoire, and Ghana. Our analysis revealed five bioregions for amphibian endemism, four of which were located within the lower Guineo-Congolian forest. Species turnover was strongly related to the geographic distance between grid cells; contributing bioclimatic variables included precipitation of the warmest quarter, mean temperature of the wettest quarter, and mean diurnal temperature range. Main conclusions: Our results indicate that geographic distance between grid cells is the primary determinant of turnover in GC endemic amphibians, with secondary but significant effects of rainfall- and temperature-related variables. Our results identify key areas of endemic amphibian richness that could be prioritized for conservation actions.

opencc-zeroJul 2023View details →

Sustained mangrove reproduction despite major turnover in pollinator community composition at expanding range edge

Background and Aims How well plants reproduce near their geographic range edge can determine whether distributions will shift in response to changing climate. Reproduction at the range edge can be limiting if pollinator scarcity leads to pollen limitation, or if abiotic stressors affect allocation to reproduction. For many animal-pollinated plants with expanding ranges, the mechanisms by which they have overcome these barriers are poorly understood. Methods In this study, we examined plant-pollinator interactions hypothesized to impact reproduction of the black mangrove, Avicennia germinans, which is expanding northward in coastal Florida, USA. We monitored insects visiting A. germinans populations varying in proximity to the geographic range edge, measured the pollen loads of the most common insect taxa and pollen receipt by A. germinans stigmas, and quantified flower and propagule production. Key Results We found that despite an 84% decline in median floral visits by insects at northernmost vs. southernmost sites, range-edge pollen receipt remained high. Notably, local floral visitor assemblages exhibited substantial turnover along the study's latitudinal gradient, with large-bodied bees and hover flies increasingly common at northern sites. We also observed elevated flower production in northern populations and higher per capita reproductive output at the range edge. Furthermore, mean propagule mass in northern populations was 18% larger than propagules from the southernmost populations. Conclusions These findings reveal no erosion of fecundity in A. germinans populations at range limits, allowing rapid expansion of mangrove cover in the region. These results also illustrate that substantial turnover in the assemblage of flower-visiting insects can occur at an expanding range edge without altering pollen receipt.

opencc-zeroSep 2023View details →

Opposing patterns of altitude-driven pollinator turnover in the tropical and temperate Americas

Abiotic factors (e.g., temperature, precipitation) vary markedly along elevational gradients and differentially affect major groups of pollinators. Ectothermic bees, for example, are impeded in visiting flowers by cold and rainy conditions common at high elevations, while endothermic hummingbirds may continue foraging under such conditions. Despite the possibly far-reaching effects of the abiotic environment on plant-pollinator interactions, we know little about how these factors play out at broad ecogeographic scales. We address this knowledge gap by investigating how pollination systems vary across elevations in 26 plant clades from the Americas. Specifically, we explore Cruden's 1972 hypothesis that the harsh montane environment drives a turnover from insect to vertebrate pollination at higher elevations. We compared the elevational distribution and bioclimatic attributes for a total of 2232 flowering plants and found that Cruden's hypothesis only holds in the tropics. Above 30° N and below 30°S, plants pollinated by vertebrates (mostly hummingbirds) tend to occur at lower elevations than those pollinated by insects. We posit that this latitudinal transition is due to the distribution of moist, forested habitats favored by vertebrate pollinators, which are common at high elevations in the tropics but not in the temperate Americas.

opencc-zeroOct 2023View details →

Frugivore-mediated seed dispersal in fragmented landscapes: Compositional and functional turnover from forest to matrix

Seed dispersal by frugivores is a fundamental function for plant community dynamics in fragmented landscapes, where forest remnants are typically embedded in a matrix of anthropogenic habitats. Frugivores can mediate both connectivity among forest remnants and plant colonization of the matrix. However, it remains poorly understood how frugivore communities change from forest to matrix due to the loss or replacement of species with traits that are less advantageous in open habitats, and whether such changes ultimately influence the composition and traits of dispersed plants via species interactions. Here, we close this gap by using a unique dataset of seed-dispersal networks that were sampled in forest patches and adjacent matrix habitats of seven fragmented landscapes across Europe. We found a similar diversity of frugivores, plants and interactions contributing to seed dispersal in forest and matrix, but a high turnover (replacement) in all these components. The turnover of dispersed seeds was smaller than that of frugivore communities because different frugivore species provided complementary seed dispersal in forest and matrix. Importantly, the turnover involved functional changes towards larger and more mobile frugivores in the matrix, which dispersed taller, larger-seeded plants with later fruiting periods. Our study provides a trait-based understanding of frugivore-mediated seed dispersal through fragmented landscapes, uncovering non-random shifts that can have cascading consequences for the composition of regenerating plant communities. Our findings also highlight the importance of forest remnants and frugivore faunas for ecosystem resilience, demonstrating a high potential for passive forest restoration of unmanaged lands in the matrix.