DOI: 10.5061/dryad.7d7wm382t
title: Circular genetic structure of the Abies nephrolepis species complex shaped by the circular landform of Northeast Asia

description: 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.
description: # Circular genetic structure of the Abies nephrolepis species complex
 shaped by the circular landform of Northeast Asia
 [https://doi.org/10.5061/dryad.7d7wm382t](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.