Inbreeding Coefficient and Distance in MHC Genes of Parents as Predictors of Reproductive Success in Domestic Cat

Simple Summary

Inbreeding and low diversity in MHC (major histocompatibility complex) genes can have a significant impact on the survival and quality of offspring in mammals. At the same time, a decrease in genetic diversity can be disastrous for animals at individual and species level. For felines, studies of the effects of inbreeding and low variety in MHC genes are conducted on populations with a low number of animals, where there is a high probability of a shortage of available partners, and, accordingly, their choice. The use of model species, especially domestic cats, allows us to identify the main consequences of inbreeding and the lack of a choice of partners for future offspring. The survival of offspring in a domestic cat is primarily affected by the degree of similarity/difference in the genes of the parents’ MHC. Parents with the maximum distance in MHC genes have a larger proportion of surviving kittens, and this effect is most pronounced immediately after birth. In parents with the minimum distance in MHC genes, a significant percentage of kittens are either stillborn or die on the first day after birth. However, inbreeding and the similarity of parents in MHC genes in domestic cats did not affect the body mass of kittens.

Abstract

Inbreeding and low diversity in MHC genes are considered to have a negative effect on reproductive success in animals. This study presents an analysis of the number and body mass of offspring in domestic cat, depending on the inbreeding coefficient and the degree of similarity in MHC genes of class I and II in parents. Inbred partners had a lower number of live kittens at birth than outbred ones. At the same time, the inbreeding coefficient did not affect the litter size and the number of offspring who survived until the period of transition to solid food. The most significant predictor for the number of surviving offspring was the degree of parental similarity in MHC genes: the parents with the maximum distance in MHC genes had more survived kittens. Moreover, this effect was most pronounced immediately after birth. A significant percentage of kittens from parents with a minimum distance in MHC genes were either stillborn or died on the first day after birth. By the age of transition to solid food, this effect is no longer so pronounced. Furthermore, neither the inbreeding coefficient nor the distance in MHC genes of parents had any effect on the body mass of kittens.

The bacterial and fungal community composition in time and space in the nest mounds of the ant Formica exsecta (Hymenoptera: Formicidae)

In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.

Nest-departure behaviour of gynes and drones in the invasive yellowjacket Vespula germanica (Hymenoptera: Vespidae)

Inbreeding costs can be high in haplodiploid hymenopterans due to their particular mechanism of sex determination (i.e., single-locus complementary sex-determination system, sl-CSD), as it can lead to the production of sterile males. Therefore, mechanisms contributing to reduced inbred matings can be beneficial. In this sense, asynchronous nest departure of sibling drones and gynes could reduce kin encounters in social hymenopterans. Using six observation colonies, we determined under field conditions the nest departure behaviour of sibling reproductives of the social wasp Vespula germanica (Hymenoptera: Vespidae). We determined that sexuals leave the nests definitively and detected asynchronous departure not fixed to a particular caste at a seasonal scale in some colonies, as gynes or drones delayed their departure as a function of the departure of the opposite sex, depending on the colony. At a higher temporal resolution (i.e., within a day), we discovered that drones consistently began to leave nests 1 h before gynes and this difference was driven by those individuals that left on the same day as did the opposite-sex kin. Even though other mechanisms such as polyandry and differential dispersal could also be important at reducing inbred matings in the species, the observed departure patterns (i.e., in some colonies actually leave together with the opposite caste, while in others temporal segregation seems to occur) from nests could be complementary to the former and be important at reducing the negative effects of inbreeding in this invasive species.

Temperature drives caste-specific morphological clines in ants

The morphology of organisms relates to most aspects of their life history and autecology. As such, elucidating the drivers of morphological variation along environmental gradients might give insight into processes limiting species distributions. In eusocial organisms, the concept of morphology is more complex than in solitary organisms. Eusocial insects such as ants exhibit drastic morphological differences between reproductive and worker castes. How environmental selection operates on the morphology of each caste, and whether caste-specific selection has fitness consequences is largely unknown, but is potentially crucial to understand what limits ant species' distributions. Here we aimed to examine whether ant shape and body size covaries with climate at the scale of an entire continent, and whether such relationship might be caste specific. We used 26,472 georeferenced morphometric measurements from 2,206 individual ants belonging to 32 closely related North American species in the genus Formica to assess how ant morphology relates to geographic variation in the abiotic environment. Although precipitation and seasonality explained some of the geographic variation in morphology, temperature was the best predictor. Specifically, geographic variation in body size was positively related to temperature, meaning that ants are smaller in cold than in warm environments. Moreover, the strength of the relationship between size and temperature was stronger for the reproductive castes (i.e. queens and males) than for the worker caste. The shape of workers and males also varied along these large-scale abiotic gradients. Specifically, the relative length of workers' legs, thoraxes and antennae positively related to temperature, meaning that they had shorter appendages in cold environments. In contrast, males had smaller heads, but larger thoraxes in more seasonal environments. Overall, our results suggest that geographic variation in ambient temperature influences the morphology of ants, but that the strength of this effect is caste specific. In conclusion, whereas ant ecology has traditionally focused on workers, our study shows that considering the ecology of the reproductive castes is imperative to move forward in this field.

