Exploring cross-species genetic diversity: unveiling new insights in Megalobrama through whole genome-wide simple sequence repeats

Relying solely on cross-species analysis of single nucleotide polymorphisms (SNPs) through single-species genome mining can introduce biases. To address this challenge, we propose a sequencing-based approach for genome-wide genotyping of simple sequence repeats (SSRs) as an alternative method. Megalobrama, belonging to the family Xenocyprididae of the order Cypriniformes, comprises four primary species: M. amblycephala (Mambl), M. terminalis (Mterm), M. pellegrini (Mpell), and M. hoffmanni (Mhoff). This study employs a sequencing-based genome-wide SSR genotyping approach, analyzing genetic information from nine Megalobrama populations using SSRs extracted from the Mambl genome. Our genotyping efforts successfully covered 916 or 24,180 SSR loci, with less than 10% or 30% of missing data, respectively. The analysis reveals significant gene flow between Mterm, Mpell, and Mambl, validated by the D-statistic test. The F3-statistic values, estimated at -0.00868676 or -0.00831186 based on 916 or 24,180 SSR loci respectively, further support these findings. Additionally, the hypothesis of extensive gene flow among Mterm, Mambl, and Mpell gains robust support from Approximate Bayesian Computation, with a posterior probability of 0.674. Species trees and phylogenetic networks, constructed using 4,116 orthogroups identified across all species, corroborate this hypothesis. Importantly, our study emphasizes the suitability of genome-wide SSRs over SNPs for cross-species genetic diversity studies. In conclusion, our study contributes to the discourse of conservation genetics, advocating for a holistic approach that integrates diverse markers while recognizing their limitations. Our findings not only illuminate the genetic landscape of Megalobrama species but also offer guiding principles for conservation efforts.