Gene flow and genetic structure of the seagrass Thalassia hemprichii in the Indo-Australian Archipelago

How genetic variation is distributed across space (genetic structure) and what factors influence the spatial genetic structuring is one of the primary questions in population genetics. The interaction between species biology (e.g. life-history traits) and physical processes operating in the seascape over time, including palaeo-historical events (e.g. sea level fluctuations) and contemporary processes (e.g. ocean currents), have been predicted to influence the extent of gene flow and the spatial genetic structuring in marine organisms. However, the relative contribution of each factor in governing the genetic pattern remains unclear. This study examined the pattern of genetic structure and the factors influencing this using multiple approaches across different temporal and spatial scales in the Indo-Australian Archipelago (IAA), the world’s hotspot of marine biodiversity. By comparing population genetic data of co-distributed marine species (e.g. fishes, molluscs, etc.), this study shows that for marine organisms, the interaction between species biological traits and the physical/environmental processes (habitat variability, water current, etc.) are the greatest drivers of genetic structure in the IAA. Since the physical/environmental processes fluctuate over time, spanning from hours to millennia, the temporal scale (palaeo-historical vs contemporary) at which physical/environmental processes generate genetic structure were examined using seascape genetic analysis. To minimise the effect of different biological traits, the seascape genetic analysis focused only on one species, Thalassia hemprichii, one of the dominant seagrass species in the IAA. The analysis revealed that both palaeo-historical processes (vicariance due to Pleistocene sea level fluctuations) and more contemporary processes (ocean currents) strongly influence the pattern of genetic structure at a regional scale (\u3e300 km). At this spatial scale, the influence of contemporary ocean currents is much smaller than that of historical vicariance. This finding contrasts with previous studies highlighting a strong effect of ocean currents in seagrass connectivity. Only when the effect of historical vicariance was minimised by spatially down-scaling the study from a regional (\u3e300 km) to local (km) scale, contemporary processes, including ocean currents and habitat heterogeneity, were shown to strongly influence the pattern of genetic structure. This study also revealed that significant genetic structure can occur at both regional and local scales. At the regional scale, the genetic clusters span distances of at least 500 km, suggesting that genetic connectivity of T. hemprichii populations occurs over very large geographic scales. At the local scale, significant spatial genetic structure was detected, negating the prediction of a single panmictic population. The strong genetic structuring occurring at both large and small spatial scales suggests that predicting seagrass connectivity solely based on geographic distance is inaccurate, and the relevant distance between populations in the marine system is not purely geographic, but rather determined by other factors operating on the seascape setting such as water currents and habitat heterogeneity. Thus, seascape setting is very important in seagrass gene flow and structure. Based on the pattern of gene flow, genetic structure, and genetic diversity, this research provides recommendations for seagrass conservation management in the IAA, including spatial design of conservation reserves and restoration including transplantation