Evolution of intraspecific floral variation in a generalist-specialist pollination system.

Intraspecific processes impact macroevolutionary patterns through individual variation, selection, and ecological specialisation. According to the niche variation hypothesis, the broader ecological niche of gen- eralist species results in an increased morphological variation among individuals, either because they are constituted of diversified specialised individuals each exploiting a fraction of the species' niche, or because they are constituted of true generalist individuals that experience relaxed selection. To test this hypoth- esis, we surveyed the individual floral morphology of species of Antillean Gesneriaceae, a group that has transitioned between specialisation for hummingbird pollination and generalisation multiple times throughout its evolutionary history. We characterised the profiles of corollas using geometric morpho- metrics and compared the intraspecific shape variance of specialists and generalists in a phylogenetic context. We used three approaches that differently accounted for the high dimensionality of morphologi- cal traits, the ancestral reconstruction of pollination syndromes over time, and the error associated with the estimation of the intraspecific variance. Our findings provide partial support for the niche variation hypothesis. If considering the whole shape in the analysis corroborated this idea, decomposing the shape into principal components indicated that not all aspects of the corolla exhibit the same pattern of vari- ation. Specifically, pollination generalists tend to display greater intraspecific variation than specialists in terms of tubularity, but not of curvature. Accounting for the error in the variance estimation also reduced the support for the hypothesis, suggesting that larger sample sizes may be required to reach stronger conclusions. This study emphasises the reciprocal influence between plants and their pollinators on floral morphology at different biodiversity scales, and suggests that ecological strategies of species can affect patterns of morphological variation at macroevolutionary scales.

Studying flowers in 3D using photogrammetry.

Flowers are intricate and integrated three-dimensional (3D) structures predominantly studied in 2D due to the difficulty in quantitatively characterising their morphology in 3D. Given the recent development of analytical methods for high-dimensional data, the reconstruction of flower models in three dimensions represents the limiting factor to studying flowers in 3D. We developed a floral photogrammetry protocol to reconstruct 3D models of flowers based on images taken with a digital single-lens reflex camera, a turntable and a portable lightbox. We demonstrate that photogrammetry allows a rapid and accurate reconstruction of 3D models of flowers from 2D images. It can reconstruct all visible parts of flowers and has the advantage of keeping colour information. We illustrated its use by studying the shape and colour of 18 Gesneriaceae species. Photogrammetry is an affordable alternative to micro-computed tomography (micro-CT) that requires minimal investment and equipment, allowing it to be used directly in the field. It has the potential to stimulate research on the evolution and ecology of flowers by providing a simple way to access 3D morphological data from a variety of flower types.

Red and yellow pigments in autumn leaves are associated with higher nitrogen resorption: A comment on Peña-Novas and Marchetti 2021 (https://doi.org/10.1111/jeb.13903).

Species with red and yellow leaves in the fall have a greater resorption of their nitrogen before leaf fall than species with green leaves. This supports the photoprotection hypothesis that proposes that red and yellow pigments protect the leaves from photooxidative stress under cool temperatures and intense light that occur in the fall with the breakdown of chlorophyl, allowing a better recycling of nutrients.

Chromosome size matters: genome evolution in the cyperid clade.

BACKGROUND AND AIMS: While variation in genome size and chromosome numbers and their consequences are often investigated in plants, the biological relevance of variation in chromosome size remains poorly known. Here, we examine genome and mean chromosome size in the cyperid clade (families Cyperaceae, Juncaceae and Thurniaceae), which is the largest vascular plant lineage with predominantly holocentric chromosomes. METHODS: We measured genome size in 436 species of cyperids using flow cytometry, and augment these data with previously published datasets. We then separately compared genome and mean chromosome sizes (2C/2n) amongst the major lineages of cyperids and analysed how these two genomic traits are associated with various environmental factors using phylogenetically informed methods. KEY RESULTS: We show that cyperids have the smallest mean chromosome sizes recorded in seed plants, with a large divergence between the smallest and largest values. We found that cyperid species with smaller chromosomes have larger geographical distributions and that there is a strong inverse association between mean chromosome size and number across this lineage. CONCLUSIONS: The distinct patterns in genome size and mean chromosome size across the cyperids might be explained by holokinetic drive. The numerous small chromosomes might function to increase genetic diversity in this lineage where crossovers are limited during meiosis.

Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species.

Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.

