2026-10-13T15:06:55Z https://www.scidb.cn/oai

10.57760/sciencedb.39499 2026-08-17T11:21:35Z

2026-08-17 Introgression shapes the genomic conflict landscape of Malus, revealing a reticulate backbone in a woody crop lineage doi:10.57760/sciencedb.39499 en Phylogenomic discordance is widespread across plants, but its evolutionary significance is often obscured when conflict is treated primarily as analytical noise rather than as evidence of underlying processes. In woody lineages in particular, incomplete lineage sorting (ILS), introgression, and genome duplication can interact over long timescales to produce complex genomic histories that are not adequately summarized by a strictly bifurcating tree. Here, we use Malus as a model woody genus to investigate how these processes structure conflict across a genus-scale phylogenomic framework. Using dense taxon sampling, hundreds of nuclear loci, plastid genomes, and genome-wide SNP summaries, we reconstruct a robust nuclear backbone for Malus and evaluate where discordance is concentrated and which processes best explain it. Nuclear analyses resolve eight major clades, whereas conflict is non-random and localized to recurrent hotspots rather than evenly distributed across the tree. Cytonuclear discordance is similarly concentrated, especially around Clade H (M. tschonoskii), where localized plastid–nuclear disagreement is consistent with plastid capture and organellar introgression. Multiple complementary analyses further indicate that the strongest conflict is not explained by ILS alone, but instead reflects lineage-structured introgression, while polyploid complexes represent additional localized sources of evolutionary complexity. Together, these results support a reticulate genomic backbone for Malus and show how integrating nuclear, plastid, and genome-wide conflict analyses can help distinguish background discordance from process-specific signals in woody plant radiations. cytonuclear discordance; introgression; hybridization; reticulate evolution; polyploidy; woody perennials. 李小丫 牛钊倩 郑雅文 黄珏琳 马代锟 黄佳欣 郝强 解思宇 徐超 刘彬彬 PUBLIC https://creativecommons.org/licenses/by-nc-sa/4.0/ dataset Science Data Bank