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Large independently evolved supergenes control colony social organization and queen reproductive strategies in several ant lineages. Their independent origins, as well as the similarities of the associated phenotypes, make ant supergenes a promising system for studying the parallel evolution of genome organization and adaptability. However, the genetic basis of differences in social organization and queen phenotypes remains unknown in many ant species, limiting the potential power of this system for comparative studies. We investigated the genetic basis of colony social organization in the queen-size dimorphic ant Myrmica ruginodis by sampling 95 queens from 31 colonies in southern Finland. Whole-genome sequencing revealed a novel 9 Mb supergene associated with both queen size and social organization. Queens homozygous for the AA haplotype were larger and found only in single-queen colonies, while queens in multiple-queen colonies were smaller and carried only AB and BB genotypes. This supergene is not homologous to previously identified supergenes in ants, suggesting it arose through a distinct evolutionary pathway.

Haplodiploid inheritance, in which females are diploid and males are haploid, is found in all species of Hymenoptera. Sex in haplodiploids is commonly determined by the alleles present at a complementary sex determination (CSD) locus, with heterozygosity triggering the female developmental pathway. The identity of this locus differs among taxa and is only known in a few species. Here, we map a single CSD locus to a 2 kbp region in the genome of the red mason bee Osmia bicornis. It overlaps the long noncoding RNA ANTSR, which has been identified as the sex-determining gene in the invasive ant Linepithema humile. This locus is homozygous in diploid males and exhibits extremely high levels of haplotype diversity, consistent with the action of frequency-dependent selection. The elevated levels of heterozygosity in the CSD locus enable us to fine-map potentially functional genetic variation within it. We also identify elevated levels of genetic diversity in the ortholog of the CSD locus in five other bee and ant genera, suggesting that it may govern sex determination widely in Hymenoptera. Our data are consistent with the hypothesis that ANTSR evolved a role in sex determination over 150 million years ago and is the ancestral sex-determination locus of bees and ants.

Population genomics can reveal trends and drivers of biodiversity loss, but it is still unclear how best to use measures of genome variation to understand population vulnerability in insects. Here we study genome variation in three species of Anthophora bees that show contrasting population trends in northern Europe. Two species, Anthophora plagiata and Anthophora retusa , have experienced declines and recoveries of different magnitudes in the last 50 years, whereas a third species, Anthophora quadrimaculata , has relative population stability. We generate highly contiguous genome assemblies and use them to study genome variation in 136 samples of these species collected throughout Sweden. We find exceedingly low genetic variation in A. plagiata , which has experienced a severe recent bottleneck, but high genetic variation in A. retusa , despite a similar recent population trajectory. Fragmented populations of the threatened species A. plagiata appear isolated from each other, but in A. retusa, there is a lack of deep population structure among geographically separated subpopulations. We infer population size in the distant past using MSMC2 and recent past using GONE. These methods are remarkably concordant and indicate ancient fluctuations in population size dating back to the Pleistocene, with moderate expansions in the past century in all three species. These results are comparable to some other studies of endangered insects, which have experienced population declines that predate the modern era. We detect long blocks of identity-by-state in A. plagiata , indicative of severe recent inbreeding. Translocations between isolated populations of this species could have a positive effect on their resilience.

Chromosomal inversions, by suppressing recombination, can profoundly shape genome evolution and drive adaptation. In the common quail (Coturnix coturnix), a highly mobile bird with a vast Palearctic breeding range, we previously identified a massive inversion on chromosome 1 associated with distinct phenotypes and restricted geographic distribution. Here, using a new de novo genome assembly, we characterise this inversion and uncover additional, ancient structural variation on chromosome 2 that segregates across the species' range: either two putatively linked inversions or a single, large inversion that appears as two due to scaffolding limitations. Together, the inversions encompass a remarkable 15.6% of the quail genome (153.6 Mbp), creating highly divergent haplotypes that diverged over a million years ago. While the chromosome 1 inversion is linked to phenotypic differences, including morphology and migratory behaviour, the chromosome 2 inversion(s) show no such association. Notably, all inversion regions exhibit reduced effective population size and a relaxation of purifying selection, evidenced by elevated nonsynonymous-to-synonymous substitution ratios (N/S). This suggests that inversions, particularly the geographically restricted one on chromosome 1, may act as engines of diversification, accelerating the accumulation of functional variation and potentially contributing to local adaptation, especially within isolated island populations. Our findings demonstrate how large-scale chromosomal rearrangements can compartmentalise a genome, fostering distinct evolutionary trajectories within a single, highly mobile species.