Judge it by its shape: a pollinator-blind approach reveals convergence in petal shape and infers pollination modes in the genus Erythrina.

PREMISE: Pollinators are thought to exert selective pressures on plants, mediating the evolution of convergent floral shape often recognized as pollination syndromes. However, little is known about the accuracy of using petal shape for inferring convergence in pollination mode without a priori pollination information. Here we studied the genus Erythrina L. as a test case to assess whether ornithophyllous pollination modes (hummingbirds, passerines, sunbirds, or mixed pollination) can be inferred based on the evolutionary analysis of petal shape. METHODS: We characterized the two-dimensional dissected shape of standard, keel, and wing petals from 106 Erythrina species using geometric morphometrics and reconstructed a phylogenetic tree of 83 Erythrina species based on plastid trnL-F and nuclear ribosomal ITS sequences. We then used two phylogenetic comparative methods based on Ornstein-Uhlenbeck models, SURFACE and l1OU, to infer distinct morphological groups using petal shape and identify instances of convergent evolution. The effectiveness of these methods was evaluated by comparing the groups inferred to known pollinators. RESULTS: We found significant petal shape differences between hummingbird- and passerine-pollinated Erythrina species. Our analyses also revealed that petal combinations generally provided better inferences of pollinator types than individual petals and that the method and optimization criterion can affect the results. CONCLUSIONS: We show that model-based approaches using petal shape can detect convergent evolution of floral shape and relatively accurately infer pollination modes in Erythrina. The inference power of the keel petals argues for a deeper investigation of their role in the pollination biology of Erythrina and other bird-pollinated legumes.

Temperate Forests Dominated by Arbuscular or Ectomycorrhizal Fungi Are Characterized by Strong Shifts from Saprotrophic to Mycorrhizal Fungi with Increasing Soil Depth.

In temperate and boreal forests, competition for soil resources between free-living saprotrophs and ectomycorrhizal (EcM) fungi has been suggested to restrict saprotrophic fungal dominance to the most superficial organic soil horizons in forests dominated by EcM trees. By contrast, lower niche overlap with arbuscular mycorrhizal (AM) fungi could allow fungal saprotrophs to maintain this dominance into deeper soil horizons in AM-dominated forests. Here we used a natural gradient of adjacent forest patches that were dominated by either AM or EcM trees, or a mixture of both to determine how fungal communities characterized with high-throughput amplicon sequencing change across organic and mineral soil horizons. We found a general shift from saprotrophic to mycorrhizal fungal dominance with increasing soil depth in all forest mycorrhizal types, especially in organic horizons. Vertical changes in soil chemistry, including pH, organic matter, exchangeable cations, and extractable phosphorus, coincided with shifts in fungal community composition. Although fungal communities and soil chemistry differed among adjacent forest mycorrhizal types, variations were stronger within a given soil profile, pointing to the importance of considering horizons when characterizing soil fungal communities. Our results also suggest that in temperate forests, vertical shifts from saprotrophic to mycorrhizal fungi within organic and mineral horizons occur similarly in both ectomycorrhizal and arbuscular mycorrhizal forests.

Development and experimental demonstration of negative first-order quasi-phase matching in a periodically poled Rb-doped KTiOPO4 crystal.

We worked on a new scheme of quasi-phase matching (QPM) based on the negative first order of the spatial modulation of the sign of the second-order nonlinearity. Applying this scheme in the case of angular-QPM (AQPM) in a biaxial crystal reveals new directions of propagation for efficient parametric frequency conversion as well as "giant" spectral acceptances. The experimental validation is performed in a periodically poled rubidium-doped KTiOPO4 biaxial crystal. This new approach naturally extends to other periodically poled uniaxial crystals such as periodically poled LiNbO3.

A four-year phytoremediation trial to decontaminate soil polluted by wood preservatives: phytoextraction of arsenic, chromium, copper, dioxins and furans.

