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publicOct 2025View details →

Data from: Flower clades and fruit clades: Trade-offs in color diversification across angiosperms

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publicOct 2025View details →

Effects of niche marginality on hotter-drought tree mortality in angiosperms and gymnosperms

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publicApr 2023View details →

Data from: Beyond pollen:ovule ratios: Evolutionary consequences of pollinator dependence and pollination efficiency for pollen and ovule production in angiosperms

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publicNov 2024View details →

Data from: Seasonal assembly of nectar microbial communities across angiosperm plant species: Assessing contributions of climate and plant traits

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opencc-zeroOct 2020View details →

The perfect storm: Gene tree estimation error, incomplete lineage sorting, and ancient gene flow explain the most recalcitrant ancient angiosperm clade, Malpighiales

The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes nine of the top ten most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 15%, 52%, and 32% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.

Data from: From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

Background: Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have been useful for reconstructing the phylogeny of numerous clades of photosynthetic organisms (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome data. Results: We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. Conclusions: Analyses of the plastid data recovered a strongly supported framework of relationships for green plants. This includes the placement of Zygnematophyceace as sister to land plants (Embryophyta) and a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining members and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees); within the monilophyte clade (Monilophyta), relationships are strongly supported with Equisetales + Psilotales sister to Marattiales + leptosporangiate ferns. We also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses and provide suggestions for future analyses that will likely incorporate plastid genome data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding protocols for the entire data set as well as subsets of the data.

opencc-zeroDec 2018View details →

Data from: Revisiting the relative growth rate hypothesis for gymnosperm and angiosperm species co‐occurrence

Premise of the study: It is unclear to what extent the co-occurrence of angiosperm and gymnosperm species in some marginal ecosystems is explained by reduced growth in angiosperms due to carbon (C) limitation, and by high stress tolerance in gymnosperms associated with lack of vessels and resource conservation. Methods: We examined growth patterns and traits associated with C balance in four evergreen angiosperm species (including one vesselless species, Drimys winteri) and three gymnosperm tree species of a cold-temperate rainforest in southern Chile. We measured the mean basal area increment for the first 50 (BAI50) and the last 10 years (BAI10), wood density, leaf lifespan, and non-structural carbohydrate (NSC) concentrations in different organs. Key results: BAI50 was 6-fold higher in angiosperms than in gymnosperms, and c. 4-fold higher in Drimys than in the fastest growing gymnosperm. BAI10 and aboveground NSC concentrations were significantly higher and leaf lifespan lower in angiosperms than in gymnosperms; these differences though were largely driven by the slow growth and low NSC concentrations of the Cupressaceae species (Pilgerodendron uviferum), while the two Podocarpaceae showed similar BAI10 and NSC concentrations to angiosperms. In angiosperms, NSC and starch concentrations were generally higher in species with lower BAI10, indicating no severe C limitation. Conclusions: The co-occurrence of angiosperms and gymnosperms in cold-temperate rainforests of southern Chile is not explained by growth disadvantages and C limitation in angiosperms. High leaf longevity, but not lack of vessels, appeared to favor resource conservation and C balance in some gymnosperms (Podocarpaceae). In compliance with data protection regulations, please contact the publication office if you would like to have your personal information removed from the database.

opencc-zeroOct 2019View details →

Angiosperm to Gymnosperm host-plant switch entails shifts in microbiota of the Welwitschia bug, Probergrothius angolensis (Distant, 1902)

Adaptation of herbivorous insects to new host plants is key to their evolutionary success in diverse environments. Many insects are associated with mutualistic gut bacteria that contribute to the host's nutrition and can thereby facilitate dietary switching in polyphagous insects. However, how gut microbial communities differ between populations of the same species that feed on different host plants remains poorly understood. Most species of Pyrrhocoridae (Hemiptera: Heteroptera) are specialist seed-feeders on plants in the family Malvaceae, however populations of one species, Probergrothius angolensis, has switched to the very distantly related Welwitschia mirabilis plant in the Namib Desert. We first compared development and survival of laboratory populations of Pr. angolensis with two other pyrrhocorids on seeds of Welwitschia and found only Pr. angolensis capable of successfully completing its development. We then collected Pr. angolensis in Namibia from Malvaceae and Welwitschia host plants, respectively, to assess their bacterial and fungal community profiles using high-throughput amplicon sequencing. Comparison with long-term lab reared insects indicated stable associations of Pr. angolensis with core bacteria (Commensalibacter, Enterococcus, Bartonella, and Klebsiella), but not fungi or yeasts. Phylogenetic analyses of core bacteria revealed relationships to other insect-associated bacteria, but also found new taxa indicating potential host-specialized nutritional roles. Importantly, the microbial community profiles of bugs feeding on Welwitschia vs. Malvaceae revealed stark and consistent differences in the relative abundance of core bacterial taxa that correlate with the host-plant switch; a result we were able to recreate through feeding experiments. Thus, a dynamic gut microbiota may provide a means for insect adaptation to new host plants in new environments when food plants are extremely divergent.

