Population genomics and phylogenomics of two African freshwater sardines in a fisheries context

Abstract

Genetic diversity forms the basis of all biodiversity, and is increasingly recognized as an important component in the conservation and management of natural resources, including fisheries. Small pelagic fishes constitute nearly one third of global fish catches and are a critical food source, especially for low- and middle-income countries, andplay key roles in aquatic ecosystems. Understanding their evolutionary history and contemporary genetic characteristics of these fish stocks is an important step in managing them sustainably. Small pelagic fishes have long been considered as panmictic with high genetic diversity due to limited barriers to gene flow. However, advancements in genomic technology have uncovered previously hidden population structure linked to genetic inversions and sex chromosomes, which can drive reproductive isolation and speciation even in seemingly well-mixed populations. Despite the growing availability of genomic data, its integration into fisheries management remains limited, largely due to communication gaps between stakeholders. Bridging these gaps requires understanding the diverse perspectives as well as regional variations in the acceptance of genomic applications in fisheries. Lake Tanganyika, the world’s second-largest freshwater lake, faces significant threats from climate change and anthropogenic pressures, including overfishing and biodiversity loss. The lake's fisheries, dominated by two small pelagic species, Stolothrissa tanganicae and Limnothrissa miodon, are crucial for the food security of millions of people, but questions remain about their genetic diversity, population structure, and evolutionary history. In this thesis, we generated high-quality genomic resources for both species, revealing that historical allopatry, ecological opportunities, and sex chromosome turnover have been the key factors in their speciation. Within species, S. tanganicae exhibits near-panmictic structure due to gene flow, while L. miodon shows stronger population structure, both within and outside of Lake Tanganyika, driven by inversion-linked divergence in genes related to vision and sperm properties. We estimated policy-relevant genetic indicators, showing consistently high genetic diversity and effective population size across populations. Using a survey of African and non-African fish and fisheries experts, we put our findings into a social and policy context, highlighting the challenges and opportunities for implementing genetic indicators in African fisheries management. Taken together, this thesis provides essential resources for the future genetic monitoring of Tanganyika sardines and offer concrete recommendations for the management of African fisheries.