Flickers of speciation: Sympatric colour morphs of the arc‐eye hawkfish,Paracirrhites arcatus,reveal key elements of divergence with gene flow

One of the primary challenges of evolutionary research is to identify ecological factors that favour reproductive isolation. Therefore, studying partially isolated taxa has the potential to provide novel insight into the mechanisms of evolutionary divergence. Our study utilizes an adaptive colour polymorphism in the arc‐eye hawkfish (Paracirrhites arcatus) to explore the evolution of reproductive barriers in the absence of geographic isolation. Dark and light morphs are ecologically partitioned into basaltic and coral microhabitats a few metres apart. To test whether ecological barriers have reduced gene flow among dark and light phenotypes, we evaluated genetic variation at 30 microsatellite loci and a nuclear exon (Mc1r) associated with melanistic coloration. We report low, but significant microsatellite differentiation among colour morphs and stronger divergence in the coding region of Mc1r indicating signatures of selection. Critically, we observed greater genetic divergence between colour morphs on the same reefs than that between the same morphs in different geographic locations. We hypothesize that adaptation to the contrasting microhabitats is overriding gene flow and is responsible for the partial reproductive isolation observed between sympatric colour morphs. Combined with complementary studies of hawkfish ecology and behaviour, these genetic results indicate an ecological barrier to gene flow initiated by habitat selection and enhanced by assortative mating. Hence, the arc‐eye hawkfish fulfil theoretical expectations for the earliest phase of speciation with gene flow.     

MHC class II‐assortative mate choice in European badgers (Meles meles)

The major histocompatibility complex (MHC) plays a crucial role in the immune system, and in some species, it is a target by which individuals choose mates to optimize the fitness of their offspring, potentially mediated by olfactory cues. Under the genetic compatibility hypothesis, individuals are predicted to choose mates with compatible MHC alleles, to increase the fitness of their offspring. Studies of MHC‐based mate choice in wild mammals are under‐represented currently, and few investigate more than one class of MHC genes. We investigated mate choice based on the compatibility of MHC class I and II genes in a wild population of European badgers (Meles meles). We also investigated mate choice based on microsatellite‐derived pairwise relatedness, to attempt to distinguish MHC‐specific effects from genomewide effects. We found MHC‐assortative mating, based on MHC class II, but not class I genes. Parent pairs had smaller MHC class II DRB amino acid distances and smaller functional distances than expected from random pairings. When we separated the analyses into within‐group and neighbouring‐group parent pairs, only neighbouring‐group pairs showed MHC‐assortative mating, due to similarity at MHC class II loci. Our randomizations showed no evidence of genomewide‐based inbreeding, based on 35 microsatellite loci; MHC class II similarity was therefore the apparent target of mate choice. We propose that MHC‐assortative mate choice may be a local adaptation to endemic pathogens, and this assortative mate choice may have contributed to the low MHC genetic diversity in this population.     

Morph‐dependent fitness and directional change of morph frequencies over time in a Dutch population of Common buzzards Buteo buteo

How genetic polymorphisms are maintained in a population is a key question in evolutionary ecology. Previous work on a plumage colour polymorphism in the common buzzard Buteo buteo suggested heterozygote advantage as the mechanism maintaining the co‐existence of three morphs (light, intermediate and dark). We took advantage of 20 years of life‐history data collected in a Dutch population to replicate earlier studies on the relationship between colour morph and fitness in this species. We examined differences between morphs in adult apparent survival, breeding success, annual number of fledglings produced and cumulative reproductive success. We found that cumulative reproductive success differed among morphs, with the intermediate morph having highest fitness. We also found assortative mating for colour morph, whereby assortative pairs were more likely to produce offspring and had longer‐lasting pair bonds than disassortative pairs. Over the 20‐year study period, the proportion of individuals with an intermediate morph increased. This apparent evolutionary change did not just arise from selection on individual phenotypes, but also from fitness benefits of assortative mating. The increased frequency of intermediates might also be due to immigration or drift. We hypothesize that genetic variation is maintained through spatial variation in selection pressures. Further studies should investigate morph‐dependent dispersal behaviour and habitat choice.     

