Genomic basis of drought resistance inFagus sylvatica

In the course of global climate change, central Europe is experiencing more frequent and prolonged periods of drought. These drought events have severe and detrimental impacts on the forest ecosystem. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) in noticeably different ways: even in the same local stand, badly drought damaged trees immediately neighboured apparently healthy trees. This led to the hypothesis that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance in a Pool-GWAS approach. Contrasting the extreme phenotypes, we identified 106 si…

Supplementary TextS26 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

This Supplement includes Supplementary Methods and Results; Table S4; List of Captions for Supplementary Tables and Supplementary Figures; List of Supplementary Archives deposited at DRYAD and Supplementary References.

Parasite presence induces gene expression changes in an ant host related to immunity and longevity

Most species are either parasites or exploited by parasites, making parasite&ndash

Gene expression patterns associated with caste and reproductive status in ants: worker-specific genes are more derived than queen-specific ones.

Variation in gene expression leads to phenotypic diversity and plays a central role in caste differentiation of eusocial insect species. In social Hymenoptera, females with the same genetic background can develop into queens or workers, which are characterized by divergent morphologies, behaviours and lifespan. Moreover, many social insects exhibit behaviourally distinct worker castes, such as brood-tenders and foragers. Researchers have just started to explore which genes are differentially expressed to achieve this remarkable phenotypic plasticity. Although the queen is normally the only reproductive individual in the nest, following her removal, young brood-tending workers often develop …

Supplement with additional information from Experimental increase in fecundity causes upregulation of fecundity and body maintenance genes in the fat body of ant queens

In most organisms, fecundity and longevity are negatively associated and the molecular regulation of these two life-history traits is highly interconnected. In addition, nutrient intake often has opposing effects on lifespan and reproduction. In contrast with solitary insects, the main reproductive individual of social hymenopterans, the queen, is also the most long-lived. During development, queen larvae are well-nourished, but we are only beginning to understand the impact of nutrition on the queens' adult life and the molecular regulation and connectivity of fecundity and longevity. Here, we used two experimental manipulations to alter queen fecundity in the ant Temnothorax rugatulus and…

Experimental increase in fecundity causes upregulation of fecundity and body maintenance genes in the fat body of ant queens.

In most organisms, fecundity and longevity are negatively associated and the molecular regulation of these two life-history traits is highly interconnected. In addition, nutrient intake often has opposing effects on lifespan and reproduction. In contrast to solitary insects, the main reproductive individual of social hymenopterans, the queen, is also the most long-lived. During development, queen larvae are well-nourished, but we are only beginning to understand the impact of nutrition on the queens' adult life and the molecular regulation and connectivity of fecundity and longevity. Here, we used two experimental manipulations to alter queen fecundity in the ant Temnothorax rugatulus and …

Temnothorax pilagens sp. n. – a new slave-making species of the tribe Formicoxenini from North America (Hymenoptera, Formicidae)

A new species of the ant genus Temnothorax Forel, 1890 – Temnothorax pilagens sp. n. is described from eastern North America. T. pilagens sp. n. is an obligate slave-making ant with two known hosts: T. longispinosus (Roger, 1863) and T. ambiguus (Emery, 1895). A differential diagnosis against Temnothorax duloticus (Wesson, 1937), the other dulotic congener from the Nearctic, is presented and a biological characteristics of the new species is given.

Dinner with the roommates: trophic niche differentiation and competition in a mutualistic ant‐ant association

1. The potential for competition is highest among species in close association. Despite net benefits for both parties, mutualisms can involve costs, including food competition. This might be true for the two neotropical ants Camponotus femoratus and Crematogaster levior, which share the same nest in a presumably mutualistic association (parabiosis). 2. While each nest involves one Crematogaster and one Camponotus partner, both taxa were recently found to comprise two cryptic species that show no partner preferences and seem ecologically similar. Since these cryptic species often occur in close sympatry, they might need to partition their niches to avoid competitive exclusion. 3. Here, we in…

Supplmementary information II from Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite

Genome of Temnothorax longispinosus: methods, assembly and annotation

Social organization and the evolution of life-history traits in two queen morphs of the ant Temnothorax rugatulus.

