Influence of genetic dissimilarity in the reproductive success and mate choice of brown trout - females fishing for optimal MHC dissimilarity

HLA Genes: A Hallmark of Functional Genetic Variation and Complex Evolution

The major histocompatibility complex (MHC) with its highly polymorphic HLA genes represents one of the most intensely studied genomic regions in the genome. MHC proteins play a key role in antigen-specific immunity and are associated with a wide range of complex diseases. Despite decades of research and many advances in the field, the characterization and interpretation of its genetic and genomic variability remain challenging. Here an overview is provided of the MHC, the nature of its exceptional variability, and the complex evolutionary processes assumed to drive this variability. Highlighted are also recent advances in the field that promise to improve our understanding of the variability in the MHC and in antigen-specific immunity more generally.

MHCtools 1.5: Analysis of MHC Sequencing Data in R

The genes of the major histocompatibility complex (MHC) play a vital role in the vertebrate immune system and have attracted considerable interest in evolutionary biology. While the MHC has been characterized in detail in humans (human leukocyte antigen, HLA) and in model organisms such as the mouse, studies in non-model organisms often lack prior knowledge about structure, genetic variability, and evolutionary properties of this locus. MHC genotyping in non-model species commonly relies on PCR-based amplicon sequencing, and while several published protocols facilitate generation of MHC sequence data, there is a lack of transparent and standardized tools for downstream data analysis.Here, I present the R package MHCtools version 1.5, which contains 15 tools that (i) assist accurate MHC genotyping from high-throughput amplicon sequencing data, and provide standardized methods to analyze (ii) MHC diversity, (iii) MHC supertypes, and (iv) MHC haplotypes.I hope that MHCtools will be helpful in future studies of the MHC in non-model species and that it may help to advance our understanding of the important roles of the MHC in ecology and evolution.

Mate Discrimination Using Chemical Cues by Male Guppies

Males often perform mate choice with the aim of maximizing reproductive success. To identify profitable mates, the males of some animals are known to use visual and chemical cues derived from females. In this study, we aimed to examine mate discrimination by male guppies (Poecilia reticulata) using chemical cues received from females under different reproductive statuses, i.e., virgin females, pregnant females, females after copulation with another male, and post-partum females. We conducted a dichotomous choice experiment for each combination of chemical stimuli from females under different reproductive statuses. In experiment 1, in which females were removed from water that was subsequently used as a chemical stimulus, male preferences did not differ significantly in all combinations of chemical stimuli from females under different reproductive statuses. However, in experiment 2, in which females remained within bottles containing the water used as a chemical stimulus, with the exception of one combination of chemical stimuli, significant differences in male preferences were detected for chemical stimuli derived from females under different reproductive statuses. Overall, males generally showed a preference for chemical stimulus received from females after copulation with other males. The findings of this study indicate that male guppies can discriminate the reproductive status of females based solely on chemical cues that may disappear or degenerate within a short period of time, thereby facilitating profitable mate choice.

Do female bluethroats without extra-pair offspring have more MHC-compatible social mates?

Abstract

Genes of the major histocompatibility complex (MHC) are crucial for adaptive immunity in jawed vertebrates, and theory predicts that there should be mate choice for optimizing MHC constitution in the offspring. In a previous study, we demonstrated a non-random female choice of extra-pair males in the bluethroat (Luscinia svecica), yielding offspring that was closer to an intermediate MHC class II (MHCII) allele count than their within-pair halfsiblings. The present study tests whether social pairs with only within-pair young (WPY) in their brood, in the same study population, had a combined MHC-constitution closer to a presumed intermediate optimum, than social pairs with extra-pair young (EPY), with a corresponding pattern in their offspring. As expected, we found that WPY from pure WPY-broods were more MHC-optimal than WPY from mixed broods, but only in broods of young (second year) males. Correspondingly, there was a tendency for social pairs with only WPY in their brood to be more MHC-compatible than social pairs with EPY in their brood, when the male was young. Older bluethroat males have considerably larger testes than young males, and their higher sperm competitiveness could help them secure paternity in their own brood, also when they are not MHC-compatible. In other words, in the sexual conflict over paternity, females may be more likely to realise their preference for a MHC-compatible mate when paired to a young male. As a possible fitness indicator, immune responsiveness to an injected antigen (PHA) was elevated for offspring closer to “the golden mean” in MHCII allele count.

Significance statement

This study contributes to our understanding of MHC-based mate choice in extra-pair mating systems, by showing that female bluethroats (Luscinia svecica) with an MHCII-compatible social mate tend to have no extra-pair young in their brood, but only when the social male is young. This elucidates a possible sexual conflict, in which older social males are able to override female preferences and prevent other males from gaining paternity in their brood through higher sperm production. Studying systems in which extra-pair paternity occurs offers an insight into the genetic benefits of mate choice, as extra-pair males, in contrast to social males, generally contribute only sperm. Further, the strict and thorough genotyping scheme applied in this study enabled us to demonstrate a preference for “the golden mean” in MHC-diversity in a species with one of the highest MHC class II-diversity known to date.

A Review of Suggested Mechanisms of MHC Odor Signaling

Simple Summary

Immune genes of the vertebrate MHC vary among individuals. Each individual collection is optimally diverse to provide resistance against some infectious diseases but not too diverse to cause autoimmune diseases. MHC-dependent mate choice aims for optimally complementary MHC alleles. Each potential partner signals through body odor his/her MHC alleles. Identifying the signal molecules was a long-lasting puzzle solved only recently after many deviations as described. Commensal microbiota which are controlled by the individual MHC genes differ among individuals. They were suspected repeatedly to provide the signal, though mice raised germ-free could still smell MHC genes. Carrier hypotheses came in various versions, centered around the specificity of each MHC molecule for binding peptides from diseases, shown to T lymphocytes to induce the immune response. Volatiles of various origins were suggested to fill the place of the peptide and thus reflect the identity of the MHC molecule. Finally, the bound peptides themselves were identified as the sought info-chemicals. Synthesized peptides affect mate choice as predicted. Specific olfactory neurons were shown to react to these peptides but only to the anchors that define the binding specificity. Even eggs choose sperm to produce offspring with optimal MHC, though the signaling pathway needs further research.

