Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis

Abstract

Background Restrictions to gene flow, genetic drift, and divergent selection associated with different environments are significant drivers of genetic differentiation. The black tiger shrimp (Penaeus monodon), is widely distributed throughout the Indian and Pacific Oceans including along the western, northern and eastern coastline of Australia, where it is an important aquaculture and fishery species. Understanding the genetic structure and the influence of environmental factors leading to adaptive differences among populations of this species is important for farm genetic improvement programs and sustainable fisheries management. Results Based on 278 individuals obtained from seven geographically disparate Australian locations, 10,624 high-quality SNP loci were used to characterize genetic diversity, population structure, genetic connectivity, and adaptive divergence. Significant population structure and differentiation were revealed among wild populations (average FST = 0.001–0.107; p < 0.05). Eighty-nine putatively outlier SNPs were identified to be potentially associated with environmental variables by using both population differentiation (BayeScan and PCAdapt) and environmental association (redundancy analysis and latent factor mixed model) analysis methods. Clear population structure with similar spatial patterns were observed in both neutral and outlier markers with three genetically distinct groups identified (north Queensland, Northern Territory, and Western Australia). Redundancy, partial redundancy, and multiple regression on distance matrices analyses revealed that both geographical distance and environmental factors interact to generate the structure observed across Australian P. monodon populations. Conclusion This study provides new insights on genetic population structure of Australian P. monodon in the face of environmental changes, which can be used to advance sustainable fisheries management and aquaculture breeding programs.

Population Structure, Genetic Connectivity, and Signatures of Local Adaptation of the Giant Black Tiger Shrimp (Penaeus monodon) throughout the Indo-Pacific Region

“…The main difference in genetic structure was that the Western Australian (WA) population was a discrete cluster (neutral SNPs) versus part of the Northern Australia and Philippines (NAP) cluster (outlier SNPs). Recently, Vu et al (2020) demonstrated that P. monodon from a Western Australian population was genetically divergent from multiple Eastern and Northern Australia populations (i.e., discrete cluster) based on outlier loci determined using EnA analyses ( n = 89 SNPs). We believe that the difference between the present study and Vu et al (2020) is most likely due to outlier determination being based on PD versus EnA analyses ( n = 663 vs. 89), respectively.…”

“…Recently, Vu et al (2020) demonstrated that P. monodon from a Western Australian population was genetically divergent from multiple Eastern and Northern Australia populations (i.e., discrete cluster) based on outlier loci determined using EnA analyses ( n = 89 SNPs). We believe that the difference between the present study and Vu et al (2020) is most likely due to outlier determination being based on PD versus EnA analyses ( n = 663 vs. 89), respectively. Other non-SNP studies also reported P. monodon from Western Australia as being genetically distinct from other Australian P. monodon populations ( Brooker et al 2000 ; Benzie et al 2002 ).…”

“… Vu et al (2020) recently demonstrated the role of environmental factors (e.g., sea surface temperature) in shaping the genetic structure and local adaptation of Australian P. monodon populations. Based on the results of Vu et al (2020) we hypothesized that P. monodon may also exhibit signatures of local adaption to sea surface temperature on a larger scale (e.g., across entire Indo-Pacific region).…”

“… Vu et al (2020) recently demonstrated the role of environmental factors (e.g., sea surface temperature) in shaping the genetic structure and local adaptation of Australian P. monodon populations. Based on the results of Vu et al (2020) we hypothesized that P. monodon may also exhibit signatures of local adaption to sea surface temperature on a larger scale (e.g., across entire Indo-Pacific region). Using two discrete analytical approaches, we identified 26 temperature correlated putatively adaptive SNPs that exhibited a significant correlation with SST_max or SST_min, which suggests that sea surface temperature could be contributing to genetic variation and/or local adaptation within and among Indo-Pacific P. monodon populations.…”

Correction to: Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis

“…After publication of this article [ 1 ], it is noticed the article contained an error: Fig. 3 erroneously contained panel B as a copy of panel A instead of the correct panel B illustration.…”