ABSTRACT During the evolution of social insects, not only did life-history traits diverge, with queens becoming highly fecund and long lived compared with their sterile workers, but also individual traits lost their importance compared with colony-level traits. In solitary animals, fecundity is largely influenced by female size, whereas in eusocial insects, colony size and queen number can affect the egg-laying rate. Here, we focused on the ant Temnothorax rugatulus, which exhibits two queen morphs varying in size and reproductive strategy, correlating with their colony's social organization. We experimentally tested the influence of social structure, colony and body size on queen fecundity…

Gene expression is more strongly associated with behavioural specialization than with age or fertility in ant workers.

The ecological success of social insects is based on division of labour, not only between queens and workers, but also among workers. Whether a worker tends the brood or forages is influenced by age, fertility and nutritional status, with brood carers being younger, more fecund and more corpulent. Here, we experimentally disentangle behavioural specialization from age and fertility in Temnothorax longispinosus ant workers and analyse how these parameters are linked to whole-body gene expression. A total of 3,644 genes were associated with behavioural specialization which is ten times more than associated with age and 50 times more than associated with fertility. Brood carers were characteri…

Life history evolution in social insects: a female perspective

Social insects are known for their unusual life histories with fecund, long-lived queens and sterile, short-lived workers. We review ultimate factors underlying variation in life history strategies in female social insects, whose social life reshapes common trade-offs, such as the one between fecundity and longevity. Interspecific life history variation is associated with colony size, mediated by changes in division of labour and extrinsic mortality. In addition to the ratio of juvenile to adult mortality, social factors such as queen number influence life history trajectories. We discuss two hypotheses explaining why queen fecundity and lifespan is higher in single-queen societies and sugg…

Offspring reverse transcriptome responses to maternal deprivation when reared with pathogens in an insect with facultative family life

Offspring of species with facultative family life are able to live with and without parents (i.e. to adjust to extreme changes in their social environment). While these adjustments are well understood on a phenotypic level, their genetic underpinnings remain surprisingly understudied. Investigating gene expression changes in response to parental absence may elucidate the genetic constraints driving evolutionary transitions between solitary and family life. Here, we manipulated maternal presence to observe gene expression changes in the fat body of juvenile European earwigs, an insect with facultative family life. Because parents typically protect offspring against pathogens, expression chan…

Pace-of-life in a social insect: behavioral syndromes in ants shift along a climatic gradient

Lay SummaryLinks between behavioral traits can shift with the local climate. We show that behavioral associations with temperature not only occur across, but also within populations. At warmer sites ant colonies increased their exploration and foraging activity, but were less aggressive. Moreover, at these warmer sites, more positive links were found between behaviors within populations compared to colder sites, where more negative links prevailed. Our study suggests that associations between behaviors shift along climatic gradients.

The genomic footprint of climate adaptation inChironomus riparius

The gradual heterogeneity of climatic factors produces continuously varying selection pressures across geographic distances that leave signatures of clinal variation in the genome. Separating signatures of clinal adaptation from signatures of other evolutionary forces, such as demographic processes, genetic drift, and adaptation to specific non-clinal conditions of the immediate local environment is a major challenge. Here, we examine climate adaptation in five natural populations of the non-biting midge Chironomus riparius sampled along a climatic gradient across Europe. Our study integrates experimental data, individual genome resequencing, Pool-Seq data, and population genetic modelling.…

Convergent Loss of Chemoreceptors across Independent Origins of Slave-Making in Ants

The evolution of an obligate parasitic lifestyle often leads to the reduction of morphological and physiological traits, which may be accompanied by loss of genes and functions. Slave-maker ants are social parasites that exploit the work force of closely related ant species for social behaviours such as brood care and foraging. Recent divergence between these social parasites and their hosts enables comparative studies of gene family evolution. We sequenced the genomes of eight ant species, representing three independent origins of ant slavery. During the evolution of eusociality, chemoreceptor genes multiplied due to the importance of chemical communication in societies. We investigated ev…

