From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics

Abstract

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.

Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

“…Our study identifies nine fusion-with-mixing events shared between bryozoans and brachiopods, of which four are confirmed as derived characters, supporting the Lophophorata topology. Fusion-with-mixing events are essentially irreversible in evolution, but convergent evolution cannot be ruled out (33). If these rare genomic changes are specific to Lophotrochozoans (excluding Entoprocta and Cycliophora), then the presence of at least eight shared derived fusion events in brachiopods and bryozoans would almost rule out convergence, becoming a conclusive piece of evidence in this ongoing debate.…”

“…These rearrangements, while disrupting gene function and expression (24) and altering recombination rates (25), also play a critical role in driving adaptation (26)(27)(28) and contributing to macroevolutionary processes like speciation (29)(30)(31)(32). This dynamic quality of chromosomal changes has also been exploited in phylogenetic studies, where macrosynteny can be a powerful tool (33). Fusion-with-mixing events could prove particularly powerful phylogenetic markers as they are considered to be irreversible rare genomic changes.…”