Dosage sensitivity shapes balanced expression and gene longevity of homoeologs after whole-genome duplications in angiosperms.

Following whole-genome duplication (WGD), duplicate gene pairs (homoeologs) can evolve varying degrees of expression divergence. However, the determinants influencing these relative expression level differences (RFPKM) between homoeologs remain elusive. Here, we analyzed the RFPKM between homoeologs in three angiosperms, Nymphaea colorata, Nelumbo nucifera, and Acorus tatarinowii, all having undergone a single WGD since the origin of angiosperms. Our results show significant positive correlations in RFPKM of homoeologs among tissues within the same species, and among orthologs across these three species, indicating convergent expression balance/bias between homoeologous gene copies following independent WGDs. We linked RFPKM between homoeologs to gene attributes associated with dosage balance constraints, such as protein-protein interactions, lethal-phenotype scores in Arabidopsis (Arabidopsis thaliana) orthologs, domain numbers, and expression breadth. Notably, homoeologs with lower RFPKM often had more interactions and higher lethal-phenotype scores, indicating selective pressures favoring balanced expression. Also, homoeologs with lower RFPKM were more likely to be retained after WGDs in angiosperms. Within Nelumbo, greater RFPKM between homoeologs correlated with increased cis- and trans-regulatory differentiation between species, highlighting the ongoing escalation of gene expression divergence. We further found that expression degeneration in one copy of homoeologs is inclined towards nonfunctionalization. Our research highlights the importance of balanced expression, shaped by dosage balance constraints, in the evolutionary retention of homoeologs in plants.

Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora.

The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap in our understanding of the World's richest flora, we present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture of Angiosperms353 universal loci for 50 of the ca. 75 spp., obtained almost entirely from herbarium specimens. We identify high phylogenomic complexity in Freziera, including the presence of data artifacts. Via by-eye observation of gene trees, detailed examination of warnings from recently improved assembly pipelines, and gene tree filtering, we identified that artifactual orthologs (i.e., the presence of only one copy of a multicopy gene due to differential assembly) were an important source of gene tree heterogeneity that had a negative impact on phylogenetic inference and support. These artifactual orthologs may be common in plant phylogenomic datasets, where multiple instances of genome duplication are common. After accounting for artifactual orthologs as source of gene tree error, we identified a significant, but nonspecific signal of introgression using Patterson's D and f4 statistics. Despite phylogenomic complexity, we were able to resolve Freziera into 9 well-supported subclades whose evolution has been shaped by multiple evolutionary processes, including incomplete lineage sorting, historical gene flow, and gene duplication. Our results highlight the complexities of plant phylogenomics, which are heightened in Andean radiations, and show the impact of filtering data processing artifacts and standard filtering approaches on phylogenetic inference.

Comparative analyses suggest a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants.

BACKGROUND: In recent years, covalent modifications on RNA nucleotides have emerged as pivotal moieties influencing the structure, function, and regulatory processes of RNA Polymerase II transcripts such as mRNAs and lncRNAs. However, our understanding of their biological roles and whether these roles are conserved across eukaryotes remains limited. RESULTS: In this study, we leveraged standard polyadenylation-enriched RNA-sequencing data to identify and characterize RNA modifications that introduce base-pairing errors into cDNA reads. Our investigation incorporated data from three Poaceae (Zea mays, Sorghum bicolor, and Setaria italica), as well as publicly available data from a range of stress and genetic contexts in Sorghum and Arabidopsis thaliana. We uncovered a strong enrichment of RNA covalent modifications (RCMs) deposited on a conserved core set of nuclear mRNAs involved in photosynthesis and translation across these species. However, the cohort of modified transcripts changed based on environmental context and developmental program, a pattern that was also conserved across flowering plants. We determined that RCMs can partly explain accession-level differences in drought tolerance in Sorghum, with stress-associated genes receiving a higher level of RCMs in a drought tolerant accession. To address function, we determined that RCMs are significantly enriched near exon junctions within coding regions, suggesting an association with splicing. Intriguingly, we found that these base-pair disrupting RCMs are associated with stable mRNAs, are highly correlated with protein abundance, and thus likely associated with facilitating translation. CONCLUSIONS: Our data point to a conserved role for RCMs in mRNA stability and translation across the flowering plant lineage.

Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm.

MAIN CONCLUSION: Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm. Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon's Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.

Reproductive development in Trithuria submersa (Hydatellaceae: Nymphaeales): the involvement of AGAMOUS-like genes.

MAIN CONCLUSION: In the early diverging angiosperm Trithuria submersa TsAG1 and TsAG2 are expressed in different flower organs, including bracts, while TsAG3 is more ovule-specific, probably functioning as a D-type gene. Species of Trithuria, the only genus of the family Hydatellaceae, represent ideal candidates to explore the biology and flower evolution of early diverging angiosperms. The life cycle of T. submersa is generally known, and the "reproductive units" are morphologically well described, but the availability of genetic and developmental data of T. submersa is still scarce. To fill this gap, a transcriptome analysis of the reproductive structures was performed and presented in this work. This analysis provided sequences of MADS-box transcription factors, a gene family known to be involved in flower and fruit development. In situ hybridization experiments on floral buds were performed to describe the spatiotemporal expression patterns of the AGAMOUS genes, revealing the existence of three AG genes with different expression domains in flower organs and in developing ovules. Trithuria may offer important clues to the evolution of reproductive function among early angiosperms and Nymphaeales in particular, and this study aims to broaden relevant knowledge regarding key genes of reproductive development in non-model angiosperms, shaping first flower appearance and evolution.

Ad fontes: divergence-time estimation and the age of angiosperms.

Accurate divergence times are essential for interpreting and understanding the context in which lineages have evolved. Over the past several decades, debates have surrounded the discrepancies between the inferred molecular ages of crown angiosperms, often estimated from the Late Jurassic into the Permian, and the fossil record, placing angiosperms in the Early Cretaceous. That crown angiosperms could have emerged as early as the Permian or even the Triassic would have major implications for the paleoecological context of the origin of one of the most consequential clades in the tree of life. Here, we argue, and demonstrate through simulations, that the older ages inferred from molecular data and relaxed-clock models are misled by lineage-specific rate heterogeneity resulting from life history changes that occurred several times throughout the evolution of vascular plants. To overcome persistent discrepancies in age estimates, more biologically informed and realistic models should be developed, and our results should be considered in the context of their biological implications before we accept inferences that are a major departure from our strongest evidence.

Systematic synthesis and identification of monolignol pathway metabolites.

Monolignol serves as the building blocks to constitute lignin, the second abundant polymer on Earth. Despite two decades of diligent efforts, complete identification of all metabolites in the currently proposed monolignol biosynthesis pathway has proven elusive. This limitation also hampers their potential application. One of the primary obstacles is the challenge of assembling a collection of all molecules, because many are commercially unavailable or prohibitively costly. In this study, we established systematic pipelines to synthesize all 24 molecules through the conversions between functional groups on a core structure followed by the application to other core structures. We successfully identified all of them in Populus trichocarpa and Eucalyptus grandis, two representative species respectively from malpighiales and myrtales in angiosperms. Knowledge about monolignol metabolite chemosynthesis and identification will form the foundation for future studies.

Syntrichia ruralis: emerging model moss genome reveals a conserved and previously unknown regulator of desiccation in flowering plants.

