Defining honeybee subspecies in an evolutionary context warrants strategized conservation

Qiu, Lifei; Dong, Jiangxing; Li, Xingan; Parey, Sajad H.; Tan, Ken; Orr, Michael C.; Majeed, Aquib; Zhang, Xue; Luo, Suxia; Zhou, Xuguo; Zhu, Chen; Ji, Ting; Niu, Qingsheng; Liu, Shanlin; Zhou, Xin

doi:10.24272/j.issn.2095-8137.2022.414

Cited by 12 publications

(17 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…At the optimal K value of 9, nine distinct populations were obtained, with one central ancestral group (referred to as Central), comprising two components and several peripheral groups, namely Aba (AB), Bomi (BM), Central (CT), Hainan (HN), Northeast (NE), Qinghai (QH), Taiwan (TW) and a subpopulation called Malay (ML) (Figure 5a and Figure S9A–C). This population structure is consistent with previous results using SNP data but a different reference genome (Ji et al., 2020; Qiu et al., 2023). Then, we investigated the population structure based on SVs, which exhibited a finer population structure with an optimal K value of 10 (Figure 5b; Figure S10A).…”

Section: Resultssupporting

confidence: 93%

“…The population structure of A. cerana is composed of one central ancestral group and multiple peripheral groups that radiated from it (Ji et al., 2020; Qiu et al., 2023). In this study, we generated a chromosome‐scale reference genome sequence for the ancestral group of A. cerana (named as HB to indicate samples were collected from the Hubei Province in China) by applying PacBio high‐fidelity (HiFi) sequencing and high‐throughput chromosome conformation capture (Hi‐C) techniques (Figure 1a; Table S2).…”

Section: Resultsmentioning

confidence: 99%

“…The Asian honeybee, A. cerana , is an important agricultural and economic insect with a widespread natural distribution in Asia (Abrol, 2013; Hung et al., 2018; Kimsey, 1989; Theisen‐Jones & Bienefeld, 2016). It has been demonstrated that mainland A. cerana is composed of one central ancestral group and multiple peripheral groups that radiated from it (Ji et al., 2020; Qiu et al., 2023). Studying locally adapted populations, with higher fitness in local environments, is essential for understanding the evolution and genetic diversity of this species and for predicting the effects of environmental change on the distribution of these honeybees (Allendorf et al., 2010; Montero‐Mendieta et al., 2019; Whitlock, 2015).…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Pan‐genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees

Li,

Yao,

Sang

et al. 2023

Molecular Ecology Resources

View full text Add to dashboard Cite

The Asian honeybee, Apis cerana, is an ecologically and economically important pollinator. Mapping its genetic variation is key to understanding population‐level health, histories and potential capacities to respond to environmental changes. However, most efforts to date were focused on single nucleotide polymorphisms (SNPs) based on a single reference genome, thereby ignoring larger scale genomic variation. We employed long‐read sequencing technologies to generate a chromosome‐scale reference genome for the ancestral group of A. cerana. Integrating this with 525 resequencing data sets, we constructed the first pan‐genome of A. cerana, encompassing almost the entire gene content. We found that 31.32% of genes in the pan‐genome were variably present across populations, providing a broad gene pool for environmental adaptation. We identified and characterized structural variations (SVs) and found that they were not closely linked with SNP distributions; however, the formation of SVs was closely associated with transposable elements. Furthermore, phylogenetic analysis using SVs revealed a novel A. cerana ecological group not recoverable from the SNP data. Performing environmental association analysis identified a total of 44 SVs likely to be associated with environmental adaptation. Verification and analysis of one of these, a 330 bp deletion in the Atpalpha gene, indicated that this SV may promote the cold adaptation of A. cerana by altering gene expression. Taken together, our study demonstrates the feasibility and utility of applying pan‐genome approaches to map and explore genetic feature variations of honeybee populations, and in particular to examine the role of SVs in the evolution and environmental adaptation of A. cerana.

show abstract

Section: Resultssupporting

confidence: 93%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Pan‐genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees

Li,

Yao,

Sang

et al. 2023

Molecular Ecology Resources

View full text Add to dashboard Cite

show abstract

“…Simulation studies have shown that low-coverage sequencing across a larger number of individuals can yield more accurate estimates of many population parameters, despite genotype uncertainty (Alex Buerkle & Gompert, 2013; Fumagalli, 2013). This approach not only reduces sequencing costs but also allows for more representative sampling; thereby, genotype likelihood-based analyses have been increasingly used in conservation genomics projects to address questions related to population genetic structure, demographic and evolutionary history, phylogeny/species delimitation, mutation load, and the genomic basis of trait variation (e.g., giant water lily [Smith et al, 2022], honey bees [Qiu et al, 2023] reef-building corals [Cooke et al, 2020], Pacific salmon [Prince et al, 2017], Aldabra giant tortoises [Çilingir et al, 2022a; 2022b], setophaga warblers [Baiz et al, 2021], Seychelles paradise flycather brown hyenas [Westbury et al, 2018], polar bears [Liu et al, 2014], muskox [Pečnerová et al, 2024], African and Asiatic cheetahs [Prost et al, 2022], Eurasian lynx [Mueller et al, 2022]).…”

