Mapping within-species biodiversity: patterns and predictors of genetic diversity on Indo-Pacific reefs

Abstract

The rate of biodiversity loss across the globe is alarming, suggesting a need to better understand the conditions favourable for generating biodiversity, especially in hyperdiverse regions. The shallow waters of the Indo-Pacific contain the highest concentration of tropical marine species on the planet; not surprisingly, the region has been the focus of extensive study by biogeographers since the 19th century. The Indian and Pacific Oceans border over 65 nations, of which 18 are classified by the UN as Least Developed Countries, with burgeoning human populations along their coastlines. These pressures make understanding the patterns and processes underlying the generation and maintenance of all levels of biodiversity a pressing need. Compared to species diversity, genetic diversity is rarely considered in conservation planning. Genetic diversity data are commonly published as studies of a single or few species, particularly phylogeographic or population genetic studies focusing on spatial patterns within species. Once published, however, these public data can be used to answer questions on a larger spatial scale than the scale of their constituent parts. In a quantitative, comparative framework, these data can be synthesised to address questions about the bewildering diversity of the Indo-Pacific by treating species as ‘replicates’. Yet, use of these data carries certain caveats. In particular, data extraction requires significant time and often returns summary statistics rather than raw genetic data. This thesis explores the availability of such data for tropical marine fauna in the Indo-Pacific and makes use of it to examine patterns of genetic diversity at an oceanic scale. The first two chapters of this thesis use publicly available data from 108 studies for 116 species of marine fauna in the tropical Indo-Pacific. In Chapter 2, I discuss the extent and scope of currently published genetic data for Indo-Pacific marine fauna, highlighting its strengths and omissions. I show that there is a distinct bias towards studies reporting genetic diversity for marine fishes compared to marine invertebrates; that most studies focus on a single species and that there is little coherence across regions in terms of species studied. I find that, generally, regions are not consistently co-sampled with neighbouring regions. For example, the same species is not often sampled from the Great Barrier Reef as well as from Indonesia, immediately to the North. I identify locations from where a disproportionately high number of species have been the focus of genetic studies, which may serve as useful ‘anchor’ locations for researchers to build a network of sampling locations. In an appropriate collaborative framework this could allow the linking of data across very broad spatial extents to explore commonalities across multiple species. The pattern of decreasing species richness of tropical marine taxa with distance from the Coral Triangle is well known. A concordant pattern has been suggested for genetic diversity, however this concordance has not been rigorously tested. In the third chapter I assess the correlation between genetic diversity and species richness of reef fauna and hard corals in the Indo-Pacific. I expected a positive correlation, given the similar processes that govern the spatial distribution of both levels of diversity: migration, extinction/drift and speciation/mutation. By using so many species to assess this question I was able to see past some of the interspecific variation in genetic diversity that has clouded the waters in previous attempts. I find a positive, albeit weak, correlation between species richness of reef fishes or hard corals and within-species genetic diversity of shallow-water marine species. Finally, in Chapter 4, I focus on a discrete species group to illustrate the advantages of combining data from multiple research groups with focused sampling to unite disconnected geographic regions in a single analysis. Here I chose three codistributed species of giant clams (Tridacna maxima, T. crocea and a cryptic species here referred to as T. sp.) to investigate the factors underlying the spatial genetic diversity within species in the Indo-Pacific. (The paper reporting our discovery of this cryptic species in included as an Appendix to this thesis). By combining new data from the West Pacific with existing data I can reveal the relative strength of the Torres Strait landbridge as a barrier to gene flow within giant clams, when compared to other barriers in the region. My analyses of population structure show that there is strong population structure among regions in Tridacna. This has significant consequences for the management of populations but also provides further evidence for the central Indo-Pacific being a region of sympatry among divergent clades. In summary, this thesis provides a statement on the problems inherent in data synthesis and provides guidance on best practice to facilitate ease of open data access; makes use of published genetic data to test one of the big questions at the interface of ecology and evolution: the species-genetic diversity correlation; and demonstrates the utility of combining raw sequence data across lab groups to allow robust assessment of both broad and fine scale patterns of genetic diversity within a group of conservation concern, the giant clams.