Evolutionary relationships of East African soda lake cichlid fish

This thesis examines the evolutionary relationships of the Alcolapia soda lake cichlid fishes of East Africa. The introduction presents background on the soda lakes in which the cichlids are found, the taxonomy and biology of the fishes, as well as the theoretical background to the study. Chapter two discusses the methods used in the thesis, addressing the benefits and limitations of each, as well as their suitability to the study in hand. Chapter three investigates the phylogenetics and phylogeography of soda lake cichlids sampled at several populations around the soda lakes and a single transplanted population outside of the focal lakes, employing a large genomic dataset generated through restriction site associated DNA (RAD) sequencing, and demonstrates low levels of interspecific genomic differentiation with high levels of ongoing gene flow. Chapter four uses the RAD dataset to test for signals of selection between Alcolapia species, employing genome-wide scans and outlier detection to characterise peaks of genomic divergence between species. Chapter five combines morphological (geometric morphometrics) and ecological (stable isotope, stomach contents) data with the RAD dataset from chapter three to consider biologically relevant diversification between Alcolapia species, testing for convergence and niche adaptation. Chapter six examines the ecomorphology of the soda lake fishes at an intraspecific level, testing for effects of geography and environment on morphological differentiation between populations. Finally, chapter seven draws together the conclusions inferred from the thesis, and discusses possible future directions for research in this system

Exploring the expression of cardiac regulators in a vertebrate adapted to an extreme environment: the cichlid fish Oreochromis (Alcolapia) alcalica

Although it is widely accepted that the cellular and molecular mechanisms of vertebrate cardiac development are evolutionarily conserved, this is on the basis of data from only a few model organisms suited to laboratory studies. Here, we investigate gene expression during cardiac development in the extremophile, non-model fish species, Oreochromis (Alcolapia) alcalica. We first characterise the early development of O. alcalica and observe extensive vascularisation across the yolk prior to hatching. We further investigate heart development by identifying and cloning O. alcalica orthologues of conserved cardiac transcription factors gata4, tbx5, and mef2c for analysis by in situ hybridisation. Expression of these three key cardiac developmental regulators also reveals other aspects of O. alcalica development, as these genes are expressed in developing blood, limb, eyes, and muscle, as well as the heart. Our data support the notion that O. alcalica is a direct-developing vertebrate that shares the highly conserved molecular regulation of the vertebrate body plan. However, the expression of gata4 in O. alcalica reveals interesting di erences in the development of the circulatory system distinct from that of the well-studied zebrafish. Understanding the development of O. alcalica embryos is an important step towards providing a model for future research into the adaptation to extreme conditions; this is particularly relevant given that anthropogenic-driven climate change will likely result in more freshwater organisms being exposed to less favourable conditions

High levels of genetic structure and striking phenotypic variability in a sexually dimorphic suckermouth catfish from the African Highveld

© 2015 The Linnean Society of London. Uncovering biological diversity to more accurately understand diversity patterns, and ultimately the processes driving diversification, is important not only from an evolutionary perspective but also a conservation perspective. This is particularly pertinent in Africa's rivers in which overall diversity, as well as how it arose, is poorly understood in comparison with lacustrine environments. Here we investigate population divergence in the sexually dimorphic suckermouth catfish species Chiloglanis anoterus (Crass, 1960) from the African Highveld, in which we observe striking variability in exaggerated male caudal fins across its range. As this trait is likely to be indirect evidence for sexual selection by female choice, a mechanism that has been shown to increase species diversity in different taxa, we used an integrated approach to test if current diversity in this species is underestimated. Results based on phylogenetic inference, population genetics and geometric morphometrics indicate that the recognized species C. anoterus represents five distinct lineages that may be considered confirmed candidate species. We suggest that diversification in these highland catfish has been facilitated through geographical isolation in upper river catchments, and that sexual selection through female choice has probably driven variation in male caudal fin morphology. In contrast to the relatively large range size of the currently recognized species (C. anoterus), our findings highlight highly restricted ranges of the lineages identified here, indicating that these highland habitats may harbour higher levels of endemic diversity than previously thought

Newly discovered cichlid fish biodiversity threatened by hybridization with non‐native species

Invasive freshwater fishes are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013–2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of O. korogwe × niloticus hybrids in three southern lakes and demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern O. korogwe populations most plausibly diverged ~140,000 years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly discovered and phenotypically unique cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions

Correction to: Widespread colonisation of Tanzanian catchments by introduced Oreochromis tilapia fishes: the legacy from decades of deliberate introduction

Due to an unfortunate turn of events, four rows in Table 2 were transposed. Hence, the original article has been corrected. The corrected section (part of ‘Minor catchments’) of Table 2 is also published here

Harnessing the power of RADseq for ecological and evolutionary genomics

High-throughput techniques based on restriction site-associated DNA sequencing (RADseq) are enabling the low-cost discovery and genotyping of thousands of genetic markers for any species, including non-model organisms, which is revolutionizing ecological, evolutionary and conservation genetics. Technical differences among these methods lead to important considerations for all steps of genomics studies, from the specific scientific questions that can be addressed, and the costs of library preparation and sequencing, to the types of bias and error inherent in the resulting data. In this Review, we provide a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past