No correlation between multi‐locus heterozygosity and fitness in the common buzzard despite heterozygote advantage for plumage colour

Correlations between heterozygosity and fitness are frequently found but rarely well understood. Fitness can be affected by single loci of large effect which correlate with neutral markers via linkage disequilibrium, or as a result of variation in genome‐wide heterozygosity following inbreeding. We explored these alternatives in the common buzzard, a raptor species in which three colour morphs differ in their lifetime reproductive success. Using 18 polymorphic microsatellite loci, we evaluated potential genetic differences among the morphs which may lead to subpopulation structuring and tested for correlations between three fitness‐related traits and heterozygosity, both genome wide and at each locus separately. Despite their assortative mating pattern, the buzzard morphs were found to be genetically undifferentiated. Multilocus heterozygosity was only found to be correlated with a single fitness‐related trait, infection with the blood parasite, Leucocytozoon buteonis, and this was via interactions with vole abundance and age. One locus also showed a significant relationship with blood parasite infection and ectoparasite infestation. The vicinity of this locus contains two genes, one of which is potentially implicated in the immune system of birds. We conclude that genome‐wide heterozygosity is unlikely to be a major determinant of parasite burden and body condition in the polymorphic common buzzard.     

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.     

SEX CHROMOSOME LINKAGE OF MATE PREFERENCE AND COLOR SIGNAL MAINTAINS ASSORTATIVE MATING BETWEEN INTERBREEDING FINCH MORPHS

Assortative mating is a key aspect in the speciation process because it is important for both initial divergence and maintenance of distinct species. However, it remains a challenge to explain how assortative mating evolves when diverging populations are undergoing gene flow (e.g., during hybridization). Here I experimentally test how assortative mating is maintained with frequent gene flow between diverged head‐color morphs of the Gouldian finch (Erythrura gouldiae). Contrary to the predominant view on the development of sexual preferences in birds, cross‐fostered offspring did not imprint on the phenotype of their conspecific (red or black morphs) or heterospecific (Bengalese finch) foster parents. Instead, the mating preferences of F₁ and F₂ intermorph‐hybrids are consistent with inheritance on the Z chromosomes, which are also the location for genes controlling color expression and the genes causing low fitness of intermorph‐hybrids. Genetic associations between color signal and preference loci on the sex chromosomes may prevent recombination from breaking down these associations when the morphs interbreed, helping to maintain assortative mating in the face of gene flow. Although sex linkage of reproductively isolating traits is theoretically expected to promote speciation, social and ecological constraints may enforce frequent interbreeding between the morphs, thus preventing complete reproductive isolation.     

No barriers to gene flow among sympatric polychromatic 'small'Telmatherina antoniae from Lake Matano, Indonesia

Genetic divergence, assortative courtship and intermale aggression were assessed between sympatric colour morphs of the sailfin silverside Telmatherina antoniae , endemic to Lake Matano, Indonesia. Genetic analysis using microsatellite markers showed no barriers to gene flow among T. antoniae primary colour morphs (blue and yellow) within sampling sites, sympatric populations or at the lake-wide level. Low but significant genetic differentiation was found between yellow morphs and mixed (blue–yellow) morphs. Behavioural surveys indicated assortative courtship does occur along primary colour lines; however, intermale aggression among paired and intruding male morphs appeared equal with respect to male colour. These observations support the hypothesis that males view other males as threats to their courtship regardless of their colour. This study supports recent work suggesting that assortative mating is present in T. antoniae despite a lack of reproductive isolation among colour morphs.     

No evidence for size‐assortative mating in the wild despite mutual mate choice in sex‐role‐reversed pipefishes

Size‐assortative mating is a nonrandom association of body size between members of mating pairs and is expected to be common in species with mutual preferences for body size. In this study, we investigated whether there is direct evidence for size‐assortative mating in two species of pipefishes, Syngnathus floridae and S. typhle, that share the characteristics of male pregnancy, sex‐role reversal, and a polygynandrous mating system. We take advantage of microsatellite‐based “genetic‐capture” techniques to match wild‐caught females with female genotypes reconstructed from broods of pregnant males and use these data to explore patterns of size‐assortative mating in these species. We also develop a simulation model to explore how positive, negative, and antagonistic preferences of each sex for body size affect size‐assortative mating. Contrary to expectations, we were unable to find any evidence of size‐assortative mating in either species at different geographic locations or at different sampling times. Furthermore, two traits that potentially confer a fitness advantage in terms of reproductive success, female mating order and number of eggs transferred per female, do not affect pairing patterns in the wild. Results from model simulations demonstrate that strong mating preferences are unlikely to explain the observed patterns of mating in the studied populations. Our study shows that individual mating preferences, as ascertained by laboratory‐based mating trials, can be decoupled from realized patterns of mating in the wild, and therefore, field studies are also necessary to determine actual patterns of mate choice in nature. We conclude that this disconnect between preferences and assortative mating is likely due to ecological constraints and multiple mating that may limit mate choice in natural populations.     