The socially parasitic ant Polyergus mexicanus has host-associated genetic population structure and related neighbouring colonies

The genetic structure of populations can be both a cause and a consequence of ecological interactions. For parasites, genetic structure may be a consequence of preferences for host species or of mating behaviour. Conversely, genetic structure can influence where conspecific interactions among parasites lay on a spectrum from cooperation to conflict. We used microsatellite loci to characterize the genetic structure of a population of the socially parasitic dulotic (aka "slave-making") ant (Polyergus mexicanus), which is known for its host-specificity and conspecific aggression. First, we assessed whether the pattern of host species use by the parasite has influenced parasite population structure. We found that host species use was correlated with subpopulation structure, but this correlation was imperfect: some subpopulations used one host species nearly exclusively, while others used several. Second, we examined the viscosity of the parasite population by measuring the relatedness of pairs of neighbouring parasitic ant colonies at varying distances from each other. Although natural history observations of local dispersal by queens suggested the potential for viscosity, there was no strong correlation between relatedness and distance between colonies. However, 35% of colonies had a closely related neighbouring colony, indicating that kinship could potentially affect the nature of some interactions between colonies of this social parasite. Our findings confirm that ecological forces like host species selection can shape the genetic structure of parasite populations, and that such genetic structure has the potential to influence parasite-parasite interactions in social parasites via inclusive fitness.

The first draft genomes of the ant Formica exsecta, and its Wolbachia endosymbiont reveal extensive gene transfer from endosymbiont to host

Background

Adapting to changes in the environment is the foundation of species survival, and is usually thought to be a gradual process. However, transposable elements (TEs), epigenetic modifications, and/or genetic material acquired from other organisms by means of horizontal gene transfer (HGTs), can also lead to novel adaptive traits. Social insects form dense societies, which attract and maintain extra- and intracellular accessory inhabitants, which may facilitate gene transfer between species. The wood ant Formica exsecta (Formicidae; Hymenoptera), is a common ant species throughout the Palearctic region. The species is a well-established model for studies of ecological characteristics and evolutionary conflict.

Results

In this study, we sequenced and assembled draft genomes for F. exsecta and its endosymbiont Wolbachia. The F. exsecta draft genome is 277.7 Mb long; we identify 13,767 protein coding genes, for which we provide gene ontology and protein domain annotations. This is also the first report of a Wolbachia genome from ants, and provides insights into the phylogenetic position of this endosymbiont. We also identified multiple horizontal gene transfer events (HGTs) from Wolbachia to F. exsecta. Some of these HGTs have also occurred in parallel in multiple other insect genomes, highlighting the extent of HGTs in eukaryotes.

Conclusion

We present the first draft genome of ant F. exsecta, and its endosymbiont Wolbachia (wFex), and show considerable rates of gene transfer from the symbiont to the host. We expect that especially the F. exsecta genome will be valuable resource in further exploration of the molecular basis of the evolution of social organization.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5665-6) contains supplementary material, which is available to authorized users.

Dispersal strategies in terrestrial insects

Terrestrial insects frequently disperse and/or migrate, either through their own self-directed actions or via other vehicles. Here, the following recent advances in the study of insect dispersal are highlighted: (1) components of classic hypotheses (marginal value theorem and inbreeding avoidance via sex-specific dispersal) have found varying degrees of recent support; (2) modern genetic tools have uncovered several candidate dispersal genes; (3) dispersal syndromes vary in their genetic and/or physiological constraints; and (4) common laboratory techniques may not accurately reflect dispersal in the field. A common theme is the tendency for breakthroughs to be concentrated in species with extremely well-defined dispersal phenotypes (e.g., long-distance migrants, wing polymorphic insects), suggesting the need for increased focus on species exhibiting less self-directed modes of dispersal.

Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta

Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon.

