Morphometric differentiation among haplochromine cichlid fish species of a satellite lake of Lake Victoria

Lake Victoria holds a young but species‐rich assemblage of cichlid fishes, which form a monophyletic assemblage with additional species from surrounding water bodies, termed the Lake Victoria superflock. Lake Victoria is surrounded by smaller lakes that are somewhat disconnected from the main lake. Lake Kanyaboli is such a small lake, having markedly reduced species diversity, in part comprised of Lake Victoria species and endemics. Here, we studied the modern haplochromine component of the cichlid fauna, represented by Lipochromis maxillaris, Astatotilapia nubila, Xystichromis phytophagus and Astatotilapia sp. ‘Bigeye’, as well as a number of unidentified modern haplochromine specimens. We used landmark‐based geometric morphometrics to study the degree of morphological divergence among those young entities. Twenty landmarks and 14 interlandmark distances were used for shape analysis. Multivariate analysis revealed significant differences between all four species, but principal component analysis and canonical variate analysis did not clearly discriminate between A. nubila and X. phytophagus, demonstrating great overall morphological similarity despite clear dietary differences. Besides coloration there was sexual dimorphism in body proportions, so that only male individuals were analysed further. In all four species, the observed similarities and differences in body shape conform to the type of ecological specialization of the fish. Most unidentified specimens overlapped the range of A. nubila and X. phytophagus, while the assignment test based on the canonical variate analysis suggested 70% of the three overlapping entities as separate units. To test their reproductive distinctness and to demonstrate potential hybridization, nuclear genetic data are needed.     

Evolution of the ribosomal RNA internal transcribed spacer one (ITS-1) in cichlid fishes of the Lake Victoria region

The nucleotide sequences of the first internal transcribed spacer (ITS-1) of the ribosomal RNA gene cluster have been determined for 11 species of closely related endemic cichlid fishes of the Lake Victoria region (LVR) and 6 related East African cichlids. The ITS-1 sequences confirmed independently derived basal phylogenies, but provide limited insight within this species flock. The line leading to Pseudocrenilabrus multicolor arose early, close to the divergence event that separated the tilapiine and haplochromine tribes of the "African Group" of the family Cichlidae. In this phylogeny, Astatoreochromis alluaudi and the riverine Astatotilapia burtoni are sister taxa, which together are a sister group to a monophyletic assemblage including both Lake Victoria and Lake Edward taxa. The ITS-1 data support the monophyly of haplochromine genera across lakes. Since Lake Victoria is believed to have been dry between 14, 500 and 12,400 BPE, the modern assemblage must have been derived from reinvasion by the products of earlier cladogenesis events. Thus, although the regional superflock is monophyletic, the haplochromines of Lake Victoria itself did not evolve in situ from a single ancestor.     

Pliocene isolation of a north‐west Saharan cichlid fish

The evolutionary origin of the only north‐west Saharan haplochromine cichlid, Astatotilapia desfontainii, was explored using mitochondrial DNA sequences. Phylogenetic analyses revealed that this species belonged to the main East African–Nilotic haplochromine clade, but was a distinct lineage that diverged from modern haplochromines in the Pliocene. The results suggest that A. desfontainii is a relict haplochromine lineage that has endured major climate fluctuations in North Africa.     

Signal and preference divergence among populations of the non‐endemic basal Lake Malawi cichlid fish Astatotilapia calliptera (Perciformes: Cichlidae)

In Lake Malawi and Lake Victoria, cichlid fishes have diversified into hundreds of species, many reproductively isolated by mate choice. Territorial males tend to be more aggressive to similar‐coloured males, facilitating coexistence of divergent colour morphs or species. Behavioural mate choice and aggression biases of species and allopatric populations of specialized rocky shore cichlids are influenced by divergent signals such as male colour. Believed to be basal to the Lake Malawi haplochromine radiation, and inhabiting shallow weedy areas of the lake and neighbouring water bodies, Astatotilapia calliptera also shows allopatric variation in colour. Here, it is demonstrated that such signal divergence is associated with tendencies of females to mate with males of their own population and also for males to preferentially attack males of their own population, indicating that preference divergence related to signal divergence in allopatry may have operated throughout the adaptive radiation of the Malawian cichlids. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 180–188.     