opencc-zeroDec 2017View details →

Data from: Endozoochory of aquatic ferns and angiosperms by mallards in Central Europe

1. Modern literature on plant dispersal by birds focuses mainly on the importance of frugivory and scatter-hoarding, yet recent studies show that endozoochory by migratory waterbirds is an important mechanism of long-distance dispersal for a broad range of plants. Nevertheless, there is a lack of empirical field studies that identify the plants dispersed by waterbirds, and relate them to expectations based on dispersal syndromes. To date, there are no detailed studies of the level of spatial variation in the plant taxa dispersed by a waterbird vector. 2. Five sets of faecal samples (total n = 215) were collected from mallards Anas platyrhynchos on autumn migration in the Tisza and Balaton regions in Hungary, central Europe. Intact diaspores were extracted, identified and their germinability assessed under standard conditions. The plant communities recorded at different sites were compared with PERMANOVA and other multivariate methods. 3. Macrospores of the floating watermoss Salvinia natans were recorded in 32 samples, and a total of 16 macrospores germinated, providing the first field demonstration of endozoochory of ferns by birds. Of 21 angiosperm taxa recorded (of which 8 germinated), 13 were terrestrial species, although the most abundant taxa were aquatic species such as the alkali bulrush Bolboschoenus maritimus and the sago pondweed Potamogeton pectinatus. Two naturalized alien species, the common fig (Ficus carica) and the hackberry (Celtis occidentalis) were also recorded. The plant taxa dispersed varied at two different spatial scales, with minor but significant differences between samples from sites separated by less than 1 km, and major differences between the two regions separated by approximately 220 km. 4. Synthesis. This is a unique study of the spatial variation in plants dispersed by endozoochory by a migratory waterfowl species, with the first demonstration of avian endozoochory of ferns. Most taxa dispersed are generally assumed to disperse by water, wind or self-dispersal, and waterfowl will provide much greater maximum dispersal distances. More such studies are essential before we can understand which plants are dispersed by migratory birds, because morphological dispersal syndromes do not allow us to make adequate a priori predictions.

Data from: From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae)

Allopolyploidisation acounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabelled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the 'correct' network for a set of polyploids depends on recovering all homoeologs, i.e. all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies ('ghost subgenome lineages'), significantly reduced the number of inferred polyploidisation events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (1) fewest possible ghost subgenome lineages, (2) fewest possible polyploidisation events, and (3) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognise Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidisations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage – between 67% and 88% – of the speciation events at this level. The theoretical and methodological approaches presented here for (1) constructing networks and (2) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidisation has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events.

opencc-zeroDec 2012View details →

Data from: Angiosperm fleshy fruits and seed dispersers: a comparative analysis of adaptation and constraints in plant-animal interactions

Variation in phenotypic traits of angiosperm fleshy fruits has been explained as the result of adaptations to their mutualistic seed dispersers. By analyzing the information available on fleshy fruit characteristics of 910 angiosperm species, I assess the hypothesis of evolutionary association between fruit phenotypic traits and type of seed disperser (birds, mammals, and mixed dispersers) and address explicitly and quantitatively alternative null hypotheses about phylogenetic effects. Phylogenetic affinity among plant taxa is accounted for by comparative methods including nested ANOVA, phylogenetic autocorrelation, and independent contrasts. Averaging over the 16 fruit traits examined, phylogenetic effects down to genus level explain 61% of total variance. Phylogenetic autocorrelations are strong among close relatives, reaching significance for 11 of the 16 fruit traits examined. When assessed by independent contrast methods, correlated evolution between type of disperser and fruit traits is confined to fruit diameter. Differences among dispersal syndromes in other traits vanish after accounting for phylogenetic effects. These analyses reveal that seed dispersal syndromes are not entirely interpretable as current adaptations to seed dispersers. Their status as exaptations can be assessed by combining experimental studies of natural selection on fruit size and rigorous comparative and cladistic tests of adaptational hypotheses.

