Steven Dodsworth

Genomic repeat abundances contain phylogenetic signal

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.

Genome skimming for next-generation biodiversity analysis.

High-throughput sequencing technologies have revolutionised the ease with which genomic data can be obtained for any plant species, from trees to bryophytes, regardless of phylogenetic proximity to model species or even the ease of cultivation. This is creating an impact on all types of biodiversity study, from phylogenomic and systematic studies through to population genetic, barcoding, and ecological investigations. A plethora of different approaches are available that differ in the expertise and time required for both the preparation of genomic DNA (gDNA) for sequencing and subsequent bioinformatic analysis of read data (Figure 1).

The effect of polyploidy and hybridization on the evolution of floral colour in Nicotiana (Solanaceae).

Background and Aims Speciation in angiosperms can be accompanied by changes in floral colour that may influence pollinator preference and reproductive isolation. This study investigates whether changes in floral colour can accompany polyploid and homoploid hybridization, important processes in angiosperm evolution. Methods Spectral reflectance of corolla tissue was examined for 60 Nicotiana (Solanaceae) accessions (41 taxa) based on spectral shape (corresponding to pigmentation) as well as bee and hummingbird colour perception in order to assess patterns of floral colour evolution. Polyploid and homoploid hybrid spectra were compared with those of their progenitors to evaluate whether hybridization has resulted in floral colour shifts. Key Results Floral colour categories in Nicotiana seem to have arisen multiple times independently during the evolution of the genus. Most younger polyploids displayed an unexpected floral colour, considering those of their progenitors, in the colour perception of at least one pollinator type, whereas older polyploids tended to resemble one or both of their progenitors. Conclusions Floral colour evolution in Nicotiana is weakly constrained by phylogeny, and colour shifts do occur in association with both polyploid and homoploid hybrid divergence. Transgressive floral colour in N. tabacum has arisen by inheritance of anthocyanin pigmentation from its paternal progenitor while having a plastid phenotype like its maternal progenitor. Potentially, floral colour evolution has been driven by, or resulted in, pollinator shifts. However, those polyploids that are not sympatric (on a regional scale) with their progenitor lineages are typically not divergent in floral colour from them, perhaps because of a lack of competition for pollinators.

Genome Size Diversity and Its Impact on the Evolution of Land Plants

Genome size is a biodiversity trait that shows staggering diversity across eukaryotes, varying over 64,000-fold. Of all major taxonomic groups, land plants stand out due to their staggering genome size diversity, ranging ca. 2400-fold. As our understanding of the implications and significance of this remarkable genome size diversity in land plants grows, it is becoming increasingly evident that this trait plays not only an important role in shaping the evolution of plant genomes, but also in influencing plant community assemblages at the ecosystem level. Recent advances and improvements in novel sequencing technologies, as well as analytical tools, make it possible to gain critical insights into the genomic and epigenetic mechanisms underpinning genome size changes. In this review we provide an overview of our current understanding of genome size diversity across the different land plant groups, its implications on the biology of the genome and what future directions need to be addressed to fill key knowledge gaps.

A roadmap for global synthesis of the plant tree of life

Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.

Petal, Sepal, or Tepal? B-Genes and Monocot Flowers

In petaloid monocots expansion of B-gene expression into whorl 1 of the flower results in two whorls of petaloid organs (tepals), as opposed to sepals in whorl 1 of typical eudicot flowers. Recently, new gene-silencing technologies have provided the first functional data to support this, in the genus Tricyrtis (Liliaceae).

Digests: Salamanders’ slow slither into genomic gigantism

Genome size varies enormously across the eukaryotic tree of life (c. 66,000-fold), with the largest reported nuclear genomes found in vertebrates (e.g. salamanders, lungfish) and angiosperms (e.g. mistletoe, fritillaries). Yet despite this huge diversity, most genomes are considerably smaller than the largest reported (c. 150 Gb), with the mean size of both vertebrate and plant genomes being similar, c. 5 Gb. This article is protected by copyright. All rights reserved

Digest: Drivers of coral diversification in a major marine biodiversity hotspot*: DIGEST

Coral reefs are of great ecological importance for marine wildlife (Knowlton 2001); despite occupying less than 0.1 percent of the surface area of the world’s oceans, they provide habitats for at least a quarter of marine species (Spalding and Grenfell 1997). They are fragile ecosystems, under threat from numerous stresses including climate change, ocean acidification, and destructive fishing practices (Pandolfi 2003). Despite their great ecological importance, relatively little is known about the evolution of coral reefs. The mode and tempo of evolution in coral reef systems are poorly understood, with data lacking on the origin and diversification of coral hotspots (Huang and Roy 2015). In this issue, Huang et al. (2017) utilize a solid phylogenetic framework based on two sets of trees of coral species: one that uses earlier supertree studies incorporating published molecular data (seven mitochondrial DNA markers) and morphological trees, and one that uses an expanded molecular dataset (seven mitochondrial plus two nuclear DNA regions). In both cases, fossil calibrations were used to date the trees. Using these different phylogenetic datasets, they tested the mode of diversification in the Indo-Pacific Coral Triangle (CT) biodiversity hotspot to test competing hypotheses regarding the temporal dynamics of coral species richness. The Coral Triangle is a geographic area encompassing the oceans around Malaysia, the Phillippines, Indonesia, TimorLeste, Papua New Guinea, and the Solomon Islands. Phylogenetic analyses indicate that diversity within the CT was driven mostly by range expansions of lineages that originated outside the CT. Speciation rates within the CT region itself were lower than surrounding regions, as endemic CT lineages were found to

Digest: Shape-shifting in Solanaceae flowers: The influence of pollinators*: DIGEST

Aside from climate, plant–pollinator interactions are thought to be one of the main drivers of diversification in tropical plant lineages (Fig. 1; Gentry 1982; Pérez-Escobar et al. 2017). It has been argued that the great variation in angiosperm flowers is largely influenced by pollinator-mediated selection (Sauquet et al. 2017), a force that has also been linked with diversification of large groups within the flowering plants, such as orchids (Pérez-Escobar et al. 2017). Micro-evolutionary studies aimed at understanding mechanisms underpinning changes in observed phenotypes have clearly demonstrated that pollinator shifts are strongly correlated with changes in floral traits (e.g., Aquilegia; Whittall and Hodges 2007). The importance of pollinator-mediated selection in driving divergence at a macro-evolutionary scale, however, remains unclear. In this issue, Smith and Kriebel (2018) explore the question of pollinator-mediated selection at a macro-evolutionary scale in the Andean shrubs of the solanaceous tribe Iochrominae. To understand drivers of deep evolutionary shifts in floral traits, they used quantitative data in a phylogenetic context to test the Grant– Stebbins model, which predicts pollinator shifts will drive divergence and potentially speciation (Johnson 2006). In addition, the authors conducted corolla shape measurements based on geometric morphometrics and reconstructed a robust species-level phylogeny. Pulling together the first such broad-scale dataset, Smith and Kriebel (2018) demonstrate that floral shape evolution within the Iochrominae, a clade that includes birdand insect-pollinated species, has been largely pollinator mediated. Using statistical re-

Salamanders' slow slither into genomic gigantism().

Genome size varies enormously across the eukaryotic tree of life (c. 66,000-fold), with the largest reported nuclear genomes found in vertebrates (e.g. salamanders, lungfish) and angiosperms (e.g. mistletoe, fritillaries). Yet despite this huge diversity, most genomes are considerably smaller than the largest reported (c. 150 Gb), with the mean size of both vertebrate and plant genomes being similar, c. 5 Gb. This article is protected by copyright. All rights reserved