Characterization of tetranucleotide microsatellite loci in a Lake Victorian,haplochromine cichlid fish: a Pundamilia pundamilia × Pundamilia nyererei hybrid

The haplochromine cichlid fishes inhabiting Lake Victoria in East Africa are of great interest to evolutionary biologists. We have isolated and optimized six tetranucleotide and a single dinucleotide locus from a hybrid of the haplochromine cichlid fishes, Pundamilia pundamilia and P. nyererei. Characterization in 18 individuals of P. nyererei from a single wild population revealed between six and 18 alleles per locus, with expected heterozygosity ranging from 0.68 to 0.94. These loci will prove useful for investigations of population structure, and elucidating relationships between closely related species. An additional 26 unoptimized loci have been deposited with GenBank and the MEN database.     

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.     

Age and spread of the haplochromine cichlid fishes in Africa

The Haplochromini are by far the most species-rich cichlid fish tribe that originated along with the so-called primary radiation of the Lake Tanganyika cichlid species flock, i.e. at the same time during which the majority of the endemic Lake Tanganyika cichlid tribes emerged. Unlike the other tribes, the haplochromines are not restricted to Lake Tanganyika but distributed throughout Africa, except for the northwestern part of the continent. Haplochromine cichlids seeded the adaptive radiation of cichlid fishes in Lakes Malawi, Kivu, Victoria, Turkana, as well as in the now extinct paleo-Lake Makgadikgadi. Here we present a comprehensive phylogenetic and phylogeographic analysis of haplochromine cichlids that is based upon DNA sequences of two mitochondrial gene segments of riverine taxa covering all major African biogeographic regions where haplochromines are found. Our analysis revealed that six lineages of haplochromines originated within a short period of time, about 5.3-4.4 MYA. These haplochromine lineages show a highly complex phylogeographic pattern, probably severely influenced by climate- and/or geology-induced changes of the environment, with river capture events most likely playing an important role for species dispersal.     

Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages

Sex determination systems are highly conserved among most vertebrates with genetic sex determination, but can be variable and evolve rapidly in some. Here, we study sex determination in a clade with exceptionally high sex chromosome turnover rates. We identify the sex determining chromosomes in three interspecific crosses of haplochromine cichlid fishes from Lakes Victoria and Malawi. We find evidence for different sex determiners in each cross. In the Malawi cross and one Victoria cross the same chromosome is sex-linked but while females are the heterogametic sex in the Malawi species, males are the heterogametic sex in the Victoria species. This chromosome has not previously been reported to be sex determining in cichlids, increasing the number of different chromosomes shown to be sex determining in cichlids to 12. All Lake Victoria species of our crosses are less than 15,000 years divergent, and we identified different sex determiners among them. Our study provides further evidence for the diversity and evolutionary flexibility of sex determination in cichlids, factors which might contribute to their rapid adaptive radiations.

     

A BAC library of the East African haplochromine cichlid fish Astatotilapia burtoni

A BAC library was constructed from Astatotilapia burtoni, a haplochromine cichlid that is found in Lake Tanganyika, East Africa, and its surrounding rivers. The library was generated from genomic DNA of blood cells and comprises 96,768 individual clones. Its median insert size is 150 kb and the coverage is expected to represent about 14 genome equivalents. The coverage evaluation was based on genome size estimates that were obtained by flow cytometry. In addition, hybridization screens with five probes largely corroborate the above coverage estimate, although the number of clones ranged from 5 to 22 authenticated clones per single copy probe. The BAC library described here is expected to be useful to the scientific community interested in cichlid genomics as an important resource to gain new insights into the rapid evolution of the great species diversity of haplochromine cichlid fishes.     

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.     