Abstract

Although an individual’s mix of MHC immune genes determines its resistance, finding MHC-dependent mate choice occurred by accident in inbred mice. Inbred mice prefer MHC dissimilar mates, even when the choice was restricted to urine. It took decades to find the info-chemicals, which have to be as polymorphic as the MHC. Microbiota were suggested repeatedly as the origin of the odor signal though germ-free mice maintained normal preference. Different versions of the ‘carrier hypothesis’ suggested MHC molecules carry volatiles after the bound peptide is released. Theory predicted an optimal individual MHC diversity to maximize resistance. The optimally complementary mate should be and is preferred as several studies show. Thus, the odor signal needs to transmit the exact information of the sender’s MHC alleles, as do MHC ligand peptides but not microbiota. The ‘MHC peptide hypothesis’ assumes that olfactory perception of the peptide ligand provides information about the MHC protein in a key-lock fashion. Olfactory neurons react only to the anchors of synthesized MHC peptides, which reflect the binding MHC molecule’s identity. Synthesized peptides supplemented to a male’s signal affect choice in the predicted way, however, not when anchors are mutated. Also, the human brain detects smelled synthesized self-peptides as such. After mate choice, the lottery of meiosis of randomly paired oocyte and sperm haplotypes would often produce MHC non-optimal offspring. In sticklebacks, eggs select MHC-compatible sperm, thus prefer the best combination close to the population optimum.

High MHC diversity confers no advantage for phenotypic quality and reproductive performance in a wild bird

1. Genes of the major histocompatibility complex (MHC) encode antigen binding molecules and are an integral part of the acquired immune response of vertebrates. In general, high individual MHC diversity is expected to increase fitness by broadening the spectrum of pathogens recognized by the immune system, in accordance with the heterozygote advantage mechanism. On the other hand, the optimality hypothesis assumes that individuals with optimal (intermediate), rather than maximum diversity of the MHC will achieve the highest fitness because of inherent costs associated with expressing diverse MHC alleles. 2. Here, we tested for associations between individual diversity of the MHC class I and class II genes (binding antigens of intra- and extra-cellular pathogens, respectively) and a range of fitness-related traits (condition, ornament expression and reproduction) in an urban population of the Eurasian coot Fulica atra. 3. Contrary to our expectation, we found that high within-individual allelic diversity of MHC genes (both class I and II) was associated with poorer condition (lower blood haemoglobin concentrations), weaker expression of the putative ornament (smaller frontal shield), later onset of breeding and smaller clutches. An analysis of functional MHC allele clusters (supertypes) provided further support for negative associations of MHC diversity with phenotypic quality and reproductive performance, but most of these relationships could not be explained by the presence of specific maladaptive supertypes. Finally, we found little empirical support for the optimality hypothesis in the Eurasian coot. 4. Our results suggest that the costs of high MHC diversity outweighed any benefits associated with broad MHC repertoire, which could be driven by depauperate pathogen diversity in an urban landscape. To the best of our knowledge, this is one of the first studies providing consistent evidence for negative associations of MHC diversity with a range of fitness-related traits in a natural avian population.

Differences in Mate Pairings of Hatchery- and Natural-Origin Coho Salmon Inferred from Offspring Genotypes

Captive breeding can affect how sexual selection acts on subsequent generations. One context where this is important is in fish hatcheries. In many salmon hatcheries, spawning is controlled artificially and offspring are reared in captivity before release into the wild. While previous studies have suggested that hatchery- and natural-origin fish may make different mate choice decisions, it remains to be determined how hatchery fish may be making different mate choice decisions compared with natural-origin fish at a genetic level. Using genotyping-by-sequencing, we identify single-nucleotide polymorphisms (SNPs) associated with variation in mate pairings from a natural context involving hatchery- and natural-origin coho salmon (Oncorhynchus kisutch). In both natural-origin and hatchery mate pairs, we observed more SNPs with negative assortment than positive assortment. However, only 3% of the negative assortment SNPs were shared between the two mating groups, and 1% of the positive assortment SNPs were shared between the two mating groups, indicating divergence in mating cues between wild and hatchery-raised salmon. These findings shed light on mate choice in general and may have important implications in the conservation management of species as well as for improving other captive breeding scenarios. There remains much to discover about mate choice in salmon and research described here reflects our intent to test the potential of ongoing advances in population genomics to develop new hatchery practices that may improve the performance of hatchery offspring, lessening the differences and thus potential impacts upon wild stocks.

Balancing selection, genetic drift, and human-mediated introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout

The extraordinary polymorphism of major histocompatibility complex (MHC) genes is considered a paradigm of pathogen-mediated balancing selection, although empirical evidence is still scarce. Furthermore, the relative contribution of balancing selection to shape MHC population structure and diversity, compared to that of neutral forces, as well as its interaction with other evolutionary processes such as hybridization, remains largely unclear. To investigate these issues, we analyzed adaptive (MHC-DAB gene) and neutral (11 microsatellite loci) variation in 156 brown trout (Salmo trutta complex) from six wild populations in central Italy exposed to introgression from domestic hatchery lineages (assessed with the LDH gene). MHC diversity and structuring correlated with those at microsatellites, indicating the substantial role of neutral forces. However, individuals carrying locally rare MHC alleles/supertypes were in better body condition (a proxy of individual fitness/parasite load) regardless of the zygosity status and degree of sequence dissimilarity of MHC, hence supporting balancing selection under rare allele advantage, but not heterozygote advantage or divergent allele advantage. The association between specific MHC supertypes and body condition confirmed in part this finding. Across populations, MHC allelic richness increased with increasing admixture between native and domestic lineages, indicating introgression as a source of MHC variation. Furthermore, introgression across populations appeared more pronounced for MHC than microsatellites, possibly because initially rare MHC variants are expected to introgress more readily under rare allele advantage. Providing evidence for the complex interplay among neutral evolutionary forces, balancing selection, and human-mediated introgression in shaping the pattern of MHC (functional) variation, our findings contribute to a deeper understanding of the evolution of MHC genes in wild populations exposed to anthropogenic disturbance.