Water scarcity, resulting from climate change, poses a significant threat to ecosystems. Syntrichia ruralis, a dryland desiccation-tolerant moss, provides valuable insights into survival of water-limited conditions. We sequenced the genome of S. ruralis, conducted transcriptomic analyses, and performed comparative genomic and transcriptomic analyses with existing genomes and transcriptomes, including with the close relative S. caninervis. We took a genetic approach to characterize the role of an S. ruralis transcription factor, identified in transcriptomic analyses, in Arabidopsis thaliana. The genome was assembled into 12 chromosomes encompassing 21 169 protein-coding genes. Comparative analysis revealed copy number and transcript abundance differences in known desiccation-associated gene families, and highlighted genome-level variation among species that may reflect adaptation to different habitats. A significant number of abscisic acid (ABA)-responsive genes were found to be negatively regulated by a MYB transcription factor (MYB55) that was upstream of the S. ruralis ortholog of ABA-insensitive 3 (ABI3). We determined that this conserved MYB transcription factor, uncharacterized in Arabidopsis, acts as a negative regulator of an ABA-dependent stress response in Arabidopsis. The new genomic resources from this emerging model moss offer novel insights into how plants regulate their responses to water deprivation.

Extinction risk predictions for the world's flowering plants to support their conservation.

More than 70% of all vascular plants lack conservation status assessments. We aimed to address this shortfall in knowledge of species extinction risk by using the World Checklist of Vascular Plants to generate the first comprehensive set of predictions for a large clade: angiosperms (flowering plants, c. 330 000 species). We used Bayesian Additive Regression Trees (BART) to predict the extinction risk of all angiosperms using predictors relating to range size, human footprint, climate, and evolutionary history and applied a novel approach to estimate uncertainty of individual species-level predictions. From our model predictions, we estimate 45.1% of angiosperm species are potentially threatened with a lower bound of 44.5% and upper bound of 45.7%. Our species-level predictions, with associated uncertainty estimates, do not replace full global, or regional Red List assessments, but can be used to prioritise predicted threatened species for full Red List assessment and fast-track predicted non-threatened species for Least Concern assessments. Our predictions and uncertainty estimates can also guide fieldwork, inform systematic conservation planning and support global plant conservation efforts and targets.

The bryophyte rhizoid-sphere microbiome responds to water deficit.

The roots of vascular plants are colonised by a multitude of microbes, which play an important role in plant health and stress resilience. Drought stress in particular is devastating for crop yield and causes major shifts in the rhizosphere microbial communities. However, the microbiome associated to the rhizoids (hereafter termed rhizoid-sphere) of the nonvascular bryophytes remains largely unexplored. Here, we use amplicon sequencing to explore the rhizoid-sphere microbiome of three bryophyte species under drought and well-watered conditions. Comparing rhizoid-sphere microbial communities associated with the two liverworts Marchantia polymorpha and Marchantia paleacea and the moss Physcomitrium patens showed characteristic differences in composition between host species and both conserved and unique changes under drought. At phylum level, these changes were similar to changes in the rhizosphere of angiosperms under drought. Furthermore, we observed strong differences in rhizoid-sphere colonisation between bryophyte species for taxa known for nitrogen fixation and plant growth promotion. Interestingly, M. polymorpha prioritised the growth of belowground organs under osmotic stress, as is the case for angiosperms under drought. Taken together, our results show interesting parallels between bryophytes and angiosperms in the relation with their rhizo(id-)sphere, suggesting evolutionary conservation among land plants in their response to drought stress.

Phylogenetic insights into the Salicaceae: The evolution of willows and beyond.

The Salicaceae includes approximately 54 genera and over 1,400 species with a cosmopolitan distribution. Members of the family are well-known for their diverse secondary plant metabolites, and they play crucial roles in tropical and temperate forest ecosystems. Phylogenetic reconstruction of the Salicaceae has been historically challenging due to the limitations of molecular markers and the extensive history of hybridization and polyploidy within the family. Our study employs whole-genome sequencing of 74 species to generate an extensive phylogeny of the Salicaceae. We generated two RAD-Seq enriched whole-genome sequence datasets and extracted two additional gene sets corresponding to the universal Angiosperms353 and Salicaceae-specific targeted-capture arrays. We reconstructed maximum likelihood-based molecular phylogenies using supermatrix and coalescent-based supertree approaches. Our fossil-calibrated phylogeny estimates that the Salicaceae originated around 128 million years ago and unravels the complex taxonomic relationships within the family. Our findings confirm the non-monophyly of the subgenus Salix s.l. and further support the merging of subgenera Chamaetia and Vetrix, both of which exhibit intricate patterns within and among different sections. Overall, our study not only enhances our understanding of the evolution of the Salicaceae, but also provides valuable insights into the complex relationships within the family.

Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications.

The tribe Astereae (Asteraceae) includes 36 subtribes and 252 genera, and is distributed worldwide in temperate and tropical regions. One of the subtribes, Celmisiinae Saldivia, has been recently circumscribed to include six genera and ca. 160 species, and is restricted to eastern Australia, New Zealand, and New Guinea. The species show an impressive range of growth habit, from small herbs and ericoid subshrubs to medium-sized trees. They live in a wide range of habitats and are often dominant in subalpine and alpine vegetation. Despite the well-supported circumscription of Celmisiinae, uncertainties have remained about their internal relationships and classification at genus and species levels. This study exploited recent advances in high-throughput sequencing to build a robust multi-gene phylogeny for the subtribe Celmisiinae. The target enrichment Angiosperms353 bait set and the hybpiper-nf and paragone-nf pipelines were used to retrieve, infer, and assemble orthologous loci from 75 taxa representing all the main putative clades within the subtribe. Because of the diploidised ploidy level in Celmisiinae, as well as missing data in the assemblies, uncertainty remains surrounding the inference of orthology detection. However, based on a variety of gene-family sets, coalescent and concatenation-based phylogenetic reconstructions recovered similar topologies. Paralogy and missing data in the gene-families caused some problems, but the estimated phylogenies were well-supported and well-resolved. The phylogenomic evidence supported Celmisiinae and three main clades: the Pleurophyllum clade (Pleurophyllum, Macrolearia and Damnamenia), mostly in the New Zealand Subantarctic Islands, Celmisia of mainland New Zealand and Australia, and Shawia (including 'Olearia pro parte' and Pachystegia) of New Zealand, Australia and New Guinea. The results presented here add to the accumulating support for the Angiosperms353 bait set as an efficient method for documenting plant diversity.

The seed morphospace, a new contribution towards the multidimensional study of angiosperm sexual reproductive biology.

BACKGROUND: The evolutionary success of flowering plants is associated with the vast diversity of their reproductive structures. Despite recent progress in understanding angiosperm-wide trends of floral structure and evolution, a synthetic view of the diversity in seed form and function across angiosperms is lacking. SCOPE: Here we present a roadmap to synthesise the diversity of seed forms in extant angiosperms, relying on the morphospace concept, i.e. a mathematical representation which relates multiple traits and describes the realised morphologies. We provide recommendations on how to broaden the range of measurable traits beyond mass, by using key morphological traits representative of the embryo, endosperm, and seed coat but also fruit attributes (e.g., dehiscence, fleshiness). These key traits were used to construct and analyse a morphospace to detect evolutionary trends and gain insight into how morphological traits relate to seed functions. Finally, we outline challenges and future research directions, combining the morphospace with macroevolutionary comparative methods to underline the drivers that gave rise to the diversity of observed seed forms. CONCLUSIONS: We conclude that this multidimensional approach has the potential, although still untapped, to improve our understanding of covariation among reproductive traits, and further elucidate angiosperm reproductive biology as a whole.

Meta-analyses of reproductive changes in angiosperm populations in response to elevation reveal a lack of global patterns.