The aim of the study was to collect data on plant phenology, density of flowers and production of floral resources in European countries, using published and grey literature written in local languages. The search was conducted in 11 European languages (Danish, Dutch, French, German, Greek, Italian, Norwegian Bokm & aring;l, Portuguese, Romanian, Spanish and Swedish) and included published and unpublished data from local journals, books, databases or master and doctoral theses. The collection contains 2382 records for 1132 plant species from 113 families. Most of the data collected is on flowering phenology, with a relatively large amount of data on nectar/sugar production and less on pollen production and floral density (1474, 1141, 325 and 152 records, respectively). Our study is unique in collecting data on floral resource traits in local European languages. The data collected are a valuable addition to existing floral resource trait databases and can help to quantify the floral resources available to pollinators and other organisms that depend on them for food in different habitats and ecosystems. At the same time, our collection, in combination with other databases on floral resource traits, allows the identification of plant genera and families for which information is scarce, as well as the best-studied plants and countries where research on floral resource traits has a long tradition. Synthesis and applications. Our research shows the value of using data published in local languages, often as grey literature, especially when building ecological databases of various kinds. Much of the basic data we collected on floral resource traits is available in literature published long ago, making it even more difficult for the research community to access. We discussed several technical issues that can be encountered when collecting such floristic data, especially if the data are to be further used in modelling.

Obtaining genome-wide data from complex samples, such as environmental material or bulk species collections, is increasingly feasible, yet inferring species presence and population genomic insights remains challenging. We applied metagenomic sequencing to 40 arthropod bulk samples collected with Malaise traps across Sweden and compared results with metabarcoding of the same material. Using a custom genome database, we achieved genus-level classification largely consistent with metabarcoding. While metagenomics detected all genera identified by metabarcoding, conservative filtering thresholds designed to minimise false positives also excluded some true signals, particularly for low-abundance taxa. Taxonomic overlap between methods was further constrained by limited reference database representation. Beyond taxonomic assignment, metagenomic sequencing yielded genome-level information: we inferred haplotype diversity, heterozygosity and geographic population structure for several abundant species, including variable degrees of hybrid origin in red wood ants and the genetic distinctiveness of Gotland bumblebees. Finally, by-catch plant DNA present in the bulk samples revealed plausible arthropod-plant interactions, several of which align with known ecological associations. Together, these results demonstrate the potential of metagenomics for biodiversity monitoring and population genomics, while underscoring the importance of filtering criteria and comprehensive reference databases.

Meiotic recombination is a fundamental evolutionary process that facilitates adaptation and the removal of deleterious genetic variation. Social Hymenoptera exhibit some of the highest recombination rates among metazoans, whereas high recombination rates have not been found among nonsocial species from this insect order. It is unknown whether elevated recombination rates are a ubiquitous feature of all social insects. In many metazoan taxa, recombination is mainly restricted to hotspots a few kilobases in length. However, little is known about the prevalence of recombination hotspots in insect genomes. Here we infer recombination rate and its fine-scale variation across the genomes of two social species from the insect order Blattodea: the termites Macrotermes bellicosus and Cryptotermes secundus. We used linkage disequilibrium–based methods to infer recombination rate. We infer that recombination rates are close to 1 cM/Mb in both species, similar to the average metazoan rate. We also observe a highly punctate distribution of recombination in both termite genomes, indicative of the presence of recombination hotspots. We infer the presence of full-length PRDM9 genes in the genomes of both species, which suggests recombination hotspots in termites might be determined by PRDM9, as they are in mammals. We also find that recombination rates in genes are correlated with inferred levels of germline DNA methylation. The finding of low recombination rates in termites indicates that eusociality is not universally connected to elevated recombination rate. We speculate that the elevated recombination rates in social Hymenoptera are instead promoted by intense selection among haploid males. 