Using Reciprocal Transplants to Assess Local Adaptation, Genetic Rescue, and Sexual Selection in Newly Established Populations

Small populations establishing on colonization fronts have to adapt to novel environments with limited genetic variation. The pace at which they can adapt, and the influence of genetic variation on their success, are key questions for understanding intraspecific diversity. To investigate these topics, we performed a reciprocal transplant experiment between two recently founded populations of brown trout in the sub-Antarctic Kerguelen Islands. Using individual tagging and genetic assignment methods, we tracked the fitness of local and foreign individuals, as well as the fitness of their offspring over two generations. In both populations, although not to the same extent, gene flow occurred between local and foreign gene pools. In both cases, however, we failed to detect obvious footprints of local adaptation (which should limit gene flow) and only weak support for genetic rescue (which should enhance gene flow). In the population where gene flow from foreign individuals was low, no clear differences were observed between the fitness of local, foreign, and F1 hybrid individuals. In the population where gene flow was high, foreign individuals were successful due to high mating success rather than high survival, and F1 hybrids had the same fitness as pure local offspring. These results suggest the importance of considering sexual selection, rather than just local adaptation and genetic rescue, when evaluating the determinants of success in small and recently founded populations.

MHC-Based Mate Choice in Wild Golden Snub-Nosed Monkeys

The genes of the major histocompatibility complex (MHC) are an important component of the vertebrate immune system and play a significant role in mate choice in many species. However, it remains unclear whether female mate choice in non-human primates is based on specific functional genes and/or genome-wide genes. The golden snub-nosed monkey (Rhinopithecus roxellana) lives in a multilevel society, which consists of several polygynous one-male-several-female units. Although adult females tend to mainly socialize with one adult male, females often initiate extra-pair copulations with other males resulting in a high proportion of offspring being fathered by extra-pair males. We investigated the effects of adaptive MHC genes and neutral microsatellites on female mate choice in a wild R. roxellana population. We sequenced 54 parent-offspring triads using two MHC class II loci (Rhro-DQA1 and Rhro-DQB1) and 20 microsatellites from 3 years of data. We found that the paternities of offspring were non-randomly associated with male MHC compositions not microsatellite genotypes. Our study showed that the fathers of all infants had significantly less variance for several estimates of genetic similarity to the mothers compared with random males at both MHC loci. Additionally, the MHC diversity of these fathers was significantly higher than random males. We also found support for choice based on specific alleles; compared with random males, Rhro-DQA1^∗ 05 and Rhro-DQB1^∗ 08 were more common in both the OMU (one-male unit) males and the genetic fathers of offspring. This study provides new evidence for female mate choice for MHC-intermediate dissimilarity (rather than maximal MHC dissimilarity) and highlights the importance of incorporating multiple MHC loci and social structure into studies of MHC-based mate choice in non-human primates.

Deciphering genetic mate choice: Not so simple in group-housed conservation breeding programs

Incorporating mate choice into conservation breeding programs can improve reproduction and the retention of natural behaviors. However, different types of genetic-based mate choice can have varied consequences for genetic diversity management. As a result, it is important to examine mechanisms of mate choice in captivity to assess its costs and benefits. Most research in this area has focused on experimental pairing trials; however, this resource-intensive approach is not always feasible in captive settings and can interfere with other management constraints. We used generalized linear mixed models and permutation approaches to investigate overall breeding success in group-housed Tasmanian devils at three nonmutually exclusive mate choice hypotheses: (a) advantage of heterozygous individuals, (b) advantage of dissimilar mates, and (c) optimum genetic distance, using both 1,948 genome-wide SNPs and 12 MHC-linked microsatellites. The managed devil insurance population is the largest such breeding program in Australia and is known to have high variance in reproductive success. We found that nongenetic factors such as age were the best predictors of breeding success in a competitive breeding scenario, with younger females and older males being more successful. We found no evidence of mate choice under the hypotheses tested. Mate choice varies among species and across environments, so we advocate for more studies in realistic captive management contexts as experimental or wild studies may not apply. Conservation managers must weigh up the need to wait for adequate sample sizes to detect mate choice with the risk that genetic changes may occur during this time in captivity. Our study shows that examining and integrating mate choice into the captive management of species housed in realistic, semi-natural group-based contexts may be more difficult than previously considered.

Songs versus colours versus horns: what explains the diversity of sexually selected traits?

Papers on sexual selection often highlight the incredible diversity of sexually selected traits across animals. Yet, few studies have tried to explain why this diversity evolved. Animals use many different types of traits to attract mates and outcompete rivals, including colours, songs, and horns, but it remains unclear why, for example, some taxa have songs, others have colours, and others horns. Here, we first conduct a systematic survey of the basic diversity and distribution of different types of sexually selected signals and weapons across the animal Tree of Life. Based on this survey, we describe seven major patterns in trait diversity and distributions. We then discuss 10 unanswered questions raised by these patterns, and how they might be addressed. One major pattern is that most types of sexually selected signals and weapons are apparently absent from most animal phyla (88%), in contrast to the conventional wisdom that a diversity of sexually selected traits is present across animals. Furthermore, most trait diversity is clustered in Arthropoda and Chordata, but only within certain clades. Within these clades, many different types of traits have evolved, and many types appear to have evolved repeatedly. By contrast, other major arthropod and chordate clades appear to lack all or most trait types, and similar patterns are repeated at smaller phylogenetic scales (e.g. within insects). Although most research on sexual selection focuses on female choice, we find similar numbers of traits (among sampled species) are involved in male contests (44%) and female choice (55%). Overall, these patterns are largely unexplained and unexplored, as are many other fundamental questions about the evolution of these traits. We suggest that understanding the diversity of sexually selected traits may require a shift towards macroevolutionary studies at relatively deep timescales (e.g. tens to hundreds of millions of years ago).

Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection

The highly polymorphic genes of the major histocompatibility complex (MHC) play a key role in adaptive immunity. Divergent allele advantage, a mechanism of balancing selection, is proposed to contribute to their exceptional polymorphism. It assumes that MHC genotypes with more divergent alleles allow for broader antigen-presentation to immune effector cells, by that increasing immunocompetence. However, the direct correlation between pairwise sequence divergence and the corresponding repertoire of bound peptides has not been studied systematically across different MHC genes. Here, we investigated this relationship for five key classical human MHC genes (human leukocyte antigen; HLA-A, -B, -C, -DRB1, and -DQB1), using allele-specific computational binding prediction to 118,097 peptides derived from a broad range of human pathogens. For all five human MHC genes, the genetic distance between two alleles of a heterozygous genotype was positively correlated with the total number of peptides bound by these two alleles. In accordance with the major antigen-presentation pathway of MHC class I molecules, HLA-B and HLA-C alleles showed particularly strong correlations for peptides derived from intracellular pathogens. Intriguingly, this bias coincides with distinct protein compositions between intra- and extracellular pathogens, possibly suggesting adaptation of MHC I molecules to present specifically intracellular peptides. Eventually, we observed significant positive correlations between an allele’s average divergence and its population frequency. Overall, our results support the divergent allele advantage as a meaningful quantitative mechanism through which pathogen-mediated selection leads to the evolution of MHC diversity.

Individual Quality and Extra-Pair Paternity in the Blue Tit: Sexy Males Bear the Costs

Adaptive explanations for the evolution of extra-pair paternity (EPP) suggest that females seek extra-pair copulations with high quality males. Still, the link between ornamentation, individual quality, and paternity remains unclear. Moreover, honest signaling is essential when explaining EPP because it is needed for sexual selection to occur; yet, it is understudied in multiple ornaments. Because blue tits (Cyanistes caeruleus) show variable color expression in several plumage patches, we tested: (i) over two seasons, whether males in better condition, more ornamented and less infected by blood parasites gain EPP and have higher reproductive success, and (ii) over three seasons, whether mating patterns affect color change. Males with more saturated yellow feathers, brighter tails, and in better condition had higher reproductive success in one of the seasons. Contrary to expectation, in another season, males that gained EPP were parasitized by blood parasites, suggesting increased vector exposure during extra-pair copulations. Our results for two seasons show that males siring more extra-pair young were older and grew brighter cheek or tail feathers for the following season. Despite the increased mating costs, in socially monogamous avian systems, high quality males incur in EPP without compromising traits that may be under sexual selection.

MHC structuring and divergent allele advantage in a urodele amphibian: a hierarchical multi-scale approach

Proteins encoded by extraordinarily polymorphic major histocompatibility complex (MHC) genes are involved in the adaptive immune response. Balancing selection is believed to maintain MHC polymorphism in the long term, although neutral processes also play a role in shaping MHC diversity. However, the relative contribution of these processes is poorly understood. Here we characterized MHC class II variation of a low-dispersal, pond-breeding newt (Triturus carnifex) over a restricted, geographically structured area. We aimed to (1) evaluate the contribution of selection and neutral processes to shaping MHC diversity at two geographic scales, and (2) test for signatures of divergent allele advantage (DAA), which is a potentially important mechanism of balancing selection. The dominant role of selection in shaping MHC variation was suggested by the lack of correlation between MHC and neutral (microsatellite) variation. Although most variation occurred within populations for both types of markers, they differed in the extent of structuring at the two spatial scales. MHC structuring was more pronounced at local scales, suggesting the role of local selection, while structuring was not detectable at a larger scale, possibly due to the effect of balancing selection. Microsatellites showed the opposite pattern. As expected under DAA, the observed genotypes combined more sequence diversity than expected under a random association of alleles. Thus, DAA may contribute to maintaining MHC polymorphism, which is ancient, as supported by signatures of historical positive selection and trans-species polymorphism. Our results point to the importance of a multi-scale approach in studying MHC variation, especially in low-dispersal taxa, which are genetically structured at fine spatial scales.

Genetic variation at MHC class II loci influences both olfactory signals and scent discrimination in ring-tailed lemurs

BACKGROUND

Diversity at the Major Histocompatibility Complex (MHC) is critical to health and fitness, such that MHC genotype may predict an individual's quality or compatibility as a competitor, ally, or mate. Moreover, because MHC products can influence the components of bodily secretions, an individual's body odors may signal its MHC composition and influence partner identification or mate choice. Here, we investigated MHC-based signaling and recipient sensitivity by testing for odor-gene covariance and behavioral discrimination of MHC diversity and pairwise dissimilarity in a strepsirrhine primate, the ring-tailed lemur (Lemur catta).

METHODS

First, we coupled genotyping of the MHC class II gene, DRB, with gas chromatography-mass spectrometry of genital gland secretions to investigate if functional genetic diversity is signaled by the chemical diversity of lemur scent secretions. We also assessed if the chemical similarity between individuals correlated with their MHC-DRB similarity. Next, we assessed if lemurs discriminated this chemically encoded, genetic information in opposite-sex conspecifics.

RESULTS

We found that both sexes signaled overall MHC-DRB diversity and pairwise MHC-DRB similarity via genital secretions, but in a sex- and season-dependent manner. Additionally, the sexes discriminated absolute and relative MHC-DRB diversity in the genital odors of opposite-sex conspecifics, suggesting that lemur genital odors function to advertise genetic quality.

CONCLUSIONS

In summary, genital odors of ring-tailed lemurs provide honest information about an individual's absolute and relative MHC quality. Complementing evidence in humans and Old World monkeys, we suggest that reliance on scent signals to communicate MHC quality may be important across the primate lineage.

