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

Patterns of sex-biased dispersal are consistent with social and ecological constraints in a group-living cichlid fish

BACKGROUND

Sex-biased dispersal is a common and widespread phenomenon that can fundamentally shape the genetic structure of the social environments in which animals live. For animals that live in and move between social groups, sex-biased dispersal can result in an asymmetry in the degree of relatedness among cohabiting males and females, which can have strong implications for their social evolution. In this study, we measured the relatedness structure within and across groups of a wild population of Neolamprologus multifasciatus, a highly-social, shell-dwelling cichlid fish endemic to Lake Tanganyika, East Africa. In total, we genotyped 812 fish from 128 social groups at 20 microsatellite loci. Neolamprologus multifasciatus live at high densities, and also experience strong ecological constraints on free movement throughout their habitat. At the same time, they exhibit sex differences in the degree of reproductive competition within their groups and this makes them an excellent model system for studying the factors associated with sex-biased dispersal.

RESULTS

Social groups of N. multifasciatus consist of multiple males and females living together. We found that cohabiting females were unrelated to one another (Lynch-Ritland estimates of relatedness = 0.045 ± 0.15, average ± SD), while males shared much higher, albeit variable, levels of relatedness to other males in their groups (0.23 ± 0.27). We uncovered a pronounced decline in relatedness between males living in separate groups as the spatial separation between them increased, a pattern that was not evident in females. Female dispersal was also markedly constrained by the distribution and availability of nearby territories to which they could emigrate.

CONCLUSIONS

Our results indicate female-biased dispersal in N. multifasciatus. Our study also highlights how the spatial distribution of suitable dispersal destinations can influence the movement decisions of animals. We also emphasize how sex-biased dispersal can influence the relatedness structure of the social environment in which individuals interact and compete with one another.

Parentage analysis across age cohorts reveals sex differences in reproductive skew in a group-living cichlid fish, Neolamprologus multifasciatus

Group-living animals are often faced with complex reproductive decisions, namely how to partition within-group reproduction, how to obtain extra-group reproduction, and how these two means of reproduction should be balanced. The solutions to these questions can be difficult to predict because ecological conditions can affect the scopes for within-group and extra-group reproduction in complex ways. For example, individuals that are restricted from moving freely around their habitats may have limited extra-group reproductive opportunities, but at the same time, groups may live in close proximities to one another, which could potentially have the opposite effect. The group-living cichlid fish, Neolamprologus multifasciatus, experiences such ecological conditions, and we conducted an intensive genetic parentage analysis to investigate how reproduction is distributed within and among groups for both males and females. We found that cohabiting males live in 'high-skew' societies, where dominant males monopolize the majority of within-group reproduction, while females live in 'low-skew' societies, where multiple females can produce offspring concurrently. Despite extremely short distances separating groups, we inferred only very low levels of extra-group reproduction suggesting that subordinate males have very limited reproductive opportunities. A strength of our parentage analysis lies in its inclusion of individuals that spanned a wide age range, from young fry to adults. We outline the logistical circumstances when very young offspring may not always be accessible to parentage researchers, and present strategies to overcome the challenges of inferring mating patterns from a wide age range of offspring.

Past lake shore dynamics explain present pattern of unidirectional introgression across a habitat barrier

Introgression patterns between divergent lineages are often characterized by asymmetry in the direction and among-marker variation in the extent of gene flow, and therefore inform on the mechanisms involved in differentiation and speciation. In the present study, we test the hypothesis that unidirectional introgression between two phenotypically and genetically distinct lineages of the littoral, rock-dwelling cichlid fish Tropheus moorii across a wide sandy bay is linked to observed differences in mate preferences between the two lineages. This hypothesis predicts bi-directional nuclear gene flow and was rejected by congruent patterns of introgression in mtDNA, AFLP and microsatellite markers, with admixture confined to the populations west of the bay. This pattern can be explained on the basis of habitat changes in the course of lake level fluctuations, which first facilitated the development of a symmetric admixture zone including the area corresponding to the present sand bay and then shaped asymmetry by causing local extinctions and cessation of gene flow when this area became once more inhabitable. This conforms with previous assumptions that habitat dynamics are a primary determinant of population-level evolution in Tropheus. In this respect, Tropheus may be representative of species whose preferred habitat is subject to frequent re-structuring.

