Population Structure, Demographic History, and Adaptation of Giant Honeybees in China Revealed by Population Genomic Data

Abstract

There have been many population-based genomic studies on human-managed honeybees (Apis mellifera and Apis cerana), but there has been a notable lack of analysis with regard to wild honeybees, particularly in relation to their evolutionary history. Nevertheless, giant honeybees have found to occupy distinct habitats and display have remarkable characteristics, which are attracting an increase amount of attention. In this study, we de novo sequenced and then assembled the draft genome sequence of the Himalayan giant honeybee, Apis laboriosa. Phylogenetic analysis based on genomic information indicated that A. laboriosa and its tropical sister species Apis dorsata diverged ∼2.61 million years ago, which supports the speciation hypothesis that link A. laboriosa to geological changes throughout history. Furthermore, we re-sequenced A. laboriosa and A. dorsata samples from five and six regions, respectively, across their population ranges in China. These analysis highlighted major genetic differences for Tibetan A. laboriosa as well as the Hainan Island A. dorsata. The demographic history of most giant honeybee populations has mirrored glacial cycles. More importantly, contrary to what has occurred among human-managed honeybees, the demographic history of these two wild honeybee species indicates a rapid decline in effective population size in the recent past, reflecting their differences in evolutionary histories. Several genes were found to be subject to selection, which may help giant honeybees to adapt to specific local conditions. In summary, our study sheds light on the evolutionary and adaptational characteristics of two wild giant honeybees species, which was useful for giant honeybee conservation.

The distribution ofApis laboriosarevisited: range extensions and biogeographic affinities

“…Further to the east, Huang et al (2022) reported on specimens housed in the National Zoological Museum of China collected in the upper regions the Brahmaputra River: one along the Yarlung Zangbo River (in Motuozhen, Medog County), and another near Bomé along the Palong Zhangbo River, a tributary to the Yarlung Zhangbo, both in Nyingche Prefecture, Xizang. Cao et al (2023) analyzed specimens collected in the nearby watershed of the Palong Zhangbo River. In Yunnan, Yang et al (2015) reported the species from Deqin County (Shengpingzhen), near the Lancang River (upper Mekong River; included in Huang et al, 2022).…”

“…Two nearly 50-year-old specimens in the National Zoological Museum of China were also collected in this same region. Cao et al (2023) collected samples from several villages in Rikaze, Xizang, in the watershed of Phung Chu (the upper reaches of the Arun River) that extends northward from eastern Nepal. Further to the east, Huang et al (2022) reported on specimens housed in the National Zoological Museum of China collected in the upper regions the Brahmaputra River: one along the Yarlung Zangbo River (in Motuozhen, Medog County), and another near Bomé along the Palong Zhangbo River, a tributary to the Yarlung Zhangbo, both in Nyingche Prefecture, Xizang.…”

“…confirmed the coordinates of the two locations from which mtDNA genomes were sequenced (Tang et al, 2003). Cao et al (2023) reported five regions within Yunnan and Xizang, China, from which colonies were sampled; we have included two of those with narrow ranges of latitude and longitude. Gautam et al (2022) studied pollination by honey bees at two sites in Uttarakhand, India.…”