The destruction of an endemic species flock: quantitative data on the decline of the haplochromine cichlids of Lake Victoria

Synopsis The Lake Victoria fish fauna included an endemic cichlid flock of more than 300 species. To boost fisheries, Nile perch (Lates sp.) was introduced into the lake in the 1950s. In the early 1980s an explosive increase of this predator was observed. Simultaneously, catches of haplochromines decreased. This paper describes the species composition of haplochromines in a research area in the Mwanza Gulf of Lake Victoria prior to the Nile perch upsurge. The decline of the haplochromines as a group and the decline of the number of species in various habitats in the Mwanza Gulf was monitored between 1979 and 1990. Of the 123+ species originally caught at a series of sampling stations ca. 80 had disappeared from the catches after 1986. In deepwater regions and in sub-littoral regions haplochromine catches decreased to virtually zero after the Nile perch boom. Haplochromines were still caught in the littoral regions where Nile perch densities were lower. However, a considerable decrease of species occurred in these regions too. It is expected that a remnant of the original haplochromine fauna will survive in the littoral region of the lake. Extrapolation of the data of the Mwanza Gulf to the entire lake would imply that approximately 200 of the 300+ endemic haplochromine species have already disappeared, or are threatened with extinction. Although fishing had an impact on the haplochromine stocks, the main cause of their decline was predation by Nile perch. The speed of decline differed between species and appeared to depend on their abundance and size, and on the degree of habitat overlap with Nile perch. Since the Nile perch upsurge, the food web of Lake Victoria has changed considerably and the total yield of the fishery has increased three to four times. Dramatic declines of native species have also been observed in other lakes as a result of the introduction of alien predators. However, such data concern less speciose communities and, in most cases, the actual process of extinction has not been monitored.     

Similar ecology,different morphology: Three new species of oral-mollusc shellers from Lake Edward

Lake Edward, East Africa, harbours a largely understudied assemblage of haplochromine cichlids that displays a range of adaptions to various specialised trophic niches. In this system, we discovered specimens of Haplochromis with morphologies similar to those of oral-mollusc shellers from Lake Victoria. These morphologies are characterised by short oral jaws with stout teeth that are used either to crush molluscs or to grab the soft bodies of snails and wrench them out of their shells. A morphometric study on 47 specimens from Lake Edward revealed the presence of three new species with an oral-shelling morphology: Haplochromis concilians sp. nov., H. erutus sp. nov. and H. planus sp. nov. All three species are formally described. Stomach-content observations confirmed an opportunistic oral-shelling ecology for H. concilians sp. nov. and H. erutus sp. nov. Within H. planus sp. nov., only large specimens displayed a specialised oral-shelling morphology, but their stomachs were nearly empty, while small specimens consumed mainly Ostracoda and Hydrachnidia. Remarkably, the three species differed considerably in morphology from each other, but they each resembled oral-sheller species from Lake Victoria.     

Phylogenetic Relationships Among East African Haplochromine Fish as Revealed by Short Interspersed Elements (SINEs)

Genomic DNA libraries were prepared from two endemic species of Lake Victoria haplochromine (cichlid) fish and used to isolate and characterize a set of short interspersed elements (SINEs). The distribution and sequences of the SINEs were used to infer phylogenetic relationships among East African haplochromines. The SINE-based classification divides the fish into four groups, which, in order of their divergence from a stem lineage, are the endemic Lake Tanganyika flock (group 1); fish of the nonendemic, monotypic, widely distributed genus Astatoreochromis (group 2); the endemic Lake Malawi flock (group 3); and group 4, which contains fish from widely dispersed East African localities including Lakes Victoria, Edward, George, Albert, and Rukwa, as well as many rivers. The group 4 haplochromines are characterized by a subset of polymorphic SINEs, each of which is present in some individuals and absent in others of the same population at a given locality, the same morphologically defined species, and the same mtDNA-defined haplogroup. SINE-defined group 4 contains six of the seven previously described mtDNA haplogroups. One of the polymorphic SINEs appears to be fixed in the endemic Lake Victoria flock; four others display the presence-or-absence polymorphism within the species of this flock. These findings have implications for the origin of Lake Victoria cichlids and for their founding population sizes.     

