Population structure and evolution in the ant Plagiolepis pygmaea and its two social parasites Plagiolepis xene and Plagiolepis grassei

Social behaviour affects dispersal of animals and is an important modifier of genetic population structures. The female sex is often philopatric, which maintains coancestry within the breeding groups and promotes cooperative behaviours. This enables also inclusive fitness returns from altruism and explains why some individuals sacrifice personal reproduction for the good of others in social insects such as ants. However, reduced dispersal and population substructuring at the level of colonies may also entail inbreeding, loss of genetic diversity, and vulnerability. In addition, the most vulnerable ants are species that are evolved to parasitize colonies of other ants, and which compromise between abilities to disperse and the efficiency to parasitize the host. On the other hand, certain social organisations of ant colonies may facilitate a species to disperse outside its natural range and become a pest. Altogether, knowledge on genetic structuring of ant populations, as well as the evolution of their life histories can contribute to conservation biology and population management. The aim of this thesis was to investigate population structures and phylogenetic evolution of the ant Plagiolepis pygmaea and its two obligatory, workerless social parasites (inquilines) P. xene and P. grassei with genetic markers and DNA sequence data. The results support the general assumption that populations of inquiline parasites are highly fragmented and genetically vulnerable. Comparison of the two parasites suggests that differences in their relative abundance may follow from their interaction with the host, i.e. how well the species is adapted to reproduce in the host colonies. The results also indicate that the most recent free living ancestor to these two parasite species is their common host. This is considered to provide evidence for the controversial issue of sympatric speciation. Further, given that the level of adaptations to parasitic life history depends on the evolutionary time since the free-living ancestor, the results establish a link between species rarity and its evolutionary age. The populations of the host species P. pygmaea displayed significantly reduced dispersal both among the females (queens) and males, and high levels of inbreeding which may enhance worker altruism. In addition, the queens were found to mate with multiple males. Given the high relatedness between the queens and their mates, this occurs probably for non-genetic reasons, e.g. without benefits associated in genetically more diverse offspring. The results hence caution that the contribution of non-genetic factors to the prevailing mating patterns and genetic population structures should not be underestimated.Sosiaalinen käyttäytyminen vaikuttaa yksilöiden leviämiseen ja siten myös perinnöllisen aineksen jakautumiseen populaatioissa. Erityisesti monen lajin naaraat ovat paikkauskollisia, mikä kasvattaa ryhmän yksilöiden sukulaisuutta ja motivoi yhteistyöhön. Sukulaisuus mahdollistaa altruistisen käyttäytymisen tuoman kokonaiskelpoisuushyödyn ja selittää miksi yhteiskuntahyönteisten kuten muurahaisten työläiset jättävät lisääntymättä itse ja sen sijaan työskentelevät muiden hyväksi. Paikkauskollisuudesta koituva rajoittunut leviäminen voi kuitenkin johtaa myös sisäsiitokseen, perinnöllisen muuntelun vähenemiseen ja lajin selviämiskykyyn muuttuvassa ympäristössä. Lisäksi suurin osa uhanalaisista muurahaisista kuuluu lajeihin, jotka loisivat muiden lajien yhteiskuntia ja joiden elinkierto joutuu osittain tasapainoilemaan hyvän leviämis- ja loisimiskyvyn välillä. Toisaalta tietyt muurahaisyhteiskuntien sosiaaliset piirteet edistävät lajin leviämistä sen alkuperäisen elinpiirin ulkopuolella ja kehittymistä haittaeläimeksi. Tieto muurahaispopulaatioiden rakenteesta ja yhteiskuntien ominaisuuksista sekä niiden evoluutiosta voi siksi palvella sekä lajien suojelun että haittaeläinkantojen säätelyn tavoitteita. Tutkimukseni tarkoituksena oli selvittää merkkigeenien ja DNA-sekvenssien avulla Plagiolepis pygmaea-muurahaisen ja sitä loisivien yhteiskuntaloismuurahaislajien (inkviliinien) P. xene ja P. grassei populaatioiden rakennetta ja näiden lajien sukulaisuussuhteita. Tulokset tukevat käsitystä, että inkviliinipopulaatiot ovat pirstoutuneita ja geneettisesti uhanalaisia. Loislajien ominaisuuksien vertailun perusteella niiden levinneisyyteen vaikuttaa kyky loisia isäntälajin yhteiskuntia. Tulokset osoittavat myös, että näiden loisten lähin vapaana elävä sukulainen on niiden yhteinen isäntälaji. Tätä pidetään osoituksena loisten sympatrisesta evoluutiosta. Lisäksi olettaen, että sopeumat isännän yhteiskuntien loisintaan riippuvat loislajin kehittymiseen kuluneesta ajasta, työ luo yhteyden loislajien esiintyvyyden ja suhteellisen evolutiivisen iän välille. Tulokset isäntälajin populaatioista sen sijaan osoittivat niiden olevan sisäisesti jakautuneita useisiin lisääntymisyksiköihin ja kuningattarien sekä koiraiden leviämisen olevan heikkoa. Tästä johtuva populaatioiden sisäsiittoisuus voi tuottaa yhteiskuntien työläisille tavallista suurempaa kokonaiskelpoisuusetua. Lisäksi kuningattarien todettiin parittelevan useasti ennen lisääntymistään. Huomioiden näiden ja koiraiden välisen korkean sukulaisuuden, moninkertainen parittelu ei todennäköisesti hyödytä kuningattarien kelpoisuutta lisäämällä niiden jälkeläisten perinnöllistä muuntelua, vaan on seurausta muista populaatioihin vaikuttavista tekijöistä. Työ osoittaakin, ettei näiden osuutta yksilöiden parittelustrategioihin ja populaatioiden geenivirtaan tule unohtaa