Gene expression is stronger associated with behaviour than with age and fertility in ant workers

AbstractThe ecological success of social insects is based on division of labour, not only between queens and workers, but also among workers. Whether a worker tends the brood or forages is strongly influenced by age, fertility and nutritional status, with brood carers being younger, more fecund and corpulent. Here, we experimentally disentangle behaviour from age and fertility inTemnothorax longispinosusant workers and analyse how these parameters are linked to whole-body gene expression. Our transcriptome analysis reveals four times more genes associated with behaviour than with age and only few fertility-associated genes. Brood carers exhibited an upregulation of genes involved in lipid b…

Supplementary information I from Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite

Tables and additional figures and methods details

A high-quality genome assembly from short and long reads for the non-biting midge Chironomus riparius (Diptera)

AbstractBackgroundChironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species.FindingsMaking use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species and the respective recombination rate as one of the first insect recombination rates at all.ConclusionsThe genome and associated resources will be h…

Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensive phenotypes

Abstract The transition to parasitism is a drastic shift in lifestyle, involving rapid changes in gene structure, function, and expression. After the establishment of antagonistic relationships, parasites and hosts co-evolve through reciprocal adaptations, often resulting in evolutionary arms-races. Repeated evolution of social parasitism and slavery among Temnothorax ants allows us to examine those gene expression patterns that characterize slavemaker raiding and reciprocal host defensive phenotypes. Previous behavioural studies have established that raiding strategies between Temnothorax slavemakers diverge, while host defense portfolios shift similarly under parasite pressure. We are the…

Evidence for a conserved queen-worker genetic toolkit across slave-making ants and their ant hosts

AbstractThe ecological success of social Hymenoptera (ants, bees, wasps) depends on the division of labour between the queen and workers. Each caste is highly specialised in its respective function in morphology, behaviour and life-history traits, such as lifespan and fecundity. Despite strong defences against alien intruders, insect societies are vulnerable to social parasites, such as workerless inquilines or slave-making (dulotic) ants. Here, we investigate whether gene expression varies in parallel ways between lifestyles (slave-making versus host ants) across five independent origins of ant slavery in the “Formicoxenus-group” of the ant tribe Crematogastrini. As caste differences are o…

Comparative analyses of caste, sex, and developmental stage‐specific transcriptomes in two Temnothorax ants

Abstract Social insects dominate arthropod communities worldwide due to cooperation and division of labor in their societies. This, however, makes them vulnerable to exploitation by social parasites, such as slave‐making ants. Slave‐making ant workers pillage brood from neighboring nests of related host ant species. After emergence, host workers take over all nonreproductive colony tasks, whereas slavemakers have lost the ability to care for themselves and their offspring. Here, we compared transcriptomes of different developmental stages (larvae, pupae, and adults), castes (queens and workers), and sexes of two related ant species, the slavemaker Temnothorax americanus and its host Temnoth…

Author response: Genomic basis for drought resistance in European beech forests threatened by climate change

Supplementary Figures from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

This supplement includes Supplementary Figure S1-S17.

Long-lived Temnothorax ant queens switch from investment in immunity to antioxidant production with age

Abstract Senescence is manifested by an increase in molecular damage and a deterioration of biological functions with age. In most organisms, body maintenance is traded-off with reproduction. This negative relationship between longevity and fecundity is also evident on the molecular level. Exempt from this negative trait association, social insect queens are both extremely long-lived and highly fecund. Here, we study changes in gene expression with age and fecundity in ant queens to understand the molecular basis of their long lifespan. We analyse tissue-specific gene expression in young founding queens and old fecund queens of the ant Temnothorax rugatulus. More genes altered their express…

Supplement 1: from Molecular regulation of lifespan extension in fertile ant workers

Additional methodological information, results and figures

Additional file 6: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Snail collection sites. (PDF 330 kb)

