Evolution of MHC IIB Diversity Across Cichlid Fish Radiations

The genes of the major histocompatibility complex (MHC) are among the most polymorphic genes in vertebrates and crucial for their adaptive immune response. These genes frequently show inconsistencies between allelic genealogies and species phylogenies. This phenomenon is thought to be the result of parasite-mediated balancing selection maintaining ancient alleles through speciation events (trans-species polymorphism [TSP]). However, allele similarities may also arise from postspeciation mechanisms, such as convergence or introgression. Here, we investigated the evolution of MHC class IIB diversity in the cichlid fish radiations across Africa and the Neotropics by a comprehensive review of available MHC IIB DNA sequence information. We explored what mechanism explains the MHC allele similarities found among cichlid radiations. Our results showed extensive allele similarity among cichlid fish across continents, likely due to TSP. Functionality at MHC was also shared among species of the different continents. The maintenance of MHC alleles for long evolutionary times and their shared functionality may imply that certain MHC variants are essential in immune adaptation, even in species that diverged millions of years ago and occupy different environments.

Divergent and non-parallel evolution of MHC IIB in the Neotropical Midas cichlid species complex

Background

Ecological diversification is the result of divergent natural selection by contrasting habitat characteristics that favours the evolution of distinct phenotypes. This process can happen in sympatry and in allopatry. Habitat-specific parasite communities have the potential to drive diversification among host populations by imposing selective pressures on their host's immune system. In particular, the hyperdiverse genes of the major histocompatibility complex (MHC) are implicated in parasite-mediated host divergence. Here, we studied the extent of divergence at MHC, and discuss how it may have contributed to the Nicaraguan Midas cichlid species complex diversification, one of the most convincing examples of rapid sympatric parallel speciation.

Results

We genotyped the MHC IIB for individuals from six sympatric Midas cichlid assemblages, each containing species that have adapted to exploit similar habitats. We recovered large allelic and functional diversity within the species complex. While most alleles were rare, functional groups of alleles (supertypes) were common, suggesting that they are key to survival and that they were maintained during colonization and subsequent radiations. We identified lake-specific and habitat-specific signatures for both allelic and functional diversity, but no clear pattern of parallel divergence among ecomorphologically similar phenotypes.

Conclusions

Colonization and demographic effects of the fish could have contributed to MHC evolution in the Midas cichlid in conjunction with habitat-specific selective pressures, such as parasites associated to alternative preys or environmental features. Additional ecological data will help evaluating the role of host–parasite interactions in the Midas cichlid radiations and aid in elucidating the potential role of non-parallel features differentiating crater lake species assemblages.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01997-9.

Genetic and ecomorphological divergence between sympatric Astyanax morphs from Central America

Intraspecific ecological and morphological polymorphism can promote ecological speciation and the build-up of reproductive isolation. Here, we evaluate correlations among morphology, trophic ecology and genetic differentiation between two divergent morphs (elongate and deep-body) of the fish genus Astyanax in the San Juan River basin in Central America, to infer the putative evolutionary mechanism shaping this system. We collected the two morphs from three water bodies and analysed: (1) the correlation between body shape and the shape of the premaxilla, a relevant trophic morphological structure, (2) the trophic level and niche width of each morph, (3) the correspondence between trophic level and body and premaxillary shape, and (4) the genetic differentiation between morphs using mitochondrial and nuclear markers. We found a strong correlation between the body and premaxillary shape of the morphs. The elongate-body morph had a streamlined body, a premaxilla with acuter angles and a narrower ascending process, and a higher trophic level, characteristic of species with predatorial habits. By contrast, the deep-body morph had a higher body depth, a premaxilla with less acute angles and a broader trophic niche, suggesting generalist habits. Despite the strong correlation between morphological and ecological divergence, the morphs showed limited genetic differentiation, supporting the idea that morphs may be undergoing incipient ecological speciation, although alternative scenarios such as stable polymorphism or plasticity should also be considered. This study provides support for the role of ecological factors promoting diversification in both lake and stream-dwelling freshwater fish.