Genetic divergence among sympatric colour morphs of the Dalmatian wall lizard (<Emphasis Type="Italic">Podarcis melisellensis</Emphasis>)

If alternative phenotypes in polymorphic populations do not mate randomly, they can be used as model systems to study adaptive diversification and possibly the early stages of sympatric speciation. In this case, non random mating is expected to support genetic divergence among the different phenotypes. In the present study, we use population genetic analyses to test putatively neutral genetic divergence (of microsatellite loci) among three colour morphs of the lizard Podarcis melisellensis, which is associated with differences in male morphology, performance and behaviour. We found weak evidence of genetic divergence, indicating that gene flow is somewhat restricted among morphs and suggesting possible adaptive diversification.     

ALLOPATRIC DIVERGENCE AND SPECIATION IN CORAL REEF FISH: THE THREE‐SPOT DASCYLLUS,DASCYLLUS TRIMACULATUS,SPECIES COMPLEX

Long pelagic larval phases and the absence of physical barriers impede rapid speciation and contrast the high diversity observed in marine ecosystems such as coral reefs. In this study, we used the three‐spot dascyllus (Dascyllus trimaculatus) species complex to evaluate speciation modes at the spatial scale of the Indo‐Pacific. The complex includes four recognized species and four main color morphs that differ in distribution. Previous studies of the group using mitochondrial DNA revealed a noncongruence between color morphs and genetic groupings; with two of the color morphs grouped together and one color morph separated into three clades. Using extensive geographic sampling of 563 individuals and a combination of mitochondrial DNA sequences and 13 nuclear microsatellites, we defined population/species boundaries and inferred different speciation modes. The complex is composed of seven genetically distinct entities, some of which are distinct morphologically. Despite extensive dispersal abilities and an apparent lack of barriers, observed genetic partitions are consistent with allopatric speciation. However, ecological pressure, assortative mating, and sexual selection, were likely important during periods of geographical isolation. This study therefore suggests that primarily historical factors later followed by ecological factors caused divergence and speciation in this group of coral reef fish.     

Adaptive associations between total body color dimorphism and climatic stress‐related traits in a stenothermal circumtropical Drosophila species

Abstract Low desiccation resistance of Drosophila ananassae reflects its rarity outside the humid tropics. However, the ability of this sensitive species to evolve under seasonally varying subtropical areas is largely unknown. D. ananassae flies are mostly lighter during the rainy season but darker and lighter flies occur in the autumn season in northern India. We tested the hypothesis whether seasonally varying alternative body color phenotypes of D. ananassae vary in their levels of environmental stress tolerances and mating behavior. Thus, we investigated D. ananassae flies collected during rainy and autumn seasons for changes in body melanization and their genetic basis, desiccation‐related traits, cold tolerance and mating propensity. On the basis of genetic crosses, we found total body color dimorphism consistent with a single gene model in both sexes of D. ananassae. A significant increase in the frequency of the dark morph was observed during the drier autumn season, and body color phenotypes showed significant deviations from Hardy‐Weinberg equilibrium, which suggests climatic selection plays a role. Resistance to desiccation as well as cold stress were two‐ to three‐fold higher in the dark body color strain as compared with the light strain. On the basis of no‐choice mating experiments, we observed significantly higher assortative matings between dark morphs under desiccation or cold stress, and between light morphs under hot or higher humidity conditions. To the best of our knowledge, this is the first report on the ecological significance of seasonally varying total body color dimorphism in a tropical species, D. ananassae.     

Mouth dimorphism in scale‐eating cichlid fish from Lake Tanganyika advances individual fitness

Random asymmetry, that is the coexistence of left‐ and right‐sided (or ‐handed) individuals within a population, is a particular case of natural variation; what triggers and maintains such dimorphisms remains unknown in most cases. Here, we report a field‐based cage experiment in the scale‐eating Tanganyikan cichlid Perissodus microlepis, which occurs in two morphs in nature: left‐skewed and right‐skewed individuals with respect to mouth orientation. Using underwater cages stocked with scale‐eaters and natural prey fish, we first confirm that, under semi‐natural conditions, left‐skewed scale‐eaters preferentially attack the right flank of their prey, whereas right‐skewed individuals feed predominantly from the left side. We then demonstrate that scale‐eaters have a higher probability for successful attacks when kept in dimorphic experimental populations (left‐ and right‐skewed morphs together) as compared to monomorphic populations (left‐ or right‐skewed morphs), most likely because prey fishes fail to accustom to strikes from both sides. The significantly increased probability for attacks appears to be the selective agent responsible for the evolution and maintenance of mouth dimorphism in P. microlepis, lending further support to the hypothesis that negative frequency‐dependent selection is the stabilizing force balancing the mouth dimorphism at quasi‐equal ratios in scale‐eating cichlids.     