Section: Discussionmentioning

confidence: 99%

Genotype likelihoods incorporated in non-linear dimensionality reduction techniques infer fine-scale population genetic structure

Gözde Çilingir,

Uzel,

Grossen

2024

Preprint

View full text Add to dashboard Cite

Understanding population structure is essential for conservation genetics, as it provides insights into population connectivity and supports the development of targeted strategies to preserve genetic diversity and adaptability. While Principal Component Analysis (PCA) is a common linear dimensionality reduction method in genomics, the utility of non-linear techniques like t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) for revealing population genetic structures has been largely investigated in humans and model organisms but less so in wild animals. Our study bridges this gap by applying UMAP and t-SNE, alongside PCA, to medium and low-coverage whole-genome sequencing data from the scimitar oryx, once extinct in the wild, and the Galápagos giant tortoises, facing various threats. By estimating genotype likelihoods from coverages as low as 0.5x, we demonstrate that UMAP and t-SNE outperform PCA in identifying genetic structure at reduced genomic coverage levels. This finding underscores the potential of these methods in conservation genomics, particularly when combined with cost-effective, low-coverage sequencing. We also provide detailed guidance on hyperparameter tuning and implementation, facilitating the broader application of these techniques in wildlife genetics research to enhance biodiversity conservation efforts.

show abstract

“…Measurements were performed on those photographs using Fiji software (Schindelin et al, 2012) . For the standard morphometric analysis we measured: the intertegular distance (ID, (Cane, 1987) , hamuli number, cubital index (described in Qiu et al, 2023), and fourteen wing characters: forewing length (lfw), forewing width (wfw), length of cubital vein 1 & 2 (Cub1, Cub2), wing vein angles-A4, B4, D7, E9, G18, J16, K19, L13, N23, 026 (Ruttner, 1988).For the geometric morphometric analysis, 20 forewing landmarks were used (Ji et al, 2020). Images of the forewings were first digitized using tpsDig v2.0 and tpsUtil v1.40 (https://sbmorphometrics.org/) and then we obtained the two-dimensional landmark coordinates for further analysis.…”

Section: Morphometric Measurementsmentioning

confidence: 99%

Tropical and montaneA.ceranashow distinct dance-distance calibration curves

Bharath Kumar,

George,

Brockmann

2024

Preprint

View full text Add to dashboard Cite

Social bees have evolved sophisticated communication systems to recruit nestmates to newly found food sources. As foraging ranges can vary from a few hundred meters to several kilometers depending on the environment or season, populations living in different climate zones likely show specific adaptations in their recruitment communication. Accordingly, studies in the western honey bee,Apis mellifera, demonstrated that temperate populations exhibit shallower dance-calibration curves compared to tropical populations. Here we report the first comparison of calibration curves for three IndianA. ceranalineages: the tropicalA. indica, and the two montane Himalayan populationsA. c. cerana(Himachal Pradesh) andA. c. kashmirensis(Jammu and Kashmir). We found that the colonies of the two montaneA. ceranapopulations show dance-distance calibration curves with significantly shallower slopes than the tropicalA. indica. Next, we transferredA. c. ceranacolonies to Bangalore (~ 2600 km away) to obtain calibration curves in the same location asA. indica. The common garden experiment confirmed this difference in slopes, implying that the lineages exhibit genetically fixed differences in dance-distance coding. However, the slopes of the calibration curves of the transferredA. c. ceranacolonies were also significantly higher than those tested in Himachal Pradesh indicating an important effect of the environment. The differences in dance-distance coding between temperate and tropicalA. ceranalineages resemble those described forA. melliferasuggesting that populations of both species independently evolved similar adaptations.

show abstract

Defining honeybee subspecies in an evolutionary context warrants strategized conservation

Cited by 12 publications

References 40 publications

Pan‐genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees

Pan‐genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees

Genotype likelihoods incorporated in non-linear dimensionality reduction techniques infer fine-scale population genetic structure

Tropical and montaneA.ceranashow distinct dance-distance calibration curves

Contact Info

Product

Resources

About