Data from: A conifer–angiosperm divergence in the growth vs shade tolerance trade-off underlies the dynamics of a New Zealand warm-temperate rain forest

1. A central tenet of forest ecology is that succession and regeneration dynamics are driven by an interspecific trade-off between juvenile growth rates in high light and shade tolerance. There is evidence, however, that a single trade-off axis may fail to explain the dynamics of mixed conifer-angiosperm rainforests in the southern hemisphere, especially in New Zealand. 2. We tested for growth vs shade tolerance trade-offs by measuring juvenile growth of five podocarps and five broadleaved canopy angiosperms across a wide range of light environments in a New Zealand warm-temperate rainforest. The light compensation point of growth was used as a measure of species light requirements, which we then compared with height growth in 10% light, approximating the environments encountered beneath small tree-fall gaps. 3. Despite considerable overlap between the ranges of both growth rates and compensation points found in the two lineages, major axis tests showed that the growth vs shade tolerance trade-off differed significantly between podocarp and angiosperm species. At a common compensation point, angiosperms were faster-growing than podocarps in 10% light. However, juveniles of these angiosperm species were notably scarce in the more open environments associated with forest margins. 4. Synthesis. A conifer–angiosperm divergence in the growth vs shade tolerance trade-off may explain long-standing problems of the dynamics of these forests. Although juveniles of most lowland podocarps can tolerate considerable shade, the more vigorous response of broadleaved angiosperms to small canopy openings enables them to out-compete podocarps in old-growth stands. The greater abundance of podocarp juveniles on forest margins cannot be attributed to them outcompeting angiosperm species where light is abundant, and is likely to reflect superior resistance to frost and/or drought. The drivers of the dynamics of New Zealand's podocarp–broadleaved forests therefore differ appreciably from those ascribed to tropical and north-temperate forests.

opencc-zeroDec 2015View details →

Data from: Ancestral gene flow and parallel organellar genome capture result in extreme phylogenomic discord in a lineage of angiosperms

While hybridization has recently received a resurgence of attention from systematists and evolutionary biologists, there remains a dearth of case studies on ancient, diversified hybrid lineages-clades of organisms that originated through reticulation. Studies on these groups are valuable in that they would speak to the long-term phylogenetic success of lineages following gene flow between species. We present a phylogenomic view of Heuchera, long known for frequent hybridization, incorporating all three independent genomes: targeted nuclear (~400,000 bp), plastid (~160,000 bp), and mitochondrial (~470,000 bp) data. We analyze these data using multiple concatenation and coalescence strategies. The nuclear phylogeny is consistent with previous work and with morphology, confidently suggesting a monophyletic Heuchera. By contrast, analyses of both organellar genomes recover a grossly polyphyletic Heuchera,consisting of three primary clades with relationships extensively rearranged within these as well. A minority of nuclear loci also exhibit phylogenetic discord; yet these topologies remarkably never resemble the pattern of organellar loci and largely present low levels of discord inter alia. Two independent estimates of the coalescent branch length of the ancestor of Heuchera using nuclear data suggest rare or nonexistent incomplete lineage sorting with related clades, inconsistent with the observed gross polyphyly of organellar genomes (confirmed by simulation of gene trees under the coalescent). These observations, in combination with previous work, strongly suggest hybridization as the cause of this phylogenetic discord.

opencc-zeroDec 2017View details →

Data from: The emergence of earliest angiosperms may be earlier than fossil evidence indicates

Gaps between molecular ages and fossils undermine the validity of time-calibrated molecular phylogenies. An example of the time gap surrounds the age of angiosperms' origin. We calculate molecular ages of the earliest flowering plant lineages using 22 fossil calibrations (101 genera, 40 families). Our results reveal the origin of angiosperms at the late Permian, ∼275 million years ago. Different prior probability curves of molecular age calculations on dense calibration point distributions had little effect on overall age estimates compared to the effects of altered calibration points. The same is true for reasonable root age constraints. We conclude that our age estimates based on multiple datasets, priors, and calibration points are robust and the true ages are likely between our extremes. Our results, when integrated with the ecophysiological evolution of early angiosperms, imply that the ecology of the earliest angiosperms is critical to understand the pre-Cretaceous evolution of flowering plants.

opencc-zeroDec 2012View details →

Data from: Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach

Despite the recent advances in generating molecular data, reconstructing species-level phylogenies for non-models groups remains a challenge. The use of a number of independent genes is required to resolve phylogenetic relationships, especially for groups displaying low polymorphism. In such cases, low-copy nuclear exons and non-coding regions, such as 3′ untranslated regions (3′-UTRs) or introns, constitute a potentially interesting source of nuclear DNA variation. Here, we present a methodology meant to identify new nuclear orthologous markers using both public-nucleotide databases and transcriptomic data generated for the group of interest by using next generation sequencing technology. To identify PCR primers for a non-model group, the genus Leucadendron (Proteaceae), we adopted a framework aimed at minimizing the probability of paralogy and maximizing polymorphism. We anchored when possible the right-hand primer into the 3′-UTR and the left-hand primer into the coding region. Seven new nuclear markers emerged from this search strategy, three of those included 3′-UTRs. We further compared the phylogenetic potential between our new markers and the ribosomal internal transcribed spacer region (ITS). The sequenced 3′-UTRs yielded higher polymorphism rates than the ITS region did. We did not find strong incongruences with the phylogenetic signal contained in the ITS region and the seven new designed markers but they strongly improved the phylogeny of the genus Leucadendron. Overall, this methodology is efficient in isolating orthologous loci and is valid for any non-model group given the availability of transcriptomic data.