Respiratory characters of three species of haplochromine cichlids: Implications for use of wetland refugia

Respiratory characters of three east African haplochromine cichlid species that differ in their use of hypoxic wetlands were examined to consider the potential of dissolved oxygen as one factor affecting habitat use. All three species had a large gill surface area, ranging from the 67th ( Pseudocrenilabrus multicolor victoriae ) to 98th ( Astatotilapia velifer ) percentile of the known gill size range for freshwater fishes. Pseudocrenilabrus multicolor victoriae was the most tolerant to hypoxia exhibiting the lowest aquatic surface respiration ( Rs )thresholds and lowest critical oxygen tension of the three species. Astatotilapia velifer had the highest ASR thresholds, gill ventilation rates, and level of surface activity of the three species, indicating a relatively low tolerance to hypoxia. Prognathochromis venator was intermediate in its response to hypoxia. These findings are discussed in light of survivorship and distribution patterns of these species following Nile perch introduction into Lake Nabugabo.     

Stable isotope evidence from formalin–ethanol-preserved specimens indicates dietary shifts and increasing diet overlap in Lake Victoria cichlids

Stable isotopes are increasingly being used to infer past and present trophic interactions in light of environmental changes. The Lake Victoria haplochromine cichlids have experienced severe environmental changes in the past decades that, amongst others, resulted in a dietary shift towards larger prey. We investigated how the changed environment and diet of the haplochromines influenced stable isotope values of formalin-then-ethanol-preserved cichlid specimens, and then investigated how these values differed among species before (1977–1982) and after substantial environmental changes (2005–2007). We found a small preservation effect on both δ¹³C and δ¹⁵N values, and significant differences in isotope values among haplochromine species collected before the environmental changes. In contrast, there was a remarkable similarity in δ¹³C and δ¹⁵N values among species collected from the contemporary ecosystem and two out three species showed significantly different stable isotope values compared to species of the historic ecosystem. In addition, we found a putative isotopic gradient effect along our 5-km-long research transect indicating that the studied demersal species are more stenotopic than previously thought. The environmental changes have resulted in dietary change and overlap of the haplochromines which provides insight into the trophic plasticity of these species, which are often considered trophic specialists.     

Evolutionary divergence in life history traits among populations of the Lake Malawi cichlid fish Astatotilapia calliptera

During the early stages of adaptive radiation, populations diverge in life history traits such as egg size and growth rates, in addition to eco‐morphological and behavioral characteristics. However, there are few studies of life history divergence within ongoing adaptive radiations. Here, we studied Astatotilapia calliptera, a maternal mouthbrooding cichlid fish within the Lake Malawi haplochromine radiation. This species occupies a rich diversity of habitats, including the main body of Lake Malawi, as well as peripheral rivers and shallow lakes. We used common garden experiments to test for life history divergence among populations, focussing on clutch size, duration of incubation, egg mass, offspring size, and growth rates. In a first experiment, we found significant differences among populations in average clutch size and egg mass, and larger clutches were associated with smaller eggs. In a second experiment, we found significant differences among populations in brood size, duration of incubation, juvenile length when released, and growth rates. Larger broods were associated with smaller juveniles when released and shorter incubation times. Although juvenile growth rates differed between populations, these were not strongly related to initial size on release. Overall, differences in life history characters among populations were not predicted by major habitat classifications (Lake Malawi or peripheral habitats) or population genetic divergence (microsatellite‐based F_ST). We suggest that the observed patterns are consistent with local selective forces driving the observed patterns of trait divergence. The results provide strong evidence of evolutionary divergence and covariance of life history traits among populations within a radiating cichlid species, highlighting opportunities for further work to identify the processes driving the observed divergence.     