BACKGROUND AND AIMS: Elevation is a major factor shaping plant populations on a global scale. At the same time, reproductive traits play a major role in plant fitness. With increasing altitude and increasingly harsh conditions, decreases in pollinator visitation rates, sexual investment, seed set, and heterozygosity (due to increased selfing) are expected. In response, selection and/or phenotypic plasticity could lead to an increase in plants' floral displays to increase their attractiveness to pollinators and compensates for the negative fitness impacts of reduced pollinator activity. A large body of literature tests these hypotheses at the among-species level, but empirical evidence at the population level (i.e., wihin-species), where adaptive change may occur, is still limited to species-specific studies. Unravelling the global patterns of change in the reproductive traits, flower visitation rates and heterozygosity of plant populations across variable environmental conditions, especially climate can help us to understand how species are able to cope with shifting conditions associated with global change, particularly in mountains. Here, we used meta-analytic approaches to assess the reproductive changes of plant populations in response to elevation on a global scale. METHODS: We used a data set with 243 paired populations of plants at 'lower' and 'higher' elevations, spanning an elevation range of 0-4380 m asl and taken from 121 angiosperm species and 115 published studies. We analyzed changes in flower number, size and longevity, pollen production, flower visitation rate, seed set and expected heterozygosity.We then tested whether the observed patterns for each trait were dependent upon plant phylogeny and various ecogeographical factors and species traits. KEY RESULTS: We found no evidence of elevation having a global effect on the reproductive traits of angiosperm populations. This null global pattern was not affected by geograph or phylogenetics. CONCLUSIONS: Our results suggest that changes in reproductive traits, flower visitation rates, and heterozygosity in plant populations across elevations are specific to each species and ecosystem. Hence, macroevolutionary (across species) and macroecological patterns of elevation of plant reproduction reported previously are apparently not simply the outcome of microevolutionary changes (within species). This apparent specificity of response across plant species poses difficulties in predicting the effects of global changes and, specifically, climatic changes, on the fate of plant species, populations, and communities.

Floral freezing tolerance is tied to flowering time in North American woody plant species.

BACKGROUND AND AIMS: As winter and spring temperatures continue to increase, the timing of flowering and leaf out is advancing in many seasonally cold regions. This advancement could put plants that flower early in the spring at risk of decreased reproduction in years when there are late freeze events. Unfortunately, relatively little is known about floral freezing tolerance in forest communities. In this study, we examined the impact of freezing temperatures on the flowers of woody plants in a region where there is rapid winter warming in North America. METHODS: We subjected the flowers of twenty-five woody species to a hard (-5ºC) and a light freeze (0ºC). We assessed tissue damage using electrolyte leakage. In a subset of species, we also examined the impact of a hard freeze on pollen tube growth. To determine if the vulnerability of flowers to freezing damage relates to flowering time and to examine the responsiveness of flowering time to spring temperature, we recorded the date of first flower for our study species for three years. KEY RESULTS AND CONCLUSIONS: Across species, we found that floral freezing tolerance was strongly tied to flowering time with the highest freezing tolerance occurring in plants that bloomed earlier in the year. We hypothesize that these early blooming species are unlikely to be impacted by a false spring. Instead, the most vulnerable species to a false spring should be those that bloom later in the season. The flowering time in these species is also more sensitive to temperature, putting them at a great risk of experiencing a false spring. Ultimately, floral damage in one year will not have a large impact on species fitness, but if false springs become more frequent, there could be long-term impacts on reproduction of vulnerable species.

Centromere drive may propel the evolution of chromosome and genome size in plants.

