Unusually fine-scale genetic structuring found in rapidly speciating Malawi cichlid fishes

Mechanisms behind the explosive radiation of over 500 cichlid fish species from a single founding population in Lake Malawi during the last 700 000 years are poorly understood. Recent studies have suggested that the degree of population subdivision among the habitat patches within the lake may be responsible, but the evidence has been circumstantial: lack of a dispersal stage in haplochromine cichlids; genetic and colour variation among populations separated by large-scale geographical barriers; and fluctuating lake levels. One reason for the rapidity of speciation in these fishes may be that population subdivision is on a much finer scale than previously thought. Here we quantify the level of population subdivision and estimate migration at a scale of 700-1400 m, in order to investigate whether cichlid populations are sufficiently isolated from each other for allopatric divergence and perhaps speciation to take place. Using six microsatellite loci, we demonstrate the existence of highly significant genetic differentiation between subpopulations on adjacent headlands in each of four rock-dwelling haplochromine cichlid species. Our results suggest that these fish populations are divided into thousands of subunits among which genetic divergence is currently occurring, and that this may provide unprecedented opportunities for allopatric speciation. <br>     

Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome‐wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here, we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next‐generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non‐cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature.     

Establishment and expansion of Lake Malawi rock fish populations after a dramatic Late Pleistocene lake level rise

Major environmental events that fragment populations among multiple island habitats have potential to drive large-scale episodes of speciation and adaptive radiation. A recent palaeolimnological study of sediment cores indicated that Lake Malawi underwent major climate-driven desiccation events 75 000–135 000 years ago that lowered the water level to at least 580 m below the present state and severely reduced surface area. After this period, lake levels rose and stabilized, creating multiple discontinuous littoral rocky habitats. Here, we present evidence supporting the hypothesis that establishment and expansion of isolated philopatric rock cichlid populations occurred after this rise and stabilization of lake level. We studied the Pseudotropheus ( Maylandia ) species complex, a group with both allopatric and sympatric populations that differ in male nuptial colour traits and tend to mate assortatively. Using coalescent analyses based on mitochondrial DNA, we found evidence that populations throughout the lake started to expand and accumulate genetic diversity after the lake level rise. Moreover, most haplotypes were geographically restricted, and the greatest genetic similarities were typically among sympatric or neighbouring populations. This is indicative of limited dispersal and establishment of assortative mating among populations following the lake level rise. Together, this evidence is compatible with a single large-scale environmental event being central to evolution of spatial patterns of genetic and species diversity in P. ( Maylandia ) and perhaps other Lake Malawi rock cichlids. Equivalent climate-driven pulses of habitat formation and fragmentation may similarly have contributed to observed rapid and punctuated cladogenesis in other adaptive radiations.     

The role of head shape and trophic variation in the diversification of the genus Herichthys in sympatry and allopatry

In the present study we evaluated the putative cases of sympatric speciation in the genus Herichthys by studying the variation in head shape using principal component analysis, phylomorphospace and reconstructions of the ancestral states of feeding preferences. Herichthys includes both allopatric and sympatric sister species, as well as sympatric unrelated species and thus offers great potential for evolutionary studies of putatively sympatric speciation. Herichthys is the northernmost group of cichlids in America and one of the most ecologically disparate genera within Middle American cichlids. Fifteen anatomical points were recorded on the heads of 293 specimens of the 11 species recognized within the genus. The results show that in spite of having wide variation in consumed diets, most species of Herichthys are close in morphospace. However, morphological variation was great among the two pairs of sympatric sister species in agreement with the suggested sympatric model of speciation.     

Can sympatric speciation by disruptive sexual selection explain rapid evolution of cichlid diversity in Lake Victoria?

Rapid speciation can occur on ecological time scales and interfere with ecological processes, resulting in species distribution patterns that are difficult to reconcile with ecological theory. The haplochromine cichlids in East African lakes are an extreme example of rapid speciation. We analyse the causes of their high speciation rates. Various studies have identified disruptive sexual selection acting on colour polymorphisms that might cause sympatric speciation. Using data on geographical distribution, colouration and relatedness from 41 species endemic to Lake Victoria, we test predictions from this hypothesis. Plotting numbers of pairs of closely related species against the amount of distributional overlap between the species reveals a bimodal distribution with modes on allopatric and sympatric. The proportion of sister species pairs that are heteromorphic for the traits under disruptive selection is higher in sympatry than in allopatry. These data support the hypothesis that disruptive sexual selection on colour polymorphisms has caused sympatric speciation and help to explain the rapid radiation of haplochromine species flocks.     