Inclusive fitness benefits mitigate costs of cuckoldry to socially paired males

Background

In socially monogamous species, reproduction is not always confined to paired males and females. Extra-pair males commonly also reproduce with paired females, which is traditionally thought to be costly to the females’ social partners. However, we suggest that when the relatedness between reproducing individuals is considered, cuckolded males can suffer lower fitness losses than otherwise expected, especially when the rate of cuckoldry is high. We combine theoretical modeling with a detailed genetic study on a socially monogamous wild fish, Variabilichromis moorii, which displays biparental care despite exceptionally high rates of extra-pair paternity.

Results

We measured the relatedness between all parties involved in V. moorii spawning events (i.e. between males and females in social pairs, females and their extra-pair partners, and paired males and their cuckolders), and we reveal that males are on average more related to their cuckolders than expected by chance. Queller–Goodnight estimates of relatedness between males and their cuckolders are on average r = 0.038 but can range up to r = 0.64. This also increases the relatedness between males and the extra-pair offspring under their care. These intriguing results are consistent with the predictions of our mathematical model, which shows that elevated relatedness between paired males and their cuckolders can be adaptive for both parties when competition for fertilizations is strong.

Conclusions

Our results show how cuckoldry by relatives can offset males’ direct fitness losses with inclusive fitness gains, which can be substantial in systems where males face almost certain paternity losses.

Electronic supplementary material

The online version of this article (10.1186/s12915-018-0620-6) contains supplementary material, which is available to authorized users.

Brood-tending males in a biparental fish suffer high paternity losses but rarely cuckold

Extra‐pair paternity within socially monogamous mating systems is well studied in birds and mammals but rather neglected in other animal taxa. In fishes, social monogamy has evolved several times but few studies have investigated the extent to which pair‐bonded male fish lose fertilizations to cuckolders and gain extra‐pair fertilizations themselves. We address this gap and present genetic paternity data collected from a wild population of Variabilichromis moorii, a socially monogamous African cichlid with biparental care of offspring. We show that brood‐tending, pair‐bonded males suffer exceptionally high paternity losses, siring only 63% of the offspring produced by their female partners on average. The number of cuckolders per brood ranged up to nine and yet, surprisingly, brood‐tending males in the population were rarely the culprits. Brood‐tending males sired very few extra‐pair offspring, despite breeding in close proximity to one another. While unpaired males were largely responsible for the cuckoldry, pair‐bonded males still enjoyed higher fertilization success than individual unpaired males. We discuss these results in the context of ecological and phenotypic constraints on cuckoldry and the fitness payoffs of alternative male tactics. Our study provides new insights into how pair‐bonded males handle the trade‐off between securing within‐pair and extra‐pair reproduction.

Weak link between dispersal and parasite community differentiation or immunogenetic divergence in two sympatric cichlid fishes

Geographical isolation, habitat variation and trophic specialization have contributed to a large extent to the astonishing diversity of cichlid fishes in the Great East African lakes. Because parasite communities often vary across space and environments, parasites can accompany and potentially enhance cichlid species diversification. However, host dispersal may reduce opportunities for parasite-driven evolution by homogenizing parasite communities and allele frequencies of immunity genes. To test for the relationships between parasite community variation, host dispersal and parasite-induced host evolution, we studied two sympatric cichlid species with contrasting dispersal capacities along the shores of southern Lake Tanganyika. Whereas the philopatric Tropheus moorii evolved into several genetically differentiated colour morphs, Simochromis diagramma is phenotypically rather uniform across its distribution range and shows only weak population structure. Populations of both species were infected with divergent parasite communities and harbour differentiated variant pools of an important set of immune genes, the major histocompatibility complex (MHC). The overall extent of geographical variation of parasites and MHC genes was similar between host species. This indicates that immunogenetic divergence among populations of Lake Tanganyika cichlids can occur even in species that are strongly dispersing. However, because this also includes species that are phenotypically uniform, parasite-induced evolution may not represent a key factor underlying species diversification in this system.

