ORCID Profile
0000-0001-8305-3236
Current Organisation
Royal Botanic Gardens and Domain Trust
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Phylogeny and Comparative Analysis | Molecular Evolution | Environmental Science and Management | Conservation and Biodiversity | Evolutionary Biology
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Flora, Fauna and Biodiversity at Regional or Larger Scales |
Related Links
Publications
Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C
Publisher: Cold Spring Harbor Laboratory
Date: 02-06-2021
DOI: 10.1101/2021.06.02.444084
Abstract: Telopea speciosissima, the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for T. speciosissima . Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8 % of Embryophyta BUSCOs complete. We present a new method in Diploidocus ( limsuite/diploidocus ) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer ( limsuite/depthsizer ), for genome size estimation from the read depth of single copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2 n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA ( CYC ) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 ‘Duplicated’ BUSCO genes suggest almost all are real duplications, increasing confidence in protein family analysis using annotated protein-coding genes, and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level T. speciosissima reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.
Open Science principles for accelerating trait-based science across the Tree of Life
Publisher: Springer Science and Business Media LLC
Date: 17-02-2020
The AusTraits Plant Dictionary
Publisher: Cold Spring Harbor Laboratory
Date: 18-06-2023
DOI: 10.1101/2023.06.16.545047
Abstract: Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. Reanalysis of data from a single database, or analyses that integrate data across multiple databases, can only occur if researchers are confident the trait concepts are consistent within and across sources. The lack of a unified, comprehensive resource for plant trait definitions has previously limited the utility of trait databases. Here we describe the AusTraits Plant Dictionary (APD), which extends the trait definitions included in the new trait database AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description addition of trait meta-data and publication in both human and machine-readable forms. Trait definitions include keywords, references and links to related trait concepts in other databases, and the traits are grouped into a hierarchy for easy searching. As well as improving the usability of AusTraits, the Dictionary will foster the integration of trait data across global and regional plant trait databases.
Early diversifications of angiosperms and their insect pollinators: were they unlinked?
Publisher: Elsevier BV
Date: 09-2022
DOI: 10.1016/J.TPLANTS.2022.04.004
Abstract: The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the notion that early ersifications of angiosperms and insects were inextricably linked. In this article, we examine (i) the discrepancies between dates of emergence for angiosperms and major clades of insects (ii) the long history of gymnosperm-insect pollination modes, which likely shaped early angiosperm-insect pollination mutualisms and (iii) how the K-Pg (Cretaceous-Paleogene) mass extinction event was vital in propelling modern angiosperm-insect mutualisms. We posit that the early ersifications of angiosperms and their insect pollinators were largely decoupled until the end of the Cretaceous.
Phylogenomics of the Major Trop ca Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes
Publisher: Frontiers Media SA
Date: 09-01-2019
Climate shapes community flowering periods across biomes
Publisher: Wiley
Date: 11-05-2022
DOI: 10.1111/JBI.14375
Abstract: Climate shapes the composition and function of plant communities globally, but it remains unclear how this influence extends to floral traits. Flowering phenology, or the time period in which a species flowers, has well‐studied relationships with climatic signals at the species level but has rarely been explored at a cross‐community and continental scale. Here, we characterise the distribution of flowering periods (months of flowering) across continental plant communities encompassing six biomes, and determine the influence of climate on community flowering period lengths. Australia. Flowering plants. We combined plant composition and abundance data from 629 standardised floristic surveys (AusPlots) with data on flowering period from the AusTraits database and additional primary literature for 2983 species. We assessed abundance‐weighted community mean flowering periods across biomes and tested their relationship with climatic annual means and the predictability of climate conditions using regression models. Combined, temperature and precipitation (annual mean and predictability) explain 29% of variation in continental community flowering period. Plant communities with higher mean temperatures and lower mean precipitation have longer mean flowering periods. Moreover, plant communities in climates with predictable temperatures and, to a lesser extent, predictable precipitation have shorter mean flowering periods. Flowering period varies by biome, being longest in deserts and shortest in alpine and montane communities. For instance, desert communities experience low and unpredictable precipitation and high, unpredictable temperatures and have longer mean flowering periods, with desert species typically flowering at any time of year in response to rain. Current climate conditions shape flowering periods across biomes, with implications for phenology under climate change. Shifts in flowering periods across climatic gradients reflect changes in plant strategies, affecting patterns of plant growth and reproduction as well as the availability of floral resources for pollinators across the landscape.
Phylogeny, Molecular and Fossil Dating, and Biogeographic History of Annonaceae and Myristicaceae (Magnoliales)
Publisher: University of Chicago Press
Date: 07-2004
DOI: 10.1086/421068
Contrasted patterns of hyperdiversification in Mediterranean hotspots
Publisher: Proceedings of the National Academy of Sciences
Date: 06-01-2009
Abstract: Dating the Tree of Life has now become central to relating patterns of bio ersity to key processes in Earth history such as plate tectonics and climate change. Regions with a Mediterranean climate have long been noted for their exceptional species richness and high endemism. How and when these biota assembled can only be answered with a good understanding of the sequence of ergence times for each of their components. A critical aspect of dating by using molecular sequence ergence is the incorporation of multiple suitable age constraints. Here, we show that only rigorous phylogenetic analysis of fossil taxa can lead to solid calibration and, in turn, stable age estimates, regardless of which of 3 relaxed clock-dating methods is used. We find that Proteaceae, a model plant group for the Mediterranean hotspots of the Southern Hemisphere with a very rich pollen fossil record, ersified under higher rates in the Cape Floristic Region and Southwest Australia than in any other area of their total distribution. Our results highlight key differences between Mediterranean hotspots and indicate that Southwest Australian biota are the most phylogenetically erse but include numerous lineages with low ersification rates.