Pervasive admixture and the spread of a large-lipped form in a cichlid fish radiation

Adaptive radiations have proven important for understanding the mechanisms and processes underlying biological diversity. The convergence of form and function, as well as admixture and adaptive introgression, are common in adaptive radiations. However, distinguishing between these two scenarios remains a challenge for evolutionary research. The Midas cichlid species complex (Amphilophus spp.) is a prime example of adaptive radiation, with phenotypic diversification occurring at various stages of genetic differentiation. One species, A. labiatus, has large fleshy lips, is associated with rocky lake substrates, and occurs patchily within Lakes Nicaragua and Managua. By contrast, the similar, but thin-lipped, congener, A. citrinellus, is more common and widespread. We investigated the evolutionary history of the large-lipped form, specifically regarding whether the trait has evolved independently in both lakes from ancestral thin-lipped populations, or via dispersal and/or admixture events. We collected samples from distinct locations in both lakes, and assessed differences in morphology and ecology. Using RAD-seq, we genotyped thousands of SNPs to measure population structure and divergence, demographic history, and admixture. We found significant between-species differences in ecology and morphology, local intraspecific differences in body shape and trophic traits, but only limited intraspecific variation in lip shape. Despite clear ecological differences, our genomic approach uncovered pervasive admixture between the species and low genomic differentiation, with species within lakes being genetically more similar than species between lakes. Taken together, our results suggest a single origin of large-lips, followed by pervasive admixture and adaptive introgression, with morphology being driven by local ecological opportunities, despite ongoing gene-flow.

Taxonomic assessment of the genus Procamallanus (Nematoda) in Middle American cichlids (Osteichthyes) with molecular data, and the description of a new species from Nicaragua and Costa Rica

Procamallanus is a species-rich genus of parasitic nematodes of marine, brackish, and freshwater fishes, occurring also occasionally in amphibians and reptiles. In the Neotropical region, this genus is highly diverse, with species described from a wide range of fish families. In this study, we reassess the taxonomic status of Procamallanus rebecae with molecular and morphological data and describe a new species endemic to Nicaragua and Costa Rica. We analyzed all Procamallanus isolated from fish from the Nicaraguan lakes and some rivers in Costa Rica after an exhaustive analysis of their freshwater fish endoparasite fauna. Procamallanus rebecae is a host-specific parasite of Middle American cichlids, previously reported in southern Mexico, Nicaragua, and Costa Rica. We therefore compared these Central American specimens with individuals of P. rebecae collected in cichlids from southeastern Mexico using two genomic regions (28S rDNA and mitochondrial cytochrome oxidase subunit 1, COI). We found high levels of sequence divergence between Procamallanus from the two geographical regions, with up to 9.8 and 10.5% for both genetic markers, respectively. We also analyzed their morphology and found conspicuous differences in the shape of the mouth and the structure of the female cauda. We therefore describe the specimens of Procamallanus from Central American cichlids as a new species. Both Procamallanus species occur in different cichlid species and are allopatrically distributed. The host specificity and ancient association patterns between cichlids and Procamallanus and the jointly colonization of both hosts and parasites during their northern dispersal from South America are briefly discussed.

Acusicola margulisae n. sp. (Copepoda: Ergasilidae) from freshwater fishes in a Nicaraguan crater lake based on morphological and molecular evidence

The ergasilid copepod Acusicola margulisae n. sp. is described based on material from three species of cichlid, Amphilophus citrinellus (Günther), Parachromis managuensis (Günther), and Oreochromis sp., and from the poecilid Poecilia mexicana (Steindachner), in the crater Lake Asososca León, Nicaragua. This constitutes the 15th species described in the genus Acusicola Cressey, 1970. The new species differs from all its congeners by the relatively longer first endopodal segment of leg 1, and the size and number of setae on second endopodal segment of leg 1. We provide the first gene sequence for a species of Acusicola. To examine the intraspecific genetic variation of the new species collected from different host species, sequences of the mitochondrial barcode region cox1 were generated. In addition, partial regions of the 18S and 28S ribosomal RNA genes were sequenced and used to infer the phylogenetic relationships of the genus Acusicola within the family Ergasilidae Burmeister, 1835. The phylogenetic trees yielded the isolates of Acusicola margulisae n. sp. as a reciprocally monophyletic lineage, and as the sister taxa of five genera of ergasilid copepods. The genus Ergasilus von Nordmann, 1832 was recovered as a paraphyletic group. These analyses indicate that phylogenetic relationships are not yet well resolved and more representative species and genera of the family are required to provide a robust classification of this highly diverse group of copepods.