Isolation and characterization of Ligustrum micranthum (Oleaceae) microsatellite loci using paired‐end Illumina reads

Twenty‐six microsatellite loci were developed and characterized for Ligustrum micranthum, a species endemic to the Ogasawara Islands, Japan. The genetic structure of this species must be clarified in order to restore the island's ecosystem. A total of 8511 primer pairs were designed from de novo sequencing. Of the 48 primer pairs selected, amplification and polymorphisms were tested using one population each from the Chichijima and Hahajima Islands of the Ogasawara Islands. Twenty‐six microsatellite loci were successfully amplified and the number of alleles for these loci ranged from five to 31 per locus, and the mean expected heterozygosities were 0.858 and 0.849, respectively. No significant deviation from the Hardy–Weinberg equilibrium was observed in either population, and no significant linkage disequilibrium was detected between any locus pair. The microsatellite loci reported in this study can be used in future studies to evaluate the genetic structure and mating system of L. micranthum.     

Microsatellite and morphological analysis of population structure in the parthenogenetic freshwater snail Melanoides tuberculata: insights into the creation of clonal variability

The distribution of variability was studied at various geographical scales in the tropical freshwater snail Melanoides tuberculata, in order to analyse the role of factors shaping this distribution, including the mating system and population dynamics. This parthenogenetic polyploid species reproduces mainly asexually, with males occurring at low frequency. About 800 individuals (38 sites) were sampled from Africa and the Middle East, where the species originated, and from recently colonized habitats in South and Central America, and especially the island of Martinique. We first described variation of general aspects and ornamentation of the shells. This analysis confirms the existence of discrete morphs. Second, individuals were studied at three microsatellite loci, showing that each morph is a genetic clone with some minor variation compatible with models of microsatellite evolution. The genetic analysis also showed much more variation within than between clones. However, two populations from Africa exhibited a large amount of variability, and a mixture of sexual and asexual reproduction might explain these genetic patterns. The worldwide distribution of variability is, therefore, compatible with the African origin of the species, and the introduction of a few clones in other parts of the world. These results also suggest that the distribution of variability in Martinique is influenced by flooding events, and that two morphs from Martinique can be interpreted as hybrids between two pre-existing morphs, based on morphological, genetic and geographical arguments.     

Sexual selection and assortative mating by size and their roles in the maintenance of a polymorphism in Swedish Littorina saxatilis populations

Two independent components of mating behaviour, sexual selection and assortative mating, were studied in two allopatric morphs, one sheltered boulder shore form (S-morph) and one exposed cliff shore form (E-morph), of Littorina saxatilis from the west coast of Sweden. Sexual selection was studied by comparing the sizes of copulating and non-copulating snails in the field. Size assortative mating was studied by collecting copulating pairs in the field, while assortative mating between morphs was investigated by bringing the pure morphs together in intermediary habitats and then noting the matings. The S-morph mated randomly in relation to size in two of the studied populations and exhibited a trend towards size assortative mating in a third, while the E-morph showed size assortative mating in both studied populations. The microdistribution of sizes of snails on the shores could not explain all the size assortative mating found, and instead it is argued that a size-based mate rejection behaviour also contributes to the assortative mating in at least some of these populations. There was sexual selection on size in both males and females in the S-morph, with large individuals being favoured as mates. In contrast, copulating snails of the E-morph were smaller than non-copulating ones. The significantly different sexual selection intensities between the two morphs may help to explain the size differences between them. There was random mating between the E- and the S-morphs of L. saxatilis, which suggests no incipient reproductive isolation between morphs on Swedish rocky shores. This is in agreement with earlier studies of Swedish populations, but is in contrast to the situation found in other geographical areas.     

