Intraspecies Genomic Divergence of a Fig Wasp Species Is Due to Geographical Barrier and Adaptation

Xun Xu,Hui Yu,Bao-Sheng Wang

doi:10.3389/fevo.2021.764828

Abstract

Understanding how intraspecies divergence results in speciation has great importance for our knowledge of evolutionary biology. Here we applied population genomics approaches to a fig wasp species (Valisia javana complex sp 1) to reveal its intraspecies differentiation and the underlying evolutionary dynamics. With re-sequencing data, we prove the Hainan Island population (DA) of sp1 genetically differ from the continental ones, then reveal the differed divergence pattern. DA has reduced SNP diversity but a higher proportion of population-specific structural variations (SVs), implying a restricted gene exchange. Based on SNPs, 32 differentiated islands containing 204 genes were detected, along with 1,532 population-specific SVs of DA overlapping 4,141 genes. The gene ontology (GO) enrichment analysis performed on differentiated islands linked to three significant GO terms on a basic metabolism process, with most of the genes failing to enrich. In contrast, population-specific SVs contributed more to the adaptation than the SNPs by linking to 59 terms that are crucial for wasp speciation, such as host reorganization and development regulation. In addition, the generalized dissimilarity modeling confirms the importance of environment difference on the genetic divergence within sp1. Hence, we assume the genetic divergence between DA and the continent due to not only the strait as a geographic barrier, but also adaptation. We reconstruct the demographic history within sp1. DA shares a similar population history with the nearby continental population, suggesting an incomplete divergence. Summarily, our results reveal how geographic barriers and adaptation both influence the genetic divergence at population-level, thereby increasing our knowledge on the potential speciation of non-model organisms.

Highlights

The origination of new species usually starts from intraspecies diversity and population subdivision
We conducted a principal component analysis (PCA) and an maximum likelihood (ML) tree based on single-nucleotide polymorphisms (SNP) to explore the genome-wide genetic structure within sp1
The Fst between differentiated islands between Hainan (DA) and either VH or SCBG is significantly higher than that between the two continental populations (Figure 2C). All those results indicate a larger genetic distance between DA and continental populations than within the continental ones. We proved that both SNPs and Structural variation (SV) contributed to the genetic difference of DA

Summary

Introduction

The origination of new species usually starts from intraspecies diversity and population subdivision. Multiple pollinator wasps were found co-existing in a single host species (Darwell et al, 2014; Yang et al, 2015; Darwell and Cook, 2017; Yu et al, 2019). Those wasps are genetically and morphologically distinct. The phylogeny among those species is complex, including populations under different phases of speciation and fully separated new species (Liu et al, 2013; Tian et al, 2015; Souto-Vilaros et al, 2019). The adaptation to different niches is an alternative hypothesis for the rapid speciation (Darwell and Cook, 2017), accompanied by others such as geographical isolation (Liu et al, 2013), hybridization (Renoult et al, 2009), host switching (Cruaud et al, 2012; Wang et al, 2021), and pollinator sharing (Bernard et al, 2020)

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Results

Conclusion