Sex-biased dispersal creates spatial genetic structure in a parthenogenetic ant with a dependent-lineage reproductive system

Reproduction and dispersal are key aspects of species life history that influence spatial genetic structure in populations. Several ant species in the genus Cataglyphis have evolved a unique breeding system in which new reproductives (that is, queens and males) are produced asexually by parthenogenesis; in contrast, non-reproductives (that is, workers) are produced via sexual reproduction by mates from distinct genetic lineages. We investigated how these two coexisting reproductive methods affect population-level spatial genetic structure using the ant Cataglyphis mauritanica as a model. We obtained genotypes for queens and their male mates from 338 colonies, and we found that the two lineages present in the study population occurred with equal frequency. Furthermore, analysis of spatial genetic structure revealed strong sex-biased dispersal. Because queens were produced by parthenogenesis and because they dispersed over short distances, there was an extreme level of spatial structuring: a mosaic of patches composed of clonal queens was formed. Males, on the other hand, dispersed over several hundred metres and, thus, across patches, ensuring successful interlineage mating.

Social Life in Arid Environments: The Case Study of Cataglyphis Ants

Unlike most desert-dwelling animals, Cataglyphis ants do not attempt to escape the heat; rather, they apply their impressive heat tolerance to avoid competitors and predators. This thermally defined niche has promoted a range of adaptations both at the individual and colony levels. We have also recently discovered that within the genus Cataglyphis there are incredibly diverse social systems, modes of reproduction, and dispersal, prompting the tantalizing question of whether social diversity may also be a consequence of the harsh environment within which we find these charismatic ants. Here we review recent advances regarding the physiological, behavioral, life-history, colony, and ecological characteristics of Cataglyphis and consider perspectives on future research that will build our understanding of organic adaptive responses to desertification.

Genetic structure of native ant supercolonies varies in space and time

Ant supercolonies are the largest cooperative units known in nature. They consist of networks of interconnected nests with hundreds of reproductive queens, where individuals move freely between nests, cooperate across nest boundaries and show little aggression towards non-nestmates. The combination of high queen numbers and free mixing of workers, queens and brood between nests results in extremely low nestmate relatedness. In such low-relatedness societies, cooperative worker behaviour appears maladaptive because it may aid random individuals instead of relatives. Here, we provide a comprehensive picture of genetic substructure in supercolonies of the native wood ant Formica aquilonia using traditional population genetic as well as network analysis methods. Specifically, we test for spatial and temporal variation in genetic structure of different classes of individuals within supercolonies and analyse the role of worker movement in determining supercolony genetic networks. We find that relatedness within supercolonies is low but positive when viewed on a population level, which may be due to limited dispersal of individuals and/or ecological factors such as nest site limitation and competition against conspecifics. Genetic structure of supercolonies varied with both sample class and sampling time point, which indicates that mobility of individuals varies according to both caste and season and suggests that generalizing has to be carried out with caution in studies of supercolonial species. Overall, our analysis provides novel evidence that native wood ant supercolonies exhibit fine-scale genetic substructure, which may explain the maintenance of cooperation in these low-relatedness societies.

Subsocial Cockroaches Nauphoeta cinerea Mate Indiscriminately with Kin Despite High Costs of Inbreeding

Many animals have evolved strategies to reduce risks of inbreeding and its deleterious effects on the progeny. In social arthropods, such as the eusocial ants and bees, inbreeding avoidance is typically achieved by the dispersal of breeders from their native colony. However studies in presocial insects suggest that kin discrimination during mate choice may be a more common mechanism in socially simpler species with no reproductive division of labour. Here we examined this possibility in the subsocial cockroach Nauphoeta cinerea, a model species for research in sexual selection, where males establish dominance hierarchies to access females and control breeding territories. When given a binary choice between a sibling male and a non-sibling male that had the opportunity to establish a hierarchy prior to the tests, females mated preferentially with the dominant male, irrespective of kinship or body size. Despite the lack of kin discrimination during mate choice, inbred-mated females incurred significant fitness costs, producing 20% less offspring than outbred-mated females. We discuss how the social mating system of this territorial cockroach may naturally limit the probability of siblings to encounter and reproduce, without the need for evolving active inbreeding avoidance mechanisms, such as kin recognition.

Starvation resistance and tissue-specific gene expression of stress-related genes in a naturally inbred ant population

Starvation is one of the most common and severe stressors in nature. Not only does it lead to death if not alleviated, it also forces the starved individual to allocate resources only to the most essential processes. This creates energetic trade-offs which can lead to many secondary challenges for the individual. These energetic trade-offs could be exacerbated in inbred individuals, which have been suggested to have a less efficient metabolism. Here, we studied the effect of inbreeding on starvation resistance in a natural population of Formica exsecta ants, with a focus on survival and tissue-specific expression of stress, metabolism and immunity-related genes. Starvation led to large tissue-specific changes in gene expression, but inbreeding had little effect on most of the genes studied. Our results illustrate the importance of studying stress responses in different tissues instead of entire organisms.