Comparative transcriptomics of social insect queen pheromones

Queen pheromones are chemical signals that mediate reproductive division of labor in eusocial animals. Remarkably, queen pheromones are composed of identical or chemically similar compounds in some ants, wasps and bees, even though these taxa diverged > 150MYA and evolved queens and workers independently. Here, we measure the transcriptomic consequences of experimental exposure to queen pheromones in workers from two ant and two bee species (genera: Lasius, Apis, Bombus), and test whether they are similar across species. Queen pheromone exposure affected transcription and splicing at many loci. Many genes responded consistently in multiple species, and the set of pheromone-sensitive genes was enriched for functions relating to lipid biosynthesis and transport, olfaction, production of cuticle, oogenesis, and histone (de)acetylation. Pheromone-sensitive genes tend to be evolutionarily ancient, positively selected, peripheral in the gene coexpression network, hypomethylated, and caste-specific in their expression. Our results reveal how queen pheromones achieve their effects, and suggest that ants and bees use similar genetic modules to achieve reproductive division of labor.Peer reviewe

Strong conservation of inbred mouse strain microRNA loci but broad variation in brain microRNAs due to RNA editing and isomiR expression

Diversity in the structure and expression of microRNAs, important regulators of gene expression, arises from SNPs, duplications followed by divergence, production of isomiRs, and RNA editing. Inbred mouse strains and crosses using them are important reference populations for genetic mapping, and as models of human disease. We determined the nature and extent of interstrain miRNA variation by (i) identifying miRNA SNPs in whole-genome sequence data from 36 strains, and (ii) examining miRNA editing and expression in hippocampus (Hpc) and frontal cortex (FCx) of six strains, to facilitate the study of miRNAs in neurobehavioral phenotypes. miRNA loci were strongly conserved among the 36 strains, but even the highly conserved seed region contained 16 SNPs. In contrast, we identified RNA editing in 58.9% of miRNAs, including 11 consistent editing events in the seed region. We confirmed the functional significance of three conserved edits in the miR-379/410 cluster, demonstrating that edited miRNAs gained novel target mRNAs not recognized by the unedited miRNAs. We found significant interstrain differences in miRNA and isomiR expression: Of 779 miRNAs expressed in Hpc and 719 in FCx, 262 were differentially expressed (190 in Hpc, 126 in FCx, 54 in both). We also identified 32 novel miRNA candidates using miRNA prediction tools. Our studies provide the first comprehensive analysis of SNP, isomiR, and RNA editing variation in miRNA loci across inbred mouse strains, and a detailed catalog of expressed miRNAs in Hpc and FCx in six commonly used strains. These findings will facilitate the molecular analysis of neurological and behavioral phenotypes in this model organism.Peer reviewe