MHC-associated mate choice under competitive conditions in captive versus wild Tasmanian devils

Mate choice contributes to driving evolutionary processes when animals choose breeding partners that confer genetic advantages to offspring, such as increased immunocompetence. The major histocompatibility complex (MHC) is an important group of immunological molecules, as MHC antigens bind and present foreign peptides to T-cells. Recent studies suggest that mates may be selected based on their MHC profile, leading to an association between an individual’s MHC diversity and their breeding success. In conservation, it may be important to consider mate choice in captive breeding programs, as this mechanism may improve reproductive rates. We investigated the reproductive success of Tasmanian devils in a group housing facility to determine whether increased MHC-based heterozygosity led individuals to secure more mating partners and produce more offspring. We also compared the breeding success of captive females to a wild devil population. MHC diversity was quantified using 12 MHC-linked microsatellite markers, including 11 previously characterized markers and one newly identified marker. Our analyses revealed that there was no relationship between MHC-linked heterozygosity and reproductive success either in captivity or the wild. The results of this study suggest that, for Tasmanian devils, MHC-based heterozygosity does not produce greater breeding success and that no specific changes to current captive management strategies are required with respect to preserving MHC diversity.

"Balancing" balancing selection? Assortative mating at the major histocompatibility complex despite molecular signatures of balancing selection

In vertebrate animals, genes of the major histocompatibility complex (MHC) determine the set of pathogens to which an individual's adaptive immune system can respond. MHC genes are extraordinarily polymorphic, often showing elevated nonsynonymous relative to synonymous sequence variation and sharing presumably ancient polymorphisms between lineages. These patterns likely reflect pathogen-mediated balancing selection, for example, rare-allele or heterozygote advantage. Such selection is often reinforced by disassortative mating at MHC. We characterized exon 2 of MHC class II, corresponding to the hypervariable peptide-binding region, in song sparrows (Melospiza melodia). We compared nonsynonymous to synonymous sequence variation in order to identify positively selected sites; assessed evidence for trans-species polymorphisms indicating ancient balancing selection; and compared MHC similarity of socially mated pairs to expectations under random mating. Six codons showed elevated ratios of nonsynonymous to synonymous variation, consistent with balancing selection, and we characterized several alleles similar to those occurring in at least four other avian families. Despite this evidence for historical balancing selection, mated pairs were significantly more similar at MHC than were randomly generated pairings. Nonrandom mating at MHC thus appears to partially counteract, not reinforce, pathogen-mediated balancing selection in this system. We suggest that in systems where individual fitness does not increase monotonically with MHC diversity, assortative mating may help to avoid excessive offspring heterozygosity that could otherwise arise from long-standing balancing selection.

Cryptic haplotype-specific gamete selection yields offspring with optimal MHC immune genes

Females choose specific mates in order to produce fitter offspring. However, several factors interfere with females' control over fertilization of their eggs, including sneaker males and phenotypically unpredictable allele segregation during meiosis. Mate choice at the individual level thus provides only a poor approximation for obtaining the best genetic match. Consequently, postcopulatory sperm selection by female oocytes has been proposed as a mechanism to achieve complementary combinations of parental haplotypes. Here, using controlled in vitro fertilization of three‐spined stickleback eggs, we find haplotype‐specific fertilization bias toward gametes with complementary major histocompatibility complex (MHC) immunogenes. The resulting zygote (and thus offspring) genotypes exhibit an intermediate level of individual MHC diversity that was previously shown to confer highest pathogen resistance. Our finding of haplotype‐specific gamete selection thus represents an intriguing mechanism for fine‐tuned optimization of the offspring's immune gene composition and an evolutionary advantage in the Red Queen dynamics of host‐parasite coevolution.

Disentangling the mechanisms of mate choice in a captive koala population

Successful captive breeding programs are crucial to the long-term survival of many threatened species. However, pair incompatibility (breeding failure) limits sustainability of many captive populations. Understanding whether the drivers of this incompatibility are behavioral, genetic, or a combination of both, is crucial to improving breeding programs. We used 28 years of pairing data from the San Diego Zoo koala colony, plus genetic analyses using both major histocompatibility complex (MHC)-linked and non-MHC-linked microsatellite markers, to show that both genetic and non-genetic factors can influence mating success. Male age was reconfirmed to be a contributing factor to the likelihood of a koala pair copulating. This trend could also be related to a pair's age difference, which was highly correlated with male age in our dataset. Familiarity was reconfirmed to increase the probability of a successful copulation. Our data provided evidence that females select mates based on MHC and genome-wide similarity. Male heterozygosity at MHC class II loci was associated with both pre- and post-copulatory female choice. Genome-wide similarity, and similarity at the MHC class II DAB locus, were also associated with female choice at the post-copulatory level. Finally, certain MHC-linked alleles were associated with either increased or decreased mating success. We predict that utilizing a variety of behavioral and MHC-dependent mate choice mechanisms improves female fitness through increased reproductive success. This study highlights the complexity of mate choice mechanisms in a species, and the importance of ascertaining mate choice mechanisms to improve the success of captive breeding programs.

Ecology can inform genetics: Disassortative mating contributes to MHC polymorphism in Leach's storm-petrels (Oceanodroma leucorhoa)

Studies of MHC-based mate choice in wild populations often test hypotheses on species exhibiting female choice and male-male competition, which reflects the general prevalence of females as the choosy sex in natural systems. Here, we examined mutual mate-choice patterns in a small burrow-nesting seabird, the Leach's storm-petrel (Oceanodroma leucorhoa), using the major histocompatibility complex (MHC). The life history and ecology of this species are extreme: both partners work together to fledge a single chick during the breeding season, a task that requires regularly travelling hundreds of kilometres to and from foraging grounds over a 6- to 8-week provisioning period. Using a 5-year data set unprecedented for this species (n = 1078 adults and 925 chicks), we found a positive relationship between variation in the likelihood of female reproductive success and heterozygosity at Ocle-DAB2, a MHC class IIB locus. Contrary to previous reports rejecting disassortative mating as a mechanism for maintaining genetic polymorphism in this species, here we show that males make significant disassortative mate-choice decisions. Variability in female reproductive success suggests that the most common homozygous females (Ocle-DAB2*01/Ocle-DAB2*01) may be physiologically disadvantaged and, therefore, less preferred as lifelong partners for choosy males. The results from this study support the role of mate choice in maintaining high levels of MHC variability in a wild seabird species and highlight the need to incorporate a broader ecological framework and sufficient sample sizes into studies of MHC-based mating patterns in wild populations in general.