Vitellogenin-like A–associated shifts in social cue responsiveness regulate behavioral task specialization in an ant

Division of labor and task specialization explain the success of human and insect societies. Social insect colonies are characterized by division of labor, with workers specializing in brood care early and foraging later in life. Theory posits that this task switching requires shifts in responsiveness to task-related cues, yet experimental evidence is weak. Here, we show that a Vitellogenin (Vg) ortholog identified in an RNAseq study on the ant T. longispinosus is involved in this process: using phylogenetic analyses of Vg and Vg-like genes, we firstly show that this candidate gene does not cluster with the intensively studied honey bee Vg but falls into a separate Vg-like A cluster. Second…

Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects.

The exceptional longevity of social insect queens despite their lifelong high fecundity remains poorly understood in ageing biology. To gain insights into the mechanisms that might underlie ageing in social insects, we compared gene expression patterns between young and old castes (both queens and workers) across different lineages of social insects (two termite, two bee and two ant species). After global analyses, we paid particular attention to genes of the insulin/insulin-like growth factor 1 signalling (IIS)/target of rapamycin (TOR)/juvenile hormone (JH) network, which is well known to regulate lifespan and the trade-off between reproduction and somatic maintenance in solitary insects…

Additional file 3: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Results and figure for the climate niche divergence PCA. (PDF 14 kb)

Additional file 1: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Results of the a) sequencing effort and b) assembly statistics. (PDF 257 kb)

Additional file 2: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Phylogenetic inference on species relationships. (PDF 255 kb)

How ants acclimate: Impact of climatic conditions on the cuticular hydrocarbon profile

1.Organisms from temperate zones are exposed to seasonal changes and must be able to cope with a wide range of climatic conditions. Especially ectotherms, including insects, are at risk to desiccate under dry and warm conditions, the more so given the changing climate. 2.To adjust to current conditions, organisms acclimate through changes in physiology, morphology and/or behaviour. Insects protect themselves against desiccation through a layer of cuticular hydrocarbons (CHC) on their body surface. Hence, acclimation may also affect the CHC profile, changing their waterproofing capacity under different climatic conditions. 3.Here, we investigated the acclimation response of two Temnothorax a…

Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

AbstractBackgroundLife history traits like developmental time, age and size at maturity are directly related to fitness in all organisms and play a major role in adaptive evolution and speciation processes. Comparative genomic or transcriptomic approaches to identify positively selected genes involved in species divergence can help to generate hypotheses on the driving forces behind speciation. Here we use a bottom-up approach to investigate this hypothesis by comparative analysis of orthologous transcripts of four closely related EuropeanRadixspecies.ResultsSnails of the genusRadixoccupy species specific distribution ranges with distinct climatic niches, indicating a potential for natural …

Tandem‐running and scouting behaviour are characterized by up‐regulation of learning and memory formation genes within the ant brain

Tandem-running is a recruitment behaviour in ants that has been described as a form of teaching, where spatial information possessed by a leader is conveyed to following nestmates. Within Temnothorax ants, tandem-running is used within a variety of contexts, from foraging and nest relocation to-in the case of slavemaking species-slave raiding. Here, we elucidate the transcriptomic basis of scouting, tandem-leading and tandem-following behaviours across two species with divergent lifestyles: the slavemaking Temnothorax americanus and its primary, nonparasitic host T. longispinosus. Analysis of gene expression data from brains revealed that only a small number of unique differentially express…

Rapid adaptation to high temperatures in Chironomus riparius

AbstractEffects of seasonal or daily temperature variation on fitness and physiology of ectothermic organisms and their ways to cope with such variations have been widely studied. However, the way multivoltines organisms cope with temperature variations from a generation to another is still not well understood and complex to identify. The aim of this study is to investigate whether the multivoltine midgeChironomus ripariusMeigen (1803) responds mainly via acclimation as predicted by current theories, or if rapid genetic adaptation is involved. To investigate this issue, a common garden approach has been applied. A mix of larvae from five European populations was raised in the laboratory at …

