Global phylogeography and Mediterranean genetic structure of the endangered dusky grouper, Epinephelus marginatus (Teleostei: Serranidae), based on mitochondrial and microsatellite genetic markers

Abstract

The aim of this research is to describe the evolutionary relationship, demographic history and connectivity patterns of the endangered marine fish Epinephelus marginatus (Lowe, 1834) on a local, regional and global scale for the purpose of aiding in conservation management strategies. Assessment was based on an integrative approach to molecular population genetics using comparative phylogeography and coalescent based methodologies which has allowed for resolution of evolutionary processes, diversification of lineages, and phylogenetic species delimitation. The basis of molecular analyses were conducted using subsets from 377 E. marginatus samples collected from 17 localities and three continents throughout their global distribution in the Atlantic Ocean, SW Indian Ocean and Mediterranean Sea. Local and regional assessment pertaining to the central Mediterranean Maltese Fisheries Management Zone was based on 14 microsatellite genetic markers and describes a population decreasing in size (θH = 2.2), which has gone through a significant size reduction in the past (M = 0.41) and consequently shows signs of moderate inbreeding (FIS = 0.10, ρ < 0.001) with an estimated effective population size (Ne) of 130. Spatially explicit Bayesian genetic cluster analysis detected two geographically distinct subpopulations within the Fisheries Management Zone and resolved that they are regionally connected to a larger network within the Sicily Channel. Evaluation of global phylogeography was based on a 398 base pair catenated alignment of high density intraspecific variation spanning part of the tRNA proline gene and d-loop from the mitochondrial control region. Spatial Bayesian inference identified five explicit biogeographic populations throughout their global range in the Azores, Brazil, Senegal, South Africa and Mediterranean Sea. Molecular clock convergence analysis founded on within lineage mutation rate divergence surmised that E. marginatus has been present in the Azores since the Calabrian Age during the Pleistocene Epoch, however establishment of the remaining global populations began more recently during the Middle Pleistocene with colonisation of the nouveau Mediterranean lineage occurring around 150,000 years ago. Analysis conducted using a Bayesian model of random coalescence estimated that the global population of E. marginatus’ has grown roughly 25% over the last 100,000 years, mostly owing to expansion in west Africa, with a modern effective population size estimate (Nef) of around 4.4 million. Global AMOVA (ΦST = 0.44647, ρ < 0.001) and an exact test of population differentiation (ρ < 0.001) detected great and significant bifurcation between global populations. These findings are likely a reflection of strong biogeographic barriers to gene flow detected by Monmonier’s algorithm (bootstrap 92-100) leading to vicariance of global lineages. The high haplotype (h = 0.51-0.99) and low nucleotide (π = 0.019-0.037) diversity found is consistent with the hypothesis of itinerant peripatetic pelagic larval dispersal as the main mode of global spatial expansion. A haplotype network constructed with the TCS algorithm also revealed several substitutions between lineages suggesting once established each region has remained historically independent. Long-term estimates of asymmetrical immigration between global populations predicted using the Metropolis-Hastings sampler method of random coalescence were found to be low (ɣ̅ji = 1.73 individuals gen-1), reinforcing the notion of independent lineage trajectory following long-distance founder events. Whilst E. marginatus’ appear to display morphological cohesiveness throughout their global distribution, intraspecific genetic partitioning of lineages can be seen reflected in significant pairwise ΦST (0.31–0.69, ρ < 0.001) and Nei’s DXY (3.5–16.3, ρ < 0.001), where objective use of Nei’s D (DXY > 0.15), ΦST (ΦST > 0.25) and the Poisson Tree Process (bootstrap > 95) collectively identified the Azorean population as a separate phylogenetic unit. Mantel tests revealed genetic isolation by distance was not a fundamental factor influencing global population vicariance or lineage divergence. The process of vicariance leading to allopatric speciation is often gradual, where lineage divergence is representative of cryptic speciation on a continuum. In conclusion, evidence presented suggests that five Evolutionarily Significant Units should be assigned to each of the biogeographically discrete global populations and that assessment of species status and conservation management should be undertaken at a local level due to habitat fragmentation and population substructuring.