Digest: Linking coordinated shifts in plant resource allocation to a chromosomal inversion

This article corresponds to Lowry, D. B., D. Popovic, D. J. Brennan, and L. M. Holeski. 2019. Mechanisms of a locally adaptive shift in allocation among growth, reproduction, and herbivore resistance in Mimulus guttatus. Evolution. https://doi.org/10.1111/evo.13699.Local adaptation in plants often requires coordinated shifts among resources. Lowry et al. provide evidence for physiological and genomic mechanisms underpinning adaptive shifts in yellow monkeyflower (Mimulus guttatus), such as the transition between annual and perennial life histories. In M. guttatus, differential activity of gibberellins, governed partially by a chromosomal inversion, is responsible for shifts between growth, reproduction, and herbivore defense (secondary compound production)

Genome skimming for phylogenomics

PhDThe advent of next-generation (or high-throughput) sequencing (NGS/HTS) has revolutionised biology, with much impact on the field of molecular phylogenetics. Traditional debates of taxa versus characters are now somewhat defunct in the phylogenomics era. In this thesis I focus on one particular HTS approach, ‘genome skimming’ as a phylogenomics and genomics method. I extend the scope of genome skimming to encompass more of the data present from low-coverage genome sequencing, using a novel method to analyse genomic repeat abundances as phylogenetic characters in addition to the assembly of high-copy organellar and nuclear DNA (plastomes and the nuclear ribosomal DNA cistron). The methodology for using nuclear repeats is initially developed, and then genome skimming is used to explore the phylogenetic relationships within a recent radiation – Nicotiana section Suaveolentes (Solanaceae). These data provide a significant improvement in our phylogenetic understanding of the group, despite low levels of genetic divergence between the core Australian species of Nicotiana section Suaveolentes and significant incomplete lineage sorting. Support is garnered for the whole genome duplication (WGD) radiation lag-time model in section Suaveolentes, with a significant increase in diversification in the last 2 million years following a lag of approximately 4 million years after the origin of the section at ~6.8 mya (allopolyploidisation event). Associated with this diversification are various processes of diploidisation including chromosome number reduction and genome downsizing. In addition to genomic patterns, there are ecological ones associated with diversification, including a general switch from perennial to annual life history strategy (with some notable reversals). These results paint Nicotiana section Suaveolentes as a recent and ongoing radiation, and are placed in the broad context of angiosperm diversification post-polyploidisationNERC, the Linnean Society, the Systematics Association and Botanical Research Fun

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

This article corresponds to Huang, D., E. E. Goldberg, L. M. Chou, and K. Roy. 2018. The origin and evolution of coral species richness in a marine biodiversity hotspot. Evolution.https://doi.org/10.1111/evo.13402

Non-destructive genome skimming for aquatic copepods

Copepods are important ecologically and represent a large amount of aquatic biomass in both freshwater and marine systems. Despite this, the taxonomy of copepods and other meiofauna is not well understood, hampered by tiny sizes, cryptic taxa, intraspecific polymorphisms and total specimen destruction where DNA methods are employed. In this article we highlight these issues and propose a more up-to-date approach for dealing with them. Namely, we recommend non-destructive DNA extraction methods, coupled with high-throughput sequencing (HTS). Whilst DNA yields may be low, they should still be sufficient for HTS library preparation and DNA sequencing. At the same time morphological specimens can be preserved and the crucial link between morphology and DNA sequence is maintained. This is critical for an integrative taxonomy and a fuller understanding of biodiversity patterns as well as evolutionary processes in meiofauna

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

This article corresponds to Smith, S. D., and R. Kriebel. 2018. Convergent evolution of floral shape tied to pollinator shifts in Iochrominae (Solanaceae). Evolution. https://doi.org/10.1111/evo.13416

989. Nicotiana walpa: Solanaceae

The Australian species Nicotiana walpa is newly described here from plants collected at the Uluru-Kata Tjuta National Park in the Northern Territory, Australia, and illustrated from plants cultivated at the Royal Botanic Gardens, Kew. Its discovery, ecology, cytology and cultivation are discussed

DNA extraction from old herbarium material of Veronica subgen. Pseudolysimachium (Plantaginaceae)