Gene expression patterns underlying parasite-induced alterations in host behaviour and life history

Many parasites manipulate their hosts' phenotype. In particular, parasites with complex life cycles take control of their intermediate hosts' behaviour and life history to increase transmission to their definitive host. The proximate mechanisms underlying these parasite-induced alterations are poorly understood. The cestode Anomotaenia brevis affects the behaviour, life history and morphology of parasitized Temnothorax nylanderi ants and indirectly of their unparasitized nestmates. To gain insights on how parasites alter host phenotypes, we contrast brain gene expression patterns of T. nylanderi workers parasitized with the cestode, their unparasitized nestmates and unparasitized workers fr…

Histone acetylation regulates the expression of genes involved in worker reproduction and lifespan in the ant Temnothorax rugatulus

In insect societies, the queen monopolizes reproduction while workers perform tasks such as brood care or foraging. Queen loss leads to ovary development and lifespan extension in workers from many ants. However, the underlying molecular mechanisms of this phenotypic plasticity remain unclear. Recent studies highlight the importance of epigenetics in regulating plastic traits in social insects. We investigated the role of histone acetylation in the regulation of worker reproduction in the ant Temnothorax rugatulus. We removed queens from their colonies to induce worker fecundity, and either fed workers with chemical inhibitors of histone acetylation (C646), deacetylation (Trichostatin A), o…

Evolutionary genomics can improve prediction of species' responses to climate change

Abstract Global climate change (GCC) increasingly threatens biodiversity through the loss of species, and the transformation of entire ecosystems. Many species are challenged by the pace of GCC because they might not be able to respond fast enough to changing biotic and abiotic conditions. Species can respond either by shifting their range, or by persisting in their local habitat. If populations persist, they can tolerate climatic changes through phenotypic plasticity, or genetically adapt to changing conditions depending on their genetic variability and census population size to allow for de novo mutations. Otherwise, populations will experience demographic collapses and species may go ext…

Molecular regulation of lifespan extension in fertile ant workers.

The evolution of sociality in insects caused a divergence in lifespan between reproductive and non-reproductive castes. Ant queens can live for decades, while most workers survive only weeks to a few years. In most organisms, longevity is traded-off with reproduction, but in social insects, these two life-history traits are positively linked. Once fertility is induced in workers, e.g. by queen removal, worker lifespan increases. The molecular regulation of this positive link between fecundity and longevity and generally the molecular underpinnings of caste-specific senescence are not well understood. Here, we investigate the transcriptomic regulation of lifespan and reproduction in fat bod…

Climate Change Genomics Calls for Standardized Data Reporting

The advent of new and affordable high-throughput sequencing techniques allows for the investigation of the genetic basis of environmental adaptation throughout the plant and animal kingdom. The framework of genotype-environment associations (GEA) provides a powerful link by correlating the geographic distribution of genotype patterns of individuals or populations with environmental factors on a spatial scale. We coarsely review the short history of GEA studies, summarizing available studies, organisms, data type, and data availability for these studies. GEA is a powerful tool in climate change research and we therefore focus on climate variables as environmental factors. While our initial a…

Little parallelism in genomic signatures of local adaptation in two sympatric, cryptic sister species.

Species living in sympatry and sharing a similar niche often express parallel phenotypes as a response to similar selection pressures. The degree of parallelism within underlying genomic levels is often unexplored, but can give insight into the mechanisms of natural selection and adaptation. Here, we use multi-dimensional genomic associations to assess the basis of local and climate adaptation in two sympatric, cryptic Crematogaster levior ant species along a climate gradient. Additionally, we investigate the genomic basis of chemical communication in both species. Communication in insects is mainly mediated by cuticular hydrocarbons (CHCs), which also protect against water loss and, hence,…

Cuticular hydrocarbons as potential mediators of cryptic species divergence in a mutualistic ant association

International audience; Upon advances in sequencing techniques, more and more morphologically identical organisms are identified as cryptic species. Often, mutualistic interactions are proposed as drivers of diversification. Species of the neotropical parabiotic ant association between Crematogaster levior and Camponotus femoratus are known for highly diverse cuticular hydrocarbon (CHC) profiles, which in insects serve as desiccation barrier but also as communication cues. In the present study, we investigated the association of the ants' CHC profiles with genotypes and morphological traits, and discovered cryptic species pairs in both genera. To assess putative niche differentiation betwee…

Characterizing a hybrid zone between a cryptic species pair of freshwater snails.