Weak population structure in the ant Formica fusca

Dispersal is a fundamental trait of a species’ biology. High dispersal results in weakly structured or even panmictic populations over large areas, whereas weak dispersal enables population differentiation and strong spatial structuring. We report on the genetic population structure in the polygyne ant Formica fusca and the relative contribution of the dispersing males and females to this. We sampled 12 localities across a ∼35 km2 study area in Finland and generated mitochondrial DNA (mtDNA) haplotype data and microsatellite data. First, we assessed queen dispersal by estimating population differentiation from mtDNA haplotype data. Second, we analysed nuclear DNA microsatellite data to determine overall population genetic substructure in the study area with principal components analysis, Bayesian clustering, hierarchical F statistics and testing for evidence of isolation-by-distance. Third, we directly compared genetic differentiation estimates from maternally inherited mtDNA and bi-parentally inherited DNA microsatellites to test for sex-bias in dispersal. Our results showed no significant spatial structure or isolation by distance in neither mtDNA nor DNA microsatellite data, suggesting high dispersal of both sexes across the study area. However, mitochondrial differentiation was weaker (Fst-mt = 0.0047) than nuclear differentiation (Fst-nuc = 0.027), which translates into a sixfold larger female migration rate compared to that of males. We conclude that the weak population substructure reflects high dispersal in both sexes, and it is consistent with F. fusca as a pioneer species exploiting unstable habitats in successional boreal forests

A Metatranscriptomic Approach to the Identification of Microbiota Associated with the Ant Formica exsecta

Peer reviewe

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.Peer reviewe

Weak patriline effects are present in the cuticular hydrocarbon profiles of isolated Formica exsecta ants but they disappear in the colony environment

Chemical recognition cues are used to discriminate among species, con-specifics, and potentially between patrilines in social insect colonies. There is an ongoing debate about the possible persistence of patriline cues despite evidence for the mixing of colony odors via a “gestalt” mechanism in social insects, because patri- line recognition could lead to nepotism. We analyzed the variation in recognition cues (cuticular hydrocarbons) with different mating frequencies or queen num- bers in 688 Formica exsecta ants from 76 colonies. We found no increase in the profile variance as genetic diversity increased, indicating that patriline effects were absent or possibly obscured by a gestalt mechanism. We then demonstrated that an isolated individual’s profile changed considerably relative to their colony pro- file, before stabilizing after 5 days. We used these isolated individuals to eliminate the masking effects of the gestalt mechanism, and we detected a weak but statisti- cally significant patriline effect in isolated adult workers and also in newly emerged callow workers. Thus, our evidence suggests that genetic variation in the cuticular hydrocarbon profile of F. exsecta ants (n-alkanes and alkenes) resulted in differences among patrilines, but they were obscured in the colony environment, thereby avoiding costly nepotistic behaviors.Peer reviewe

Prolyl oligopeptidase inhibition reduces alpha-synuclein aggregation in a cellular model of multiple system atrophy

Multiple system atrophy (MSA) is a fatal neurodegenerative disease where the histopathological hallmark is glial cytoplasmic inclusions in oligodendrocytes, rich of aggregated alpha-synuclein (aSyn). Therefore, therapies targeting aSyn aggregation and toxicity have been studied as a possible disease-modifying therapy for MSA. Our earlier studies show that inhibition of prolyl oligopeptidase (PREP) with KYP-2047 reduces aSyn aggregates in several models. Here, we tested the effects of KYP-2047 on a MSA cellular models, using rat OLN-AS7 and human MO3.13 oligodendrocyte cells. As translocation of p25α to cell cytosol has been identified as an inducer of aSyn aggregation in MSA models, the cells were transiently transfected with p25α. Similar to earlier studies, p25α increased aSyn phosphorylation and aggregation, and caused tubulin retraction and impaired autophagy in OLN-AS7 cells. In both cellular models, p25α transfection increased significantly aSyn mRNA levels and also increased the levels of inactive protein phosphatase 2A (PP2A). However, aSyn or p25α did not cause any cellular death in MO3.13 cells, questioning their use as a MSA model. Simultaneous administration of 10 µM KYP-2047 improved cell viability, decreased insoluble phosphorylated aSyn and normalized autophagy in OLN-AS7 cells but similar impact was not seen in MO3.13 cells.Peer reviewe