Phylogeography and Ecological Niche Shape the Cichlid Fish Gut Microbiota in Central American and African Lakes

Cichlid fishes, with their repeated colonization of lakes and subsequent radiations at different scales of phylogenetic and ecological diversification, offer an excellent model system to understand the factors shaping the host-gut microbiota association in nature. Here, we characterized the gut microbiota of the Amphilophus species complex from Central America (known as the Midas cichlid complex), encompassing 158 wild specimens (13 species) collected from seven Nicaraguan lakes, and combined these data with previously published data from two African lakes (spanning 29 species). Our aim was to comprehensively explore trends in microbiota variation and persistence along the large spatial and temporal scales of cichlid diversification (from the oldest radiation in L. Tanganyika, 9-12 My old, to young ones in Nicaraguan crater lakes, <0.5 My old), in allopatry and sympatry (within and across lakes), and across the range of dietary niches (from highly specialized to generalist feeders). Despite their extraordinary diversity, cichlids shared a remarkably conserved microbial taxonomic profile, which argues for a primary role of the host genetics in the assembly and maintenance of these microbial communities. Within this partly constrained microbiota profile, geographic isolation (continent and lake) represented the first level of discrimination. For the Midas cichlid, a partial congruency was found between host microbiota and genetic distances, suggesting that microbial communities have partly diversified along their cichlid phylogeographic history of crater lake colonization. In sympatry (within lakes), the young and poorly ecologically diversified cichlid assemblages of Central American lakes display largely unresolved gut microbiotas (in terms of both alpha and beta diversities), whereas the phylogenetically and ecologically diverse species found in African lakes showed greater microbial interspecific diversity. This pattern largely points to the level of habitat segregation, trophic niche overlap, and reproductive barriers as major modulators of the gut microbiota connectivity among sympatric species.

Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids

BACKGROUND

The Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC remains to be characterized in many species including any Neotropical cichlid fish. Neotropical crater lake cichlids are ideal models to study evolutionary processes as they display one of the most convincing examples of sympatric and repeated parallel radiation events within and among isolated crater lakes.

RESULTS

Here, we characterized the genes of MHC class IIB chain of the Midas cichlid species complex (Amphilophus cf. citrinellus) including fish from five lakes in Nicaragua. We designed 19 new specific primers anchored in a stepwise fashion in order to detect all alleles present. We obtained 866 genomic DNA (gDNA) sequences from thirteen individuals and 756 additional sequences from complementary DNA (cDNA) of seven of those individuals. We identified 69 distinct alleles with up to 25 alleles per individual. We also found considerable intron length variation and mismatches of alleles detected in cDNA and gDNA suggesting that some loci have undergone pseudogenization. Lastly, we created a model of protein structure homology for each allele and identified their key structural components.

CONCLUSIONS

Overall, the Midas cichlid has one of the most diverse repertoires of MHC class IIB genes known, which could serve as a powerful tool to elucidate the process of divergent radiations, colonization and speciation in sympatry.

