Variation in habitat preference and population structure among three species of the Lake Malawi cichlid genus Protomelas

Several studies have demonstrated strong population structuring over small distances in the rocky-shore mbuna cichlid fishes from Lake Malawi, suggesting the potential for allopatric speciation. However, many endemic Lake Malawi cichlids are neither mbuna, nor confined to rocky shores. Using microsatellites, we investigated the population structure in three species of the non-mbuna genus Protomelas. The rocky-shore P. taeniolatus showed high levels of population structure even over distances of less than 1 km, while the sandy-shore species P. similis showed no significant structure over distances up to 21 km. Protomelas fenestratus, which is generally found at the interface between rocks and sand, also showed low levels of population structure. Our results suggest that the model of allopatric speciation based on habitat fragmentation within the current lake basin may be equally applicable to rocky-shore non-mbuna as to mbuna, but that an alternative model is required to explain speciation among sandy-shore species as well as the deep-water and pelagic species.     

Extreme microallopatric divergence in a cichlid species from Lake Malawi

We demonstrate significant population structuring on an extremely small spatial scale between adjacent demes of a Lake Malawi haplochromine cichlid species of the mbuna group, Pseudotropheus callainos, separated by only 35 m of habitat discontinuity. This substantiates further the notion that intralacustrine allopatric divergence may help to explain the high level of species richness of the mbuna in comparison to other Malawian cichlids, as well as of the Malawian haplochromines as a whole.     

No evidence for parallel sympatric speciation in cichlid species of the genus Pseudotropheus from north-western Lake Malawi

To test the hypothesis of parallel speciation by sexual selection, we examined length variation at six microsatellite loci of samples from four sites of four to six putative species belonging to two subgenera of rocky shore mbuna cichlids from Lake Malawi. Almost all fixation indices were significantly different from zero, suggesting that there is presently little or no gene flow among allopatric populations or sympatric species. Analysis of variance indicated that genetic distances among allopatric populations of putative conspecifics were significantly lower than among sympatric populations of heterospecifics. The topology of trees based on distance matrices was also largely consistent with the hypothesis that the putative species are monophyletic and have thus not evolved in parallel in their present locations. If parallel speciation does occur in Malawi cichlids, it may be on a larger spatial scale than investigated in our study.     

Isotopic change throughout the life history of a Lake Malawi cichlid fish

Clear changes in body size-isotope (carbon and nitrogen) trajectories of Pseudotropheus callainos , a cichlid belonging to the endemic haplochromine species radiation in Lake Malawi, were found that corresponded with an ontogenetic dietary shift from predominantly planktonic to benthic food sources. The results indicated that dietary switching was a proximate cause of isotopic change over the life history of this species and confirmed the value of stable isotope signatures for inferring diet. The data also illustrated that possible variability of signatures over the life history of a species should be considered when using stable isotope ratios to investigate fine-scale ecological differentiation among taxa.     

Nuclear gene variation and molecular dating of the cichlid species flock of Lake Malawi

The cichlid fishes of Lake Malawi are famously diverse. However, evolutionary studies have been difficult because of their recent and uncertain phylogenetic history. Portions of 12 nuclear loci were sequenced in nine rock-dwelling species (mbuna) and three representatives of pelagic nonmbuna species. In contrast to the pattern of variation at mitochondrial genes, which do provide phylogenetic resolution at the level of mbuna versus nonmbuna, and among some genera, the nuclear loci were virtually devoid of phylogenetic signal. Only a small minority of variable positions were phylogenetically informative, and no phylogenetic branches are supported by more than one site. From the nuclear gene perspective the Malawian radiation appears to be a star phylogeny, as if the founding of the lake was accompanied by a partial bottleneck. The pattern is different from that found in Lake Victoria, in which nuclear loci share large amounts of ancestral variation. In the case of nuclear genes of Lake Malawi, the absence of phylogenetically informative variation suggests a relative absence of ancestral variation. Nuclear genes also differed from the mitochondria in having nearly twice the amount of divergence from Oreochromis (tilapia). An approximate splitting time between mbuna and nonmbuna lineages was estimated as 0.7 Myr. Oreochromis is estimated to have diverged from the cichlids in Lake Malawi and Lake Tanganyika about 18 MYA.     