Nile perch and the transformation of Lake Victoria

The transformation of Lake Victoria that began in 1980 followed the population explosion of Nile perch Lates niloticus, causing the apparent extirpation of 500+ endemic haplochromine species and dramatic physico-chemical changes. Officially introduced in 1962–1963, but present earlier, the reasons for the long delay before its population exploded are discussed. The hypothesis that it occurred only after the haplochromine decline is evaluated, but haplochromines declined only after the Nile perch expansion began. The sudden eutrophication of the lake was attributed to Nile perch, but evidence of eutrophication from 1950 onwards led some researchers to conclude that it was the result of climatic changes. We conclude that the haplochromine destruction disrupted the complex food webs that existed prior to the upsurge of Nile perch. The depletion of fish biomass by Nile perch may have been the source of extra phosphorus responsible for the eutrophication of the lake. After the Nile perch explosion in 1980 the fish population came to be dominated by only three species, but fisheries productivity increased at least 10-fold. Fishing has caused demographic changes in Nile perch, which may have allowed some haplochromine species to recover. The condition of the lake appears to have stabilised since 2000, partly because the fish biomass has risen to at least 2 × 10⁶ t, replacing the ‘lost’ biomass and restoring some ecosystem functioning.     

Patterns in fish radiation are compatible with Pleistocene desiccation of Lake Victoria and 14,600 year history for its cichlid species flock

Geophysical data are currently being interpreted as evidence for a late Pleistocene desiccation of Lake Victoria and its refilling 14,600 years ago. This implies that between 500 and 1000 endemic cichlid fish species must have evolved in 14,600 years, the fastest large-scale species radiation known. A recent review concludes that biological evidence clearly rejects the postulated Pleistocene desiccation of the lake: a 14,600 year history would imply exceptionally high speciation rates across a range of unrelated fish taxa. To test this suggestion, I calculated speciation rates for all 41 phylogenetic lineages of fish in the lake. Except for one cichlid lineage, accepting a 14 600 year history does not require any speciation rates that fall outside the range observed in fishes in other young lakes around the world. The exceptional taxon is a lineage of haplochromine cichlids that is also known for its rapid speciation elsewhere. Moreover, since it is unknown how many founding species it has, it is not certain that its speciation rates are really outside the range observed in fishes in other young lakes. Fish speciation rates are generally faster in younger than in older lakes, and those in Lake Victoria, by far the largest of the young lakes of the world, are no exception. From the speciation rates and from biogeographical observations that Lake Victoria endemics, which lack close relatives within the lake basin, have such relatives in adjacent drainage systems that may have had Holocene connections to Lake Victoria, I conclude that the composition of the fish assemblage does not provide biological evidence against Pleistocene desiccation. It supports a hypothesis of recent colonization from outside the lake basin rather than survival of a diverse assemblage within the basin.     

Mitochondrial phylogeny of the endemic mouthbrooding lineages of cichlid fishes from Lake Tanganyika in eastern Africa

Of the three cichlid species flocks in eastern Africa, Lake Tanganyika harbors the oldest species assemblage, which is also the most diverse morphologically and behaviorally. For 12 species (20 individuals) of 12 genera of the tribe Ectodini, 852 bp from two segments (cytochrome b and control region) of the mitochondrial genome were sequenced. In addition, orthologous sequences were obtained from eight species (11 individuals) representing other mouthbrooding lineages from Lake Tanganyika. Comparisons of sequence divergences revealed that the single Tanganyikan tribe Ectodini appears to be approximately five times older than the whole Lake Malawi cichlid species flock, suggesting that the radiation of the Tanganyikan mouthbrooding lineages took place long before the species flocks of Lakes Malawi and Victoria evolved. Seven of nine surveyed tribes of Tanganyikan cichlids appear to be approximately equally divergent, and this seems to corroborate the hypothesis of a rapid simultaneous formation of lineages at an early stage in the history of the Lake Tanganyika species flock. The close genetic relationship between the endemic Tropheus lineage and a nonendemic "Haplochromine," Astatotilapia burtoni, indicates that members of the tribe Tropheini may be the sister group of the cichlid flocks of Lakes Malawi and Victoria. The phylogenetic analyses demonstrate the monophyly of the Ectodini and identify the Cyprichromini as their sister group among the Tanganyikan cichlids. Within the tribe Ectodini the molecular data suggest both a branching pattern different than that previously proposed and a subdivision of the Ectodini into four clades, instead of the two originally described. The previously postulated model of morphological transformations believed to be responsible for the drastically different types of ecological specialization found among the Ectodini might therefore be in need of reinterpretation. Characters immediately related to foraging and nutrition seem to be particularly prone to homoplasy, even among members of a single lineage of cichlid fishes.