Untangling the evolutionary history of a highly polymorphic species: introgressive hybridization and high genetic structure in the desert cichlid fish Herichtys minckleyi

Understanding the origin of biodiversity requires knowledge on the evolutionary processes that drive divergence and speciation, as well as on the processes constraining it. Intraspecific polymorphisms can provide insight into the mechanisms that generate and maintain phenotypic, behavioural and life history diversification, and can help us understand not only the processes that lead to speciation but also the processes that prevent local fixation of morphs. The 'desert cichlid' Herichtys minckleyi is a highly polymorphic species endemic to a biodiversity hotspot in northern Mexico, the Cuatro Ciénegas valley. This species is polymorphic in body shape and trophic apparatus, and eco-morphotypes coexist in small spring-fed lagoons across the valley. We investigated the genetic structure of these polymorphisms and their phylogeographic history by analysing the entire control region of the mitochondrial DNA and 10 nuclear microsatellite markers in several populations from different sites and morphs. We found two very divergent mitochondrial lineages that most likely predate the closing of the valley and are not associated with morphotypes or sites. One of these lineages is also found in the sister species Herichthys cyanoguttatus. Data from neutral microsatellite markers suggest that most lagoons or drainages constitute their own genetic cluster with sympatric eco-morphotypes forming panmictic populations. Alternative mechanisms such as phenotypic plasticity and a few loci controlled traits provide possible explanations for the sympatric coexistence of discrete nonoverlapping eco-morphotypes with apparent lack of barriers to gene flow within multiple lagoons and drainages.

Origins of shared genetic variation in African cichlids

Cichlid fishes have evolved tremendous morphological and behavioral diversity in the waters of East Africa. Within each of the Great Lakes Tanganyika, Malawi, and Victoria, the phenomena of hybridization and retention of ancestral polymorphism explain allele sharing across species. Here, we explore the sharing of single nucleotide polymorphisms (SNPs) between the major East African cichlid assemblages. A set of approximately 200 genic and nongenic SNPs was ascertained in five Lake Malawi species and genotyped in a diverse collection of ∼160 species from across Africa. We observed segregating polymorphism outside of the Malawi lineage for more than 50% of these loci; this holds similarly for genic versus nongenic SNPs, as well as for SNPs at putative CpG versus non-CpG sites. Bayesian and principal component analyses of genetic structure in the data demonstrate that the Lake Malawi endemic flock is not monophyletic and that river species have likely contributed significantly to Malawi genomes. Coalescent simulations support the hypothesis that river cichlids have transported polymorphism between lake assemblages. We observed strong genetic differentiation between Malawi lineages for approximately 8% of loci, with contributions from both genic and nongenic SNPs. Notably, more than half of these outlier loci between Malawi groups are polymorphic outside of the lake. Cichlid fishes have evolved diversity in Lake Malawi as new mutations combined with standing genetic variation shared across East Africa.

The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes

The evolution of convergent phenotypes is one of the most interesting outcomes of replicate adaptive radiations. Remarkable cases of convergence involve the thick-lipped phenotype found across cichlid species flocks in the East African Great Lakes. Unlike most other convergent forms in cichlids, which are restricted to East Africa, the thick-lipped phenotype also occurs elsewhere, for example in the Central American Midas Cichlid assemblage. Here, we use an ecological genomic approach to study the function, the evolution and the genetic basis of this phenotype in two independent cichlid adaptive radiations on two continents. We applied phylogenetic, demographic, geometric morphometric and stomach content analyses to an African (Lobochilotes labiatus) and a Central American (Amphilophus labiatus) thick-lipped species. We found that similar morphological adaptations occur in both thick-lipped species and that the 'fleshy' lips are associated with hard-shelled prey in the form of molluscs and invertebrates. We then used comparative Illumina RNA sequencing of thick vs. normal lip tissue in East African cichlids and identified a set of 141 candidate genes that appear to be involved in the morphogenesis of this trait. A more detailed analysis of six of these genes led to three strong candidates: Actb, Cldn7 and Copb. The function of these genes can be linked to the loose connective tissue constituting the fleshy lips. Similar trends in gene expression between African and Central American thick-lipped species appear to indicate that an overlapping set of genes was independently recruited to build this particular phenotype in both lineages.