Variable discrimination and asymmetric preferences in laboratory tests of reproductive isolation between cichlid colour morphs

Mating behaviour affects reproductive isolation and phenotypic differentiation. In Lake Tanganyika, the cichlid fish Tropheus moorii diversified into numerous, currently allopatric colour variants. Allopatric isolation is periodically interrupted by dispersal and secondary contact during lake level fluctuations, making long‐term differentiation partly dependent on assortative mating. Laboratory experiments with two moderately distinct morphs revealed assortative female preferences in one (Nakaku), but random mate choice in the other morph (Mbita). No discrimination was apparent between two subtly differentiated morphs (Chimba and Moliro). Tested against each other in a previous study, the highly distinct Moliro and Nakaku exhibited strong assortative preferences. The correlation between colour pattern similarity and mate discrimination suggests that allopatry and philopatric behaviour are less crucial for the maintenance of differentiation between highly distinct morphs than for more similar morphs. Interestingly, the asymmetric isolation in one pair of morphs is congruent with a pattern of unidirectional mitochondrial introgression between populations.     

Disassortative mating prevails in style‐dimorphic Narcissus papyraceus despite low reciprocity and compatibility of morphs

Evolution to reduce inbreeding can favor disassortative (intermorph) over assortative (intramorph) mating in hermaphroditic sexually polymorphic plant species. Heterostyly enhances disassortative pollination through reciprocal placement of stigmas and anthers of morphs and appropriate pollinators. Stylar dimorphism in which there is not reciprocal anther placement may compromise disassortative mating, particularly when there is not intramorph incompatibility. Variable rates of disassortative mating along with differential female fecundity or siring success among floral morphs could lead to variation in morph ratio. We investigated mating patterns, female fecundity, and siring success of style‐length morphs in Narcissus papyraceus, a self‐incompatible but morph‐compatible species with dimorphic (long‐ and short‐styled) and monomorphic (long‐styled) populations in central and north regions of its range, respectively. We established experimental populations in both regions and exposed them to ambient pollinators. Using paternity analysis, we found similar siring success of morphs and high disassortative mating in most populations. Female fecundity of morphs was similar in all populations. Although these results could not completely explain the loss of dimorphism in the species’ northern range, they provided evidence for the evolutionary stability of stylar dimorphism in N. papyraceus in at least some populations. Our findings support the hypothesis that prevailing intermorph mating is key for the maintenance of stylar dimorphism.     

Seeking signatures of reinforcement at the genetic level: a hitchhiking mapping and candidate gene approach in the house mouse

Reinforcement is the process by which prezygotic isolation is strengthened as a response to selection against hybridization. Most empirical support for reinforcement comes from the observation of its possible phenotypic signature: an accentuated degree of prezygotic isolation in the hybrid zone as compared to allopatry. Here, we implemented a novel approach to this question by seeking for the signature of reinforcement at the genetic level. In the house mouse, selection against hybrids and enhanced olfactory‐based assortative mate preferences are observed in a hybrid zone between the two European subspecies Mus musculus musculus and M. m. domesticus, suggesting a possible recent reinforcement event. To test for the genetic signature of reinforcing selection and identify genes involved in sexual isolation, we adopted a hitchhiking mapping approach targeting genomic regions containing candidate genes for assortative mating in mice. We densely scanned these genomic regions in hybrid zone and allopatric samples using a large number of fast evolving microsatellite loci that allow the detection of recent selection events. We found a handful of loci showing the expected pattern of significant reduction in variability in populations close to the hybrid zone, showing assortative odour preference in mate choice experiments as compared to populations further away and displaying no such preference. These loci lie close to genes that we pinpoint as testable candidates for further investigation.     

Extremely variable di‐ and tetranucleotide microsatellite loci in Brazilian free‐tailed bats (Tadarida brasiliensis)

We present three dinucleotide and six tetranucleotide microsatellite loci that were developed for the Brazilian free‐tailed bat, Tadarida brasiliensis (Chiroptera, Molossidae). Ninety‐one individuals from two populations were scored at each locus, revealing extremely high levels of polymorphism (15–55 alleles per locus). These loci provide genetic markers for studying gene flow, migration and mating behaviour.     

Characterization of microsatellite loci in the dusky‐footed woodrat,Neotoma fuscipes

Six moderately to highly polymorphic microsatellite loci were developed for dusky‐footed woodrats (Neotoma fuscipes) using a modified enrichment protocol. Of the 149 clones sequenced, 33 (22%) contained inserts with greater than 10 repeat units. These loci are currently being used to study various aspects of the ecology and evolution of N. fuscipes ranging from their mating and social system to individual population histories and geographical differentiation.