Recent speciation between sympatric Tanganyikan cichlid colour morphs

Lake Tanganyika, Africa's oldest lake, harbours an impressive diversity of cichlid fishes. Although diversification in its radiating groups is thought to have been initially rapid, cichlids from Lake Tanganyika show little evidence for ongoing speciation. In contrast, examples of recent divergence among sympatric colour morphs are well known in haplochromine cichlids from Lakes Malawi and Victoria. Here, we report genetic evidence for recent divergence between two sympatric Tanganyikan cichlid colour morphs. These Petrochromis morphs share mitochondrial haplotypes, yet microsatellite loci reveal that their sympatric populations form distinct genetic groups. Nuclear divergence between the two morphs is equivalent to that which arises geographically within one of the morphs over short distances and is substantially smaller than that among other sympatric species in this genus. These patterns suggest that these morphs diverged only recently, yet that barriers to gene flow exist which prevent extensive admixture despite their sympatric distribution. The morphs studied here provide an unusual example of active diversification in Lake Tanganyika's generally ancient cichlid fauna and enable comparisons of speciation processes between Lake Tanganyika and other African lakes.     

Microsatellites reveal high levels of population substructuring in the species-poor Eretmodine cichlid lineage from Lake Tanganyika

This study investigated fine-scale population substructuring in an apparently monogamous, biparental mouth-brooding cichlid. Microsatellite allele frequencies were determined at four polymorphic loci for nine populations of Eretmodus cyanostictus. We provide empirical support for the hypothesis that a species employing this breeding strategy should exhibit high levels of population substructuring. Stretches of sand represent considerable barriers to dispersal and, in contrast to the rock-dwelling cichlids of Lake Malawi, distance alone, along a continuous rocky shoreline, is sufficient to reduce gene flow significantly There was a significant pattern of isolation by distance both along the whole study area and over the stretch of continuous shoreline, suggesting that this species has poor dispersal capabilities and that juveniles establish territories close to their natal site. Despite limited dispersal, E. cyanostictus populations are not significantly more inbred than a more-widely dispersing rock-dwelling cichlid from Lake Malawi. This finding may cast doubt on the hypothesis that polyandry has evolved as a mechanism for maintaining genetic diversity in Lake Malawi cichlids. High levels of substructuring may not always promote high levels of speciation, and other factors, such as the intensity of sexual selection, may be more important in determining the speciation potential of a lineage.     

How does the taxonomic status of allopatric populations influence species richness within African cichlid fish assemblages?

Aim Current estimates of species richness within rapidly evolving species flocks are often highly dependent on the species status of allopatric populations that differ in phenotypic traits. These traits may be unreliable indicators of biological species status and systematists may have inconsistently assigned species among lineages or locations on the basis of these traits, thus hampering comparative studies of regional species richness and speciation rates. Our aim was to develop a method of generating standardized estimates of regional species richness suitable for comparative analysis, and to use these estimates to examine the extent and consistency of species assignment of allopatric populations within rapidly evolving cichlid fish flocks present in three east African lakes. Location Lakes Malawi, Victoria and Tanganyika. Methods Using published taxon co-occurrence data, a novel approach was employed to calculate standardized ‘minimum’ estimates of regional species richness for hard substrate associated complexes of cichlids within each of the lakes. Minimum estimates were based on an explicit assumption that if taxa present on equivalent habitats have disjunct distributions, then they are allopatric forms of the same species. These estimates were compared with current observed ‘high-end’ regional species richness estimates for those complexes to determine the consistency of species assignment of allopatric populations between lineages within a lake. A ‘sympatry’ index was developed to enable comparisons of levels of species assignment of allopatric populations between-lakes to be made. Results Within each lake, the minimum and high-end estimates for species richness were significantly correlated across complexes, indicating that the complexes that contain more recognized species contain the most genuine biological species. However, comparisons of complexes among lakes revealed considerable differences. For equivalent geographical areas, substantially higher proportions of recognized species were totally allopatric within the studied Lake Malawi and Lake Victoria complexes, than those of Lake Tanganyika. Main Conclusions Among African lakes, levels of assignment to species status of allopatric populations were found to be distinctly different. It is unclear whether the discrepancies are a consequence of differences between the lake faunas in degrees of phenotypic divergence among allopatric populations, or are simply the result of inconsistent taxonomic practices. In either case, these results have considerable wider relevance for they emphasize that quantitative measures of regional and beta diversity are critically dependent on the species status of allopatric populations, an issue usually neglected in comparative studies of species richness. The technique introduced here can be used to standardize measures of regional diversity of lineages for comparative analyses, potentially enabling more accurate identification of processes influencing rates of speciation.     

