Family-level sampling of mitochondrial genomes in Coleoptera: Compositional heterogeneity and phylogenetics

Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be sampled more densely. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5 and nad6 genes. Credible tree topologies were obtained with the nhPhyML (‘non-homogeneous’) algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher-level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia (Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia)))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, whilst compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees

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)

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

Background and Aims: We investigate whether changes in floral colour accompany polyploid and homoploid hybridisation, important processes in angiosperm evolution. Potentially, changes in floral colour can facilitate speciation through pollinator shifts. Methods: We examined spectral reflectance of corolla tissue from 60 Nicotiana (Solanaceae) accessions (41 taxa) based on spectral shape (corresponding to pigmentation) as well as bee and hummingbird colour perception to assess patterns of floral colour evolution. We compared polyploid and homoploid hybrid spectra to those of their progenitors to evaluate whether hybridisation 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. Polyploid and homoploid hybrids can display a floral colour: 1) intermediate between progenitors, 2) like one or other progenitor, or 3) a transgressive or divergent colour not present in either progenitor. Conclusions: Floral colour evolution in Nicotiana is weakly constrained by phylogeny, but colour shifts occur and are sometimes associated with allopolyploid or homoploid speciation. 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

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

Using genomic repeats for phylogenomics: A case study in wild tomatoes (Solanum section Lycopersicon: Solanaceae)

High-throughput sequencing data have transformed molecular phylogenetics and a plethora of phylogenomic approaches are now readily available. Shotgun sequencing at low genome coverage is a common approach for isolating high-copy DNA, such as the plastid or mitochondrial genomes, and ribosomal DNA. These sequence data, however, are also rich in repetitive elements that are often discarded. Such data include a variety of repeats present throughout the nuclear genome in high copy number. It has recently been shown that the abundance of repetitive elements has phylogenetic signal and can be used as a continuous character to infer tree topologies. In the present study, we evaluate repetitive DNA data in tomatoes (Solanum section Lycopersicon) to explore how they perform at the inter- and intraspecific levels, utilizing the available data from the 100 Tomato Genome Sequencing Consortium. The results add to previous examples from angiosperms where genomic repeats have been used to resolve phylogenetic relationships at varying taxonomic levels. Future prospects now include the use of genomic repeats for population-level analyses and phylogeography, as well as potentially for DNA barcoding

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

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