Male size, not female preferences influence female reproductive success in a poeciliid fish (Poecilia latipinna): a combined behavioural/genetic approach

Objective

We investigated the potential role of indirect benefits for female mate preferences in a highly promiscuous species of live-bearing fishes, the sailfin molly Poecilia latipinna using an integrative approach that combines methods from animal behavior, life-history evolution, and genetics. Males of this species solely contribute sperm for reproduction, and consequently females do not receive any direct benefits. Despite this, females typically show clear mate preferences. It has been suggested that females can increase their reproductive success through indirect benefits from choosing males of higher quality.

Results

Although preferences for large body size have been recorded as an honest signal for genetic quality, this particular study resulted in female preference being unaffected by male body size. Nonetheless, larger males did sire more offspring, but with no effect on offspring quality. This study presents a methodical innovation by combining preference testing with life history measurements—such as the determination of the dry weight of fish embryos—and paternity analyses on single fish embryos.

Electronic supplementary material

The online version of this article (10.1186/s13104-018-3487-2) contains supplementary material, which is available to authorized users.

Mate choice in sticklebacks reveals that immunogenes can drive ecological speciation

Adaptation to ecologically contrasting niches can lead to the formation of new species. Theoretically, this process of ecological speciation can be driven by pleiotropic "magic traits" that genetically link natural and sexual selection. To qualify as a true magic trait, the pleiotropic function of a gene must be reflected in biologically relevant mechanisms underlying both local adaptation and mate choice. The immune genes of the major histocompatibility complex (MHC) contribute to parasite resistance and also play a major role in sexual selection. Hence, the MHC may encode a candidate magic trait. Using diverging 3-spined stickleback populations from a connected lake-river habitat, we show with mate choice experiments in a flow channel that polymorphic MHC genes probably underlie assortative mating with respect to particular habitat-adapted ecotypes, potentially resulting in reproductive isolation. By manipulating olfactory cues in controlled experiments, we show that female sticklebacks employ MHC-dependent male olfactory signals to select mates with which they can achieve a habitat-specific MHC gene structure that optimally protects their offspring against local parasites. By using MHC-based olfactory signals, females thus select individuals of their own population as mates. Our results demonstrate how mate choice and parasite resistance may be functionally linked. These findings suggest that MHC genes are pleiotropic and encode a true magic trait of biologically significant effect.

Testing mate choice and overdominance at MH in natural families of Atlantic salmon Salmo salar

This study aimed to test mate choice and selection during early life stages on major histocompatibility (MH) genotype in natural families of Atlantic salmon Salmo salar spawners and juveniles, using nine microsatellites to reconstruct families, one microsatellite linked to an MH class I gene and one minisatellite linked to an MH class II gene. MH-based mate choice was only detected for the class I locus on the first year, with lower expected heterozygosity in the offspring of actually mated pairs than predicted under random mating. The genotype frequencies of MH-linked loci observed in the juveniles were compared with frequencies expected from Mendelian inheritance of parental alleles to detect selection during early life stages. No selection was detected on the locus linked to class I gene. For the locus linked to class II gene, observed heterozygosity was higher than expected in the first year and lower in the second year, suggesting overdominance and underdominance, respectively. Within family, juveniles' body size was linked to heterozygosity at the same locus, with longer heterozygotes in the first year and longer homozygotes in the second year. Selection therefore seems to differ from one locus to the other and from year to year.

Sexual Selection and the differences between the sexes in Mandrills (Mandrillus sphinx)

Sexual selection has become a major focus in evolutionary and behavioral ecology. It is also a popular research topic in primatology. I use studies of mandrills (Mandrillus sphinx), a classic example of extravagant armaments and ornaments in animals, to exemplify how a long-term, multidisciplinary approach that integrates field observations with laboratory methods can contribute to on-going theoretical debates in the field of sexual selection. I begin with a brief summary of the main concepts of sexual selection theory and the differences between the sexes. I then introduce mandrills and the study population and review mandrill life history, the ontogeny of sex differences, and maternal effects. Next, I focus on male-male competition and female choice, followed by the less well-studied questions of female-female competition and male choice. This review shows how different reproductive priorities lead to very different life histories and divergent adaptations in males and females. It demonstrates how broadening traditional perspectives on sexual selection beyond the ostentatious results of intense sexual selection on males leads to an understanding of more subtle and cryptic forms of competition and choice in both sexes and opens many productive avenues in the study of primate reproductive strategies. These include the potential for studies of postcopulatory selection, female intrasexual competition, and male choice. These studies of mandrills provide comparison and, I hope, inspiration for studies of both other polygynandrous species and species with mating systems less traditionally associated with sexual selection.

