Pygmy seahorse population genomics: insights from RADsequencing on a population from West Papua, Indonesia.
Supervisor: Laurent Pouyaud Charles Perrier (Inst Sci l’Evol Montpellier).
Pygmy seahorse (H. bargibanti) is a sessile marine fish, found exclusively in association with gorgonian genus Muricella spp on which it displays similar colors as its host. It is yet unknown whether the variation among pygmy seahorse color morphs is due to plasticity on the gorgonian host or whether it is genetically determined and possibly corresponding to genetically divergent ecotypes or to variations at a few loci. The primary aim of this thesis was to produce phylogenetic and genomic information about H. bargibanti to test putative genetic structure among different seahorse morphotypes and according to gorgonian-associated host specificity. Thirty-two samples were collected from Triton Bay (West Papua, Indonesia) from 4 different gorgon mitotypes and consisted of 4 distinct color morphotypes. Partial COI mtDNA gene was PCR amplified and obtained DNA sequences confirmed that all specimens belonged to the species H. bargibanti. Tajima’s D test and measures of haplotype diversity revealed that all studied specimens of H. bargibanti are part of a single large and diverse population likely at equilibrium. Genomic results obtained from RADseq confirmed that H. bargibanti specimens originated from a single large population, by showing very little genetic distance between the individuals and a large effective population size. These results suggest high gene flow between gorgons, independently from their color, and hence suggest an absence of ecotypes corresponding to the distinct color morphs. In addition, our genome scan did not find prominent gene associated with color morphs, further suggesting that color variation is rather plastic than genetic. Further research recommendation would be sampling and sequencing additional individuals from other locations to infer spatial distance of gene flow. Moreover, our RADseq approach was representative of only a fraction of the genome and using whole genome sequencing could provide additional loci potentially associated to color morph or confirm the absence of genetic determinism in color variation.

Keywords: H. bargibanti, seahorse, phylogenetics, genomics, population genetics, RADseq, conservation, Indonesia