Population structure on breeding grounds of Lake Malawi’s ‘twilight zone’ cichlid fishes

Aim Free‐ranging benthopelagic fishes often have large population sizes and high rates of dispersal. These traits can act to homogenize population structure across the distributional range of a species and to reduce the likelihood of allopatric speciation. The apparent absence of any barriers to gene flow among populations, together with prior molecular evidence for panmixia across the ranges of three species, has resulted in Diplotaxodon, a genus of benthopelagic cichlid fishes of Lake Malawi, being proposed as a candidate case of sympatric speciation. Our aim was to further investigate this possibility by testing for intraspecific genetic subdivision among breeding populations, and intraspecific differences in breeding habitat. Location Lake Malawi, central‐east Africa. Methods We analysed eight microsatellite DNA loci to test for spatial genetic differences among populations on breeding grounds of eight Diplotaxodon species. We also tested for temporal population genetic differences within breeding grounds of three species. Records of ripe Diplotaxodon encountered during sampling were analysed to test if spatial variation in assemblage structure was linked to nearshore water depth and geographic proximity of sampling sites. Results Consistent with previous molecular evidence, within four of the eight species tested we found no evidence of spatial genetic structuring among breeding populations. However, within the other four species we found slight yet significant spatial genetic differences, indicating restricted gene flow among breeding grounds. There was no evidence of temporal genetic differences within sites. Analyses of the distributions of ripe Diplotaxodon revealed differences in assemblage structure linked to nearshore water depth. Main conclusions Together, these results demonstrate both the evolution of fidelity to deep‐water breeding locations in some Diplotaxodon species, and differences in breeding habitat among species. These findings are consistent with a role for divergence of breeding habitat in speciation of these cichlids, possibly promoted by dispersal limitation among geographically segregated spawning aggregations.     

Genetic population structure indicates sympatric speciation of Lake Malawi pelagic cichlids.

Allopatric processes of speciation have routinely been presented to explain the extraordinary radiation of the East African Great Lakes cichlid fish species flocks. The 21 or more species of pelagic cichlids within the Lake Malawi flock appear to have lake-wide distributions that challenge such a concept. Data from six microsatellite DNA loci indicate single, panmictic populations across the lake of three Diplotaxodon species. Levels of variability at these loci suggest that populations have been large and stable. Mitochondrial DNA sequence data (872 bp of control region + 981 bp of the NADH-2) from 90 species, representing all major clades within the Lake Malawi flock, indicate reciprocal monophyly of the pelagic clade. We suggest that these data support a hypothesis that speciation in sympatry is more plausible (and widespread) within the cichlid species flocks than previously thought.     

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.     

Comparison of gene flow among species that occur within the same geographic locations versus gene flow among populations within species reveals introgression among several Elymus species

One of the challenges in evolutionary biology is to understand the evolution of speciation with incomplete reproductive isolation as many taxa have continued gene flow both during and after speciation. Comparison of population structure between sympatric and allopatric populations can reveal specific introgression and determine if introgression occurs in a unidirectional or bidirectional manner. Simple sequence repeat markers were used to characterize sympatric and allopatric population structure of plant species, Elymus alaskanus (Scribn. and Merr.) Löve, E. caninus L., E. fibrosus (Schrenk) Tzvel., and E. mutabilis (Drobov) Tzvelev. Our results showed that genetic diversity (H_E) at species level is E. caninus (0.5355) > E. alaskanus (0.4511) > E. fibrosus (0.3924) > E. mutabilis (0.3764), suggesting that E. caninus and E. alaskanus are more variable than E. fibrosus and E. mutabilis. Gene flow between species that occurs within the same geographic locations versus gene flow between populations within species was compared to provide evidence of introgression. Our results indicated that gene flow between species that occur within the same geographic location is higher than that between populations within species, suggesting that gene flow resulting from introgressive hybridization might have occurred among the sympatric populations of these species, and may play an important role in partitioning of genetic diversity among and within populations. The migration rate from E. fibrosus to E. mutabilis is highest (0.2631) among the four species studied. Asymmetrical rates of gene flow among four species were also observed. The findings highlight the complex evolution of these four Elymus species.     