Differences in stable isotope composition within and among zooplanktivorous Utaka cichlid populations from Lake Malawi

Stable isotope analysis was used to determine whether five sympatric zooplanktivorous cichlids of the Utaka assemblage from Lake Malawi vary in isotopic signature as an indication of possible differences in food resource composition. The isotopic composition of the Utaka in combination with literature data about diet composition suggests that these species exploit a narrow range of zooplanktonic prey types. At five sampling locations, significant differences in δ¹³C and δ¹⁵N were detected among species but a consistent pattern across locations was absent. Significant intraspecific differences between locations were found. These differences were relatively low in view of the large geographic distances between the populations and there was no consistent spatial pattern among the species. The observed differences may be indicative of local variations in diet composition, which may help in reducing niche overlap among these zooplanktivores.     

Aggressive biases towards similarly coloured males in Lake Malawi cichlid fishes

In haplochromine cichlids, female mate choice based on male nuptial coloration has played an important role in speciation. Recent studies suggest that male coloration strongly influences the distribution of these fishes based on male-male aggression; males direct more aggression towards similarly coloured opponents while tolerating differently coloured individuals. We explored the role of male nuptial colour in aggression among the mbuna of Lake Malawi, examining aggression by male Metriaclima mbenjii, the red top cobalt zebra, towards conspecific opponents, similarly coloured heterospecific opponents and differently coloured heterospecifics. In trials in which focal males were offered a single opponent, while the total number of aggressive behaviours did not vary among opponent species, the types of behaviours did; focal males directed more lateral displays towards conspecifics than towards the other opponent species. When focal males were offered two opponents simultaneously, M. mbenjii directed more aggressive behaviours and more lateral displays towards similarly coloured opponents, regardless of species. Furthermore, when offered a conspecific and a similarly coloured opponent simultaneously, there were no differences in behaviour towards either opponent. Thus, nuptial coloration is used by males to identify competitors, and it suggests that male-male aggression may have also been an important diversifying force in speciation in rock-dwelling Lake Malawi cichlids.     

Elevated mtDNA diversity in introduced populations of Cynotilapia afra (Günther 1894) in Lake Malawi National Park is evidence for multiple source populations and hybridization

Genetic variation in many invasive species shows little or no signs of a founder event, suggesting that high genetic diversity may facilitate establishment success. The rocky‐shore, plankton‐feeding cichlid fish Cynotilapia afra is endemic to Lake Malawi, but naturally absent from many suitable sites. In the 1960s, this species was introduced to the southern areas of the lake, presumably as a result of the aquarium fish trade. It has now become established on a number of rocky areas within the Lake Malawi National Park. Here, we analysed DNA sequence variation in the mitochondrial control region of six native and four introduced populations of C. afra, and three populations of the closely‐related and hybridizing Pseudotropheus zebra. In contrast to previous studies of Lake Malawi rock dwelling cichlids, network analyses suggested that native populations of C. afra showed high levels of lineage sorting in mtDNA. Introduced populations showed higher sequence and haplotype diversity than their native counterparts. Our analyses suggested that the elevated gene diversity was largely attributed to the fact that the introduced C. afra populations were derived from several genetically distinct and geographically separate populations, and to a lesser extent because of introgressive hybridization with native P. zebra. The establishment and spread of C. afra may be partly because of its ability to occupy a vacant ecological niche, but it may also have been facilitated by its enhanced genetic diversity.     

Speciation in rapidly diverging systems: lessons from Lake Malawi

Rapid evolutionary radiations provide insight into the fundamental processes involved in species formation. Here we examine the diversification of one such group, the cichlid fishes of Lake Malawi, which have radiated from a single ancestor into more than 400 species over the past 700 000 years. The phylogenetic history of this group suggests: (i) that their divergence has proceeded in three major bursts of cladogenesis; and (ii) that different selective forces have dominated each cladogenic event. The first episode resulted in the divergence of two major lineages, the sand- and rock-dwellers, each adapted to a major benthic macrohabitat. Among the rock-dwellers, competition for trophic resources then drove a second burst of cladogenesis, which resulted in the differentiation of trophic morphology. The third episode of cladogenesis is associated with differentiation of male nuptial colouration, most likely in response to divergent sexual selection. We discuss models of speciation in relation to this observed pattern. We advocate a model, divergence with gene flow, which reconciles the disparate selective forces responsible for the diversification of this group and suggest that the nonadaptive nature of the tertiary episode has significantly contributed to the extraordinary species richness of this group.     

PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite loci in the cichlid fish in Lake Victoria, Haplochromis chilotes

Twelve short tandem repeat markers were successfully isolated from a cichlid, Haplochromis chilotes, in Lake Victoria, and characterized in Haplochromis pyrrhocephalus. The microsatellite regions of these markers were found to have between two and 48 alleles with heterozygosity ranging from 0.07 to 0.97. No loci showed significant departures from the Hardy–Weinberg or linkage equilibrium after the Bonferroni correction (P > 0.05). Cross‐species amplification in other cichlids of Lake Victoria, Haplochromis laparogramma, Lithochromis rubripinnis, L. rufus and Haplochromis sp. ‘rockkribensis’, was successful.     

Biogeography and population genetics of the Lake Malawi cichlid Melanochromis auratus: habitat transience, philopatry and speciation

Migration rates among nine populations of the endemic Lake Malawi cichlid Melanochromis auratus were estimated along a 42-km stretch of habitat in the southern end of the lake. Allele frequencies were surveyed at four simple sequence repeat (SSR) loci. The data suggest migration rates among populations are quite low. Exact tests indicate that statistically detectable allele frequency differences exist between many adjacent populations in the study. The F_ST value among all populations was estimated to be 0.151 (P < 0.0002). A biogeographic survey suggests that the highest levels of genetic differentiation exist between populations separated by stretches of deep water. Migration is more common between populations separated by shallower water or with shoreline dispersal routes. Reduced allelic diversity was observed at more recently created habitat patches, suggesting that either bottlenecks are associated with the colonization of new habitat patches or that these shallower sites were all founded by genetically depauperate ancestral populations. The extreme philopatry of M. auratus, coupled with the patchy distribution and transient nature of its preferred habitat, provides opportunities for both selection and genetic drift to produce genetic differentiation among populations. Both processes may be important to the evolution of taxonomic diversity in the East African cichlid species flocks.     

Population-structure and genetic diversity in a haplochromine cichlid fish [corrected] of a satellite lake of Lake Victoria

The approximately 500 species of the cichlid fish species flock of Lake Victoria, East Africa, have evolved in a record-setting 100,000 years and represent one of the largest adaptive radiations. We examined the population structure of the endangered cichlid species Xystichromis phytophagus from Lake Kanyaboli, a satellite lake to Lake Victoria in the Kenyan Yala wetlands. Two sets of molecular markers were analysed--sequences of the mitochondrial control region as well as six microsatellite loci--and revealed surprisingly high levels of genetic variability in this species. Mitochondrial DNA sequences failed to detect population structuring among the three sample populations. A model-based population assignment test based on microsatellite data revealed that the three populations most probably aggregate into a larger panmictic population. However, values of population pairwise FST indicated moderate levels of genetic differentiation for one population. Eleven distinct mitochondrial haplotypes were found among 205 specimens of X. phytophagus, a relatively high number compared to the total number of 54 haplotypes that were recovered from hundreds of specimens of the entire cichlid species flock of Lake Victoria. Most of the X. phytophagus mitochondrial DNA haplotypes were absent from the main Lake Victoria, corroborating the putative importance of satellite lakes as refugia for haplochromine cichlids that went extinct from the main lake in the last decades and possibly during the Late Pleistocene desiccation of Lake Victoria.     