Widely used as wood preservatives for the last century, Pentachlorophenol (PCP) and chromated copper arsenate (CCA) have been shown to leach from treated surfaces and contaminate soil of wood storage sites. We performed a four-year field phytoremediation trial in southern Quebec (Canada) on a site contaminated with PCP and CCA with the following objectives: (1) assess the potential of willow, fescue, alfalfa and Indian mustard to tolerate and translocate CCA and PCP residues in their aerial tissues, (2) investigate the possibility of phytoextraction of dioxins and furans, and (3) test the effect of nitrogen fertilizer on phytoremediation performance. We showed that while nitrogen fertilization increased the chlorophyll content of plants, it did not result in a significantly greater plant biomass. We also showed that plants grown in the presence of PCP/CCA residues were able to translocate and concentrate trace elements in their aerial tissues, but also dioxins and furans (PCDD/F). This suggests that plants grown on sites polluted by PCP might contain dioxins and furans and should be treated as contaminated by these toxic chemicals. Finally, the reduction of soil contaminants at the end of the trial suggests that phytoremediation is a promising approach for decontaminating such sites.

An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus).

Cytonuclear discordance is commonly observed in phylogenetic studies, yet few studies have tested whether these patterns reflect incomplete lineage sorting or organellar introgression. Here, we used whole-chloroplast sequence data in combination with over 1000 nuclear single-nucleotide polymorphisms to clarify the extent of cytonuclear discordance in wild annual sunflowers (Helianthus), and to test alternative explanations for such discordance. Our phylogenetic analyses indicate that cytonuclear discordance is widespread within this group, both in terms of the relationships among species and among individuals within species. Simulations of chloroplast evolution show that incomplete lineage sorting cannot explain these patterns in most cases. Instead, most of the observed discordance is better explained by cytoplasmic introgression. Molecular tests of evolution further indicate that selection may have played a role in driving patterns of plastid variation - although additional experimental work is needed to fully evaluate the importance of selection on organellar variants in different parts of the geographic range. Overall, this study represents one of the most comprehensive tests of the drivers of cytonuclear discordance and highlights the potential for gene flow to lead to extensive organellar introgression in hybridizing taxa.

Validation of the angular quasi-phase-matching theory for the biaxial optical class using PPRKTP.

We report the first experimental validation of angular quasi-phase-matching (AQPM) theory in a biaxial crystal by performing second-harmonic generation (SHG) in the periodically-poled Rb-doped KTiOPO4 (PPRKTP) crystal cut as a sphere. Both AQPM and birefringence phase-matching (BPM) angles were measured thanks to a Kappa circle.

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants.

Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, α/ß-tubulin, and elongation factor 1-α. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system.

Meta-transcriptomics indicates biotic cross-tolerance in willow trees cultivated on petroleum hydrocarbon contaminated soil.

BACKGROUND: High concentrations of petroleum hydrocarbon (PHC) pollution can be hazardous to human health and leave soils incapable of supporting agricultural crops. A cheap solution, which can help restore biodiversity and bring land back to productivity, is cultivation of high biomass yielding willow trees. However, the genetic mechanisms which allow these fast-growing trees to tolerate PHCs are as yet unclear. METHODS: Salix purpurea 'Fish Creek' trees were pot-grown in soil from a former petroleum refinery, either lacking or enriched with C10-C50 PHCs. De novo assembled transcriptomes were compared between tree organs and impartially annotated without a priori constraint to any organism. RESULTS: Over 45% of differentially expressed genes originated from foreign organisms, the majority from the two-spotted spidermite, Tetranychus urticae. Over 99% of T. urticae transcripts were differentially expressed with greater abundance in non-contaminated trees. Plant transcripts involved in the polypropanoid pathway, including phenylalanine ammonia-lyase (PAL), had greater expression in contaminated trees whereas most resistance genes showed higher expression in non-contaminated trees. CONCLUSIONS: The impartial approach to annotation of the de novo transcriptomes, allowing for the possibility for multiple species identification, was essential for interpretation of the crop's response treatment. The meta-transcriptomic pattern of expression suggests a cross-tolerance mechanism whereby abiotic stress resistance systems provide improved biotic resistance. These findings highlight a valuable but complex biotic and abiotic stress response to real-world, multidimensional contamination which could, in part, help explain why crops such as willow can produce uniquely high biomass yields on challenging marginal land.

Species radiation by niche shifts in New Zealand's rockcresses (Pachycladon, Brassicaceae).