Adaptive phenotypic plasticity in the Midas cichlid fish pharyngeal jaw and its relevance in adaptive radiation

Background

Phenotypic evolution and its role in the diversification of organisms is a central topic in evolutionary biology. A neglected factor during the modern evolutionary synthesis, adaptive phenotypic plasticity, more recently attracted the attention of many evolutionary biologists and is now recognized as an important ingredient in both population persistence and diversification. The traits and directions in which an ancestral source population displays phenotypic plasticity might partly determine the trajectories in morphospace, which are accessible for an adaptive radiation, starting from the colonization of a novel environment. In the case of repeated colonizations of similar environments from the same source population this "flexible stem" hypothesis predicts similar phenotypes to arise in repeated subsequent radiations. The Midas Cichlid (Amphilophus spp.) in Nicaragua has radiated in parallel in several crater-lakes seeded by populations originating from the Nicaraguan Great Lakes. Here, we tested phenotypic plasticity in the pharyngeal jaw of Midas Cichlids. The pharyngeal jaw apparatus of cichlids, a second set of jaws functionally decoupled from the oral ones, is known to mediate ecological specialization and often differs strongly between sister-species.

Results

We performed a common garden experiment raising three groups of Midas cichlids on food differing in hardness and calcium content. Analyzing the lower pharyngeal jaw-bones we find significant differences between diet groups qualitatively resembling the differences found between specialized species. Observed differences in pharyngeal jaw expression between groups were attributable to the diet's mechanical resistance, whereas surplus calcium in the diet was not found to be of importance.

Conclusions

The pharyngeal jaw apparatus of Midas Cichlids can be expressed plastically if stimulated mechanically during feeding. Since this trait is commonly differentiated - among other traits - between Midas Cichlid species, its plasticity might be an important factor in Midas Cichlid speciation. The prevalence of pharyngeal jaw differentiation across the Cichlidae further suggests that adaptive phenotypic plasticity in this trait could play an important role in cichlid speciation in general. We discuss several possibilities how the adaptive radiation of Midas Cichlids might have been influenced in this respect.

Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes

Background

Elucidation of the mechanisms driving speciation requires detailed knowledge about the phylogenetic relationships and phylogeography of the incipient species within their entire ranges as well as their colonization history. The Midas cichlid species complex Amphilophus spp. has been proven to be a powerful model system for the study of ecological specialization, sexual selection and the mechanisms of sympatric speciation. Here we present a comprehensive and integrative phylogeographic analysis of the complete Midas Cichlid species complex in Nicaragua (> 2000 individuals) covering the entire distributional range, using two types of molecular markers (the mitochondrial DNA control region and 15 microsatellites). We investigated the majority of known lake populations of this species complex and reconstructed their colonization history in order to distinguish between alternative speciation scenarios.

Results

We found that the large lakes contain older and more diverse Midas Cichlid populations, while all crater lakes hold younger and genetically less variable species assemblages. The large lakes appear to have repeatedly acted as source populations for all crater lakes, and our data indicate that faunal exchange among crater lakes is extremely unlikely. Despite their very recent (often only a few thousand years old) and common origin from the two large Nicaraguan lakes, all crater lake Midas Cichlid radiations underwent independent, but parallel, evolution, and comprise distinct genetic units. Indeed several of these crater lakes contain multiple genetically distinct incipient species that most likely arose through sympatric speciation. Several crater lake radiations can be traced back to a single ancestral line, but some appear to have more than one founding lineage. The timing of the colonization(s) of each crater lake differs, although most of them occurred more (probably much more) recently than 20,000 years ago.

Conclusion

The genetic differentiation of the crater lake populations is directly related to the number of founding lineages, but independent of the timing of colonization. Interestingly, levels of phenotypic differentiation, and speciation events, appeared independent of both factors.

