Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups characterized by pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model to examine the influence of reticulation on generic circumscription, particularly where hybridization and allopolyploidy dominate the evolutionary history. In this study, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stran..., 2.1. Taxon sampling, DNA extraction, and sequencing
To refine our understanding of the phylogenetic placement and generic circumscription of Stranvaesia within the apple tribe framework, we undertook a comprehensive taxon sampling of Stranvaesia and its allies. Based on the redefinition by Liu et al. (2019), our sample included six individuals from three accepted species: two from S. bodinieri, one from S. nussia (the type species), and three from S. oblanceolata. Given the unclear phylogenies between Stranvaesia and Photinia, our study also encompassed 19 individuals from Photinia, representing 16 species out of 20 currently recognized species (referring to Yu and Ku, 1974; Lu and Spongberg, 2003). Furthermore, to ascertain the phylogenetic position of the target lineages, we also selected 41 outgroup species spanning 19 genera. These encompassed one genus from the tribe Gillenieae, specifically Gillenia stipulata (Muhl. ex Willd.) Nutt. Additionally, they included 18 currently recogni..., , # Data from: Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era

[https://doi.org/10.5061/dryad.hx3ffbghm](https://doi.org/10.5061/dryad.hx3ffbghm)

This package contains the data and software outputs - Analyses_data.tar.gz

## Description of the data and file structure

### Analyses_data.zip

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

Data 2. Stranvaesia_78_plastid_coding_genes.fasta = concatenated alignments of 78 plastid coding genes of Stranvaesia
Stranvaesia_78_plastid_coding_genes.partitions.txt = partition file for concatenated alignments of 78 plastid coding genes of Stranvaesia

Data 3. Stranvaesia_426_SCN_genes_dataset.fasta = concatenated alignments of 426 SCN genes dataset
Stranvaesia_426_SCN_genes_dataset.partitions.txt = partition file for concatenated alignments of 426 SCN genes dataset

Data 4. 13-taxa_sampling(Stranvaesia)_for...