Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

The concluding chapter: recircumscription of Goodenia (Goodeniaceae) to include four allied genera with an updated infrageneric classification

Close scrutiny of Goodenia (Goodeniaceae) and allied genera in the 'Core Goodeniaceae' over recent years has clarified our understanding of this captivating group. While expanded sampling, sequencing of multiple regions, and a genome skimming reinforced backbone clearly supported Goodenia s.l. as monophyletic and distinct from Scaevola and Coopernookia, there appears to be no synapomorphic characters that uniquely characterise this morphologically diverse clade. Within Goodenia s.l., there is strong support from nuclear, chloroplast and mitochondrial data for three major clades (Goodenia Clades A, B and C) and various subclades, which lead to earlier suggestions for the possible recognition of these as distinct genera. Through ongoing work, it has become evident that this is impractical, as conflict remains within the most recently diverged Clade C, likely due to recent radiation and incomplete lineage sorting. In light of this, it is proposed that a combination of morphological characters is used to circumscribe an expanded Goodenia that now includes Velleia, Verreauxia, Selliera and Pentaptilon, and an updated infrageneric classification is proposed to accommodate monophyletic subclades. A total of twenty-five new combinations, three reinstatements, and seven new names are published herein including Goodenia subg. Monochila sect. Monochila subsect. Infracta K.A.Sheph. subsect. nov. Also, a type is designated for Goodenia subg. Porphyranthus sect. Ebracteolatae (K.Krause) K.A.Sheph. comb. et stat. nov., and lectotypes or secondstep lectotypes are designated for a further three names.

Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l. (Goodeniaceae)

Goodeniaceae is a primarily Australian flowering plant family with a complex taxonomy and evolutionary history. Previous phylogenetic analyses have successfully resolved the backbone topology of the largest clade in the family, Goodenia s.l., but have failed to clarify relationships within the species-rich and enigmatic Goodenia clade C, a prerequisite for taxonomic revision of the group. We used genome skimming to retrieve sequences for chloroplast, mitochondrial, and nuclear markers for 24 taxa representing Goodenia s.l., with a particular focus on Goodenia clade C. We performed extensive hypothesis tests to explore incongruence in clade C and evaluate statistical support for clades within this group, using datasets from all three genomic compartments. The mitochondrial dataset is comparable to the chloroplast dataset in providing resolution within Goodenia clade C, though backbone support values within this clade remain low. The hypothesis tests provided an additional, complementary means of evaluating support for clades. We propose that the major subclades of Goodenia clade C (C1-C3 + Verreauxia) are the result of a rapid radiation, and each represents a distinct lineage.

The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes

PREMISE OF THE STUDY

The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae.

METHODS

Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes.

RESULTS

Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions.

DISCUSSION

Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.

The unexpected depths of genome-skimming data: A case study examining Goodeniaceae floral symmetry genes

PREMISE OF THE STUDY

The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae.

METHODS

Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their utility in mining low-copy nuclear genes involved in floral symmetry, specifically the CYCLOIDEA (CYC)-like genes. De novo assemblies were generated using multiple assemblers, and BLAST searches were performed for CYC1, CYC2, and CYC3 genes.

RESULTS

Overall Trinity, SOAPdenovo-Trans, and SOAPdenovo implementing lower k-mer values uncovered the most data, although no assembler consistently outperformed the others. Using SOAPdenovo-Trans across all 24 data sets, we recovered four CYC-like gene groups (CYC1, CYC2, CYC3A, and CYC3B) from a majority of the species. Alignments of the fragments included the entire coding sequence as well as upstream and downstream regions.

DISCUSSION

Genome-skimming data sets can provide a significant source of low-copy nuclear gene sequence data that may be used for multiple downstream applications.

Characterizing Floral Symmetry in the Core Goodeniaceae with Geometric Morphometrics

Core Goodeniaceae is a clade of ~330 species primarily distributed in Australia. Considerable variation in flower morphology exists within this group and we aim to use geometric morphometrics to characterize this variation across the two major subclades: Scaevola sensu lato (s.l.) and Goodenia s.l., the latter of which was hypothesized to exhibit greater variability in floral symmetry form. We test the hypothesis that floral morphological variation can be adequately characterized by our morphometric approach, and that discrete groups of floral symmetry morphologies exist, which broadly correlate with subjectively determined groups. From 335 images of 44 species in the Core Goodeniaceae, two principal components were computed that describe >98% of variation in all datasets. Increasing values of PC1 ventralize the dorsal petals (increasing the angle between them), whereas increasing values of PC2 primarily ventralize the lateral petals (decreasing the angle between them). Manipulation of these two morphological “axes” alone was sufficient to recreate any of the general floral symmetry patterns in the Core Goodeniaceae. Goodenia s.l. exhibits greater variance than Scaevola s.l. in PC1 and PC2, and has a significantly lower mean value for PC1. Clustering clearly separates fan-flowers (with dorsal petals at least 120° separated) from the others, whereas the distinction between pseudo-radial and bilabiate clusters is less clear and may form a continuum rather than two distinct groups. Transitioning from the average fan-flower to the average non-fan-flower is described almost exclusively by PC1, whereas PC2 partially describes the transition between bilabiate and pseudo-radial morphologies. Our geometric morphometric method accurately models Core Goodeniaceae floral symmetry diversity.

Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies

Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments' ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia+Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A+Goodenia B) (Velleia+Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.

End-of-life care in end-stage renal disease: renal and palliative care

The numbers of patients with end-stage renal disease are growing, with a disproportionate increase among those who are elderly, dependent and with multiple co-morbidities. More of these patients are choosing to be managed conservatively, without dialysis. Palliative provision for these patients within UK renal services is limited, but the recent National Service Framework for Renal Services (Department of Health, 2005) has promoted service development. However, few models of service provision have been described. This article describes a retrospective review of a new service for conservatively-managed patients with end-stage renal disease. The range and complexity of the health needs of this population is demonstrated, and an example of service development described. A model of the stages of the conservative pathway and appropriate interventions was developed. The absence of research evidence prevented development of formal audit standards, and highlighted the urgent need for evaluation of models of care.

Morphology, anatomy and histochemistry of Salicornioideae (Chenopodiaceae) fruits and seeds

BACKGROUND AND AIMS

The subfamily Salicornioideae (Chenopodiaceae) are a taxonomically difficult group largely due to the lack of diagnostic characters available to delineate tribal- and generic-level boundaries; a consequence of their reduced floral and vegetative features. This study examined the variation in fruits and seeds across both tribes of the Salicornioideae to assess if characters support traditional taxonomic sections.

METHODS

Light microscopy, environmental scanning electron microscopy and anatomical ultra-thin sectioning were employed to examine variation in fruits and seeds. Sixty-eight representatives across 14 of the 15 genera currently recognized within the tribes Halopeplideae and Salicornieae were examined to determine whether characters support current taxonomic groups.

KEY RESULTS

Characters such as seed coat structure, embryo shape, seed orientation, the forms of seed storage proteins and carbohydrates show variation within the Salicornioideae and may be phylogenetically useful. The campylotropous ovule typical of the Chenopodiaceae generally results in a curved embryo; however, many Halosarcia and Sclerostegia species have straight embryos and in Salicornia and Sarcocornia the large peripheral embryo appears bent rather than curved. Seed coat ornamentation of Microcnemum and Arthrocnemum is distinct from other Salicornioideae as the elongated epidermal cells of the exotesta have convex walls. Histochemical stains of anatomical sections of cotyledon cells showed protein bodies were variable in shape, and starch grains were present in some species, namely Salicornia bigelovii, S. europaea and Allenrolfea occidentalis.

CONCLUSIONS

While fruits and seeds were found to be variable within the subfamily, no synapomorphic characters support the tribe Halopeplideae as these genera have crustaceous seed coats, curved embryos and abundant perisperm; features characteristic of many of the tribe Salicornieae. The endemic Australian genera are closely related and few seed and fruit characters are diagnostic at the generic level. Nineteen characters identified as being potentially informative will be included in future phylogenetic analyses of the subfamily.

Radiation of the Australian Salicornioideae (Chenopodiaceae)--based on evidence from nuclear and chloroplast DNA sequences

In phylogenetic analyses of nuclear ITS and chloroplast trnL DNA sequences, the mostly endemic Australian genera; Halosarcia, Pachycornia, Sclerostegia, Tecticornia, and Tegicornia of the subfamily Salicornioideae (Chenopodiaceae) together form a monophyletic group, congruent with the hypothesis that they evolved from a common ancestor. However, limited genetic differentiation evident in both nrDNA and cpDNA sequences among these taxa suggests a possible rapid radiation. Based on fossil pollen records and climatic models of other authors, it is hypothesized that the expansion of the Australian endemic Salicornioideae most likely occurred during the Late Miocene to Pliocene, when increasing aridity caused the formation of extensive salt lakes along endorheic paleodrainage channels. Moreover, Australian Sarcocornia representatives were supported as monophyletic, nested within a paraphyletic Sarcocornia clade that also comprised European Salicornia in the ITS analysis. This suggests that Sarcocornia arrived in Australia subsequent to the ancestor of the Australian endemic genera most likely via long-distance dispersal.