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Population genetics of the cichlid, Cynotilapia afra (Günther 1894), in its native and introduced ranges in Lake Malawi

Zidana, Hastings K.


Hastings K. Zidana


Cock Van Oosterhout

Bernd Ha¨nfling

George F. Turner


Species introductions can provide unplanned and occasionally replicated experiments that can be studied to understand fundamental ecological and evolutionary processes associated with range expansions in the natural world. The cichlid species flock of Lake Malawi consists of an estimated 451-800 species and is a textbook example of explosive speciation that has been studied as a model system of evolution in the past three decades. In addition, fish are of major socio-economic importance to Malawian people, and they form an important source (circa 70%) of animal protein in their diet. Furthermore, fisheries activity employs 3% of the country's population and contributes to 4% of the country's Gross Domestic Product (GDP).

This thesis studies a well documented, human mediated introduction of a rocky-shore, plankton-feeding cichlid fish Cynotilapia afra into Lake Malawi National Park. This introduction has important evolutionary and ecological consequences on the native populations of Pseudotropheus zebra, and here I investigate its population genetic impacts using contemporary molecular genetic tools and analyses. Three hypotheses were tested:

1. Introduction events are usually associated with a small founder population size, and the resulting genetic bottleneck is expected to reduce genetic variation of C. afra in the introduced range.
2. The invasive scenario during the introduction followed a stepping stone pattern, or alternatively, it occurred as several independent introductions of C. afra in Lake Malawi National Park.
3. Introgressive hybridisation between C. afra and P. zebra may have facilitated the introduction of the invading C. afra population and restored its depleted genetic variation associated with the founder event. Furthermore, the gene pool of C. afra has more non-native genetic material as compared to P. zebra. Samples were collected from six native and four introduced populations of C. afra, as well as three native populations of P. zebra. The latter species is from a different genus, although laboratory experiments indicate that both species hybridise in laboratory conditions. Sequence variation in the mitochondrial DNA (mtDNA) control region was analysed using 15 individuals per sample population and 60 individuals per sample population were genotyped at six microsatellite loci. These data were analysed to test the three hypotheses and identify potential source populations, infer introduction patterns (stepping stone or independent), and deduct whether introgressive hybridisation may have facilitated the founder event and subsequent establishment of C. afra in the invasive range in Lake Malawi Natural Park. The three data chapters in this thesis discuss the findings of the mtDNA sequence study (Chapter 2) and the microsatellite study (Chapter 3). In Chapter 4, I analyse the microsatellite data in further detail and consider the role of introgression by using Bayesian analysis tools.

The mtDNA study presented in Chapter 2 reveals that C. afra and P. zebra mtDNA sequences show high levels of lineage sorting (i.e. the DNA sequences of both species are remarkably distinct). This finding is in sharp contrast to previous studies on Lake Malawi rock-dwelling cichlids which have shown that cichlid species share the same or very similar mtDNA haplotypes. Furthermore, the introduced populations showed a higher sequence and haplotype diversity than their native counterparts. This analysis suggests that elevated gene diversity was largely due to C. afra populations being founded by individuals from several genetically distinct and geographically separate populations. In Chapter 4, I discuss the role of introgressive hybridisation with native P. zebra, and its impact on mtDNA variation in the introduced C. afra gene pool.

In Chapter 3, I show that in contrast to the signal obtained from the mtDNA, the genetic variation at the microsatellite loci exhibited a significant reduction in the introduced range. Introduced C. afra populations have a lower mean effective number of alleles (ne) than C. afra populations in their native range. I use an approximate Bayesian analysis and show compelling evidence that at least two independent introductions have contributed to the introduced C. afra gene pool, a conclusion that is supported by high probability values. This conclusion differs from that of previous studies which suggested a stepping stone introduction pattern around Thumbi West Island. Surprisingly, a population of C. afra at Domwe Island was founded by a source population from Thumbi West Island, and this stepping stone introduction pattern is supported with a high probability (95%).

Microsatellite analysis furthermore suggests that the founder event of C. afra in Lake Malawi National Park was associated with strong genetic drift associated with a genetic bottleneck. I was not able to detect this signal from the mtDNA genetic marker alone, which showed an increase in genetic variation at the mtDNA due to different source populations contributing to the founder event (see Chapter 2). These combined studies reported in Chapter 2 and 3 thus demonstrate that microsatellites may be well-suited to investigate questions related to conservation issues such as bottlenecks associated with founder events, while mtDNA is more suited to reveal the evolutionary processes and establish different source populations that have contributed to the introduction.

In Chapter 4, I analyse the level of genetic differentiation at microsatellite loci, and show that the introduced C. afra and native P. zebra populations at Thumbi West Island are genetically more similar (G'ST=0.36+/-0.05) than the species-pair at Otter point (G'ST=0.94+/-0.18) and Domwe Island (G'ST=0.55+/-0.09). In addition, C. afra and P. zebra at Thumbi West Island showed a lower genetic distance than allopatric C. afra or P. zebra populations from Otter point and Domwe Island. Further analysis using a Bayesian assignment approach supports previous findings and demonstrates the likelihood of introgressive hybridisation between an introduced C. afra and a native P. zebra population at Thumbi West Island. No evidence of introgression is found at Otter point and Domwe Island, where the C. afra and P. zebra populations show distinct genetic structure. The occurrence of introgressive hybridisation at Thumbi West between species from distinct genera shows that translocations can have a dramatic impact even on the gene pools of heterospecific recipient populations. The results from this work have crucial implications in evolution of cichlid fishes and in invasion biology when predicting the evolution of invasiveness.

In summary, the thesis shows that hybridisation, as well as the introduction of multiple genetically differentiated source populations has increased the genetic diversity of introduced C. afra populations, and this may have facilitated their establishment in Lake Malawi National Park. Translocation of cichlid species in Lake Malawi can have a dramatic impact even on heterospecific gene pools.


Zidana, H. K. (2010). Population genetics of the cichlid, Cynotilapia afra (Günther 1894), in its native and introduced ranges in Lake Malawi. (Thesis). University of Hull. Retrieved from

Thesis Type Thesis
Deposit Date Aug 15, 2011
Publicly Available Date Feb 22, 2023
Keywords Biological sciences
Public URL
Additional Information Department of Biological Sciences, The University of Hull
Award Date Jan 1, 2010


Thesis (3.9 Mb)

Copyright Statement
© 2010 Zidana, Hastings K. All rights reserved. No part of this publication may be reproduced without the written permission of the copyright holder.

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