Possible species specific courtship sounds by two sympatric cichlid fishes in Lake Malawi, Africa

Sounds were produced by the males of two species of cichlid fishes while courting females. Each courtship sound consisted of a series of distinct pulses occurring in rapid succession. Courtship sounds produced by Tramitichromis cf. intermedius and Copadichromis conophorus were significantly different in pulse rate and individual pulse durations. For C. conophorus calls (n=127) the mean ± sd number of pulses per call was 10 ± 3 and call duration was 181 ± 59 ms. There was a significant positive linear relationship between call duration and the number of pulses (r²=0.912, p < 0.001). The dominant frequency of the pulses in calls was 471 ± 50 (range 372–594) Hz (n=40 calls). T. cf. intermedius also produced a pulsed courtship call; data (mean ± sd) from two male T. cf. intermedius: 9 ± 2 pulses per call and duration 199 ± 44 ms (n=20 calls). The linear regression between call duration and number of pulses was positive (r²=0.463, p=0.001). Pulse rate within calls of T. cf. intermedius compared to C. conophorus were significantly different (p=0.018). Individual pulse durations were also significantly different (p=0.043) between species. However, interpulse intervals were not significantly different (p=0.177). These cichlids produced courtship sounds that were distinct by individual pulse durations and by pulse repition rate in a call.     

Assortative mating among rock-dwelling cichlid fishes supports high estimates of species richness from Lake Malawi

It has been estimated that Lake Malawi, Africa, contains 500–650 endemic species of cichlid fishes, the largest number of vertebrate species endemic to any comparable sized area on the planet. As many of these putative species cannot be distinguished anatomically, these estimates of species richness depend to a great extent on the assumption that sympatrically occurring male colour morphs represent biological species. We have tested this assumption using a combination of behavioural observations of courtship and microsatellite DNA analysis for six putative species of the Pseudotropheus ( Tropheops ) complex and three of the Pseudotropheus ( Maylandia ) complex occurring sympatrically at Nkhata Bay. We were unable to demonstrate assortative courtship for the species pairs Pseudotropheus ( Maylandia ) zebra / P . 'gold zebra' or P. ( Tropheops ) 'band'/ P. ( T .) 'rust' because we were unable to distinguish between the females of these taxa. All other taxa showed clear assortative courtship, except for P. ( T .) 'deep', a deep-water species which was rarely observed. Fixation indices (θ_ST for the infinite allele model, and R _ST for the stepwise mutation model) calculated from six microsatellite DNA loci demonstrated significant deviations from panmixia in all pairwise comparisons of putative species, indicating little or no gene flow between populations. All taxa showed high levels of allelic diversity providing evidence that genetic bottlenecking may have been of limited importance in the speciation process. Assortative mating among taxa differing only in male colouration is supportive of theories that speciation in these fishes has been driven by sexual selection by female choice.     

High prevalence of non-synonymous substitutions in mtDNA of cichlid fishes from Lake Victoria

When a population size is reduced, genetic drift may fix slightly deleterious mutations, and an increase in nonsynonymous substitution is expected. It has been suggested that past aridity has seriously affected and decreased the populations of cichlid fishes in Lake Victoria, while geographical studies have shown that the water levels in Lake Tanganyika and Lake Malawi have remained fairly constant. The comparably stable environments in the latter two lakes might have kept the populations of cichlid fishes large enough to remove slightly deleterious mutations. The difference in the stability of cichlid fish population sizes between Lake Victoria and the Lakes Tanganyika and Malawi is expected to have caused differences in the nonsynonymous/synonymous ratio, ω (= d_N/d_S), of the evolutionary rate. Here, we estimated ω and compared it between the cichlids of the three lakes for 13 mitochondrial protein-coding genes using maximum likelihood methods. We found that the lineages of the cichlids in Lake Victoria had a significantly higher ω for several mitochondrial loci. Moreover, positive selection was indicated for several codons in the mtDNA of the Lake Victoria cichlid lineage. Our results indicate that both adaptive and slightly deleterious molecular evolution has taken place in the Lake Victoria cichlids' mtDNA genes, whose nonsynonymous sites are generally conserved.     

Microsatellite analysis of population structure in Canadian polar bears

Attempts to study the genetic population structure of large mammals are often hampered by the low levels of genetic variation observed in these species. Polar bears have particularly low levels of genetic variation with the result that their genetic population structure has been intractable. We describe the use of eight hypervariable microsatellite loci to study the genetic relationships between four Canadian polar bear populations: the northern Beaufort Sea, southern Beaufort Sea, western Hudson Bay, and Davis Strait - Labrador Sea. These markers detected considerable genetic variation, with average heterozygosity near 60% within each population. Interpopulation differences in allele frequency distribution were significant between all pairs of populations, including two adjacent populations in the Beaufort Sea. Measures of genetic distance reflect the geographic distribution of populations, but also suggest patterns of gene flow which are not obvious from geography and may reflect movement patterns of these animals. Distribution of variation is sufficiently different between the Beaufort Sea populations and the two more eastern ones that the region of origin for a given sample can be predicted based on its expected genotype frequency using an assignment test. These data indicate that gene flow between local populations is restricted despite the long-distance seasonal movements undertaken by polar bears.     