Genetic support for random mating between left and right-mouth morphs in the dimorphic scale-eating cichlid fish Perissodus microlepis from Lake Tanganyika

Population genetic analyses were conducted to investigate whether random mating occurs between left and right-mouth morphs of the dimorphic scale-eating cichlid fish Perissodus microlepis from two geographical sites in southern Lake Tanganyika. The mitochondrial and nuclear DNA markers (13 microsatellite loci) revealed no genetic differentiation between left and right morphs (i.e. widespread interbreeding). The observed lack of genetic divergence between the different morphs allowed for the exclusion of the possibility of assortative mating between same morph types. The microsatellite data showed no significant departures of heterozygosity from Hardy-Weinberg equilibrium, suggesting purely random mating between the morphs. Overall, this study indicated no genetic evidence for either assortative or disassortative mating, but it did provide support for the random mating hypothesis. Highly significant, albeit weak, spatial population structure was also found when samples of different morphs were pooled according to geographical sites. An additional analysis of two microsatellite loci that were recently suggested to be putatively linked to the genetic locus that determines the laterality of these mouth morphs did not show any such association.

Fine-scale spatial genetic structure and gene dispersal in Silene latifolia

Plants are sessile organisms, often characterized by limited dispersal. Seeds and pollen are the critical stages for gene flow. Here we investigate spatial genetic structure, gene dispersal and the relative contribution of pollen vs seed in the movement of genes in a stable metapopulation of the white campion Silene latifolia within its native range. This short-lived perennial plant is dioecious, has gravity-dispersed seeds and moth-mediated pollination. Direct measures of pollen dispersal suggested that large populations receive more pollen than small isolated populations and that most gene flow occurs within tens of meters. However, these studies were performed in the newly colonized range (North America) where the specialist pollinator is absent. In the native range (Europe), gene dispersal could fall on a different spatial scale. We genotyped 258 individuals from large and small (15) subpopulations along a 60 km, elongated metapopulation in Europe using six highly variable microsatellite markers, two X-linked and four autosomal. We found substantial genetic differentiation among subpopulations (global F(ST)=0.11) and a general pattern of isolation by distance over the whole sampled area. Spatial autocorrelation revealed high relatedness among neighboring individuals over hundreds of meters. Estimates of gene dispersal revealed gene flow at the scale of tens of meters (5-30 m), similar to the newly colonized range. Contrary to expectations, estimates of dispersal based on X and autosomal markers showed very similar ranges, suggesting similar levels of pollen and seed dispersal. This may be explained by stochastic events of extensive seed dispersal in this area and limited pollen dispersal.

Case studies and mathematical models of ecological speciation. 1. Cichlids in a crater lake

A recent study of a pair of sympatric species of cichlids in Lake Apoyo in Nicaragua is viewed as providing probably one of the most convincing examples of sympatric speciation to date. Here, we describe and study a stochastic, individual-based, explicit genetic model tailored for this cichlid system. Our results show that relatively rapid (<20,000 generations) colonization of a new ecological niche and (sympatric or parapatric) speciation via local adaptation and divergence in habitat and mating preferences are theoretically plausible if: (i) the number of loci underlying the traits controlling local adaptation, and habitat and mating preferences is small; (ii) the strength of selection for local adaptation is intermediate; (iii) the carrying capacity of the population is intermediate; and (iv) the effects of the loci influencing nonrandom mating are strong. We discuss patterns and timescales of ecological speciation identified by our model, and we highlight important parameters and features that need to be studied empirically to provide information that can be used to improve the biological realism and power of mathematical models of ecological speciation.

Genetic admixture of burbot (Teleostei: Lota lota) in Lake Constance from two European glacial refugia

The burbot, Lota lota, is the only freshwater species of the codfish family and has a Holarctic distribution. Pleistocene glaciations caused significant geographical differentiation in the past, but its life history characterized by winter spawning migrations over large distances is likely to homogenize populations by contemporary gene flow. We investigated the population genetic structure of 541 burbots from Lake Constance and adjacent Rhine and Danube tributaries in Europe using the entire mitochondrial DNA (mtDNA) control region and 11 microsatellites. Microsatellites revealed considerable population divergence (F(ST) = 0.26) and evidenced recent bottlenecks in two Central European rivers. In accordance to previous evidence two main phylogeographic lineages (Atlantic and Danubian) were found co-occurring at similar frequencies in Lake Constance, where they currently undergo random mating as indicated by microsatellites. The Danubian lineage contributed only a small proportion to the lake's mtDNA diversity, and probably expanded within the lake shortly after its formation approximately 10,000-15,000 BP. The larger Atlantic haplotype diversity suggested a population expansion older than the lake itself. Levels of admixture at microsatellite loci were less obvious due to their high variability, and coalescence methods were used to estimate past admixture proportions. Our results reinforce a model of a two-step colonization of Europe by burbot from an ancestral Danubian refuge, and confirm the persistence of a secondary Atlantic refuge, as proposed to exist for other freshwater fish. We conclude that the present-day burbot population in Lake Constance bears the genetic signature of both contemporary gene flow and historical separation events.

