The genus Picea (spruce) is widely distributed across the Northern Hemisphere and is a dominant component of boreal and montane forests. Understanding the evolutionary processes that have shaped diversification and regional differentiation across the genus requires a well-resolved phylogeny of Picea. However, the evolutionary history of Picea has long been obscure due to conflicting genetic signals.

In a study published in Cladistics on October 24, researchers from Lanzhou University and the Xishuangbanna Tropical Botanical Garden (XTBG) of the Chinese Academy of Sciences investigated the phylogenetic relationships and evolutionary mechanisms of spruces. They did so by integrating transcriptomic data from 37 species. Their results showed that incomplete lineage sorting, rather than hybridization, was the dominant source of phylogenetic conflict in the genus.

The researchers adopted a pan-transcriptomic framework that circumvented the technical challenges posed by massive repetitive sequences in conifer genomes. By combining coalescent models, discordance region analysis, and network inference, they established a quantitative analytical framework for resolving complex evolutionary conflicts.

The researchers drew on 118 transcriptomic datasets, 43 of which were newly generated. They revealed that most spruce genes are highly variable. Only about 9% are shared by all species and are associated with basic cellular functions. The remaining 90% of genes differ among species and are linked to ecology and stress responses.

Using 405 low-copy genes, the researchers identified four major spruce groups, with a rare western North American species, Picea breweriana, as the earliest-diverging lineage. They also found that about 275 genes are sufficient to reliably reconstruct the genus's backbone.

However, beneath this stable framework, gene trees conflict extensively. The researchers traced most of this conflict (approximately 28%) to incomplete lineage sorting, a natural consequence of rapid and recent speciation in large and long-lived populations, rather than to hybridization (approximately 7%). While crossbreeding did occur, it was geographically localized and not the main driver of conflict.

The study also linked gene families to regional environments. Spruce lineages on the Qinghai-Tibet Plateau exhibited changes in stress and low-oxygen response genes, which may reflect waterlogged alpine soils. East Asian lineages exhibited shifts in protein regulation, and boreal lineages displayed changes in photosynthesis and wood-related genes adapted to short, harsh growing seasons.

Analysis of diversification rates indicated higher rates in early branches during the Miocene, whereas extant groups generally exhibited lower rates.

"Our findings provide a phylogenomic framework for understanding diversification mechanisms in Picea. Conservation strategies should consider not only taxonomic units but also the evolutionary processes that generate and maintain genetic diversity. As climate change accelerates ,we should protect genetically diverse refugial populations and regionally differentiated variation," said SUN Yongshuai of XTBG.