Phylogenomics reveals patterns of ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives

Abstract

Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a ‘spectacular failure’ due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed polyphyly of others. Using an fbranch analysis we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix-Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Salix and Populus have played important roles in the diversification and diversity in these two genera.

Climate and geography shape hybrid zone dynamics across space and time: insights fromPopulus trichocarpaxP. balsamifera

“…The estimates observed herein suggest 2.11 -2.13 million years ago P. trichocarpa and P. balsamifera diverged and are congruent with observations for this species-pair from (Sanderson et al, 2023). The differentiation we observed in the chloroplast not only aligns with patterns of nuclear differentiation among the three assigned parental-types but also supports the observations and interpretations of previous chloroplast assessments of divergence in Populus.…”

Genomic insights into hybrid zone formation: The role of climate, landscape, and demography in the emergence of a novel hybrid lineage

“…The estimates observed herein suggest 2.11-2.13 million years ago P. trichocarpa and P. balsamifera diverged and are congruent with observations for this species-pair from (Sanderson et al, 2023).…”

Sex chromosome turnover plays an important role in the maintenance of barriers to post-speciation introgression in willows

“…Turnover of 15XY to 15ZW changed the heterogamety and appeared at the origin of a major group of the Vetrix clade that includes more than 300 species ( He et al, 2021b ). A burst of diversification near the origin of the Vetrix clade was found in Sanderson et al (2023) , which is likely to match the 15XY to 15ZW transition in this clade. Furthermore, a turnover of 15XY to 7XY likely triggered the speciation of the Salix clade, which includes ~60 species ( He et al, 2021b ).…”

“…More recently, genomic approaches were applied to detect hybridization. Sanderson et al (2023) identified several cases of hybridization between species from different branches among the ancestors of subgenera Longifoliae , Vetrix , and Chamaetia ( Vetrix clade) of Salix based on the ABBA-BABA statistics.…”