Adaptive radiations such as the Darwin finches in the Galapagos or the cichlid fishes from the Eastern African Great Lakes have been a constant source of inspiration for biologists and a stimulus for evolutionary thinking. A central concept behind adaptive radiation is that of evolution by niche shifts, or ecological speciation. Evidence for adaptive radiations generally requires a strong correlation between phenotypic traits and the environment. But adaptive traits are often cryptic, hence making this phenotype-environment approach difficult to implement. Here we propose a procedure for detecting adaptive radiation that focuses on species' ecological niche comparisons. It evaluates whether past ecological disparity in a group fits better a neutral Brownian motion model of ecological divergence or a niche shift model. We have evaluated this approach on New Zealand rockcresses (Pachycladon) that recently radiated in the New Zealand Alps. We show that the pattern of ecological divergence rejects the neutral model and is consistent with that of a niche shift model. Our approach to detect adaptive radiation has the advantage over alternative approaches that it focuses on ecological niches, a key concept behind adaptive radiation. It also provides a way to evaluate the importance of ecological speciation in adaptive radiations and will have general application in evolutionary studies. In the case of Pachycladon, the high estimated diversification rate, the distinctive ecological niches of species, and the evidence for ecological speciation suggest a remarkable example of adaptive radiation.

Phylogeny and biogeography of wild roses with specific attention to polyploids.

BACKGROUND AND AIMS: The genus Rosa (150-200 species) is widely distributed throughout temperate and sub-tropical habitats from the northern hemisphere to tropical Asia, with only one tropical African species. In order to better understand the evolution of roses, this study examines infrageneric relationships with respect to conventional taxonomy, considers the extent of allopolyploidization and infers macroevolutionary processes that have led to the current distribution of the genus. METHODS: Phylogenetic relationships among 101 species of the genus Rosa were reconstructed using sequences from the plastid psbA-trnH spacer, trnL intron, trnL-F spacer, trnS-G spacer and trnG intron, as well as from nuclear glyceraldehyde 3-phosphate dehydrogenase (GAPDH), which was used to identify putative allopolyploids and infer their possible origins. Chloroplast phylogeny was used to estimate divergence times and reconstruct ancestral areas. KEY RESULTS: Most subgenera and sections defined by traditional taxonomy are not monophyletic. However, several clades are partly consistent with currently recognized sections. Allopolyploidy seems to have played an important role in stabilizing intersectional hybrids. Biogeographic analyses suggest that Asia played a central role as a genetic reservoir in the evolution of the genus Rosa. CONCLUSIONS: The ancestral area reconstruction suggests that despite an early presence on the American continent, most extant American species are the results of a later re-colonization from Asia, probably through the Bering Land Bridge. The results suggest more recent exchanges between Asia and western North America than with eastern North America. The current distribution of roses from the Synstylae lineage in Europe is probably the result of a migration from Asia approx. 30 million years ago, after the closure of the Turgai strait. Directions for a new sectional classification of the genus Rosa are proposed, and the analyses provide an evolutionary framework for future studies on this notoriously difficult genus.

Phenology varies with phylogeny but not by trophic level with climate change.

Shifts in phenology with climate change can lead to asynchrony between interacting species, with cascading impacts on ecosystem services. Previous meta-analyses have produced conflicting results on whether asynchrony has increased in recent decades, but the underlying data have also varied-including in species composition, interaction types and whether studies compared data grouped by trophic level or compared shifts in known interacting species pairs. Here, using updated data from previous studies and a Bayesian phylogenetic model, we found that species have advanced an average of 3.1 days per decade across 1,279 time series across 29 taxonomic classes. We found no evidence that shifts vary by trophic level: shifts were similar when grouped by trophic level, and for species pairs when grouped by their type of interaction-either as paired species known to interact or as randomly paired species. Phenology varied with phylogeny (λ = 0.4), suggesting that uneven sampling of species may affect estimates of phenology and potentially phenological shifts. These results could aid forecasting for well-sampled groups but suggest that climate change has not yet led to widespread increases in phenological asynchrony across interacting species, although substantial biases in current data make forecasting for most groups difficult.

Herbarium collections remain essential in the age of community science.

The past decade has yielded more biodiversity observations from community science than the past century of traditional scientific collection. This rapid influx of data is promising for overcoming critical biodiversity data shortfalls, but we also have vast untapped resources held in undigitized natural history collections. Yet, the ability of these undigitized collections to fill data gaps, especially compared against the constant accumulation of community science data, remains unclear. Here, we compare how well community science (iNaturalist) observations and digitized herbarium specimens represent the diversity, distributions, and modeling needs of vascular plants in Canada. We find that, despite having only a third as many records, herbarium specimens capture more taxonomic, phylogenetic, and functional diversity and more efficiently capture species' environmental niches. As such, the digitization of Canada's 7.3M remaining specimens has the potential to more than quintuple our ability to model biodiversity. In contrast, it would require over 27M more iNaturalist observations to produce similar benefits. Our findings indicate that digitizing Earth's remaining herbarium specimens is likely an efficient, feasible, and potentially critical investment when it comes to improving our ability to predict and protect biodiversity into the future.