Populations of many bumblebee species are declining, with distributions shifting northwards to track suitable climates. Climate change is considered a major contributing factor. Arctic species are particularly vulnerable as they cannot shift further north, making assessment of their population viability important. Analysis of levels of whole-genome variation is a powerful way to analyse population declines and fragmentation. Here, we use genome sequencing to analyse genetic variation in seven species of bumblebee from the Scandinavian mountains, including two classified as vulnerable. We sequenced 333 samples from across the ranges of these species in Sweden. Estimates of effective population size (N_E) vary from ~55,000 for species with restricted high alpine distributions to 220,000 for more widespread species. Population fragmentation is generally very low or undetectable over large distances in the mountains, suggesting an absence of barriers to gene flow. The relatively high N_E and low population structure indicate that none of the species are at immediate risk of negative genetic effects caused by high levels of genetic drift. However, reconstruction of historical fluctuations in N_E indicates that the arctic specialist species Bombus hyperboreus has experienced population declines since the last ice age and we detected one highly inbred diploid male of this species close to the southern limit of its range, potentially indicating elevated genetic load. Although the levels of genetic variation in montane bumblebee populations are currently relatively high, their ranges are predicted to shrink drastically due to the effects of climate change and monitoring is essential to detect future population declines.

Insects are essential not only for ecosystem functioning and food security but also comprise some of the world's most destructive invasive species. Therefore, both insect declines and invasions raise major conservation concerns globally and call for respective conservation or mitigation measures. However, studies of insects are hampered by intrinsic biological features of these organisms, which include extreme population fluctuations, a huge diversity of ecological strategies, and common cryptic species. Population genetics provides a large toolkit to adequately accommodate those features, thereby enabling researchers to inform and monitor the efficacy of conservation and mitigation programs. Here, we provide an overview of the molecular and analytical methods that are relevant to insect conservation or mitigation and highlight the challenges involved in their implementation. We detail how and why temporal changes in genetic diversity, population structure and migration, and the genetic basis of adaptation should be taken into account to inform insect management programs. Finally, we review the barriers to the broad adoption of population genetics in insect research and provide guidelines to facilitate the use of these methods by stakeholders. Overall, this review provides theoretical and practical guidelines for implementing population genetics in both insect conservation and control.

Insects constitute vital components of ecosystems. There is alarming evidence for global declines in insect species diversity, abundance, and biomass caused by anthropogenic drivers such as habitat degradation or loss, agricultural practices, climate change, and environmental pollution. This raises important concerns about human food security and ecosystem functionality and calls for more research to assess insect population trends and identify threatened species and the causes of declines to inform conservation strategies. Analysis of genetic diversity is a powerful tool to address these goals, but so far animal conservation genetics research has focused strongly on endangered vertebrates, devoting less attention to invertebrates, such as insects, that constitute most biodiversity. Insects' shorter generation times and larger population sizes likely necessitate different analytical methods and management strategies. The availability of high-quality reference genome assemblies enables population genomics to address several key issues. These include precise inference of past demographic fluctuations and recent declines, measurement of genetic load levels, delineation of evolutionarily significant units and cryptic species, and analysis of genetic adaptation to stressors. This enables identification of populations that are particularly vulnerable to future threats, considering their potential to adapt and evolve. We review the application of population genomics to insect conservation and the outlook for averting insect declines.