Phylogenomic Approaches to Deal with Particularly Challenging Plant Lineages

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Background

Recent advances in high-throughput sequencing, HTS (i.e., next generation sequencing), now allow genomic-level approaches to the study of evolutionary processes (e.g., hybridization, adaptive radiations) that have historically challenged our ability to make compelling phylogenetic hypotheses for some plant lineages. This molecular revolution, coupled with the development of bioinformatic and analytical tools, has resulted in the phylogenetic analysis of hundreds to thousands of genomic regions to emerge as a new standard in evolutionary biology.

In spite of these developments, whole genome sequencing is still not a viable option across Land Plants, given that genome sizes range from 60 Mb to 140 Gb in flowering plants. Reduced representation approaches - including untargeted (i.e., genome skimming or shotgun sequencing), targeted (i.e., RNA seq, Genotyping-by-Sequencing, Amplicon-sequencing, etc.), and hybrid (e.g., hyb-seq) approaches - can accommodate this genome size diversity and allow non-model organisms to join the genomic revolution.

Inferring phylogenetic relationships among recently or rapidly diverged lineages remains a major challenge in Evolutionary Biology. The difficulties underlying this challenge include finding genetic markers with enough phylogenetic signal to disentangle genealogical relationships at the shallowest evolutionary levels, and discordance among gene trees which may differ significantly from the species or population tree. Such discordance may originate from hybridization among distinct lineages with subsequent fixation of alleles or incomplete lineage sorting of alleles due to short intervals between divergence events.

HTS technologies and bioinformatic and analytical tools have revolutionized the questions that can be addressed and the taxa that can be studied using genome-wide approaches. Large, genome-scale datasets can be used both to address phylogenetic relationships among very closely related species and at the same time examine patterns of lineage sorting and historical hybridization; two of the most pervading obstacles in phylogenetic inference. However, considerable challenges remain.

This Research Topic is intended to serve as a key resource for researchers studying plant groups whose phylogenetic histories have proven difficult to resolve in the past. With this, we aim to highlight the strengths, difficulties, and obstacles of emerging sequencing and analytical techniques to improve our understanding of the evolution of these so-called challenging plant lineages. Ultimately, our aim is that this Research Topic will serve to set the new standard of phylogenetics in the genomic era.

We welcome articles falling under, but not limited to, the following:
- New phylogenomic approaches to disentangle the tree of life of challenging plant lineages, especially those that involve recent rapid divergence (e.g., radiations) and/or hybridization.
- The development of new analytical approaches and laboratory protocols that adequately tackle the underlying processes of biological diversification, while accounting for the particularities of incipient differentiation.
- Novel phylogenomic insights in lineages where extensive gene duplications (resulting from, i.e., whole genome duplications or the activity of transposable elements) or losses (e.g., parasitic plants) hindered phylogenetic reconstructions.

Keywords: Challenging Plant Lineages, Hybrid Speciation, Phylogenomics, Plant Species Evolution, Radiations.

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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