The genomic basis of evolutionary differentiation among honey bees
- Bertrand Fouks1,
- Philipp Brand2,
- Hung N Nguyen3,
- Jacob Herman1,
- Francisco Camara4,
- Daniel Ence5,
- Darren Hagen6,
- Katherina J Hoff7,
- Stefanie Nachweide7,
- Lars Romoth7,
- Kimberly KO Walden8,
- Roderic Guigo4,
- Mario Stanke9,
- Giuseppe Narzisi10,
- Mark Yandell11,
- Hugh M. Robertson8,
- Nikolaus Koeniger12,
- Panuwan Chantawannakul13,
- Michael C Schatz14,
- Kim C. Worley15,
- Gene E Robinson16,
- Christine G Elsik17 and
- Olav Rueppell1,18
- 1 University of North Carolina Greensboro;
- 2 University of California, Davis;
- 3 Institute for Data Science & Informatics, University of Missouri;
- 4 Centre for Genomic Regulation, The Barcelona Institute of Science and Technology;
- 5 University of Florida;
- 6 Oklahoma State University;
- 7 University of Greifswald, Institute for Mathematics and Computer Science;
- 8 University of Illinois at Urbana-Champaign;
- 9 University of Greifswald;
- 10 New York Genome Center;
- 11 University of Utah;
- 12 University of Würzburg;
- 13 Chiang Mai University;
- 14 Johns Hopkins University;
- 15 Baylor College of Medicine;
- 16 University of Illinois at Urbana Champaign;
- 17 University of Missouri
Abstract
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 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.
- Received September 30, 2020.
- Accepted April 22, 2021.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International license), as described at http://creativecommons.org/licenses/by/4.0/.