opencc-zeroAug 2019View details →

Data from: Palaeoclimatic reconstruction for a Cenomanian-aged angiosperm flora near Schefferville, Labrador

An understanding of local and regional climate trends is essential to investigate the remarkable angiosperm radiation that happened during the Albian-Cenomanian transition. However, many of the inland depositional environments pioneered by the first modern angiosperms are poorly represented in the fossil record. Eastern Canada in particular has a very poor Mesozoic record. In this paper, we present the first multivariate palaeoclimate analysis (CLAMP) for the environment of a geologically isolated woody dicot dominated flora found in the Redmond no.1 mine, Labrador, near Schefferville, with an estimated Cenomanian age. It reveals that the Redmond flora would have experienced a mean annual temperature of 15.1 ± 2.1 °C, one of the coolest recorded for North America at this time. These results confer the Redmond no.1 site a warm temperate and fully humid climate with a hot summer, in accordance with previous qualitative palaeoclimate estimates. This flora fits smoothly into palaeolatitudinal MAT gradients that use other Cenomanian-estimated North American floras. Despite an inland setting, the climate analysis does not recover a significantly higher degree of seasonality than the sites to which it is compared, which agrees with established climate equability models for the Cretaceous and Paleogene. This study also introduces 15 new morphotypes discovered in recent fieldwork. The eventual description of the species they represent may refine our dating estimates for the Redmond Formation. A greater understanding of the depositional environment and of the natural history of these angiosperms is required to improve this community's characterization, along with estimates from other proxies.

Data from: Conserved genetic regions across angiosperms as tools to develop single copy nuclear markers in gymnosperms: an example using cycads

Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: 1) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and, 2) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single Copy genes (APVO SSC) against the EST Zamia databases in Genbank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases the matching Genbank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginko biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Z. pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.

opencc-zeroDec 2017View details →

Data from: Light and growth form interact to shape stomatal ratio among British angiosperms

In most plants, stomata are located only on the abaxial leaf surface (hypostomy), but many plants have stomata on both surfaces (amphistomy). High light and herbaceous growth form have been hypothesized to favor amphistomy, but these hypotheses have not been rigorously tested together using phylogenetic comparative methods. I leveraged a large dataset including stomatal ratio, Ellenberg light indicator value, growth form and phylogenetic relationships for 372 species of British angiosperms. I used phylogenetic comparative methods to test how light and/or growth form influence stomatal ratio and density. High light and herbaceous growth form are correlated with amphistomy, as predicted, but they also interact; the effect of light is pronounced in therophytes (annuals) and perennial herbs, but muted in phanerophytes (shrubs and trees). Furthermore, amphistomy and stomatal density evolve together in response to light. Comparative analyses of British angiosperms reveal two major insights. First, light and growth form interact to shape stomatal ratio; amphistomy is common under high light, but mostly for herbs. Second, coordinated evolution of adaxial stomatal density and light tolerance indicates that amphistomy helps to optimally balance light acquisition with gas exchange. Stomatal ratio may have potential as a functional trait for paleoecology and crop improvement.

opencc-zeroMay 2019View details →

Data from: Early wasp plucks the flower: disparate extant diversity of sawfly superfamilies (Hymenoptera: 'Symphyta') may reflect asynchronous switching to angiosperm hosts

The insect order Hymenoptera originated during the Permian nearly 300 million years ago. Ancestrally herbivorous hymenopteran lineages today make up the paraphyletic suborder 'Symphyta,' which encompasses circa 8200 species with very diverse host-plant associations. We used phylogeny-based statistical analyses to explore drivers of diversity dynamics within the 'Symphyta,' with a particular focus on the hypothesis that diversification of herbivorous insects has been driven by the explosive radiation of angiosperms during and after the Cretaceous. Our ancestral-state estimates reveal that the first symphytans fed on gymnosperms, and that shifts onto angiosperms and pteridophytes—and back—have occurred at different time intervals in different groups. Trait-dependent analyses indicate that average net diversification rates do not differ between symphytan lineages feeding on angiosperms, gymnosperms, or pteridophytes, but trait-independent models show that the highest diversification rates are found in a few angiosperm-feeding lineages that may have been favored by the radiations of their host taxa during the Cenozoic. Intriguingly, lineages-through-time plots exhibit signs of an early Cretaceous mass extinction, with a recovery starting first in angiosperm-associated clades. Hence, the oft-invoked assumption of herbivore diversification driven by the rise of flowering plants may overlook a Cretaceous global turnover in insect herbivore communities during the rapid displacement of gymnosperm- and pteridophyte-dominated floras by angiosperms.