Angiosperm phylogeny based on <011>matK sequence information
Publisher: Wiley
Date: 12-2003
Abstract: Plastid matK gene sequences for 374 genera representing all angiosperm orders and 12 genera of gymnosperms were analyzed using parsimony (MP) and Bayesian inference (BI) approaches. Traditionally, slowly evolving genomic regions have been preferred for deep-level phylogenetic inference in angiosperms. The matK gene evolves approximately three times faster than the widely used plastid genes rbcL and atpB. The MP and BI trees are highly congruent. The robustness of the strict consensus tree supercedes all in idual gene analyses and is comparable only to multigene-based phylogenies. Of the 385 nodes resolved, 79% are supported by high jackknife values, averaging 88%. Amborella is sister to the remaining angiosperms, followed by a grade of Nymphaeaceae and Austrobaileyales. Bayesian inference resolves Amborella + Nymphaeaceae as sister to the rest, but with weak (0.42) posterior probability. The MP analysis shows a trichotomy sister to the Austrobaileyales representing eumagnoliids, monocots + Chloranthales, and Ceratophyllum + eudicots. The matK gene produces the highest internal support yet for basal eudicots and, within core eudicots, resolves a crown group comprising Berberidopsidaceae/Aextoxicaceae, Santalales, and Caryophyllales + asterids. Moreover, matK sequences provide good resolution within many angiosperm orders. Combined analyses of matK and other rapidly evolving DNA regions with available multigene data sets have strong potential to enhance resolution and internal support in deep level angiosperm phylogenetics and provide additional insights into angiosperm evolution.
Photographs as an essential biodiversity resource: drivers of gaps in the vascular plant photographic record
Publisher: Wiley
Date: 13-03-2023
DOI: 10.1111/NPH.18813
Abstract: The photographic record is increasingly becoming an important bio ersity resource for primary research and conservation monitoring. However, globally, there are important gaps in this record even in relatively well‐researched floras. To quantify the gaps in the Australian native vascular plant photographic record, we systematically surveyed 33 sources of well‐curated species photographs, assembling a list of species with accessible and verifiable photographs, as well as the species for which this search failed. Of 21 077 Australian native species, 3715 lack a verifiable photograph across our 33 surveyed resources. There are three major geographic hotspots of unphotographed species in Australia, all far from current population centres. Many unphotographed species are small in stature or uncharismatic, and many are also recently described. The large number of recently described species without accessible photographs was surprising. There are longstanding efforts in Australia to organise the plant photographic record, but in the absence of a global consensus to treat photographs as an essential bio ersity resource, this has not become common practice. Many recently described species are small‐range endemics and some have special conservation status. Completing the botanical photographic record across the globe will facilitate a virtuous feedback loop of more efficient identification, monitoring and conservation.
The ancestral flower of angiosperms and its early diversification
Publisher: Springer Science and Business Media LLC
Date: 08-2017
DOI: 10.1038/NCOMMS16047
Abstract: Recent advances in molecular phylogenetics and a series of important palaeobotanical discoveries have revolutionized our understanding of angiosperm ersification. Yet, the origin and early evolution of their most characteristic feature, the flower, remains poorly understood. In particular, the structure of the ancestral flower of all living angiosperms is still uncertain. Here we report model-based reconstructions for ancestral flowers at the deepest nodes in the phylogeny of angiosperms, using the largest data set of floral traits ever assembled. We reconstruct the ancestral angiosperm flower as bisexual and radially symmetric, with more than two whorls of three separate perianth organs each (undifferentiated tepals), more than two whorls of three separate stamens each, and more than five spirally arranged separate carpels. Although uncertainty remains for some of the characters, our reconstruction allows us to propose a new plausible scenario for the early ersification of flowers, leading to new testable hypotheses for future research on angiosperms.
Early Eocene fossil plants from the Mwadui kimberlite pipe, Tanzania
Publisher: Elsevier BV
Date: 09-2013
Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C
Publisher: Wiley
Date: 11-01-2022
Abstract: Telopea speciosissima , the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome‐level genome for T . speciosissima . Combining Oxford Nanopore long‐reads, 10x Genomics Chromium linked‐reads and Hi‐C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8% of Embryophyta BUSCOs “Complete”. We present a new method in Diploidocus ( limsuite/diploidocus ) for classifying, curating and QC‐filtering scaffolds, which combines read depths, k ‐mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer ( limsuite/depthsizer ), for genome size estimation from the read depth of single‐copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1% of the assembly, conforming to the expected number of chromosomes (2 n = 22). Genome annotation predicted 40,158 protein‐coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA ( CYC ) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 “Duplicated” BUSCO genes using a new tool, DepthKopy ( limsuite/depthkopy ), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome‐level T . speciosissima reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.
Profile of a flower: How rates of morphological evolution drive floral diversification in Ericales and angiosperms
Publisher: Wiley
Date: 08-2023
DOI: 10.1002/AJB2.16213
Abstract: Recent studies of floral disparity in the asterid order Ericales have shown that flowers vary strongly among families and that disparity is unequally distributed between the three flower modules (perianth, androecium, gynoecium). However, it remains unknown whether these patterns are driven by heterogeneous rates of morphological evolution or other factors. Here, we compiled a data set of 33 floral characters scored for 414 species of Ericales s led from 346 genera and all 22 families. We conducted ancestral state reconstructions using an equal‐rates Markov model for each character. We estimated rates of morphological evolution for Ericales and for a separate angiosperm‐wide data set of 19 characters and 792 species, creating “rate profiles” for Ericales, angiosperms, and major angiosperm subclades. We compared morphological rates among flower modules within each data set separately and between data sets, and we compared rates among angiosperm subclades using the angiosperm data set. The androecium exhibits the highest evolutionary rates across most characters, whereas most perianth and gynoecium characters evolve more slowly in both Ericales and angiosperms. Both high and low rates of morphological evolution can result in high floral disparity in Ericales. Analyses of an angiosperm‐wide floral data set reveal that this pattern appears to be conserved across most major angiosperm clades. Elevated rates of morphological evolution in the androecium of Ericales may explain the higher disparity reported for this floral module. Comparing rates of morphological evolution through rate profiles proves to be a powerful tool in understanding floral evolution.
Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa
Publisher: Oxford University Press (OUP)
Date: 10-09-2016
How (much) do flowers vary? Unbalanced disparity among flower functional modules and a mosaic pattern of morphospace occupation in the order Ericales
Publisher: The Royal Society
Date: 05-04-2017
Abstract: The staggering ersity of angiosperms and their flowers has fascinated scientists for centuries. However, the quantitative distribution of floral morphological ersity (disparity) among lineages and the relative contribution of functional modules (perianth, androecium and gynoecium) to total floral disparity have rarely been addressed. Focusing on a major angiosperm order (Ericales), we compiled a dataset of 37 floral traits scored for 381 extant species and nine fossils. We conducted morphospace analyses to explore phylogenetic, temporal and functional patterns of disparity. We found that the floral morphospace is organized as a continuous cloud in which most clades occupy distinct regions in a mosaic pattern, that disparity increases with clade size rather than age, and that fossils fall in a narrow portion of the space. Surprisingly, our study also revealed that among functional modules, it is the androecium that contributes most to total floral disparity in Ericales. We discuss our findings in the light of clade history, selective regimes as well as developmental and functional constraints acting on the evolution of the flower and thereby demonstrate that quantitative analyses such as the ones used here are a powerful tool to gain novel insights into the evolution and ersity of flowers.