Characterizing hybrid zones and their dynamics is a central goal in evolutionary biology, but this is particularly challenging for morphologically cryptic species. The lack of conspicuous divergence between parental types means intermediate hybrid forms often go undetected. We aimed to detect and characterize a suspected hybrid zone between a pair of morphologically cryptic lineages of the freshwater snail, Radix. We sampled Radix from across a contact zone between two mitochondrial lineages (Radix balthica and an undescribed lineage termed 'MOTU3') and detected admixture between two nuclear genotype clusters, which were significantly but not categorically associated with the mitochondrial …

How does climate change affect social insects?

Climate change poses a major threat to global biodiversity, already causing sharp declines of populations and species. In some social insect species we already see advanced phenologies, changes in distribution ranges, and changes in abundance Rafferty (2017) and Diamond et al. (2017). Physiologically, social insects are no different from solitary insects, but they possess a number of characteristics that distinguish their response to climate change. Here, we examine these traits, which might enable them to cope better with climate change than solitary insects, but only in the short term. In addition, we discuss how climate change will alter biotic interactions and ecosystem functions, and h…

Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite.

The geographical mosaic theory of coevolution predicts that species interactions vary between locales. Depending on who leads the coevolutionary arms race, the effectivity of parasite attack or host defence strategies will explain parasite prevalence. Here, we compare behaviour and brain transcriptomes of Temnothorax longispinosus ant workers when defending their nest against an invading social parasite, the slavemaking ant Temnothorax americanus . A full-factorial design allowed us to test whether behaviour and gene expression are linked to parasite pressure on host populations or to the ecological success of parasite populations. Albeit host defences had been shown before to covary with …

Data from: Gene expression patterns underlying parasite-induced alterations in host behaviour and life history

Many parasites manipulate their hosts’ phenotype. In particular, parasites with complex life cycles take control of their intermediate hosts’ behaviour and life history to increase transmission to their definitive host. The proximate mechanisms underlying these parasite-induced alterations are poorly understood. The cestode Anomotaenia brevis affects the behaviour, life history and morphology of parasitized Temnothorax nylanderi ants and indirectly of their unparasitized nestmates. To gain insights on how parasites alter host phenotypes, we contrast brain gene expression patterns of T. nylanderi workers parasitized with the cestode, their unparasitized nestmates and unparasitized workers fr…

Data from: Pace-of-life in a social insect: behavioral syndromes in ants shift along a climatic gradient

Behavioral syndromes are correlations between behavioral traits, but their selective advantage under different environmental conditions is not well understood. Here, we used the pace-of-life hypothesis to predict how behavioral syndromes could vary along climatic gradients. This hypothesis states that populations experiencing different ecological conditions should differ in suites of physiological characteristics associated with behavioral and life-history traits. We examined the persistence of behavioral syndromes at multiple levels in the ant Temnothorax longispinosus along a climatic gradient in north-eastern USA. “Across populations”, we predicted that proactive phenotypes, which show h…

Supplement 4: from Molecular regulation of lifespan extension in fertile ant workers

Result tables of GO enrichments

Supplemental Material for Schmidt et al., 2020

Supplementary Information and Data

Additional file 5: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Results enrichment analyses. (XLSX 11 kb)

Excel table with differentially expressed genes slavemaker origin from Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite

slavemaker origin

Supplement 2: from Molecular regulation of lifespan extension in fertile ant workers

R scripts of DeSeq2 and statistical analyses

Table S5 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Additional file 4: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Selected genes with annotations. (XLSX 35 kb)

Table S1 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM 1.

