Integrating Morphometrics, K-mer–based Genomic, and Phylogenomics Reveals a Complex Reticulate History of Cypripedium × ventricosum
Description
Research hypothesis Cypripedium × ventricosum is a morphologically variable and widely distributed natural orchid hybrid complex in northeastern China. Its evolutionary history remains poorly understood, largely because species of the genus Cypripedium possess exceptionally large genomes (28–45 Gb), which pose major challenges for genome assembly and conventional population genomic analyses. This study aims to test whether the observed morphological and genomic variation within this complex is more consistent with a single origin, multiple independent origins, or more complex reticulate processes such as introgression, organelle capture, and polyploidization. By integrating multiple lines of evidence—including morphology, flow cytometry, phylogenomics, and k‑mer‑based genome‑wide similarity analyses—we seek to resolve the evolutionary dynamics of this taxonomically challenging group without relying on a reference genome. Data content This dataset contains all raw and processed data generated from 67 Cypripedium samples collected in northeastern China (Inner Mongolia, Heilongjiang, Jilin, and Liaoning provinces) and 5 out groups. These data support the major findings reported in the associated manuscript. Key findings The key finding of this dataset is that C. × ventricosum is not a simple, uniform hybrid entity, but rather a morphologically variable and genomically heterogeneous complex. The observed patterns of morphological intermediacy, genome‑wide similarity, and cytonuclear discordance are collectively consistent with a reticulate evolutionary history shaped by multiple interacting processes, including hybridization, incomplete lineage sorting (ILS), potential introgression, and polyploidization. Data interpretation and usage This dataset can be used to independently verify the reported results or to conduct additional analyses. Morphological data (Morphological.zip): Contains continuous, ordinal, and categorical trait measurements for 67 individuals. These data can be used for further multivariate analyses or comparative morphometric studies. Sequence alignments and phylogenetic trees (alignments.zip and trees.zip): Contain alignments for 46 plastid and mitochondrial sequences and 44 nrDNA sequences, as well as the corresponding maximum‑likelihood trees with bootstrap support. These can be used for independent phylogenetic reconstruction or to test alternative evolutionary hypotheses. Sourmash signatures and scripts (sourmashsig.zip): Contain 50 .sig files (k‑mer sketches, k = 31, scaled = 500). These can be used to reproduce the genome‑wide similarity comparisons or to perform additional sourmash analyses. Haplotype network files (haplotype.zip): Provide input data for TCS network reconstruction from 39 samples, allowing independent assessment of haplotype sharing patterns. All data files are organised in folders according to analysis type.