Diversification of Dombeyoideae (Malvaceae) in the Mascarenes: Old Taxa on Young Islands?
Publisher: University of Chicago Press
Date: 03-2015
DOI: 10.1086/679350
More than sixty origins of pantoporate pollen in angiosperms
Publisher: Wiley
Date: 12-2017
DOI: 10.3732/AJB.1700289
Abstract: Apertures in pollen grains are key structures of the wall, involved in pollen tube germination and exchanges with the environment. Aperture types in angiosperms are erse, but pollen with one and three apertures (including monosulcate and tricolpate, respectively) are the two most common types. Here, we investigate the phylogenetic distribution in angiosperms of pollen with many round, scattered apertures called pantoporate pollen. We constructed a morphological data set with species producing pantoporate pollen and representative angiosperm species with other pollen types, s led from every angiosperm order, with a total of 1260 species distributed in 330 families. This data set was analyzed with parsimony to characterize the phylogenetic distribution of pantoporate pollen in angiosperms. We show that pantoporate pollen is distributed throughout most of the angiosperm tree, including early erging angiosperms, monocots, and eudicots. However, this pollen type is usually restricted to a few species in a given group, and is seldom fixed at large taxonomical scales, with a few notable exceptions. Pantoporate pollen evolved many times during angiosperm history, but the persistence of this morphology in the long term is infrequent. This distribution pattern could indicate conflicting short-term and long-term selective pressures, pantoporate pollen being selected in the short run, but eliminated in the long run. Biological hypotheses supporting this scenario are discussed, in the context of both theoretical and empirical data on pollen biology.
Perianth symmetry changed at least 199 times in angiosperm evolution
Publisher: Wiley
Date: 10-2016
DOI: 10.12705/655.1
Presence in Mediterranean hotspots and floral symmetry affect speciation and extinction rates in Proteaceae
Publisher: Wiley
Date: 23-12-2015
DOI: 10.1111/NPH.13244
Abstract: The Proteaceae is a large angiosperm family displaying the common pattern of uneven distribution of species among genera. Previous studies have shown that this disparity is a result of variation in ersification rates across lineages, but the reasons for this variation are still unclear. Here, we tested the impact of floral symmetry and occurrence in Mediterranean climate regions on speciation and extinction rates in the Proteaceae. A rate shift analysis was conducted on dated genus‐level phylogenetic trees of the Proteaceae. Character‐dependent analyses were used to test for differences in ersification rates between actinomorphic and zygomorphic lineages and between lineages located within or outside Mediterranean climate regions. The rate shift analysis identified 5–10 major ersification rate shifts in the Proteaceae tree. The character‐dependent analyses showed that speciation rates, extinction rates and net ersification rates of the Proteaceae were significantly higher for lineages occurring in Mediterranean hotspots. Higher speciation and extinction rates were also detected for zygomorphic species, but net ersification rates appeared to be similar in actinomorphic and zygomorphic Proteaceae. Presence in Mediterranean hotspots favors Proteaceae ersification. In contrast with observations at the scale of angiosperms, floral symmetry is not a trait that strongly influences their evolutionary success.
Key questions and challenges in angiosperm macroevolution
Publisher: Wiley
Date: 25-03-2018
DOI: 10.1111/NPH.15104
Abstract: Contents Summary 1170 I. Introduction 1170 II. Six key questions 1172 III. Three key challenges 1177 IV. Conclusions 1181 Acknowledgements 1182 References 1183 SUMMARY: The origin and rapid ersification of angiosperms (flowering plants) represent one of the most intriguing topics in evolutionary biology. Despite considerable progress made in complementary fields over the last two decades (paleobotany, phylogenetics, ecology, evo-devo, genomics), many important questions remain. For instance, what has been the impact of mass extinctions on angiosperm ersification? Are the angiosperms an adaptive radiation? Has morphological evolution in angiosperms been gradual or pulsed? We propose that the recent and ongoing revolution in macroevolutionary methods provides an unprecedented opportunity to explore long-standing questions that probably hold important clues to understand present-day bio ersity. We present six key questions that explore the origin and ersification of angiosperms. We also identify three key challenges to address these questions: (1) the development of new integrative models that include ersification, multiple intrinsic and environmental traits, biogeography and the fossil record all at once, whilst accounting for s ling bias and heterogeneity of macroevolutionary processes through time and among lineages (2) the need for large and standardized synthetic databases of morphological variation and (3) continuous effort on s ling the fossil record, but with a revolution in current paleobotanical practice.
Myristicaceae
Publisher: Springer Berlin Heidelberg
Date: 1993
The floral morphospace – a modern comparative approach to study angiosperm evolution
Publisher: Wiley
Date: 18-08-2014
DOI: 10.1111/NPH.12969
Abstract: Morphospaces are mathematical representations used for studying the evolution of morphological ersity and for the evaluation of evolved shapes among theoretically possible ones. Although widely used in zoology, they – with few exceptions – have been disregarded in plant science and in particular in the study of broad‐scale patterns of floral structure and evolution. Here we provide basic information on the morphospace approach we review earlier morphospace applications in plant science and as a practical ex le, we construct and analyze a floral morphospace. Morphospaces are usually visualized with the help of ordination methods such as principal component analysis ( PCA ) or nonmetric multidimensional scaling ( NMDS ). The results of these analyses are then coupled with disparity indices that describe the spread of taxa in the space. We discuss these methods and apply modern statistical tools to the first and only angiosperm‐wide floral morphospace published by Stebbins in 1951. Despite the incompleteness of Stebbins’ original dataset, our analyses highlight major, angiosperm‐wide trends in the ersity of flower morphology and thereby demonstrate the power of this previously neglected approach in plant science.
Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae
Publisher: Frontiers Media SA
Date: 25-01-2019
Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution
Publisher: Oxford University Press (OUP)
Date: 11-09-2023
Evolutionary radiations of Proteaceae are triggered by the interaction between traits and climates in open habitats
Publisher: Wiley
Date: 03-06-2016
DOI: 10.1111/GEB.12481
Estimating divergence times and ancestral breeding systems inFicusand Moraceae
Publisher: Oxford University Press (OUP)
Date: 07-09-2018
DOI: 10.1093/AOB/MCY159
A Seed Related to Myristicaceae in the Early Eocene of Southern England
Publisher: American Society of Plant Taxonomists
Date: 10-2008
Characterization of CYCLOIDEA-like genes in Proteaceae, a basal eudicot family with multiple shifts in floral symmetry
Publisher: Oxford University Press (OUP)
Date: 26-12-2017
DOI: 10.1093/AOB/MCW219
Fossil calibration of Magnoliidae, an ancient lineage of angiosperms
Publisher: Coquina Press
Date: 2015
DOI: 10.26879/435
Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms
Publisher: Springer Science and Business Media LLC
Date: 21-06-2018
DOI: 10.1038/S41598-018-27750-1
Abstract: Ancestral state reconstruction is an important tool to study morphological evolution and often involves estimating transition rates among character states. However, various factors, including taxonomic scale and s ling density, may impact transition rate estimation and indirectly also the probability of the state at a given node. Here, we test the influence of rate heterogeneity using maximum likelihood methods on five binary perianth characters, optimized on a phylogenetic tree of angiosperms including 1230 species s led from all families. We compare the states reconstructed by an equal-rate (Mk1) and a two-rate model (Mk2) fitted either with a single set of rates for the whole tree or as a partitioned model, allowing for different rates on five partitions of the tree. We find strong signal for rate heterogeneity among the five sub isions for all five characters, but little overall impact of the choice of model on reconstructed ancestral states, which indicates that most of our inferred ancestral states are the same whether heterogeneity is accounted for or not.
Five major shifts of diversification through the long evolutionary history of Magnoliidae (angiosperms)
Publisher: Springer Science and Business Media LLC
Date: 18-03-2015
Fossil berries reveal global radiation of the nightshade family by the early Cenozoic
Publisher: Wiley
Date: 07-04-2023
DOI: 10.1111/NPH.18904
Abstract: Fossil discoveries can transform our understanding of plant ersification over time and space. Recently described fossils in many plant families have pushed their known records farther back in time, pointing to alternative scenarios for their origin and spread. Here, we describe two new Eocene fossil berries of the nightshade family (Solanaceae) from the Esmeraldas Formation in Colombia and the Green River Formation in Colorado (USA). The placement of the fossils was assessed using clustering and parsimony analyses based on 10 discrete and five continuous characters, which were also scored in 291 extant taxa. The Colombian fossil grouped with members of the tomatillo subtribe, and the Coloradan fossil aligned with the chili pepper tribe. Along with two previously reported early Eocene fossils from the tomatillo genus, these findings indicate that Solanaceae were distributed at least from southern South America to northwestern North America by the early Eocene. Together with two other recently discovered Eocene berries, these fossils demonstrate that the erse berry clade and, in turn, the entire nightshade family, is much older and was much more widespread in the past than previously thought.
Publisher Correction: Open Science principles for accelerating trait-based science across the Tree of Life
Publisher: Springer Science and Business Media LLC
Date: 09-03-2020
Phylogenetic analysis of fossil flowers using an angiosperm‐wide data set: proof‐of‐concept and challenges ahead
Publisher: Wiley
Date: 10-2020
DOI: 10.1002/AJB2.1538
Pollen diversity and evolution in Proteoideae (Proteales : Proteaceae)
Publisher: American Society of Plant Taxonomists
Date: 04-2007
Macroevolutionary Patterns of Flowering Plant Speciation and Extinction
Publisher: Annual Reviews
Date: 29-04-2018
DOI: 10.1146/ANNUREV-ARPLANT-042817-040348
Abstract: Species ersity is remarkably unevenly distributed among flowering plant lineages. Despite a growing toolbox of research methods, the reasons underlying this patchy pattern have continued to perplex plant biologists for the past two decades. In this review, we examine the present understanding of transitions in flowering plant evolution that have been proposed to influence speciation and extinction. In particular, ploidy changes, transitions between tropical and nontropical biomes, and shifts in floral form have received attention and have offered some surprises in terms of which factors influence speciation and extinction rates. Mating systems and dispersal characteristics once predominated as determining factors, yet recent evidence suggests that these changes are not as influential as previously thought or are important only when paired with range shifts. Although range extent is an important correlate of speciation, it also influences extinction and brings an applied focus to ersification research. Recent studies that find that past ersification can predict present-day extinction risk open an exciting avenue for future research to help guide conservation prioritization.
Subfamilial and tribal relationships of Ranunculaceae: evidence from eight molecular markers
Publisher: Springer Science and Business Media LLC
Date: 09-02-2016
A practical guide to molecular dating
Publisher: Elsevier BV
Date: 08-2013
Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes
Publisher: Cold Spring Harbor Laboratory
Date: 11-10-2018
DOI: 10.1101/440925
Abstract: Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 109 genera and ca. 2450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis s ling 65 genera and a species level analysis of tribe Piptostigmateae s ling 29 species with multiple in iduals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two s les from herbarium dried leaves. Our kit targets 469 exons (364 653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked eaually well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia . We also reconstructed a well resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.
Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil-Rich Group: The Case of Nothofagus (Fagales)
Publisher: Oxford University Press (OUP)
Date: 26-12-2011
Abstract: Although temporal calibration is widely recognized as critical for obtaining accurate ergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using "early but risky" fossil constraints in addition to "safe but late" constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of ergence times. For ex le, our estimates for the crown group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.
Increased sampling of both genes and taxa improves resolution of phylogenetic relationships within Magnoliidae, a large and early-diverging clade of angiosperms
Publisher: Elsevier BV
Date: 2014
DOI: 10.1016/J.YMPEV.2013.09.010
Abstract: Magnoliidae have been supported as a clade in the majority of large-scale molecular phylogenetic studies of angiosperms. This group consists of about 10,000 species assigned to 20 families and four orders, Canellales, Piperales, Laurales, and Magnoliales. Some relationships among the families are still largely debated. Here, we reconstruct the phylogenetic relationships of Magnoliidae as a whole, s ling 199 species (representing ca. 75% of genera) and 12 molecular markers from the three genomes (plastid atpB, matK, trnL intron, trnL-trnF spacer, ndhF, rbcL mitochondrial atp1, matR, mtSSU, mtLSU nuclear 18s rDNA, 26S rDNA). Maximum likelihood, Bayesian and maximum parsimony analyses yielded congruent trees, with good resolution and high support values for higher-level relationships. This study further confirms, with greater levels of support, two major clades in Magnoliidae: Canellales+Piperales and Laurales+Magnoliales. Relationships among the 20 families are, in general, well resolved and supported. Several previously ambiguous relationships are now well supported. For instance, the Aristolochiaceae s.l. (incl. Asaroideae, Aristolochioideae, and Lactoris) are monophyletic with high support when Hydnoraceae are excluded. The latter family was not included in most previous studies because of the lack of suitable plastid sequences, a consequence of the parasitic habit of its species. Here, we confirm that it belongs in Aristolochiaceae. Our analyses also provide moderate support for a sister group relationship between Lauraceae and Monimiaceae. Conversely, the exact position of Magnoliaceae remains very difficult to determine. This study provides a robust phylogenetic background to address the evolutionary history of an important and highly erse clade of early- erging angiosperms.