Data from: Gene expression is more strongly associated with behavioural specialisation than with age or fertility in ant workers

The ecological success of social insects is based on division of labour, not only between queens and workers, but also among workers. Whether a worker tends the brood or forages is influenced by age, fertility and nutritional status, with brood carers being younger, more fecund and more corpulent. Here, we experimentally disentangle behavioural specialisation from age and fertility in Temnothorax longispinosus ant workers and analyse how these parameters are linked to whole-body gene expression. A total of 3644 genes were associated with behavioural specialisation which is ten times more than associated with age and 50 times more than associated with fertility. Brood carers were characteriz…

Table S16 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Table S6 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Table S20 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Table S12 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Data from: Tandem-running and scouting behavior are characterized by up-regulation of learning and memory formation genes within the ant brain

Tandem-running is a recruitment behavior in ants that has been described as a form of teaching, where spatial information possessed by a leader is conveyed to following nestmates. Within Temnothorax ants, tandem-running is used within a variety of contexts, from foraging and nest relocation to – in the case of slavemaking species – slave raiding. Here, we elucidate the transcriptomic basis of scouting, tandem-leading, and tandem-following behavior across two species with divergent lifestyles: the slavemaking Temnothorax americanus and its primary, non-parasitic host T. longispinosus. Analysis of gene expression data from brains revealed that only a small number of unique differentially-expr…

Data from: Characterising a hybrid zone between a cryptic species pair of freshwater snails

Characterising hybrid zones and their dynamics is a central goal in evolutionary biology, but this is particularly challenging for morphologically cryptic species. The lack of conspicuous divergence between parental types means intermediate hybrid forms often go undetected. We aimed to detect and characterise a suspected hybrid zone between a pair of morphologically cryptic lineages of the freshwater snail, Radix. We sampled Radix from across a contact zone between two mitochondrial lineages (Radix balthica and an undescribed lineage termed MOTU3) and detected admixture between two nuclear genotype clusters, which were significantly but not categorically associated with the mitochondrial li…

Table S3 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Supplement 3: from Molecular regulation of lifespan extension in fertile ant workers

List of differentially expressed genes

Supplement 5: from Molecular regulation of lifespan extension in fertile ant workers

Information on all differentially expressed transcripts

Data from: Cuticular hydrocarbons as potential mediators of cryptic species divergence in a mutualistic ant association

Upon advances in sequencing techniques, more and more morphologically identical organisms are identified as cryptic species. Often, mutualistic interactions are proposed as drivers of diversification. Species of the Neotropical parabiotic ant association between Crematogaster levior and Camponotus femoratus are known for highly diverse cuticular hydrocarbon (CHC) profiles, which in insects serve as desiccation barrier but also as communication cues. In the present study we investigated the association of the ants’ CHC profiles to genotypes and morphological traits, and discovered cryptic species pairs in both genera. To assess putative niche differentiation between the cryptic species, we c…

Table S10 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Data from: Gene expression patterns associated with caste and reproductive status in ants: worker-specific genes are more derived than queen-specific ones

Variation in gene expression leads to phenotypic diversity and plays a central role in caste differentiation of eusocial insect species. In social Hymenoptera, females with the same genetic background can develop into queens or workers, which are characterized by divergent morphologies, behaviors and lifespan. Moreover, many social insects exhibit behaviorally distinct worker castes, such as brood-tenders and foragers. Researchers have just started to explore which genes are differentially expressed to achieve this remarkable phenotypic plasticity. Although the queen is normally the only reproductive individual in the nest, following her removal, young brood-tending workers often develop ov…

Table S26 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Excel Table with differentially expressed genes host origin from Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite

Host origin

Table S24 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Additional file 7: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Radix mt-genome primers. (XLS 36 kb)

Table S15 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Table S19 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Data from: Vitellogenin-like A–associated shifts in social cue responsiveness regulate behavioral task specialization in an ant