Asymmetric dominance and asymmetric mate choice oppose premating isolation after allopatric divergence

Assortative mating promotes reproductive isolation and allows allopatric speciation processes to continue in secondary contact. As mating patterns are determined by mate preferences and intrasexual competition, we investigated male–male competition and behavioral isolation in simulated secondary contact among allopatric populations. Three allopatric color morphs of the cichlid fish Tropheus were tested against each other. Dyadic male–male contests revealed dominance of red males over bluish and yellow-blotch males. Reproductive isolation in the presence of male–male competition was assessed from genetic parentage in experimental ponds and was highly asymmetric among pairs of color morphs. Red females mated only with red males, whereas the other females performed variable degrees of heteromorphic mating. Discrepancies between mating patterns in ponds and female preferences in a competition-free, two-way choice paradigm suggested that the dominance of red males interfered with positive assortative mating of females of the subordinate morphs and provoked asymmetric hybridization. Between the nonred morphs, a significant excess of negative assortative mating by yellow-blotch females with bluish males did not coincide with asymmetric dominance among males. Hence, both negative assortative mating preferences and interference of male–male competition with positive assortative preferences forestall premating isolation, the latter especially in environments unsupportive of competition-driven spatial segregation.

A microsatellite-based genetic linkage map and putative sex-determining genomic regions in Lake Victoria cichlids

Cichlid fishes in East Africa have undergone extensive adaptive radiation, which has led to spectacular diversity in their morphology and ecology. To date, genetic linkage maps have been constructed for several tilapias (riverine), Astatotilapia burtoni (Lake Tanganyika), and hybrid lines of Lake Malawi cichlids to facilitate genome-wide comparative analyses. In the present study, we constructed a genetic linkage map of the hybrid line of Lake Victoria cichlids, so that maps of cichlids from all the major areas of East Africa will be available. The genetic linkage map shown here is derived from the F2 progeny of an interspecific cross between Haplochromis chilotes and Haplochromis sauvagei and is based on 184 microsatellite and two single-nucleotide polymorphism (SNP) markers. Most of the microsatellite markers used in the present study were originally designed for other genetic linkage maps, allowing us to directly compare each linkage group (LG) among different cichlid groups. We found 25 LGs, the total length of which was 1133.2cM with an average marker spacing of about 6.09cM. Our subsequent linkage mapping analysis identified two putative sex-determining loci in cichlids. Interestingly, one of these two loci is located on cichlid LG5, on which the female heterogametic ZW locus and several quantitative trait loci (QTLs) related to adaptive evolution have been reported in Lake Malawi cichlids. We also found that V1R1 and V1R2, candidate genes for the fish pheromone receptor, are located very close to the recently detected sex-determining locus on cichlid LG5. The genetic linkage map study presented here may provide a valuable foundation for studying the chromosomal evolution of East African cichlids and the possible role of sex chromosomes in generating their genomic diversity.

Genetic structure of pelagic and littoral cichlid fishes from Lake Victoria

The approximately 700 species of cichlids found in Lake Victoria in East Africa are thought to have evolved over a short period of time, and they represent one of the largest known examples of adaptive radiation. To understand the processes that are driving this spectacular radiation, we must determine the present genetic structure of these species and elucidate how this structure relates to the ecological conditions that caused their adaptation. We analyzed the genetic structure of two pelagic and seven littoral species sampled from the southeast area of Lake Victoria using sequences from the mtDNA control region and 12 microsatellite loci as markers. Using a Bayesian model-based clustering method to analyze the microsatellite data, we separated these nine species into four groups: one group composed of pelagic species and another three groups composed mainly of rocky-shore species. Furthermore, we found significant levels of genetic variation between species within each group at both marker loci using analysis of molecular variance (AMOVA), although the nine species often shared mtDNA haplotypes. We also found significant levels of genetic variation between populations within species. These results suggest that initial groupings, some of which appear to have been related to habitat differences, as well as divergence between species within groups took place among the cichlid species of Lake Victoria.