Sympatric speciation in Nicaraguan crater lake cichlid fish

Sympatric speciation, the formation of species in the absence of geographical barriers, remains one of the most contentious concepts in evolutionary biology. Although speciation under sympatric conditions seems theoretically possible, empirical studies are scarce and only a few credible examples of sympatric speciation exist. Here we present a convincing case of sympatric speciation in the Midas cichlid species complex (Amphilophus sp.) in a young and small volcanic crater lake in Nicaragua. Our study includes phylogeographic, population-genetic (based on mitochondrial DNA, microsatellites and amplified fragment length polymorphisms), morphometric and ecological analyses. We find, first, that crater Lake Apoyo was seeded only once by the ancestral high-bodied benthic species Amphilophus citrinellus, the most common cichlid species in the area; second, that a new elongated limnetic species (Amphilophus zaliosus) evolved in Lake Apoyo from the ancestral species (A. citrinellus) within less than approximately 10,000 yr; third, that the two species in Lake Apoyo are reproductively isolated; and fourth, that the two species are eco-morphologically distinct.

Old fish in a young lake: stone loach (Pisces: Barbatula barbatula) populations in Lake Constance are genetically isolated by distance

The genetic structure of 10 populations (453 individuals) of stone loach (Barbatula barbatula L.), a small bottom-dwelling cyprinid fish, in the littoral zone of Lake Constance, central Europe, was investigated by analysing the mitochondrial control region sequences and five microsatellite loci. An unexpectedly high degree of genetic diversity (up to 0.36%) and old estimated age of these populations (> 150 000 years) based on mitochondrial DNA (mtDNA) was found. These findings contrast with the relatively young age of the lake, which could be colonized by fish only after the last ice age around 15 000 bp. Stone loach appears to be an old species in a young lake. Both types of molecular markers showed population genetic structure pronounced in mtDNA (overall F(ST) = 0.15) but moderate in microsatellites (F(ST) = 0.03). As predicted by its life history, philopatry, and limited capacity for dispersal, stone loach populations of Lake Constance show a clear pattern of isolation by distance. Geographic distances along the shores are the best explanation for the observed geographical distribution of genetic differentiation (r = 0.88), indicating that open water represents a barrier for the dispersal of the stone loach. The colonization of Lake Constance might have occurred initially at one location and then populations spread throughout the lake in a stepwise manner following the shoreline, and subsequently remained largely genetically isolated as suggested by the large observed differences among them.

Post-mating clutch piracy in an amphibian

Female multiple mating and alternative mating systems can decrease the opportunity for sexual selection. Sperm competition is often the outcome of females mating with multiple males and has been observed in many animals, and alternative reproductive systems are widespread among species with external fertilization and parental care. Multiple paternity without associated complex behaviour related to mating or parental care is also seen in simultaneously spawning amphibians and fishes that release gametes into water. Here we report 'clutch piracy' in a montane population of the common frog Rana temporaria, a reproductive behaviour previously unknown in vertebrates with external fertilization. Males of this species clasp the females and the pair deposits one spherical clutch of eggs. No parental care is provided. 'Pirate' males search for freshly laid clutches, clasp them as they would do a female and fertilize the eggs that were left unfertilized by the 'parental' male. This behaviour does not seem to be size-dependent, and some males mate with a female and perform clutch piracy in the same season. Piracy affected 84% of the clutches and in some cases increased the proportion of eggs fertilized, providing direct fitness benefits both for the pirate males and the females. Sexual selection--probably caused by a strong male-biased sex ratio--occurs in this population, as indicated by size-assortative mating; however, clutch piracy may reduce its impact. This provides a good model to explore how alternative mating strategies can affect the intensity of sexual selection.

