Plastid genomes are in general highly conserved given their slow evolutionary rate, thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridisation, both processes usually complicating systematic inferences. In this study, we have generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity, and repeat composition of these sequences. By comparing the whole plastome sequences obtained, we confirmed the double inversion located in the long single copy region, for most of the species analysed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also show that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae -as well as in the sister family Calyceraceae - are lacking the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, are overall consistent with the general consensus for the family’s phylogeny, while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.

Reconstructing the Tree of Life remains a central goal in biology. Early methods, relying on small numbers of morphological or genetic characters, often yielded conflicting evolutionary histories, undermining confidence in the results. Investigations based on phylogenomics, which use hundreds to thousands of loci for phylogenetic inquiry, have provided a clearer picture of life's history, but certain branches remain problematic. To resolve difficult nodes on the Tree of Life, two recent studies tested the utility of synteny, the conserved collinearity of orthologous genetic loci in two or more organisms, for phylogenetics. Synteny exhibits compelling phylogenomic potential while also raising new challenges. We identify and discuss specific opportunities and challenges that bear on the value of synteny data and other rare genomic changes for phylogenomic studies. Synteny-based analyses of highly contiguous genome assemblies mark a new chapter in the phylogenomic era and the quest to reconstruct the Tree of Life.

Phylogenomics has enriched our understanding of the Tree of Life. Non-vertical modes of evolution—such as hybridization/introgression and horizontal gene transfer—deviate from a strictly bifurcating tree model, mirroring a network-like or reticulate structure. Here, we present an overview of a phylogenomic workflow for inferring organismal histories, calibrating those histories to evolutionary time, and detecting reticulate evolution. Mitigating analytical sources of error facilitates accurate reconstructions of evolutionary history and, in turn, characterization of non-vertical modes of evolution. Workflows and methods discussed herein may aid in the rigorous inference of organismal histories in geologic time and reticulation, providing a clearer understanding of the evolutionary process.