Dead-End Hybridization in Walnut Trees Revealed by Large-Scale Genomic Sequence Data

Abstract

Although hybridization plays a large role in speciation, some unknown fraction of hybrid individuals never reproduces, instead remaining as genetic dead-ends. We investigated a morphologically distinct and culturally important Chinese walnut, Juglans hopeiensis, suspected to have arisen from hybridization of Persian walnut (J. regia) with Asian butternuts (J. cathayensis, J. mandshurica, and hybrids between J. cathayensis and J. mandshurica). Based on 151 whole-genome sequences of the relevant taxa, we discovered that all J. hopeiensis individuals are first-generation hybrids, with the time for the onset of gene flow estimated as 370,000 years, implying both strong postzygotic barriers and the presence of J. regia in China by that time. Six inversion regions enriched for genes associated with pollen germination and pollen tube growth may be involved in the postzygotic barriers that prevent sexual reproduction in the hybrids. Despite its long-recurrent origination and distinct traits, J. hopeiensis does not appear on the way to speciation.

Keywords: chromosomal rearrangements; gene flow; hybridization; postzygotic reproductive barriers; speciation; walnuts.

Fig. 1

The geographic locations and representative nuts of Juglans hopeiensis and its parents. The Asian butternuts, J. cathayensis, Jc–Jm hybrids, and J. mandshurica all have similar nuts (ovoid with a distinct apical, shell rough ridged, and deeply pitted). The species geographic distributions were mainly referred from the Global Biodiversity Information Facility (GBIF: http://www.gbif.org/).

Fig. 2

Genomic variation in Juglans hopeiensis and its parents. (A) Results of a STRUCTURE analysis with the optimal K showing individual ancestry proportions. (B) PCA showing the first two principal components (excluding four outlying individuals of J. regia). (C) Individual heterozygosity for polymorphic sites across the genome. (D) NgsAdmix analysis assignments for 50-kb stepping windows across contig 1.

Fig. 3

Inferring population demographic history. (A) Changes in effective population size (N_e) over the past 4.5 My in Asian butternuts and Juglans regia as inferred with PSMC. Within J. hopeiensis and Jc–Jm hybrids, results were obtained by using J. mandshurica as the reference genome. Each color and line represent one group and individual, respectively, and g, generation time (year), μ, mutation rate (per site per year). (B) Simplified graphical summary of the best-fitting demographic model inferred by fastsimcoal2 based on SNPs from Asian butternuts and Persian walnut. The joint past population is shown as the light green bar. Gray-shaded area and arrows indicate the bidirectional gene flow. The orange and blue bars represent Asian butternuts and Persian walnut. Populations of Asian butternuts and Persian walnut were set to decline from past to present based on the PSMC results.

Fig. 4

The maternal origin of hybrids. ML phylogeny obtained from 22 chloroplast haplotypes. ML bootstrap values (MLBS) ≥95% are labeled on each node.

Fig. 5

High genetic differentiation regions with 50-kb stepping windows across the 16 chromosomes. (A) F_ST analysis between Juglans cathayensis and J. regia. (B) F_ST analysis between J. mandshurica and J. regia. (C) D_XY analysis between J. cathayensis and J. regia. (D) D_XY analysis between J. mandshurica and J. regia. Windows that exceeded the gray-dotted line were identified as F_ST and D_XY outliers, represented by black or red dots. C, M, and R are the abbreviations of J. cathayensis, J. mandshurica, and J. regia.

Fig. 6

Six inversions longer than 10 kb in syntenic chromosome regions between Asian butternuts and Juglans regia.