Circular genetic structure of the Abies nephrolepis species complex shaped by the circular landform of Northeast Asia
Data files
May 31, 2024 version files 20.28 MB
Abstract
Aim:
Pinaceae have been noted for their tendency towards reticulation as a result of interspecific hybridization. Here, we demonstrated the phylogeographic dynamics of the native Northeast Asian sub-alpine conifer, Abies nephrolepis species complex (ANSC), evolving in circular overlaps along the Northeast Asian landform, which functions as a corridor with the sea, thus acting as a geographic barrier.
Location: Northeast Asia: the Korean Peninsula, Japanese Archipelago, Russian Far East, and northeastern China
Taxon: Abies nephrolepis species complex (Family Pinaceae, Genus Abies, Section Balsamea, Abies nephrolepis, A. koreana, A. veitchii, and A. sachalinensis)
Methods: A total of 728 individuals from 38 ANSC populations were analysed using multiplexed inter-simple sequence repeat genotyping by sequencing to capture variations in bi-parental nuclear genomes. Eight mitochondrial regions and eight chloroplast regions of each individual were sequenced using the MiSeq platform and Sanger sequencing. Species distribution models were generated.
Results: Bayesian clustering with 507 nuclear single nucleotide polymorphisms and the discrepancy between cytoplasmic and nuclear genome lineages implied contemporary and ancient connections between neighbouring species in the form of circular overlap. This genetic connectivity was supported by principal component analysis. Strong correlations between genetic distance and geographic distance were observed, suggesting that gene flow occurs through a continuous chain around the sea. We also found that gene flow direction and intensity changed over time, with support from paleodistribution modelling.
Conclusion: Past hybridization events were captured in cytoplasmic genomes, generating heterogeneity across maternal ancestries. This intensive phylogeographic study demonstrates speciation with incomplete reproductive isolation (continuous gene flow) among neighbouring species with an alteration of the direction and intensity of gene flow due to climate change. The divergence of ANSC due to repeated isolation and reconnection caused by heterogenous physiological environments and climate fluctuation provides a model to solve evolutionary scenarios for reticulate evolution in Pinaceae and other plants.
README: Circular genetic structure of the Abies nephrolepis species complex shaped by the circular landform of Northeast Asia
https://doi.org/10.5061/dryad.7d7wm382t
Description of the data and file structure
Movie S1 : Three-dimensional principal component analysis of 728 individuals from the A. nephrolepis species complex based on 507 SNPs. The different colors correspond to sampling sites . The raw data is included in dataset S7
Movie S2 : Three-dimensional principal component analysis of A. nephrolepis species complex populations based on 507 SNPs in 728 individuals. The different colors correspond to sampling sites. The raw data is included in dataset S8
Dataset S1: Genotype of 728 samples from the Abies nephrolepis species complex for a selected set of 507 SNPs with MIG-seq population filtering option p = 38 and r = 5 in Structure format. Individual IDs are displayed in the first column and population IDs are displayed in the second column. The first row indicates loci identifiers
Dataset S2 : Concatenated aligned sequences of eight chloroplast regions from 728 individuals of the A. nephrolepis species complex
Dataset S3 : Concatenated aligned sequences of eight mitochondrial regions from 728 individuals of the A. nephrolepis species complex
Dataset S4 : Raw occurrence data of A. nephrolepis, A. koreana, A. veitchii, and A. sachalinensis
Dataset S5 : Number of reads and number of bases per individual with MIG-seq output
Dataset S6 : Membership coefficients of individuals at K = 2 and K = 4 inferred from 507 SNPs in 728 individuals of the A. nephrolepis species complex and their chlorotype- and mitotype-identified network analysis
Dataset S7 : Data matrix for Three-dimensional principal component analysis of 728 individuals from the A. nephrolepis species complex based on 507 SNPs. Three-dimensional principal component analysis is shown in movie S1.
Dataset S8 : Data matrix for Three-dimensional principal component analysis of A. nephrolepis species complex populations based on 507 SNPs in 728 individuals. The different colors correspond to sampling sites. Three-dimensional principal component analysis is shown in movie S2.
Sharing/Access information
The research described in this publication complies with the relevant national laws implementing the Convention on Biological Diversity and Nagoya Protocol agreements. Benefits from this research accrue from the sharing of our data and results on public databases as described above.