Data from: Unraveling the web of life: Incomplete lineage sorting and hybridization as primary mechanisms over polyploidization in the evolutionary dynamics of pear species

The traditional Tree of Life (ToL) model is increasingly challenged by the
Web of Life (WoL) paradigm, which offers a more accurate depiction of
organismal phylogeny, particularly in light of the incongruences often
observed between gene and species trees. However, the absence of a
standardized method for resolving evolutionary mechanisms—such as
Incomplete Lineage Sorting (ILS), hybridization, introgression,
polyploidization, and whole-genome duplication—remains a significant
obstacle in defining the WoL. Characterized by extensive hybridization
events, the pear genus Pyrus provides an ideal model for exploring these
complexities. In this study, we present a Step-by-Step Exclusion approach
for investigating the evolutionary pathways of Pyrus, and our results
demonstrate that: 1) ILS, rather than polyploidization, plays a dominant
role in the origination of Pyrus; 2) the two subgenera of Pyrus followed
independent evolutionary paths, influenced by geographical barriers formed
through the uplift of the Tibetan Plateau and increased aridity in Central
Asia; 3) both ILS and hybridization have driven the diversification of
subg. Pashia, while hybridization alone has shaped the reticulate
evolution of subg. Pyrus; 4) the establishment of the Silk Road during the
Han Dynasty facilitated genetic exchange between subg. Pyrus and subg.
Pashia. The SSE approach offers a versatile framework for studying the
evolutionary mechanisms underlying the WoL paradigm.