BACKGROUND: Genome size is influenced by natural selection and genetic drift acting on variations from polyploidy and repetitive DNA sequences. We hypothesized that centromere drive, where centromeres compete for inclusion in the functional gamete during meiosis, may also affect genome and chromosome size. This competition occurs in asymmetric meiosis, where only one of the four meiotic products becomes a gamete. If centromere drive influences chromosome size evolution, it may also impact post-polyploid diploidization, where a polyploid genome is restructured to function more like a diploid through chromosomal rearrangements, including fusions. We tested if plant lineages with asymmetric meiosis exhibit faster chromosome size evolution compared to those with only symmetric meiosis, which lack centromere drive as all four meiotic products become gametes. We also examined if positive selection on centromeric histone H3 (CENH3), a protein that can suppress centromere drive, is more frequent in these asymmetric lineages. METHODS: We analyzed plant groups with different meiotic modes: asymmetric in gymnosperms and angiosperms, and symmetric in bryophytes, lycophytes, and ferns. We selected species based on available CENH3 gene sequences and chromosome size data. Using Ornstein-Uhlenbeck evolutionary models and phylogenetic regressions, we assessed the rates of chromosome size evolution and the frequency of positive selection on CENH3 in these clades. RESULTS: Our analyses showed that clades with asymmetric meiosis have a higher frequency of positive selection on CENH3 and increased rates of chromosome size evolution compared to symmetric clades. CONCLUSIONS: Our findings support the hypothesis that centromere drive accelerates chromosome and genome size evolution, potenatially also influencing the process of post-polyploid diploidization. We propose a model which in a single famework helps explain the stability of chromosome size in symmetric lineages (bryophytes, lycophytes, and ferns) and its variability in asymmetric lineages (gymnosperms and angiosperms), providing a foundation for future research in plant genome evolution.

Fire effects on pollination and plant reproduction: a quantitative review.

BACKGROUND AND AIMS: Fire may favour plant flowering by opening the vegetation and increasing abiotic resource availability. Increased floral display size can attract more pollinators and increase the absolute fruit and seed production immediately after the fire. However, anthropogenic increases in fire frequency may alter these responses. We aim to assess the effects of fire on pollination and reproductive success of plants at the global scale. METHODS: We performed a systematic literature review and meta-analyses to examine overall fire effects as well as different fire parameters on pollination and on plant reproduction. We also explored to what extent the responses vary among pollinators, pollination vectors, plant regeneration strategies, compatibility systems, vegetation types and biomes. KEY RESULTS: Most studies were conducted in fire-prone ecosystems. Overall, single fires increased pollination and plant reproduction but this effect was overridden by recurrent fires. Floral visitation rates of pollinators were enhanced immediately following a wildfire, and especially in bee-pollinated plants. Fire increased the absolute production of fruits or seeds but not the fruit or seed set. The reproductive benefits were mostly observed in wind-pollinated (graminoids), herbaceous and resprouter species. Finally, fire effects on pollination were positively correlated with fire effects on plant reproductive success. CONCLUSIONS: Fire has a central role in pollination and plant sexual reproduction in fire-prone ecosystems. The increase in the absolute production of fruits and seeds suggests that fire benefits on plant reproduction are likely driven by increased abiotic resources and the consequent floral display size. However, reproduction efficiency, as measured by fruit or seed set, does not increase with fire. In contrast, when assessed on the same plant simultaneously, fire effects on pollination are translated into reproduction. Increased fire frequency due to anthropogenic changes can alter the nature of the response to fire.

Cretaceous chloranthoids: early prominence, extinct diversity and missing links.