Phylogenomics of Brosimum (Moraceae) and allied genera, including a revised subgeneric system
Publisher: Wiley
Date: 19-04-2021
DOI: 10.1002/TAX.12503
Abstract: We present a phylogenomic study of Brosimum (Moraceae) and the allied genera Trymatococcus and Helianthostylis , with near‐complete taxon s ling. Distributed from Mexico and the Greater Antilles to the Amazon, this clade contains the underutilized crop ramón (bread nut) ( Brosimum alicastrum ) as well as other species valued for timber or medicinal uses. Target enrichment for 333 genes produced a well‐resolved phylogenetic tree and showed that Trymatococcus and Helianthostylis are nested within Brosimum . We present a revised subgeneric classification of Brosimum (19 spp.) based on phylogenetic and morphological considerations, including the reduction of Trymatococcus and Helianthostylis to subgenera. The monophyletic subgenera can be diagnosed based on stipule, pistillode, and cotyledon synapomorphies. Divergence date estimates suggest a Miocene origin for Brosimum , and ancestral area reconstruction indicated that all four subgenera originated and initially ersified in Amazonia before dispersing into other parts of South and Central America.
Integrating Fossil Flowers into the Angiosperm Phylogeny using a Total Evidence Approach
Publisher: Cold Spring Harbor Laboratory
Date: 19-02-2022
DOI: 10.1101/2022.02.17.480913
Abstract: Fossil flowers are essential to infer past angiosperm evolutionary processes. The assignment of fossil flowers to extant clades has traditionally relied on morphological similarity and on apomorphies shared with extant taxa. The use of explicit phylogenetic analyses to establish their affinity has so far remained limited. In this study, we built a comprehensive framework to investigate the phylogenetic placement of 24 exceptionally preserved fossil flowers. For this, we assembled a new species-level dataset of 30 floral traits for 1201 extant species that were s led to represent the stem and crown nodes of all angiosperm families. We explored multiple analytical approaches to integrate the fossils into the phylogeny, including different phylogenetic estimation methods, topological-constrained analyses, and a total evidence approach combining molecular and morphological data of extant and fossil species. Our results were widely consistent across approaches, with minor differences in the support of fossils at different phylogenetic positions. The placement of some fossils is in agreement with previously suggested relationships, but for others, a new placement is indicated. We also identified fossils that are well constrained within particular extant families, whereas others showed high phylogenetic uncertainty. Finally, we present recommendations for future total evidence analyses, regarding the selection of fossils and appropriate methodologies, and provide some perspectives on how to integrate fossils into the investigation of ergence times and the temporal evolution of morphological traits.
Profile of a flower: How rates of morphological evolution drive floral diversification in Ericales
Publisher: Cold Spring Harbor Laboratory
Date: 29-11-2022
DOI: 10.1101/2022.11.28.518258
Abstract: Recent studies of floral disparity in the asterid order Ericales have shown that flowers vary strongly among families and that disparity is unequally distributed between the three flower modules (perianth, androecium, gynoecium). However, it remains unknown whether these patterns are driven by heterogeneous rates of morphological evolution or other factors. Here, we compiled a dataset of 33 floral characters scored for 414 extant ericalean species s led from 346 genera and all 22 families. We conducted ancestral state reconstructions using an equal rates Markov models for each trait. We used the rates estimated during the ancestral state reconstruction for comparing evolutionary rates between flower modules, creating a “rate profile” of ericalean flowers. The androecium exhibits the highest evolutionary rates across most characters, whereas most perianth and gynoecium characters evolve slower. High and low rates of morphological evolution can result in high floral disparity in Ericales. Analyses of an angiosperm-wide floral dataset reveal that this pattern appears to be conserved across most major angiosperm clades. Elevated rates of morphological evolution in the androecium of Ericales may explain the higher disparity reported for this floral module. We discuss the implications of heterogenous morphological rates of evolution among floral modules from a functional perspective. Comparing rates of morphological evolution through rate profiles proves to be a powerful tool in understanding floral evolution.
Global patterns and a latitudinal gradient of flower disparity: perspectives from the angiosperm order Ericales
Publisher: Wiley
Date: 04-03-2021
DOI: 10.1111/NPH.17195
Abstract: Morphological ersity (disparity) is an essential but often neglected aspect of bio ersity. Hence, it seems timely and promising to re‐emphasize morphology in modern evolutionary studies. Disparity is a good proxy for the ersity of functions and interactions with the environment of a group of taxa. In addition, geographical and ecological patterns of disparity are crucial to understand organismal evolution and to guide bio ersity conservation efforts. Here, we analyse floral disparity across latitudinal intervals, growth forms, climate types, types of habitats, and regions for a large and representative s le of the angiosperm order Ericales. We find a latitudinal gradient of floral disparity and a decoupling of disparity from species richness. Other factors investigated are intercorrelated, and we find the highest disparity for tropical trees growing in African and South American forests. Explanations for the latitudinal gradient of floral disparity may involve the release of abiotic constraints and the increase of biotic interactions towards tropical latitudes, allowing tropical lineages to explore a broader area of the floral morphospace. Our study confirms the relevance of bio ersity parameters other than species richness and is consistent with the importance of species interactions in the tropics, in particular with respect to angiosperm flowers and their pollinators.
Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution
Publisher: Cold Spring Harbor Laboratory
Date: 25-07-2022
DOI: 10.1101/2022.07.24.501330
Abstract: Determining the link between genomic and phenotypic evolution is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of five statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, the performance of all five methods improved when there was greater rate variation among lineages. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.
Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling
Publisher: Oxford University Press (OUP)
Date: 06-10-2021
Abstract: Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape bio ersity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth–death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticized such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study has shown that there are an infinite number of equally likely ersification scenarios that can generate any timetree. This has led to questioning whether or not ersification rates should be estimated at all. Here, we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle ersification histories. Using simulations, we illustrate the characteristics of newly proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modeling, but they in no way suggest we should abandon ersification modeling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community. [Birth–death models extinction phylogenetics speciation.]
Exceptional evolutionary lability of flower‐like inflorescences (pseudanthia) in Apiaceae subfamily Apioideae
Publisher: Wiley
Date: 03-2022
DOI: 10.1002/AJB2.1819
Abstract: Pseudanthia are widespread and have long been postulated to be a key innovation responsible for some of the angiosperm radiations. The aim of our study was to analyze macroevolutionary patterns of these flower‐like inflorescences and their potential correlation with ersification rates in Apiaceae subfamily Apioideae. In particular, we were interested to investigate evolvability of pseudanthia and evaluate their potential association with changes in the size of floral display. The framework for our analyses consisted of a time‐calibrated phylogeny of 1734 representatives of Apioideae and a morphological matrix of inflorescence traits encoded for 847 species. Macroevolutionary patterns in pseudanthia were inferred using Markov models of discrete character evolution and stochastic character mapping, and a principal component analysis was used to visualize correlations in inflorescence architecture. The interdependence between net ersification rates and the occurrence of pseudocorollas was analyzed with trait‐independent and trait‐dependent approaches. Pseudanthia evolved in 10 major clades of Apioideae with at least 36 independent origins and 46 reversals. The morphospace analysis recovered differences in color and compactness between floral and hyperfloral pseudanthia. A correlation between pseudocorollas and size of inflorescence was also strongly supported. Contrary to our predictions, pseudanthia are not responsible for variation in ersification rates identified in this subfamily. Our results suggest that pseudocorollas evolve as an answer to the trade‐off between enlargement of floral display and costs associated with production of additional flowers. The high evolvability and architectural differences in apioid pseudanthia may be explained on the basis of adaptive wandering and evolutionary developmental biology.
Planning the future of plant systematics: Report on a special colloquium at the Royal Netherlands Academy of Arts and Sciences
Publisher: Wiley
Date: 12-2016
DOI: 10.3732/AJB.1600327
Using fossils and molecular data to reveal the origins of the Cape proteas (subfamily Proteoideae)
Publisher: Elsevier BV
Date: 04-2009
DOI: 10.1016/J.YMPEV.2008.12.013
Abstract: The angiosperm family Proteaceae is a distinct component of the Cape Floristic Region bio ersity hotspot with 330 endemic species. Phylogenetic analyses of subfamily Proteoideae using sequence data from one nuclear and six plastid loci show that most of this ersity is contained in two distinct Cape floral clades. Molecular dating analyses, using Bayesian and penalized likelihood methods and four phylogenetically supported fossil age constraints, reveal contrasting histories for these two clades. The genus Protea belongs to a lineage that may have been in Africa since the Late Cretaceous but began to ersify in the Cape only 5-18 Myr ago. In contrast, the Leucadendrinae clade presumably arrived in the region no earlier than 46 Myr ago by long-distance dispersal from an Australian ancestor and the extant members of this clade began to ersify in the Cape 22-39 Myr ago. These results join a growing number of case studies that challenge the commonly accepted view that most of the Cape flora radiated synchronously in the Late Miocene and Early Pliocene when a Mediterranean climate settled in the region.
The Angiosperm Terrestrial Revolution and the origins of modern biodiversity
Publisher: Wiley
Date: 16-11-2021
DOI: 10.1111/NPH.17822
Abstract: Bio ersity today has the unusual property that 85% of plant and animal species live on land rather than in the sea, and half of these live in tropical rainforests. An explosive boost to terrestrial ersity occurred from c . 100–50 million years ago, the Late Cretaceous and early Palaeogene. During this interval, the Earth‐life system on land was reset, and the biosphere expanded to a new level of productivity, enhancing the capacity and species ersity of terrestrial environments. This boost in terrestrial bio ersity coincided with innovations in flowering plant biology and evolutionary ecology, including their flowers and efficiencies in reproduction coevolution with animals, especially pollinators and herbivores photosynthetic capacities adaptability and ability to modify habitats. The rise of angiosperms triggered a macroecological revolution on land and drove modern bio ersity in a secular, prolonged shift to new, high levels, a series of processes we name here the Angiosperm Terrestrial Revolution.
Climate shapes flowering periods across plant communities
Publisher: Cold Spring Harbor Laboratory
Date: 12-10-2021
DOI: 10.1101/2021.10.10.463841
Abstract: Climate shapes the composition and function of plant communities globally, but it remains unclear how this influence extends to floral traits. Flowering phenology, or the time period in which a species flowers, has well-studied relationships with climatic signals at the species level but has rarely been explored at a cross-community and continental scale. Here, we characterise the distribution of flowering periods (months of flowering) across continental plant communities encompassing six biomes, and determine the influence of climate on community flowering period lengths. Australia Flowering plants We combined plant composition and abundance data from 629 standardised floristic surveys (AusPlots) with data on flowering period from the AusTraits database and additional primary literature for 2,983 species. We assessed abundance-weighted community mean flowering periods across biomes and tested their relationship with climatic annual means and the predictability of climate conditions using regression models. Combined, temperature and precipitation (annual mean and predictability) explain 29% of variation in continental community flowering period. Plant communities with higher mean temperatures and lower mean precipitation have longer mean flowering periods. Moreover, plant communities in climates with predictable temperatures and, to a lesser extent, predictable precipitation have shorter mean flowering periods. Flowering period varies by biome, being longest in deserts and shortest in alpine and montane communities. For instance, desert communities experience low and unpredictable precipitation and high, unpredictable temperatures and have longer mean flowering periods, with desert species typically flowering at any time of year in response to rain. Our findings demonstrate the role of current climate conditions in shaping flowering periods across biomes, with implications under climate change. Shifts in flowering periods across climatic gradients reflect changes in plant strategies, affecting patterns of plant growth and reproduction as well as the availability of floral resources across the landscape.