Division of labor and task specialization explain the success of human and insect societies. Social insect colonies are characterized by division of labor with workers specializing on brood care early and foraging later in life. Theory posits that this task switching requires shifts in responsiveness to task-related cues, yet experimental evidence is weak. Here we show that a Vitellogenin (Vg) ortholog identified in a RNAseq study on the ant Temnothorax longispinosus is involved in this process: Using phylogenetic analyses of Vg and Vg-like genes, we firstly show that this candidate gene does not cluster with the intensively studied honey bee Vg, but falls into a separate Vg-like A cluster.…

Additional file 8: of Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Annotations and evolutionary models of the clusters used for phylogenetic inference. (XLSX 10 kb)

Table S7 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Table S11 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Table S2 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Table S17 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Figure S1 from Offspring reverse transcriptome responses to maternal deprivation when reared with pathogens in an insect with facultative family life

Genes affected by the presence of the pathogen, independently of maternal presence. Y-axis represents normalized expression across samples per gene (Z-Score).

Table S21 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Table S23 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Table S25 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Data from: How ants acclimate: impact of climatic conditions on the cuticular hydrocarbon profile

1. Organisms from temperate zones are exposed to seasonal changes and must be able to cope with a wide range of climatic conditions. Especially ectotherms, including insects, are at risk to desiccate under dry and warm conditions, the more so given the changing climate. 2. To adjust to current conditions, organisms acclimate through changes in physiology, morphology and/or behaviour. Insects protect themselves against desiccation through a layer of cuticular hydrocarbons (CHC) on their body surface. Hence, acclimation may also affect the CHC profile, changing their waterproofing capacity under different climatic conditions. 3. Here, we investigated the acclimation response of two Temnothora…

Table S13 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Data from: Rapid adaptation to high temperatures in Chironomus riparius

Effects of seasonal or daily temperature variation on fitness and physiology of ectothermic organisms and their ways to cope with such variations have been widely studied. However, the way multivoltines organisms cope with temperature variations from a generation to another is still not well understood and complex to identify. The aim of this study is to investigate whether the multivoltine midge Chironomus riparius Meigen (1803) responds mainly via acclimation as predicted by current theories, or if rapid genetic adaptation is involved. To investigate this issue, a common garden approach has been applied. A mix of larvae from five European populations was raised in the laboratory at three …

Table S9 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Data from: Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix

Background: Life history traits like developmental time, age and size at maturity are directly related to fitness in all organisms and play a major role in adaptive evolution and speciation processes. Comparative genomic or transcriptomic approaches to identify positively selected genes involved in species divergence can help to generate hypotheses on the driving forces behind speciation. Here we use a bottom-up approach to investigate this hypothesis by comparative analysis of orthologous transcripts of four closely related European Radix species. Results: Snails of the genus Radix occupy species specific distribution ranges with distinct climatic niches, indicating a potential for natural…

Table S22 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Excel Table with differentially expressed genes parasite success and attack from Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite

Parasite success and attack no Attack

Table S18 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Table S8 from Comparative transcriptomic analysis of the mechanisms underpinning ageing and fecundity in social insects

Overview of all Supplementary tables provided as separate Excel files, except Table S4 which is included in ESM1.

Tables S1 & S2 from Offspring reverse transcriptome responses to maternal deprivation when reared with pathogens in an insect with facultative family life

Table S1. Comparisons of different transcriptome assemblies. The table on the sheet "Transrate output" shows data obtained using Transrate v.1.03 (Smith-unna et al., 2016). We compared assemblies created using Trinity and CLC Assembly Cell, as well as a merged "hybrid" obtained using CAP3 (Huang and Madan, 1999). The assembly comparison was used to determine the best assembly for continued analyses. Table S2. Full list of all DEGs revealed by the LRTs testing for main and interaction effects, as well as the associated annotations and read counts per sample. Note that no DEGs depended on maternal presence alone. Table headers are default DEseq2 headers, while the Blast annotation was added b…