Genomic Signature of Shifts in Selection in a Subalpine Ant and Its Physiological Adaptations

Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae)

Formica is a large genus in the family Formicidae with high diversity in its distribution, morphology, and physiology. To better understand evolutionary characteristics of Formica, the complete mitochondrial genomes (mitogenomes) of two Formica species were determined and a comparative mitogenomic analysis for this genus was performed. The two newly sequenced Formica mitogenomes each included 37 typical mitochondrial genes and a large non-coding region (putative control region), as observed in other Formica mitogenomes. Base composition, gene order, codon usage, and tRNA secondary structure were well conserved among Formica species, whereas diversity in sequence size and structural characteristics was observed in control regions. We also observed several conserved motifs in the intergenic spacer regions. These conserved genomic features may be related to mitochondrial function and their highly conserved physiological constraints, while the diversity of the control regions may be associated with adaptive evolution among heterogenous habitats. A negative AT-skew value on the majority chain was presented in each of Formica mitogenomes, indicating a reversal of strand asymmetry in base composition. Strong codon usage bias was observed in Formica mitogenomes, which was predominantly determined by nucleotide composition. All 13 mitochondrial protein-coding genes of Formica species exhibited molecular signatures of purifying selection, as indicated by the ratio of non-synonymous substitutions to synonymous substitutions being less than 1 for each protein-coding gene. Phylogenetic analyses based on mitogenomic data obtained fairly consistent phylogenetic relationships, except for two Formica species that had unstable phylogenetic positions, indicating mitogenomic data are useful for constructing phylogenies of ants. Beyond characterizing two additional Formica mitogenomes, this study also provided some key evolutionary insights into Formica.

Foraging valor linked with aggression: selection against completely abandoning aggression in the high-elevation ant Tetramorium alpestre?

Aggression has multiple benefits and is often coupled with other behaviors ("behavioral syndromes"). The level of aggressiveness is influenced by an adaptive benefit-cost ratio suggesting that benefits should outweigh the costs of aggression. Here, we assess if several behaviors are coupled in two behaviorally different populations (aggressive, peaceful) of the high-elevation ant Tetramorium alpestre. For three weeks, we collected colony fragments and analyzed boldness, exploring, foraging, and risk-taking behaviors. We hypothesized that the aggressive population is bolder, more explorative and risk-prone, and forages more food than the peaceful population. To test whether (a) the combination of experiments and parameters used yields a good setup, (b) populations differ behaviorally, and (c) populations display behavioral syndromes, we assessed (a) the frequency of repeatable behaviors of each experiment, (b) the behavioral means among populations, and (c) the behavioral repeatability, respectively. We found that (a) boldness and exploring were most repeatable and represent a good experimental setup, (b) the aggressive population was bolder and more explorative and risk-prone than the peaceful population, (c) boldness and exploring behaviors were highly repeatable in both populations, thus corroborating our hypothesis. The results suggest that boldness, exploring, and risk-taking but not foraging are presumably coupled with aggression and indicate the presence of behavioral syndromes in this ant. Under specific ecological conditions, aggression may be coupled with other behaviors and important for finding food. Aggression is probably adaptive in T. alpestre, possibly indicating that selection favors aggression at least partially, which may counteract the complete loss of intraspecific aggression.

Scrutinising an inscrutable bark-nesting ant: Exploring cryptic diversity in the Rhopalomastix javana (Hymenoptera: Formicidae) complex using DNA barcodes, genome-wide MIG-seq and geometric morphometrics

Overlooking cryptic species diversity has grave implications on assessments of climate change impacts on biodiversity, ecosystems and organismal populations. Discriminating between cryptic species has long been challenging even for seasoned taxonomists, as interspecies morphological differences are often indiscernible by visual observation. Multi-disciplinary methods involving genetic analyses in conjunction with quantitative morphological data, should therefore be used to investigate boundaries between cryptic species. We adopted an integrated approach combining analyses of mitochondrial COI barcodes, a genome-wide dataset obtained via multiplexed inter-simple sequence repeats (ISSRs) genotyping by sequencing (MIG-seq), and geometric morphometrics to investigate species divergences in the inscrutable Rhopalomastix javana species complex. Objective clustering of COI suggested five putative molecular species units divergent from each other by thresholds within 4.2-10.6% uncorrected pairwise distance. Phylogenetic analyses based on concatenated MIG-seq data also recovered and strongly supported the monophyly of five major lineages in agreement with COI clusters. Co-ancestry analyses based on MIG-seq data using fineRADstructure resolved variable patterns of admixture linked to geography, and potential genetic drift within some putative species. Geometric morphometric analyses of specimen images further detected statistically significant differences in at least one of three anatomical aspects (Head, Meso, Profile) between all pairs of putative species. Head shape (full-face view) was determined to be the most informative character for species diagnosis, with relatively high classification accuracy. Thin-plate spline deformation grids highlighted areas of high variation between species in each shape for deeper taxonomic scrutiny. The presence of species from multiple distinct lineages existing in near-sympatry firmly demonstrates that R. javana comprises more than one closely-related species, but exact species boundaries are difficult to ascertain. Differences in elevation and its associated abiotic effects on ant adaptations and reproductive phenology may contribute to restricting gene flow and maintaining species boundaries between sympatric populations of the R. javana complex. We further assess the advantages and limitations of geometric morphometrics as a taxonomic tool. Despite its drawbacks, our combined approach has helped draw important insights on cryptic diversity in R. javana, and also identified gaps of knowledge that await address. Results from this study will inform and prime future in-depth taxonomic investigation on the R. javana complex, including formal descriptions and establishment of the five putative species.

Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

Heliconius butterflies, a speciose genus of Müllerian mimics, represent a classic example of an adaptive radiation that includes a range of derived dietary, life history, physiological and neural traits. However, key lineages within the genus, and across the broader Heliconiini tribe, lack genomic resources, limiting our understanding of how adaptive and neutral processes shaped genome evolution during their radiation. Here, we generate highly contiguous genome assemblies for nine Heliconiini, 29 additional reference-assembled genomes, and improve 10 existing assemblies. Altogether, we provide a dataset of annotated genomes for a total of 63 species, including 58 species within the Heliconiini tribe. We use this extensive dataset to generate a robust and dated heliconiine phylogeny, describe major patterns of introgression, explore the evolution of genome architecture, and the genomic basis of key innovations in this enigmatic group, including an assessment of the evolution of putative regulatory regions at the Heliconius stem. Our work illustrates how the increased resolution provided by such dense genomic sampling improves our power to generate and test gene-phenotype hypotheses, and precisely characterize how genomes evolve.

Short-time development of among-colony behaviour in a high-elevation ant

Standardised assays are often used to characterise aggression in animals. In ants,such assays can be applied at several organisational levels (e.g., colony, population) and at specific times during the season. However, whether the behaviour differs at these levels and changes over a few weeks remains largely unexplored. Here, six colonies from the high-elevation ant Tetramorium alpestre were collected weekly for five weeks from two behaviourally-different populations (aggressive and peaceful in intraspecific encounters). We conducted one-on-one worker encounters at the colony and population levels. When analysing the colony combinations separately, the behaviour was peaceful and remained so within the peaceful population; initial aggression became partially peaceful within the aggressive population; and initial aggression decreased occasionally and increased in one combination but remained constant for most across-population combinations. When analysing all colony combinations together, within-population behaviour remained similar, but acrosspopulation behaviour became peaceful. The observed behavioural differences among organisational levels emphasise the relevance of assessing both. Moreover, the effect of decreasing aggression is discernible already over a few weeks. Compression of the vegetation period at high elevations may compress such behavioural changes.Addressing both organisational levels and seasonality is important, particularly in studies of behavioural complexity such as in this ant.

Global change may make hostile - Higher ambient temperature and nitrogen availability increase ant aggression

Behaviour is a response of organisms to internal and external stimuli and comprises various activities such as searching for food. Aggression is important in such activities, for example, improving the chances of winning competition for food, but animals differ in their level of aggression. This behavioural plasticity allows individuals to respond to environmental changes and is important for the survival of animals. It may be an important asset in facing global changes, which affect all organisms, for example, via rising temperature and eutrophication. The latter have steadily increased since 1900, especially in high elevations. Their effects may first become visible in stationary organisms such as ants because their nests are strictly associated with the conditions on site. Here, we analysed eight populations of the high-elevation ant Tetramorium alpestre along several elevations spanning the European Alps. We conducted a correlative approach and analysed several genetic and environmental proxies, namely within- and across-colony genetic relatedness, cuticular hydrocarbons, body size, across-colony geographic distance, air temperature, and worker nitrogen values additionally to within-population aggressive behaviour. We hypothesised that a) these proxies and aggressive behaviour differ among populations and that b) one or more of these proxies influence aggression. We found that a) some environmental proxies and aggression differed among populations but not the genetic proxies and that b) air temperature and worker nitrogen-isotope values correlated positively with worker aggression. The results indicate an environmental but not social-structural influence on this ant's aggressive behaviour, even though social structure varied among populations (single- and multiple-queened colonies). We infer that global change affects aggression in our study system and propose five mutually non-exclusive scenarios to explain the behavioural change mechanistically. Using the space-for-time principle, we speculate that aggression may increase due to future increases in temperature and nitrogen availability in this ant and other species living in high elevations.

