Studying the genetic signatures of climate-driven selection can produce insights into local adaptation and the potential impacts of climate change on populations. The honey bee (Apis mellifera) is an interesting species to study local adaptation because it originated in tropical/subtropical climatic regions and subsequently spread into temperate regions. However, little is known about the genetic basis of its adaptation to temperate climates. Here, we resequenced the whole genomes of ten individual bees from a newly discovered population in temperate China and downloaded resequenced data from 35 individuals from other populations. We found that the new population is an undescribed subspecies in the M-lineage of A. mellifera (Apis mellifera sinisxinyuan). Analyses of population history show that long-term global temperature has strongly influenced the demographic history of A. m. sinisxinyuan and its divergence from other subspecies. Further analyses comparing temperate and tropical populations identified several candidate genes related to fat body and the Hippo signaling pathway that are potentially involved in adaptation to temperate climates. Our results provide insights into the demographic history of the newly discovered A. m. sinisxinyuan, as well as the genetic basis of adaptation of A. mellifera to temperate climates at the genomic level. These findings will facilitate the selective breeding of A. mellifera to improve the survival of overwintering colonies.

The mechanisms by which organisms adapt to variable environments are a fundamental question in evolutionary biology and are important to protect important species in response to a changing climate. An interesting candidate to study this question is the honey bee Apis cerana, a keystone pollinator with a wide distribution throughout a large variety of climates, that exhibits rapid dispersal. Here, we resequenced the genome of 180 A. cerana individuals from 18 populations throughout China. Using a population genomics approach, we observed considerable genetic variation in A. cerana. Patterns of genetic differentiation indicate high divergence at the subspecies level, and physical barriers rather than distance are the driving force for population divergence. Estimations of divergence time suggested that the main branches diverged between 300 and 500 Ka. Analyses of the population history revealed a substantial influence of the Earth’s climate on the effective population size of A. cerana, as increased population sizes were observed during warmer periods. Further analyses identified candidate genes under natural selection that are potentially related to honey bee cognition, temperature adaptation, and olfactory. Based on our results, A. cerana may have great potential in response to climate change. Our study provides fundamental knowledge of the evolution and adaptation of A. cerana.

There is growing concern that massive loss of honey bees can cause serious negative effects on biodiversity and ecosystems. Surveys of colony losses have been performed worldwide to monitor the dynamic changes and health status of honey bee colonies. Here, we present the results of surveys regarding winter colony losses from 21 provinces in China from 2009 to 2021, with a total of 1,744,324 colonies managed by 13,704 beekeepers. The total colony losses were low (9.84%; 95% Confidence Interval (CI): 9.60–10.08%) but varied among years, provinces, and scales of apiaries. As little is known about the overwintering mortality of Apis cerana, in this study, we surveyed and compared the loss rates between Apis mellifera and A. cerana in China. We found colonies of A. mellifera suffered significantly lower losses than A. cerana in China. Larger apiaries resulted in higher losses in A. mellifera, whereas the opposite was observed in A. cerana. Furthermore, we used generalized linear mixed-effects models (GLMMs) to evaluate the effects of potential risk factors on winter colony losses and found that the operation size, species, migration, migration×species interaction, and queen problems were significantly related to the loss rates. New queens can increase their colony overwintering survival. Migratory beekeepers and large operations reported lower loss rates.

Background: Whole-genome sequencing has become routine for population genetic studies. Sequencing of individuals provides maximal data but is rather expensive and fewer samples can be studied. In contrast, sequencing a pool of samples (pool-seq) can provide sufficient data, while presenting less of an economic challenge. Few studies have compared the two approaches to infer population genetic structure and diversity in real datasets. Here, we apply individual sequencing (ind-seq) and pool-seq to the study of Western honey bees (Apis mellifera). Methods: We collected honey bee workers that belonged to 14 populations, including 13 subspecies, totaling 1347 colonies, who were individually (139 individuals) and pool-sequenced (14 pools). We compared allele frequencies, genetic diversity estimates, and population structure as inferred by the two approaches. Results: Pool-seq and ind-seq revealed near identical population structure and genetic diversities, albeit at different costs. While pool-seq provides genome-wide polymorphism data at considerably lower costs, ind-seq can provide additional information, including the identification of population substructures, hybridization, or individual outliers. Conclusions: If costs are not the limiting factor, we recommend using ind-seq, as population genetic structure can be inferred similarly well, with the advantage gained from individual genetic information. Not least, it also significantly reduces the effort required for the collection of numerous samples and their further processing in the laboratory.

Surveys of managed honey bee colony losses worldwide have become fundamental for engineering a sustainable and systematic approach to protect honey bees. Though China is a member of the world’s apiculture superpowers, the investigation of honey bee colony losses from Chinese government was not formally launched until recently. In this study, we investigated the colony winter losses of the western honey bee (Apis mellifera) of four consecutive years in 2013–2017 from 19 provinces in China, with a total of 2387 responding Chinese beekeepers (195 hobby beekeepers, 1789 side-line beekeepers, 403 commercial beekeepers) providing the records of overwintering mortality of honey bee colonies. The calculated colony losses were 8.7%, a relatively low mortality below the world average. There still exist considerable variations in total losses among provinces (ranging from 0.9% to 22.0%), years (ranging from 8.1% to 10.6%) and scales of apiaries (ranging from 7.5% to 10.0%). Furthermore, we deeply analyzed and estimated the effects of potential risk factors on the colonies’ winter losses, and speculated that the queen problems, the operation sizes and proportion of new queens are leading causes of the high honey bee colony mortality in China. More research and advanced technical methods are still required for correlation analysis and verification in future surveys of managed honey bee colony winter losses.