Phylogenomics reveals patterns of ancient hybridization and differential diversification contributing to phylogenetic conflict inPopulusL. andSalixL

Abstract

Despite the economic, ecological, and scientific importance of the genera Populus L. (poplars, cottonwoods, and aspens) and Salix L. Salicaceae (willows), 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 Populus and Salix have played important roles in the diversification and diversity in these two genera.

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). 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 .…”

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

“…Divergence between P. balsamifera and coastal P. trichocarpa was initiated ~930,000 years ago, aligning with the Mid-Pleistocene Transition, when glacial cycles became longer and shifts to interglacial climates became more abrupt and extreme (Willeit et al, 2019). Our divergence time estimates are much older than the 75,000 years estimated by Levsen et al (2012) for P. trichocarpa and P. balsamifera but are congruent with observations for this species-pair from Sanderson et al (2023). Furthermore, the divergence timing between the interior genetic cluster of P. trichocarpa from P. balsamifera aligned with the last glacial maxima (~26,000 years ago), and yet still low levels of gene flow persisted.…”

Sex determination system turnovers play important roles in the willows speciation

“…However, 15XY to 15ZW and 15XY to 7XY, that carried same sex determination factors (Wang et al, 2023b), are insufficient to form a complete reproductive barrier between the species pair, at least in early generations of their separation. However, Sanderson et al (2023) found a burst of diversification near the origin of the Vetrix clade, which is likely match the SDSs 15XY 15ZW transition in this clade.…”

“…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.…”