BACKGROUND: The Chloranthaceae comprise four extant genera (Hedyosmum, Ascarina, Chloranthus and Sarcandra), all with simple flowers. Molecular phylogenetics indicates that the Chloranthaceae diverged very early in angiosperm evolution, although how they are related to eudicots, magnoliids, monocots and Ceratophyllum is uncertain. Fossil pollen similar to that of Ascarina and Hedyosmum has long been recognized in the Early Cretaceous, but over the last four decades evidence of extinct Chloranthaceae based on other types of fossils has expanded dramatically and contributes significantly to understanding the evolution of the family. SCOPE: Studies of fossils from the Cretaceous, especially mesofossils of Early Cretaceous age from Portugal and eastern North America, recognized diverse flowers, fruits, seeds, staminate inflorescences and stamens of extinct chloranthoids. These early chloranthoids include forms related to extant Hedyosmum and also to the Ascarina, Chloranthus and Sarcandra clade. In the Late Cretaceous there are several occurrences of distinctive fossil androecia related to extant Chloranthus. The rich and still expanding Cretaceous record of Chloranthaceae contrasts with a very sparse Cenozoic record, emphasizing that the four extant genera are likely to be relictual, although speciation within the genera might have occurred in relatively recent times. In this study, we describe three new genera of Early Cretaceous chloranthoids and summarize current knowledge on the extinct diversity of the group. CONCLUSIONS: The evolutionary lineage that includes extant Chloranthaceae is diverse and abundantly represented in Early Cretaceous mesofossil floras that provide some of the earliest evidence of angiosperm reproductive structures. Extinct chloranthoids, some of which are clearly in the Chloranthaceae crown group, fill some of the morphological gaps that currently separate the extant genera, help to illuminate how some of the unusual features of extant Chloranthaceae evolved and suggest that Chloranthaceae are of disproportionate importance for a more refined understanding of ecology and phylogeny of early angiosperm diversification.

Species-tree topology impacts the inference of ancient whole-genome duplications across the angiosperm phylogeny.

PREMISE: The history of angiosperms is marked by repeated rounds of ancient whole-genome duplications (WGDs). Here we used state-of-the-art methods to provide an up-to-date view of the distribution of WGDs in the history of angiosperms that considers both uncertainty introduced by different WGD inference methods and different underlying species-tree hypotheses. METHODS: We used the distribution synonymous divergences (Ks) of paralogs and orthologs from transcriptomic and genomic data to infer and place WGDs across two hypothesized angiosperm phylogenies. We further tested these WGD hypotheses with syntenic inferences and Bayesian models of duplicate gene gain and loss. RESULTS: The predicted number of WGDs in the history of angiosperms (~170) based on the current taxon sampling is largely similar across different inference methods, but varies in the precise placement of WGDs on the phylogeny. Ks-based methods often yield alternative hypothesized WGD placements due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation. However, errors in species-tree inference can still produce spurious WGD hypotheses, regardless of method used. CONCLUSIONS: Here we showed that different WGD inference methods largely agree on an average of 3.5 WGD in the history of individual angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the WGD inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods.

Tangled webs and spider-flowers: Phylogenomics, biogeography, and seed morphology inform the evolutionary history of Cleomaceae.

PREMISE: Cleomaceae is an important model clade for studies of evolutionary processes including genome evolution, floral form diversification, and photosynthetic pathway evolution. Diversification and divergence patterns in Cleomaceae remain tangled as research has been restricted by its worldwide distribution, limited genetic sampling and species coverage, and a lack of definitive fossil calibration points. METHODS: We used target sequence capture and the Angiosperms353 probe set to perform a phylogenetic study of Cleomaceae. We estimated divergence times and biogeographic analyses to explore the origin and diversification of the family. Seed morphology across extant taxa was documented with multifocal image-stacking techniques and morphological characters were extracted, analyzed, and compared to fossil records. RESULTS: We recovered a well-supported and resolved phylogenetic tree of Cleomaceae generic relationships that includes 236 (~86%) species. We identified 11 principal clades and confidently placed Cleomella as sister to the rest of the family. Our analyses suggested that Cleomaceae and Brassicaceae diverged ~56 mya, and Cleomaceae began to diversify ~53 mya in the Palearctic and Africa. Multiple transatlantic disjunct distributions were identified. Seeds were imaged from 218 (~80%) species in the family and compared to all known fossil species. CONCLUSIONS: Our results represent the most comprehensive phylogenetic study of Cleomaceae to date. We identified transatlantic disjunctions and proposed explanations for these patterns, most likely either long-distance dispersals or contractions in latitudinal distributions caused by climate change over geological timescales. We found that seed morphology varied considerably but mostly mirrored generic relationships.