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. 2022 Nov 12;23(1):750.
doi: 10.1186/s12864-022-08984-w.

Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies

Ahmad Farhadi  1   2 , Andrew G Jeffs  3 , Shane D Lavery  3
Affiliations

Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies

Ahmad Farhadi et al. BMC Genomics. .

Abstract

Background: Evolutionary divergence and speciation often occur at a slower rate in the marine realm due to the higher potential for long-distance reproductive interaction through larval dispersal. One common evolutionary pattern in the Indo-Pacific, is divergence of populations and species at the peripheries of widely-distributed organisms. However, the evolutionary and demographic histories of such divergence are yet to be well understood. Here we address these issues by coupling genome-wide SNP data with mitochondrial DNA sequences to test the patterns of genetic divergence and possible secondary contact among geographically distant populations of the highly valuable spiny lobster Panulirus homarus species complex, distributed widely through the Indo-Pacific, from South Africa to the Marquesas Islands.

Result: After stringent filtering, 2020 SNPs were used for population genetic and demographic analyses, revealing strong regional structure (FST = 0.148, P < 0001), superficially in accordance with previous analyses. However, detailed demographic analyses supported a much more complex evolutionary history of these populations, including a hybrid origin of a North-West Indian Ocean (NWIO) population, which has previously been discriminated morphologically, but not genetically. The best-supported demographic models suggested that the current genetic relationships among populations were due to a complex series of past divergences followed by asymmetric migration in more recent times.

Conclusion: Overall, this study suggests that alternating periods of marine divergence and gene flow have driven the current genetic patterns observed in this lobster and may help explain the observed wider patterns of marine species diversity in the Indo-Pacific.

Keywords: Admixture; Demography; Genome-wide SNPs; Panulirus homarus complex.

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Conflict of interest statement

The authors declare no potential competing interest of interest.

Figures

Fig. 1
Fig. 1
Species distribution and sampling locations for P. homarus spiny lobsters in the Indo-Pacific Ocean. Circles are sampling locations in this study and color represents the morphotypes (orange: South Africa P. h. rubellus (SA); blue: Northwest Indian Ocean (previously P. h. megasculpta) (NWIO), green: Central P. h. homarus (C); purple: Marquesas Islands (MI) (previously P. h. Brown). Color dashed lines show the hybrid zones
Fig. 2
Fig. 2
DAPC scatter plot of P. homarus main lineages using SNP dataset in this study, a) all SNP dataset b) outlier SNP dataset
Fig. 3
Fig. 3
Bar-plot of admixture (top, at optimal K = 4), admixture bar-plot of outlier loci (middle, k = 4), mtCR BAPS plot (bottom, optimal K = 3) on P. homarus populations. Each vertical bar represents an individual
Fig. 4
Fig. 4
Minimum spanning network representing the phylogeographic relationship between P. homarus lineages, left: using genome wide SNPs, right: using mtCR
Fig. 5
Fig. 5
∂a∂i best-fit models for S. Africa-Central (SA-C), NWIO-Central (NWIO-C), and Central-Marquesas Islands (C-MI) population pairs. A Demographic model diagrams indicating relative time since population split, relative timing and direction of asymmetric gene flow (> 10-fold difference in m), and relative population sizes. B Joint allele frequency spectra (AFS) obtained from data. C joint AFS obtained from the best fit model. Further detail in Supplementary file 1- Fig. S6 and Table S3
See this image and copyright information in PMC

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