Latitudinal gradients in seed predation persist in urbanized environments.

Urbanization is creating a new global biome, in which cities and suburbs around the world often resemble each other more than the local natural areas they replaced. But while urbanization can profoundly affect ecology at local scales, we know little about whether it disrupts large-scale ecological patterns. Here we test whether urbanization disrupts a macroecological pattern central to ecological and evolutionary theory: the increase in seed predation intensity from high to low latitudes. Across 14,000 km of latitude spanning the Americas, we compared predation intensity on two species of standardized experimental seeds in urbanized and natural areas. In natural areas, predation on both seed species increased fivefold from high latitudes to the tropics, one of the strongest latitudinal gradients in species interactions documented so far. Surprisingly, latitudinal gradients in predation were equally strong in urbanized areas despite significant habitat modification. Nevertheless, urbanization did affect seed predation. Compared with natural areas, urbanization reduced overall predation and vertebrate predation, did not affect predation by invertebrates in general, and increased predation by ants. Our results show that macroecological patterns in predation intensity can persist in urbanized environments, even as urbanization alters the relative importance of predators and potentially the evolutionary trajectory of urban populations.

Fast diploidization in close mesopolyploid relatives of Arabidopsis.

Mesopolyploid whole-genome duplication (WGD) was revealed in the ancestry of Australian Brassicaceae species with diploid-like chromosome numbers (n = 4 to 6). Multicolor comparative chromosome painting was used to reconstruct complete cytogenetic maps of the cryptic ancient polyploids. Cytogenetic analysis showed that the karyotype of the Australian Camelineae species descended from the eight ancestral chromosomes (n = 8) through allopolyploid WGD followed by the extensive reduction of chromosome number. Nuclear and maternal gene phylogenies corroborated the hybrid origin of the mesotetraploid ancestor and suggest that the hybridization event occurred approximately 6 to 9 million years ago. The four, five, and six fusion chromosome pairs of the analyzed close relatives of Arabidopsis thaliana represent complex mosaics of duplicated ancestral genomic blocks reshuffled by numerous chromosome rearrangements. Unequal reciprocal translocations with or without preceeding pericentric inversions and purported end-to-end chromosome fusions accompanied by inactivation and/or loss of centromeres are hypothesized to be the main pathways for the observed chromosome number reduction. Our results underline the significance of multiple rounds of WGD in the angiosperm genome evolution and demonstrate that chromosome number per se is not a reliable indicator of ploidy level.

Variation in flower size and shape of Impatiens capensis is correlated with urbanization in Montreal, Canada.

Urbanization is changing the conditions in which many species live, forcing them to adjust to these novel environments. Floral size and shape are critical traits for the reproduction of plants pollinated by animals as they are involved in the attraction of pollinators and in efficient pollination. Variation in size and shape could be affected by urbanization via its modification of the abiotic environment (habitat fragmentation, water availability, temperature, soil properties), or via its impact on the biotic environment of plants (pollination, herbivory). Although numerous studies have assessed the impact of urbanization on pollinator communities and many plant traits, few have investigated its impact on floral size and shape while quantifying the proportion of the total urbanization effect that is due to biotic interactions. In this study, we tested if urbanization and pollinator visitation rates affect the flower shape of the spotted jewelweed, Impatiens capensis. We quantified the size and shape of flowers in frontal and profile views using geometric morphometrics for 228 individuals from six populations from the region of Montreal, Canada. Pollinator visitation rates were estimated at each site and the main pollinators were found to be bumblebees, honeybees and hummingbirds. We found that floral size and shape are significantly correlated with urbanization as measured by the amount of vegetation in the surrounding environment of the plants (mean normalized vegetation index, NDVI) and by the visitation rates of bumblebees and honey bees. Partitioning of the total flower shape variation suggests that urbanization affects flower shape through abiotic factors and via its impact on pollinator visitation rates. While further studies from other cities are necessary to confirm the role of urbanization in shaping the floral shape of I. capensis, these results support the idea that urbanization could affect flower shapes.