Microsatellites Cross-Species Amplification across Some African Cichlids

The transfer of the genomic resources developed in the Nile tilapia, Oreochromis niloticus, to other Tilapiines sensu lato and African cichlid would provide new possibilities to study this amazing group from genetics, ecology, evolution, aquaculture, and conservation point of view. We tested the cross-species amplification of 32 O. niloticus microsatellite markers in a panel of 15 species from 5 different African cichlid tribes: Oreochromines (Oreochromis, Sarotherodon), Boreotilapiines (Tilapia), Chromidotilapines, Hemichromines, and Haplochromines. Amplification was successfully observed for 29 markers (91%), with a frequency of polymorphic (P₉₅) loci per species around 70%. The mean number of alleles per locus and species was 3.2 but varied from 3.7 within Oreochromis species to 1.6 within the nontilapia species. The high level of cross-species amplification and polymorphism of the microsatellite markers tested in this study provides powerful tools for a wide range of molecular genetic studies within tilapia species as well as for other African cichlids.

The function of anal fin egg-spots in the cichlid fish Astatotilapia burtoni

Color and pigmentation patterns of animals are often targets of sexual selection because of their role in communication. Although conspicuous male traits are typically implicated with intersexual selection, there are examples where sex-specific displays play a role in an intrasexual context, e.g. when they serve as signals for aggression level and/or status. Here, we focus on the function of a conspicuous male ornament in the most species-rich tribe of cichlid fishes, the haplochromines. A characteristic feature of these ca. 1500 species are so-called egg-spots in form of ovoid markings on the anal fins of males, which are made up of carotenoid based pigment cells. It has long been assumed that these yellow, orange or reddish egg-spots play an important role in the courtship and spawning behavior of these maternal mouth-brooding fishes by mimicking the eggs of a conspecific female. The exact function of egg-spots remains unknown, however, and there are several hypotheses about their mode of action. To uncover the function of this cichlid-specific male ornament, we used female mate choice experiments and a male aggression test in the haplochromine species Astatotilapia burtoni. We manipulated the number and arrangement of egg-spots on the anal fins of males, or removed them entirely, and tested (1) female preference with visual contact only using egg-traps, (2) female preference with free contact using paternity testing with microsatellites and (3) male aggression. We found that females did not prefer males with many egg-spots over males with fewer egg-spots and that females tended to prefer males without egg-spots over males with egg-spots. Importantly, males without egg-spots sired clutches with the same fertilization rate as males with egg-spots. In male aggression trials, however, males with fewer egg-spots received significantly more attacks, suggesting that egg-spots are an important signal in intrasexual communication.

Population structure of two closely related pelagic cichlids in Lake Victoria, Haplochromis pyrrhocephalus and H. laparogramma

Cichlid fishes in Lake Victoria show spectacular diversification that is thought to be recent. Therefore, by investigating those fishes, we may be able to elucidate recently completed or ongoing speciation processes. We studied the population structures of two closely related pelagic cichlid species, Haplochromis pyrrhocephalus and H. laparogramma, using a mitochondrial DNA locus and 12 nuclear microsatellite loci as putative neutral markers. Ten and two populations of H. pyrrhocephalus and H. laparogramma, respectively, were sampled from the southern part of Lake Victoria. We grouped those 12 populations into four mutually differentiated regional populations, one of which consisted of the two H. laparogramma populations. The levels of differentiation were substantial at the mitochondrial locus (F(ST) = 0.03-0.54), but very low at microsatellite loci (R(ST) = 0.008-0.116). The data from both types of loci indicated that the regional population of H. laparogramma was first separated from those of H. pyrrhocephalus if we set aside one erratic population of H. pyrrhocephalus. The data also suggested recent population expansions of the two species, the time scales for which were estimated to be on the order of 10(4)-10(5) years. These data suggested that dynamic speciation processes accompanied occasional spawning of new species and population size changes in this lake.