TY - JOUR
T1 - The genomic basis of evolutionary differentiation among honey bees
AU - Fouks, Bertrand
AU - Brand, Philipp
AU - Nguyen, Hung N.
AU - Herman, Jacob
AU - Camara, Francisco
AU - Ence, Daniel
AU - Hagen, Darren E.
AU - Hoff, Katharina J.
AU - Nachweide, Stefanie
AU - Romoth, Lars
AU - Walden, Kimberly K.O.
AU - Guigo, Roderic
AU - Stanke, Mario
AU - Narzisi, Giuseppe
AU - Yandell, Mark
AU - Robertson, Hugh M.
AU - Koeniger, Nikolaus
AU - Chantawannakul, Panuwan
AU - Schatz, Michael C.
AU - Worley, Kim C.
AU - Robinson, Gene E.
AU - Elsik, Christine G.
AU - Rueppell, Olav
N1 - Funding Information:
We thank Salim Tingek for hosting O.R. and N.K. at the Agricultural Research Station, Tenom, Malaysia. Research reported by O.R. in this publication was supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number R15GM102753, the National Institute on Aging under award number R21AG046837, and the UNC Greensboro Florence Schaeffer Endowment. C.G.E. was supported by the National Science Foundation under award number IIA-1355406 and Agriculture and Food Research Initiative Competitive grant number 2018-67013-27536 from the U.S. Department of Agriculture National Institute of Food and Agriculture. Further support was provided to G.E.R. by the Illinois Sociogenomics Initiative. Funding for A. florea genome sequencing and assembly was provided by National Human Genome Research Institute grant U54 HG003273 to R.A. Gibbs. M.C.S. acknowledges the U.S. National Science Foundation award number DBI-1627442 and P.C. acknowledges the support of the Chiang Mai University fund. Other parts of this work were supported by the INB (“Instituto Nacional de Bioinformatica”)–Elixir Spain Project PT13/0001/0021 (ISCIII-FEDER) and the Spanish Ministry of Economy and Competitiveness, under “Centro de Excelencia Severo Ochoa 2013–2017,” SEV-2012-0208.
Publisher Copyright:
© 2021 Fouks et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
PY - 2021/7
Y1 - 2021/7
N2 - In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.
AB - In contrast to the western honey bee, Apis mellifera, other honey bee species have been largely neglected despite their importance and diversity. The genetic basis of the evolutionary diversification of honey bees remains largely unknown. Here, we provide a genome-wide comparison of three honey bee species, each representing one of the three subgenera of honey bees, namely the dwarf (Apis florea), giant (A. dorsata), and cavity-nesting (A. mellifera) honey bees with bumblebees as an outgroup. Our analyses resolve the phylogeny of honey bees with the dwarf honey bees diverging first. We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation, which is in agreement with previous studies. However, this process seems to be related to pathways other than transcriptional control. Positive selection patterns across Apis reveal a trade-off between maintaining genome stability and generating genetic diversity, with a rapidly evolving piRNA pathway leading to genomes depleted of transposable elements, and a rapidly evolving DNA repair pathway associated with high recombination rates in all Apis species. Diversification within Apis is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior.
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U2 - 10.1101/gr.272310.120
DO - 10.1101/gr.272310.120
M3 - Article
C2 - 33947700
AN - SCOPUS:85109023709
SN - 1088-9051
VL - 31
SP - 1203
EP - 1215
JO - Genome Research
JF - Genome Research
IS - 7
ER -