Variation in hostplant relations and courtship signals of weed-associated populations of the brown planthopper, Nilaparvata lugens (Stål), from Australia and Asia: a test of the recognition species concept

Populations of the morphological species, Nilaparvata lugens (Stål), were found to breed and feed on the grass, Leersia hexandra Schwartz, at six sites in Queensland, Australia. They differ from sympatric rice-feeding populations in characters of pulse repetition frequencies of male and female acoustic courtship signals. The two host-derived populations hybridize freely in the laboratory, but in mate choice experiments show very significant preferences for homogametic matings. No indication of field hybridization has been found, so that the two morphologically inseparable populations represent sympatric biological species in Australia.
Populations from L. hexandra are also reported from four localities in Sri Lanka and one in Orissa, India. These resemble previously studied populations from the Philippines. They differ significantly in courtship call characters, both from sympatric rice-associated populations and from allopatric Leersia -associated populations from Australia.
The geographical variation reported for acoustic signals is not consistent with Paterson's recognition concept of species, but may be interpreted in terms of theories of allopatric speciation involving sexual selection for mate recognition signals.     

REINFORCEMENT OF STICKLEBACK MATE PREFERENCES: SYMPATRY BREEDS CONTEMPT

Detailed studies of reproductive isolation and how it varies among populations can provide valuable insight into the mechanisms of speciation. Here we investigate how the strength of premating isolation varies between sympatric and allopatric populations of threespine sticklebacks to test a prediction of the hypothesis of reinforcement: that interspecific mate discrimination should be stronger in sympatry than in allopatry. In conducting such tests, it is important to control for ecological character displacement between sympatric species because ecological character divergence may strengthen prezygotic isolation as a by-product. We control for ecological character displacement by comparing mate preferences of females from a sympatric population (benthics) with mate preferences of females from two allopatric populations that most closely resemble the sympatric benthic females in ecology and morphology. No-choice mating trials indicate that sympatric benthic females mate less readily with heterospecific (limnetic) than conspecific (benthic) males, whereas two different populations of allopatric females resembling benthics show no such discrimination. These differences demonstrate reproductive character displacement of benthic female mate choice. Previous studies have established that hybridization between sympatric species occurred in the past in the wild and that hybrid offspring have lower fitness than either parental species, thus providing conditions under which natural selection would favor individuals that do not hybridize. Results are therefore consistent with the hypothesis that female mate preferences have evolved as a response to reduced hybrid fitness (reinforcement), although direct effects of sympatry or a biased extinction process could also produce the pattern. Males of the other sympatric species (limnetics) showed a preference for smaller females, in contrast to the inferred ancestral preference for larger females, suggesting reproductive character displacement of limnetic male mate preferences as well.     

The distribution and dispersal of introduced fish at Thumbi West Island in Lake Malawi, Africa

The rock-dwelling cichlids, or mbuna, of Lake Malawi are exceptionally diverse. Explanations of this diversity have used limited dispersal by the mbuna as the basis for allopatric models of speciation. However, there have been no studies that have attempted to define the extent and rates of dispersal of mbuna populations in the field. The present work took advantage of some translocations in which several species of mbuna were introduced to the Cape Maclear region of Lake Malawi from elsewhere in the lake. A detailed series of transects involving observations at four depths was undertaken at Thumbi West Island to define the distribution of the introduced species. There are large differences between species in the extent to which they have spread. Some species are now present all round the island while others have dispersed only a limited distance from the site of the initial introductions. This survey provides the first comprehensive data set on the distribution of the introduced species and it raises a number of important questions regarding their dispersal ability and their likely impact on the endemic community.     

Visual adaptation could aid sympatric speciation in a deep crater lake

Allopatric speciation was originally suggested to be the primary mechanism of animal speciation (Mayr, 1942; Figure 1). During allopatric speciation, populations diverge when gene flow is reduced across significant biogeographic barriers. Sympatric speciation, where species diverge while inhabiting the same location, was thought to be essentially impossible. However, the advent of theoretical models followed by new experimental evidence made sympatric speciation more plausible (Via, 2001). The cichlid fishes of Barombi Mbo, a small crater lake in western Cameroon, became one of the most widely accepted examples of sympatric speciation (Schliewen, Tautz, & Paabo, 1994). Although the phylogenetic history of this clade is not quite as simple as originally thought, it remains one of the best examples of sympatric speciation (Richards, Poelstra, & Martin, 2018). However, little is known about the molecular mechanisms contributing to the splitting of these species in situ. In a From the Cover article in this issue of Molecular Ecology, Musilova et al. (2019) focus on the diversity of visual systems among these fishes. They identify genetic changes associated with several aspects of visual adaptation that may have contributed to the ecological specialization and sympatric speciation of cichlids in this lake.     