Gene duplication and divergence produce divergent MHC genotypes without disassortative mating

Genes of the major histocompatibility complex (MHC) exhibit heterozygote advantage in immune defence, which in turn can select for MHC-disassortative mate choice. However, many species lack this expected pattern of MHC-disassortative mating. A possible explanation lies in evolutionary processes following gene duplication: if two duplicated MHC genes become functionally diverged from each other, offspring will inherit diverse multilocus genotypes even under random mating. We used locus-specific primers for high-throughput sequencing of two expressed MHC Class II B genes in Leach's storm-petrels, Oceanodroma leucorhoa, and found that exon 2 alleles fall into two gene-specific monophyletic clades. We tested for disassortative vs. random mating at these two functionally diverged Class II B genes, using multiple metrics and different subsets of exon 2 sequence data. With good statistical power, we consistently found random assortment of mates at MHC. Despite random mating, birds had MHC genotypes with functionally diverged alleles, averaging 13 amino acid differences in pairwise comparisons of exon 2 alleles within individuals. To test whether this high MHC diversity in individuals is driven by evolutionary divergence of the two duplicated genes, we built a phylogenetic permutation model. The model showed that genotypic diversity was strongly impacted by sequence divergence between the most common allele of each gene, with a smaller additional impact of monophyly of the two genes. Divergence of allele sequences between genes may have reduced the benefits of actively seeking MHC-dissimilar mates, in which case the evolutionary history of duplicated genes is shaping the adaptive landscape of sexual selection.

HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection

The main function of HLA class I molecules is to present pathogen-derived peptides to cytotoxic T lymphocytes. This function is assumed to drive the maintenance of an extraordinary amount of polymorphism at each HLA locus, providing an immune advantage to heterozygote individuals capable to present larger repertories of peptides than homozygotes. This seems contradictory, however, with a reduced diversity at individual HLA loci exhibited by some isolated populations. This study shows that the level of functional diversity predicted for the two HLA-A and HLA-B genes considered simultaneously is similar (almost invariant) between 46 human populations, even when a reduced diversity exists at each locus. We thus propose that HLA-A and HLA-B evolved through a model of joint divergent asymmetric selection conferring all populations an equivalent immune potential. The distinct pattern observed for HLA-C is explained by its functional evolution towards killer cell immunoglobulin-like receptor (KIR) activity regulation rather than peptide presentation.

A limit to the divergent allele advantage model supported by variable pathogen recognition across HLA-DRB1 allele lineages

Genetic diversity in human leukocyte antigen (HLA) molecules is thought to have arisen from the co-evolution between host and pathogen and maintained by balancing selection. Heterozygote advantage is a common proposed scenario for maintaining high levels of diversity in HLA genes, and extending from this, the divergent allele advantage (DAA) model suggests that individuals with more divergent HLA alleles bind and recognize a wider array of antigens. While the DAA model seems biologically suitable for driving HLA diversity, there is likely an upper threshold to the amount of sequence divergence. We used peptide-binding and pathogen-recognition capacity of DRB1 alleles as a model to further explore the DAA model; within the DRB1 locus, we examined binding predictions based on two distinct phylogenetic groups (denoted group A and B) previously identified based on non-peptide-binding region (PBR) nucleotide sequences. Predictions in this study support that group A allele and group B allele lineages have contrasting binding/recognition capacity, with only the latter supporting the DAA model. Furthermore, computer simulations revealed an inconsistency in the DAA model alone with observed extent of polymorphisms, supporting that the DAA model could only work effectively in combination with other mechanisms. Overall, we support that the mechanisms driving HLA diversity are non-exclusive. By investigating the relationships among HLA alleles, and pathogens recognized, we can provide further insights into the mechanisms on how humans have adapted to infectious diseases over time.

Characterization of MHC class IIB for four endangered Australian freshwater fishes obtained from ecologically divergent populations

Genetic diversity is an essential aspect of species viability, and assessments of neutral genetic diversity are regularly implemented in captive breeding and conservation programs. Despite their importance, information from adaptive markers is rarely included in such programs. A promising marker of significance in fitness and adaptive potential is the major histocompatibility complex (MHC), a key component of the adaptive immune system. Populations of Australian freshwater fishes are generally declining in numbers due to human impacts and the introduction of exotic species, a scenario of particular concern for members of the family Percichthyidae, several of which are listed as nationally vulnerable or endangered, and hence subject to management plans, captive breeding, and restoration plans. We used a next-generation sequencing approach to characterize the MHC IIB locus and provide a conservative description of its levels of diversity in four endangered percichthyids: Gadopsis marmoratus, Macquaria australasica, Nannoperca australis, and Nannoperca obscura. Evidence is presented for a duplicated MHC IIB locus, positively selected sites and recombination of MHC alleles. Relatively moderate levels of diversity were detected in the four species, as well as in different ecotypes within each species. Phylogenetic analyses revealed genus specific clustering of alleles and no allele sharing among species. There were also no shared alleles observed between two ecotypes within G. marmoratus and within M. australasica, which might be indicative of ecologically-driven divergence and/or long divergence times. This represents the first characterization and assessment of MHC diversity for Percichthyidae, and also for Australian freshwater fishes in general, providing key genetic resources for a vertebrate group of increasing conservation concern.

Copy number variation and genetic diversity of MHC Class IIb alleles in an alien population of Xenopus laevis

Xenopus laevis (the African clawed frog), which originated through hybridisation and whole genome duplication, has been used as a model for genetics and development for many years, but surprisingly little is known about immune gene variation in natural populations. The purpose of this study was to use an isolated population of X. laevis that was introduced to Wales, UK in the past 50 years to investigate how variation at the MHC compares to that at other loci, following a severe population bottleneck. Among 18 individuals, we found nine alleles based on exon 2 sequences of the Class IIb region (which includes the peptide binding region). Individuals carried from one to three of the loci identified from previous laboratory studies. Genetic variation was an order of magnitude higher at the MHC compared with three single-copy nuclear genes, but all loci showed high levels of heterozygosity and nucleotide diversity and there was not an excess of homozygosity or decrease in diversity over time that would suggest extensive inbreeding in the introduced population. Tajima’s D was positive for all loci, which is consistent with a bottleneck. Moreover, comparison with published sequences identified the source of the introduced population as the Western Cape region of South Africa, where most commercial suppliers have obtained their stocks. These factors suggest that despite founding by potentially already inbred individuals, the alien population in Wales has maintained substantial genetic variation at both adaptively important and neutral genes.

