Genomic Analyses Reveal Demographic History and Temperate Adaptation of the Newly Discovered Honey Bee SubspeciesApis mellifera sinisxinyuann. ssp

Abstract

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.

Genomic evidence for asymmetric introgression by sexual selection in the common wall lizard

“…We also calculated population fixation statistics ( F ST ) between the two groups and Z‐transformed the value. The putative selection targets were extracted based on being in the top 5% of log‐odds ratios for both π and F ST (Chen et al., ) (Figure a). The genetic differentiation patterns were compared between candidate loci and non‐candidate (“neutral”) loci using pairwise F ST analysis for populations from different regions (Izuno et al., ).…”

“…We also calculated population fixation statistics (F ST ) between the two groups and Z-transformed the value. The putative selection targets were extracted based on being in the top 5% of log-odds ratios for both π and F ST (Chen et al, 2016) (Figure 2a).…”

Developing reduced SNP assays from whole‐genome sequence data to estimate introgression in an organism with complex genetic patterns, the Iberian honeybee (Apis mellifera iberiensis)

“…The honeybee exhibits high diversity, with 31 currently recognized subspecies (Chen et al., 2016; Engel, 1999; Meixner, Leta, Koeniger, & Fuchs, 2011; Sheppard & Meixner, 2003) belonging to four main evolutionary lineages (western and northern Europe, M; south‐eastern Europe, C; Africa, A; Middle East and Central Asia, O). Of the 31 subspecies, the Iberian honeybee A. m. iberiensis (M‐lineage) has received the most attention with numerous genetic surveys (Chávez‐Galarza et al., 2015; and references therein).…”

Computer software for identification of honey bee subspecies and evolutionary lineages

“…The western honey bee (Apis mellifera ) has a wide geographical range, which covers almost the entire area of Europe, Africa, the Near East and central Asia (Ruttner 1988;Sheppard and Meixner 2003;Chen et al 2016). Within this range, there are markedly different climates and environments.…”