The soursop genome and comparative genomics of basal angiosperms provide new insights on evolutionary incongruence
Publisher: Cold Spring Harbor Laboratory
Date: 17-05-2019
DOI: 10.1101/639153
Abstract: Deep relationships and the sequence of ergence among major lineages of angiosperms (magnoliids, monocots and eudicots) remain ambiguous and differ depending on analytical approaches and datasets used. Complete genomes potentially provide opportunities to resolve these uncertainties, but two recently published magnoliid genomes instead deliver further conflicting signals. To disentangle key angiosperm relationships, we report a high-quality draft genome for the soursop ( Annona muricata , Annonaceae). We reconstructed phylogenomic trees and show that the soursop represents a genomic mosaic supporting different histories, with scaffolds almost exclusively supporting single topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previous whole genome-based studies remained inconclusive. This result is clear and consistent with recent studies using plastomes. The soursop genome highlights the need for more early erging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history.
Pulled Diversification Rates, Lineages-Through-Time Plots and Modern Macroevolutionary Modelling
Publisher: Cold Spring Harbor Laboratory
Date: 04-01-2021
DOI: 10.1101/2021.01.04.424672
Abstract: Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape bio ersity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely ersification scenarios that can generate any timetree. This has lead to questioning whether or not ersification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle ersification histories. Using simulations we demonstrate the characteristics of newly-proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon ersification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methodological shortcomings, but by acknowledging them we can better target our joint efforts as a scientific community.
Landscape Patterns in Rainforest Phylogenetic Signal: Isolated Islands of Refugia or Structured Continental Distributions?
Publisher: Public Library of Science (PLoS)
Date: 02-12-2013
Systematic revision of Myristicaceae (Magnoliales) in Madagascar, with four new species of Mauloutchia
Publisher: Oxford University Press (OUP)
Date: 11-2004
Insect pollination for most of angiosperm evolutionary history
Publisher: Wiley
Date: 05-06-2023
DOI: 10.1111/NPH.18993
Abstract: Most contemporary angiosperms (flowering plants) are insect pollinated, but pollination by wind, water or vertebrates occurs in many lineages. Though evidence suggests insect pollination may be ancestral in angiosperms, this is yet to be assessed across the full phylogeny. Here, we reconstruct the ancestral pollination mode of angiosperms and quantify the timing and environmental associations of pollination shifts. We use a robust, dated phylogeny and species‐level s ling across all angiosperm families to model the evolution of pollination modes. Data on the pollination system or syndrome of 1160 species were collated from the primary literature. Angiosperms were ancestrally insect pollinated, and insects have pollinated angiosperms for c. 86% of angiosperm evolutionary history. Wind pollination evolved at least 42 times, with few reversals to animal pollination. Transitions between insect and vertebrate pollination were more frequent: vertebrate pollination evolved at least 39 times from an insect‐pollinated ancestor with at least 26 reversals. The probability of wind pollination increases with habitat openness (measured by Leaf Area Index) and distance from the equator. Our reconstruction gives a clear overview of pollination macroevolution across angiosperms, highlighting the long history of interactions between insect pollinators and angiosperms still vital to bio ersity today.
Challenges and questions in reconstructing the ancestral flower of angiosperms: A reply to Sokoloff et al.
Publisher: Wiley
Date: 02-2018
DOI: 10.1002/AJB2.1023
Androecium diversity and evolution in Myristicaceae (Magnoliales), with a description of a new Malagasy genus, Doyleanthus gen. nov
Publisher: Wiley
Date: 09-2003
Abstract: Myristicaceae (Magnoliales) consist of 20 genera and nearly 500 species of lowland rainforest trees with a pantropical distribution. They are distinctive in having small, unisexual flowers with stamens fused into a synandrium, which consists of a single whorl of sessile anthers borne around a sterile central column. With its short filaments and more complex anther phyllotaxy, the Malagasy genus Mauloutchia represents a notable exception to this pattern. New scanning electron microscope (SEM) examinaitons of Brochoneura, Cephalosphaera, Knema, Mauloutchia, and Staudtia are incorporated into a broader review of androecium ersity across the family. These new results are discussed in the context of a phylogenetic study of the family, based on combined molecular and morphological data. The unusual synandrium of Mauloutchia, nested among genera with strictly sessile anthers fused to the column, appears to be secondarily derived. Furthermore, the ersity of patterns observed within the genus may be interpreted as the result of a stepwise transformation involving reappearance and elongation of filaments, increase of anther number, and modification of anther phyllotaxy. However, the question of the origin of stamen fusion in Myristicaceae remains unanswered and requires more developmental studies. Finally, a new Malagasy genus of Myristicaceae (Doyleanthus) is described, which is similar to Mauloutchia in most characters but fundamentally different in androecial traits.
Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale
Publisher: Oxford University Press (OUP)
Date: 20-09-2017
Abstract: The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon s ling, gene s ling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene s ling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subs ling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest ergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon s ling, significant methodological changes, and new information from the fossil record. [Angiospermae, chloroplast, genome, molecular dating, Triassic.].
Zygomorphy evolved from disymmetry in Fumarioideae (Papaveraceae, Ranunculales): new evidence from an expanded molecular phylogenetic framework
Publisher: Oxford University Press (OUP)
Date: 26-03-2015
DOI: 10.1093/AOB/MCV020
The delayed and geographically heterogeneous diversification of flowering plant families
Publisher: Springer Science and Business Media LLC
Date: 06-07-2020
DOI: 10.1038/S41559-020-1241-3
Abstract: The Early Cretaceous (145-100 million years ago (Ma)) witnessed the rise of flowering plants (angiosperms), which ultimately lead to profound changes in terrestrial plant communities. However, palaeobotanical evidence shows that the transition to widespread angiosperm-dominated biomes was delayed until the Palaeocene (66-56 Ma). Important aspects of the timing and geographical setting of angiosperm ersification during this period, and the groups involved, remain uncertain. Here we address these aspects by constructing and dating a new and complete family-level phylogeny, which we integrate with 16 million geographic occurrence records for angiosperms on a global scale. We show substantial time lags (mean, 37-56 Myr) between the origin of families (stem age) and the ersification leading to extant species (crown ages) across the entire angiosperm tree of life. In turn, our results show that families with the shortest lags are overrepresented in temperate and arid biomes compared with tropical biomes. Our results imply that the ersification and ecological expansion of extant angiosperms was geographically heterogeneous and occurred long after most of their phylogenetic ersity originated during the Cretaceous Terrestrial Revolution.
Early diversifications of angiosperms and their insect pollinators: Were they unlinked?