Population-structure and genetic diversity in a haplochromine fish cichlid 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.

The Midas cichlid species complex: incipient sympatric speciation in Nicaraguan cichlid fishes?

Abstract Sympatric speciation is a contentious concept, although theoretical models as well as empirical evidence support its relevance in evolutionary biology. The Midas cichlid species complex (Amphilophus citrinellus, labiatus, zaliosus) from several crater lakes in Nicaragua fits several of the key characteristics of a sympatric speciation model. In particular, in A. citrinellus (i) strong assortative mating on the basis of colour polymorphism and (ii) ecological differentiation based on morphological polymorphisms involving the feeding apparatus and body shape might both be mechanisms of incipient speciation. Seven microsatellite markers and mtDNA control region sequences [836 base pairs (bp)] were used to study the population genetic structure of 519 specimens of Midas cichlid populations from the two Great Lakes Managua and Nicaragua, and three crater lakes in Nicaragua, Central America. The three named species of the species complex occupy different ecological niches, are morphologically distinct and can be distinguished genetically. We uncovered allopatric genetic differentiation of populations of A. citrinellus from different lakes and distant locations within Lake Managua and, more interestingly, incipient genetic differentiation of several sympatric populations based on colouration (in A. citrinellus and A. labiatus) but not on the morphology of the pharyngeal jaws (in A. citrinellus). Sexual selection and assortative mating might be the driven forces of diversification within named species. The Midas cichlid species complex in Nicaragua is an excellent model system for the study of the incipient stages of adaptation, speciation and the formation of species flocks.

Shape analysis of symmetric structures: quantifying variation among individuals and asymmetry

Morphometric studies often consider parts with internal left-right symmetry, for instance, the vertebrate skull. This type of symmetry is called object symmetry and is distinguished from matching symmetry, in which two separate structures exist as mirror images of each other, one on each body side. We explain a method for partitioning the total shape variation of landmark configurations with object symmetry into components of symmetric variation among individuals and asymmetry. This method is based on the Procrustes superimposition of the original and a reflected copy of each landmark configuration and is compatible with the two-factor ANOVA model customary in studies of fluctuating asymmetry. We show a fully multivariate framework for testing the effects in the two-factor model with MANOVA statistics, which also applies to shapes with matching symmetry. We apply the new methods in a small case study of pharyngeal jaws of the Neotropical cichlid fish Amphilophus citrinellus. The analysis revealed that the symmetric component of variation in the pharyngeal jaws is dominated by the contrast between two alternative trophic morphs in this species and that there is subtle but statistically significant directional asymmetry. Finally, we provide some general recommendations for morphometric studies of symmetric shapes.

Ecological plasticity by morphological design reduces costs of subordination: influence on species distribution

We studied the feeding behaviour of two subordinate tit species (Parus spp.) in two competitive contexts: feeding solitarily versus feeding in the presence of the dominant great tit. Considering ecological plasticity as the within-species component of mean behavioural performance associated with different morphologies in different species, we test the hypothesis that subordinate species with morphological designs allowing a greater ecological plasticity (e.g. blue tit whose hindlimb morphology is modified for greater leg flexion) may gain an advantage against subordinate species with a less plastic design (e.g. crested tit whose hindlimb morphology is modified for aid in leg extension) in a competitive context. Our results demonstrate that the blue tit has greater foraging abilities than the crested tit, as the former is able to modify its feeding behaviour in the presence of the dominant great tit significantly more than the crested tit. In light of these results we propose that some subordinate species can take advantage of their greater ecological plasticity against another less plastic, subordinate species, suggesting that ecological plasticity due to morphological design is a way of reducing costs of subordination as well as a novel, alternative mechanism explaining species distribution.