An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time

Native Americans domesticated maize (Zea mays ssp. mays) from lowland teosinte parviglumis (Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 (HPC1), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.

Genomic shifts, phenotypic clines and fitness costs associated with cold-tolerance in the Asian tiger mosquito

Climatic variation is a key driver of genetic differentiation and phenotypic traits evolution, and local adaptation to temperature is expected in widespread species. We investigated phenotypic and genomic changes in the native range of the Asian tiger mosquito, Aedes albopictus. We first refine the phylogeographic structure based on genome-wide regions (1,901 ddRAD SNPs) from 41 populations. We then explore the patterns of cold adaptation using phenotypic traits measured in common garden (wing size and cold tolerance) and genotype–temperature associations at targeted candidate regions (51,706 exon capture SNPs) from 9 populations. We confirm the existence of three evolutionary lineages including clades A (Malaysia, Thailand, Cambodia, and Laos), B (China and Okinawa), and C (South Korea and Japan). We identified temperature-associated differentiation in fifteen out of 221 candidate regions but none in ddRAD regions, supporting the role of directional selection in detected genes. These include genes involved in lipid metabolism and a circadian clock gene. Most outlier SNPs are differently fixed between clades A and C, while clade B has an intermediate pattern. Females are larger at higher latitude yet produce no more eggs, which might favor the storage of energetic reserves in colder climate. Non-diapausing eggs from temperate populations survive better to cold exposure than those from tropical populations, suggesting they are protected from freezing damages but this cold tolerance has a fitness cost in terms of egg viability. Altogether, our results provide strong evidence for the thermal adaptation of A. albopictus across its wide temperature range.

A high-quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation

The hyperdiverse order Coleoptera comprises a staggering ~25% of known species on Earth. Despite recent breakthroughs in next generation sequencing, there remains a limited representation of beetle diversity in assembled genomes. Most notably, the ground beetle family Carabidae, comprising more than 40,000 described species, has not been studied in a comparative genomics framework using whole genome data. Here we generate a high-quality genome assembly for Nebria riversi, to examine sources of novelty in the genome evolution of beetles, as well as genetic changes associated with specialization to high-elevation alpine habitats. In particular, this genome resource provides a foundation for expanding comparative molecular research into mechanisms of insect cold adaptation. Comparison to other beetles shows a strong signature of genome compaction, with N. riversi possessing a relatively small genome (~147 Mb) compared to other beetles, with associated reductions in repeat element content and intron length. Small genome size is not, however, associated with fewer protein-coding genes, and an analysis of gene family diversity shows significant expansions of genes associated with cellular membranes and membrane transport, as well as protein phosphorylation and muscle filament structure. Finally, our genomic analyses show that these high-elevation beetles have endosymbiotic Spiroplasma, with several metabolic pathways (e.g., propanoate biosynthesis) that might complement N. riversi, although its role as a beneficial symbiont or as a reproductive parasite remains equivocal.

Effect of social structure and introduction history on genetic diversity and differentiation

Invasive species are a global threat to biodiversity, and understanding their history and biology is a major goal of invasion biology. Population-genetic approaches allow insights into these features, as population structure is shaped by factors such as invasion history (number, origin and age of introductions) and life-history traits (e.g., mating system, dispersal capability). We compared the relative importance of these factors by investigating two closely related ants, Tetramorium immigrans and Tetramorium tsushimae, that differ in their social structure and invasion history in North America. We used mitochondrial DNA sequences and microsatellite alleles to estimate the source and number of introduction events of the two species, and compared genetic structure among native and introduced populations. Genetic diversity of both species was strongly reduced in introduced populations, which also differed genetically from native populations. Genetic differentiation between ranges and the reduction in microsatellite diversity were more severe in the more recently introduced and supercolonial T. tsushimae. However, the loss of mitochondrial haplotype diversity was more pronounced in T. immigrans, which has single-queen colonies and was introduced earlier. Tetramorium immigrans was introduced at least twice from Western Europe to North America and once independently to South America. Its monogyny might have limited genetic diversity per introduction, but new mutations and successive introductions over a long time may have added to the gene pool in the introduced range. Polygyny in T. tsushimae probably facilitated the simultaneous introduction of several queens from a Japanese population to St. Louis, USA. In addition to identifying introduction pathways, our results reveal how social structure can influence the population-genetic consequences of founder events.