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 t...,
Materials and Methods
In the following section, we provide a brief overview of the materials and methods used in this project; additional details can be found in the supplementary methods.

1 | Taxon Sampling, DNA Extraction, and Sequencing
A comprehensive phylogenetic analysis of Pyrus was conducted, including all seven subsections defined by Phipps et al. (1990), the most detailed global taxonomic framework for pear species. Due to the self-incompatibility and hybrid formation of Pyrus, species like P. sinkiangensis were excluded. To accurately estimate divergence times, 41 outgroups from 26 genera in the apple tribe Maleae were selected, with a focus on close relatives, such as Malus and Sorbus sensu lato. Gillenia trifoliata from the tribe Gillenieae was used as an outgroup for rooting the Maleae phylogeny. Of the 92 samples analyzed, 58 came from Whole Genome Sequencing (WGS) and/or Deep Genome Skimming (DGS) data from the NCBI Sequence Read Archive (SRA), while 34 DGS (2 × 150bp)..., , # Title of Dataset:

Unraveling the Web of Life: Incomplete lineage sorting and hybridization as primary mechanisms over polyploidization in the evolutionary dynamics of pear species

This package contains the data and software outputs - Analyses_data.zip

## Description of the Data and file structure

Analyses_data.zip

### ALIGNMENTS

Data 1. Pyrus_nuclear.fasta = 801 nuclear single-copy reference genes filtered from thirteen genomes

Data 2. Pyrus_77_plastid_coding_genes.fasta = concatenated alignments of 77 plastid coding genes of Pyrus
Pyrus_77_plastid_coding_genes.partitions.txt = partition file for concatenated alignments of 77 plastid coding genes of Pyrus

Data 3. Pyrus_771_MO_genes_dataset.fasta = concatenated alignments of 771 MO ortholog genes dataset
Pyrus_771_MO_genes_dataset.partitions.txt = partition file for concatenated alignments of 771 MO ortholog genes dataset

Data 4. Pyrus_905_RT_genes_dataset.fasta = concatenated alignments of 905 RT ortholog genes dataset
Pyrus_...,