Publisher: California Digital Library (CDL)
Date: 18-11-2021
Sirdavidia, an extraordinary new genus of Annonaceae from Gabon
Publisher: Pensoft Publishers
Date: 04-02-2015
Molecular dating of the ‘Gondwanan’ plant family Proteaceae is only partially congruent with the timing of the break-up of Gondwana
Publisher: Wiley
Date: 30-07-2007
Trait-dependent diversification in angiosperms: patterns, models and data
Publisher: Cold Spring Harbor Laboratory
Date: 19-05-2022
DOI: 10.1101/2022.05.18.490882
Abstract: Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species ersification. Angiosperms are a highly erse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species ersification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about how these interact and their relative importance. Here, we synthesized data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to ersification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, dataset properties were correlated to SSE model results - trees that were larger, older, or less well-s led tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species’ ecology, demography and genetics.
An updated phylogeny and infrageneric classification of the genus Sisyrinchium (Iridaceae): Challenges of molecular and morphological evidence
Publisher: Wiley
Date: 12-2017
DOI: 10.12705/666.4
Phylogenomics ofBrosimumSw. (Moraceae) and allied genera, including a revised subgeneric system
Publisher: Cold Spring Harbor Laboratory
Date: 16-05-2020
DOI: 10.1101/2020.05.15.098566
Abstract: We present a phylogenomic study of Brosimum and the allied genera Trymatococcus and Helianthostylis , with near-complete taxon s ling. Distributed from Mexico and the Greater Antilles to the Amazon, this clade contains the underutilized crop ramón (bread nut) ( Brosimum alicastrum ) as well as other species valued for timber or medicinal uses. Target enrichment for 333 genes produced a well-resolved phylogenetic tree and showed that Trymatoccocus and Helianthostylis are nested within Brosimum . We present a revised subgeneric classification of Brosimum based on phylogenetic and morphological considerations, including the reduction of Trymatococcus and Helianthostylis to subgenera. The monophyletic subgenera can be diagnosed based on stipule, pistillode, and cotyledon synapomorphies. Divergence date estimates suggest a Miocene origin for Brosimum , and ancestral area reconstruction indicated that all four subgenera originated and initially ersified in Amazonia before dispersing into other parts of South and Central America. Presentamos un estudio filogenómico del género Brosimum y sus aliados, Trymatococcus y Helianthostylis , y que incluye prácticamente todas las especies descritas. Su distribución va desde México y las Antillas Mayores hasta el Amazonas y comprende especies como el ramón ( B. alicastrum ), un cultivo infrautilizado, y otras especies empleadas como madera o en medicina. La secuenciación masiva dirigida de 333 marcadores nucleares de copia única permitió la reconstrucción de una filogenia bien resuelta, en la que se demuestra que Trymatococcus y Helianthostylis están anidados en Brosimum . Presentamos, por lo tanto, una clasificación revisada a nivel de especies, teniendo en cuenta los resultados moleculares y las características morfológicas, y donde Trymatococcus y Helianthostylis pasan a ser subgéneros de Brosimum . Estos subgéneros monofiléticos pueden ser identificados por caracteres de las estípulas y de los pistilodios.
Phylogenetic analysis of Magnoliales and Myristicaceae based on multiple data sets: implications for character evolution
Publisher: Oxford University Press (OUP)
Date: 30-05-2003
Insects pollinated flowering plants for most of angiosperm evolutionary history
Publisher: Cold Spring Harbor Laboratory
Date: 02-2023
DOI: 10.1101/2023.01.31.526530
Abstract: Pollination is a fundamental process driving the speciation of angiosperms (flowering plants). Most contemporary angiosperms are insect pollinated, but abiotic pollination by wind or water and vertebrate pollination by birds or mammals occurs in many lineages. We model the evolution of pollination across angiosperms and quantify the timing and environmental associations of pollination shifts. We use a robust dated phylogeny and trait-independent species-level s ling across all families of angiosperms to model the evolution of pollination modes. Data on the pollination system or syndrome of 1160 species were collated from primary literature. Angiosperms were ancestrally insect pollinated, and insects have pollinated angiosperms for approximately 86% of angiosperm evolutionary history. Wind pollination evolved at least 42 times, with few reversals back to animal pollination. Transitions between insect and vertebrate pollination were more frequent: vertebrate pollination evolved at least 39 times from an insect pollinated ancestor with at least 26 reversals. The probability of wind pollination increases with habitat openness (measured by Leaf Area Index) and with distance from the equator. Our reconstruction of pollination across angiosperms sheds light on a key question in angiosperm macroevolution, highlighting the long history of interactions between insect pollinators and angiosperms still vital to global bio ersity today.
Analysis of shared heritability in common disorders of the brain
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-06-2018
Abstract: Consistent classification of neuropsychiatric diseases is problematic because it can lead to misunderstanding of etiology. The Brainstorm Consortium examined multiple genome-wide association studies drawn from more than 200,000 patients for 25 brain-associated disorders and 17 phenotypes. Broadly, it appears that psychiatric and neurologic disorders share relatively little common genetic risk. However, different and independent pathways can result in similar clinical manifestations (e.g., psychosis, which occurs in both schizophrenia and Alzheimer's disease). Schizophrenia correlated with many psychiatric disorders, whereas the immunopathological affliction Crohn's disease did not, and posttraumatic stress syndrome was also largely independent of underlying traits. Essentially, the earlier the onset of a disorder, the more inheritable it appeared to be. Science , this issue p. eaap8757
Pollen Diversity and Evolution in Myristicaceae (Magnoliales)
Publisher: University of Chicago Press
Date: 07-2003
DOI: 10.1086/375424
What is the age of flowering plants?
Publisher: Oxford University Press (OUP)
Date: 19-04-2022
DOI: 10.1093/JXB/ERAC130
Abstract: The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ~140 million years (Ma Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both macroevolutionary analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their ergence with acrogymnosperms (stem age) the age(s) of emergence of their unique, distinctive features including flowers (morphological age) and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior distribution (typically a calibration density set by the user in Bayesian analyses). Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as largely unknown (140–270 Ma) and that contrasting age estimates in the literature mostly reflect conflicting prior distributions. We also suggest that future work that depends on the time scale of flowering plant ersification be designed to integrate over this vexing uncertainty.
Related Organisations
Related Funding Activities
Discovery Projects - Grant ID: DP220103265
Start Date: 03-2022
End Date: 02-2025
Amount: $461,510.00
Funder: Australian Research Council
View Funded ActivityDiscovery Projects - Grant ID: DP200102927
Start Date: 08-2020
End Date: 08-2024
Amount: $390,000.00
Funder: Australian Research Council
View Funded Activity