The genetic architecture of male colour differences between a sympatric Lake Malawi cichlid species pair

The genetic basis of traits involved in reproductive isolation is a key parameter in models of sympatric speciation by sexual selection, a potential mechanism driving the explosive radiation of East African cichlids. Analysis of hybrid crosses between two sympatric Lake Malawi cichlid species, representing the extremes of the extant colour distribution, generated Castle-Wright estimates of four to seven loci controlling colour differences. Segregation patterns deviated from a purely additive model with a significant contribution from dominance, and possibly also epistasis. Evidence was found for a strong influence of autosomal loci. As departures from simple additive variation could effect the operation of models of sympatric speciation, dominance and epistasis should not be neglected.     

Genetic differentiation among host-associated Alebra leafhoppers (Hemiptera: Cicadellidae)

The limited importance ascribed to sympatric speciation processes via host race formation is partially due to the few cases of host races that have been reported among host populations. This work sheds light on the taxonomy of Alebra leafhoppers and examines the possible existence of host races among host-associated populations. The species of this genus show varying degrees of host association with deciduous trees and shrubs and, frequently, host populations of uncertain taxonomic status coexist and occasionally become pests. Allozyme electrophoresis of 21 Greek populations including sympatric, local and geographically distant samples collected on 13 different plant species, show that they represent at least five species: A. albostriella Fallén, A. viridis (Rey) (sensu Gillham), A. wahlbergi Boheman and two new species. Of these, one is associated to Quercus frainetto and other is specific to Crataegus spp. Significant genetic differences among sympatric and local host populations were found only in A. albostriella, between populations on Turkey oak, beech and common alder. It is suggested that the last two of these host populations may represent different host races. The results show that both the host plant and geographical distance affect the patterns of differentiation in the genus. The formation of some species seems to have been the result of allopatric speciation events while, for others, their origin can be equally explained either by sympatric or allopatric speciation.     

Speciation of Iberian diving beetles in Pleistocene refugia (Coleoptera, Dytiscidae)

The Mediterranean basin is an area of high diversity and endemicity, but the age and origin of its fauna are still largely unknown. Here we use species-level phylogenies based on approximately 1300 base pairs of the genes 16S rRNA and cytochrome oxidase I to establish the relationships of 27 of the 34 endemic Iberian species of diving beetles in the family Dytiscidae, and to investigate their level of divergence. Using a molecular clock approach, 18-19 of these species were estimated to be of Pleistocene origin, with four to six of them from the Late Pleistocene ( approximately 100 000 years). A second, lower speciation frequency peak was assigned to Late Miocene or Early Pliocene. Analysis of the distributional ranges showed that endemic species placed in the tip nodes of the trees are significantly more likely to be allopatric with their sisters than endemic species at lower node levels. Allopatric sister species are also significantly younger than sympatric clades, in agreement with an allopatric mode of speciation and limited subsequent range movement. These results strongly suggest that for some taxa Iberian populations were isolated during the Pleistocene long enough to speciate, and apparently did not expand their ranges to recolonize areas north of the Pyrenees. This is in contradiction to observations from fossil beetles in areas further north, which document large range movements associated with the Pleistocene glacial cycles hypothesized to suppress population isolation and allopatric speciation.     

Color patterns and species recognition in four closely related species of Lake Malawi cichlid

We examined interspecific female mating preferences in fourclosely related species of cichlid belonging to the Pseudotropheuszebra species complex of Lake Malawi. These species differin coloration but are similar in other respects, suggestingthat male color patterns may be important to female mate choicein species recognition. To test this hypothesis, we presented females from each species with a choice of four males, one ofher own species and three others that were each of a differentspecies. We also gave each female a choice between the threeheterospecific males only. In all four species, females showeda significant preference for conspecific males in the four-waychoice and chose the male with the most similar color patternto the conspecific male in the three-way choice. These resultsare discussed with reference to the theory of sexual selectionon color patterns as a means of sympatric speciation in cichlids.