Herbarium specimens have become a major source of information in molecular biodiversity research, framing the term "herbarium genomics". However, obtaining good DNA from old herbarium specimens is still a challenge. Currently, DNA extraction methods from old herbarium material often yield highly degraded and fragmented DNA. A number of studies have discussed such methods, especially how to avoid further DNA fragmentation. This study aims to compare different DNA extraction methods applied to old herbarium material from Veronica subg. Pseudolysimachium. One such method is a CTABbased DNA extraction followed by a clean-up with paramagnetic beads that is used in the Jodrell Laboratory, Royal Botanic Gardens Kew, UK. This method was compared to a modified NucleoSpin Plant II protocol, based on silica columns, as used at the Technical University Munich-Freising, which was already successfully used for extracting DNA from a Linnean type specimen. Further tests were conducted on the influence of incubation time on the CTAB DNA extraction protocol with a subsample of specimens. Our preliminary results suggest that CTAB DNA extraction might have some advantages in specific cases but also that silica column-based methods have fewer problems with contamination by polysaccharides and polyphenolic compounds. Regarding the incubation time, we did not observe a clear pattern, but we developed several ideas on how to proceed with tests to find an optimal DNA extraction protocol to deal with highly fragmented DNA. Taking practical considerations into account, the column-based method proves to be preferable, especially when trying to reduce the amount of leaf tissue used, but further modifications of both methods should be explored

Digest: Multiple factors influence mountain orchid diversity and distribution

How have orchid species diversified in the campos rupestres, Brazil? Fiorini et al. (2023) use genomic data sets and multidisciplinary approaches, including phylogenetics and population genomics, to investigate the diversity of Bulbophyllum. They demonstrate that geographic isolation alone does not explain diversification patterns in Bulbophyllum species throughout the sky forests. Some taxa show considerable evidence of gene flow, and lineages not previously identified as closely related could present a novel source of their genetic diversity

Flower-specific KNOX phenotype in the orchid Dactylorhiza fuchsii

The KNOTTED1-like homeobox (KNOX) genes are best known for maintaining a pluripotent stem-cell population in the shoot apical meristem that underlies indeterminate vegetative growth, allowing plants to adapt their development to suit the prevailing environmental conditions. More recently, the function of the KNOXgene family has been expanded to include additional roles in lateral organ development such as complex leaf morphogenesis, which has come to dominate the KNOX literature. Despite several reports implicating KNOX genes in the development of carpels and floral elaborations such as petal spurs, few authors have investigated the role of KNOX genes in flower development. Evidence is presented here of a flower-specific KNOX function in the development of the elaborate flowers of the orchid Dactylorhiza fuchsii, which have a three-lobed labellum petal with a prominent spur. Using degenerate PCR, four Class I KNOX genes (DfKN1–4) have been isolated, one from each of the four major Class I KNOX subclades and by reverse transcription PCR (RT-PCR), it is demonstrated that DfKNOXtranscripts are detectable in developing floral organs such as the spur-bearing labellum and inferior ovary. Although constitutive expression of the DfKN2 transcript in tobacco produces a wide range of floral abnormalities, including serrated petal margins, extra petal tissue, and fused organs, none of the vegetative phenotypes typical of constitutive KNOX expression were produced. These data are highly suggestive of a role for KNOX expression in floral development that may be especially important in taxa with elaborate flowers

Potential of herbariomics for studying repetitive DNA in angiosperms

Repetitive DNA has an important role in angiosperm genomes and is relevant to our understanding of genome size variation, polyploidisation and genome dynamics more broadly. Much recent work has harnessed the power of high-throughput sequencing (HTS) technologies to advance the study of repetitive DNA in flowering plants. Herbarium collections provide a useful historical perspective on genome diversity through time, but their value for the study of repetitive DNA has not yet been explored. We propose that herbarium DNA may prove as useful for studies of repetitive DNA content as it has for reconstructed organellar genomes and low-copy nuclear sequence data. Here we present a case study in the tobacco genus (Nicotiana; Solanaceae), showing that herbarium specimens can provide accurate estimates of the repetitive content of angiosperm genomes by direct comparison with recently-collected material. We show a strong correlation between the abundance of repeat clusters, e.g., different types of transposable elements and satellite DNA, in herbarium collections versus recent material for four sets of Nicotiana taxa. These results suggest that herbarium specimen genome sequencing (herbariomics) holds promise for both repeat discovery and analyses that aim to investigate the role of repetitive DNAs in genomic evolution, particularly genome size evolution and/or contributions of repeats to the regulation of gene space