Major histocompatibility complex and mate choice in the polygynous primate: the Sichuan snub-nosed monkey (Rhinopithecus roxellana)

The highly polymorphic genes within the major histocompatibility complex (MHC) not only play a major role in immunity resistance, but also seem to provide hints for mate choice in some animal populations. In the present study we investigated MHC-related mate choice in a small natural population (group size 40-55 individuals) of a polygynous primate, the Sichuan snub-nosed monkey (Rhinopithecus roxellana). We found that there was no evidence either for MHC-disassortative mating, or for females to mate with males based on MHC heterozygosity or specific alleles. Nevertheless, of the 11 alleles identified, we found that the frequencies of 2 alleles, Rhro-DRB2 (P < 0.01) and Rhro-DRB5 (P < 0.05) were higher in offspring than in their parents. These findings suggest that MHC-DRB in this population of R. roxellana is unlikely to be associated with mating preferences. Limited female opportunities for mate choice are likely due, in part, to the harem breeding structure present in R. roxellana, and the relatively small number of resident adult males in our study band (N = 4-6). In addition, we suggest that differences in the frequency of particular alleles across generations may be linked to parasite resistance in a fluctuating environment; however, confirmation of this finding requires further study.

Major histocompatibility complex similarity and sexual selection: different does not always mean attractive

Females that mate multiply have the possibility to exert postcopulatory choice and select more compatible sperm to fertilize eggs. Prior work suggests that dissimilarity in major histocompatibility complex (MHC) plays an important role in determining genetic compatibility between partners. Favouring a partner with dissimilar MHC alleles would result in offspring with high MHC diversity and therefore with enhanced survival thanks to increased resistance to pathogens and parasites. The high variability of MHC genes may further allow discrimination against the sperm from related males, reducing offspring homozygosity and inbreeding risk. Despite the large body of work conducted at precopulatory level, the role of MHC similarity between partners at postcopulatory level has been rarely investigated. We used an internal fertilizing fish with high level of multiple matings (Poecilia reticulata) to study whether MHC similarity plays a role in determining the outcome of fertilization when sperm from two males compete for the same set of eggs. We also controlled for genomewide similarity by determining similarity at 10 microsatellite loci. Contrary to prediction, we found that the more MHC-similar male sired more offspring while similarity at the microsatellite loci did not predict the outcome of sperm competition. Our results suggest that MHC discrimination may be involved in avoidance of hybridization or outbreeding rather than inbreeding avoidance. This, coupled with similar findings in salmon, suggests that the preference for MHC-dissimilar mates is far from being unanimous and that pre- and postcopulatory episodes of sexual selection can indeed act in opposite directions.

Influence of immune-relevant genotype on the reproductive success of a salmonid alternative mating strategy

Major histocompatibility complex (MHC) and immune-relevant gene markers were used to evaluate differences in reproductive success (RS) among naturally spawning coho salmon Oncorhynchus kisutch mate pairs involving an alternative male reproductive phenotype, known as jacks. These mate pairs included both hatchery-reared and wild origin fish such that three classes were evaluated in two consecutive years (2005 and 2006) using a previously constructed multigenerational genetic pedigree: wild × wild (W × W), hatchery × hatchery (H × H) and wild × hatchery (W × H). Oncorhynchus kisutch jack mate pairs mated randomly based on immune-relevant genotype in both years; a result consistent with the opportunistic mating strategy of jacks. An association between greater number of alleles shared at three immune-relevant gene markers and increased RS was found for: W × H mate pairs in 2005 (BHMS429), W × H pairs in 2006 (SsalR016TKU) and W × W pairs in 2006 (OMM3085). No correlation between immune gene diversity and RS was found for H × H pairs in either year. The results suggest that the influence of immune-relevant genotype on mating success may be different for jacks when compared with previous studies of large adult male O. kisutch.

Variation in female guppy preference for male olfactory and visual traits

Animals often use different sensory systems to assess different sexually selected signals from potential mates. However, the relative importance of different signals on mate choice is not well understood in many animal species. In this study, we examined the relative importance of male olfactory and visual cues on female preference in the guppy Poecilia reticulata. We used digitally modified male images to standardize visual stimuli. We found that, regardless of whether females were presented without male visual stimuli or with identical male visual stimuli, they preferred stimuli with the odor of males to those without. However, when females were allowed to choose between dull male visual stimuli with male odor, and brightly colored male visual stimuli without male odor, there was no clear preference for either. Some females preferred the dull male visual stimuli with male odor, whereas some other females preferred the brightly colored male visual stimuli without male odor. These results indicate that the relative importance of olfactory and visual cues in female mate preference varied between individuals.

Crozier's paradox revisited: maintenance of genetic recognition systems by disassortative mating

Background

Organisms are predicted to behave more favourably towards relatives, and kin-biased cooperation has been found in all domains of life from bacteria to vertebrates. Cooperation based on genetic recognition cues is paradoxical because it disproportionately benefits individuals with common phenotypes, which should erode the required cue polymorphism. Theoretical models suggest that many recognition loci likely have some secondary function that is subject to diversifying selection, keeping them variable.

Results

Here, we use individual-based simulations to investigate the hypothesis that the dual use of recognition cues to facilitate social behaviour and disassortative mating (e.g. for inbreeding avoidance) can maintain cue diversity over evolutionary time. Our model shows that when organisms mate disassortatively with respect to their recognition cues, cooperation and recognition locus diversity can persist at high values, especially when outcrossed matings produce more surviving offspring. Mating system affects cue diversity via at least four distinct mechanisms, and its effects interact with other parameters such as population structure. Also, the attrition of cue diversity is less rapid when cooperation does not require an exact cue match. Using a literature review, we show that there is abundant empirical evidence that heritable recognition cues are simultaneously used in social and sexual behaviour.

Conclusions

Our models show that mate choice is one possible resolution of the paradox of genetic kin recognition, and the literature review suggests that genetic recognition cues simultaneously inform assortative cooperation and disassortative mating in a large range of taxa. However, direct evidence is scant and there is substantial scope for future work.