Genetic homogeneity among breeding grounds and nursery areas of an exploited Lake Malawi cichlid fish

1. Nursery areas are commonly recognized as important habitats for the management and conservation of fish stocks. Here we report the use of nursery areas by an exploited offshore cichlid in Lake Malawi, Rhamphochromis longiceps .
2. Like all haplochromine cichlids that have been studied, the species is a maternal mouthbrooder that broods eggs for several weeks following spawning. We found evidence that during this brooding period females migrate from open water to release juveniles in three shallow peripheral waterbodies (Chia Lagoon, Unaka Lagoon, Lake Malombe). However, it was unclear whether there is geographical population structuring within the species, which could indicate stock differences in their use of these nursery habitats, or if the lake contains a genetically panmictic population that employs nursery habitats opportunistically.
3. To investigate spatial and temporal population structuring within the lake we genotyped populations at seven microsatellite DNA loci. Overall, we found no significant spatial structuring among juveniles from the peripheral lagoons or among breeding males within the main lake body. Moreover, we found no evidence of temporal structuring among males on the breeding grounds within Lake Malawi or females entering Chia lagoon. Together, these results suggest that Lake Malawi contains a genetically homogeneous population of R. longiceps .
4. At present we know little of the distribution of juvenile R. longiceps elsewhere in the Lake Malawi basin, but their absence from surveyed rocky and sandy littoral habitats makes it possible that the species is dependent upon a small number of nearshore nursery areas, including these lagoons. As such, conservation of lagoon habitats and monitoring of exploited fish stocks within them may be important for effective preservation of biodiversity within the catchment.     

Does the time spent near a male predict female mate choice in a Malawian cichlid?

Gravid female Malawian Pseudotropheus cichlids spent significantly more time with males that they subsequently chose as mates, indicating that time spent near a male is a valid and accurate method of measuring female preference. Furthermore, females preferred to mate with males that had longer pelvic fins and a larger number of eggspots on their anal fins. In some instances, females chose to mate with both of the males with which they were presented, possibly because they were unable to discriminate between them.     

Evolutionary history of the endemic Lake Tanganyika cichlid fish Tylochromis polylepis: a recent intruder to a mature adaptive radiation

With an age of 9–12 million years (Myr) Lake Tanganyika holds the oldest and most complex species flock of cichlid fishes. It is believed to be of polyphyletic origin and rooted in nine ancient African lineages, six of which underwent diversification, while three remained monotypic. Here, the evolutionary history, route and timing of colonization were analyzed, as well as intraspecific genetic diversity of Tylochromis polylepis , the single albeit endemic representative of the tribe Tylochromini in Lake Tanganyika. The role of Tylochromis in the radiation was uncertain and the species was suggested to be either an ancient colonizer or a recent addition to the fauna. With 2.8–4.2% sequence divergence to four congeners living in Lakes Bangweulu and Mweru (Upper Congo River) as well as from Luozi River and Lake Etsotso (Lower Congo River), the species appears to be a recent colonizer, which is likely to have diverged from its riverine allies less than 510 000 years ago. The ability to enter an adaptive radiation at a highly mature stage with its densely packed species community and fine-tuned niche segregation seems remarkable. So far it was assumed that all Tanganyikan endemics evolved within the lake ecosystem by intralacustrine speciation, and that complex competitive interactions among endemics tighten the system against intruders. The intruding species can be classified as a generalist living over muddy bottom in the lake and in river estuaries. Microgeographic substructuring is suggested, possibly because of geographic segregation of breeding sites. Concerning the route of colonization, a downstream movement via one of the inflowing rivers situated in the south of Lake Tanganyika is suggested.