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Nagarajan‐Radha V, Cordina N, Beekman M. Diet and mitonuclear haplotype interactions affect growth rate in a slime mould. Ecol Evol 2023; 13:e10508. [PMID: 37674651 PMCID: PMC10477482 DOI: 10.1002/ece3.10508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/12/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
Trait expression in metazoans is strongly influenced by the balance of macronutrients (i.e. protein, carbohydrate and fat) in the diet. At the same time, an individual's genetic background seems to regulate the magnitude of phenotypic response to a particular diet. It needs to be better understood whether interactions between diet, genetic background and trait expression are found in unicellular eukaryotes. A protist-the slime mould, Physarum polycephalum can choose diets based on protein-to-carbohydrate (P:C) content to support optimal growth rate. Yet, the role of genetic background (variation in the mitochondrial and nuclear DNAs) in mediating growth rate response to dietary P:C ratios in the slime mould is unknown. Here, we studied the effects of interactions between mitochondrial and nuclear DNA haplotypes and diet (i.e. G × G × E interactions) on the growth rate of P. polycephalum. A genetic panel of six distinct strains of P. polycephalum that differ in their mitochondrial and nuclear DNA haplotypes was used to measure growth rate across five diets that varied in their P:C ratio and total calories. We first determined the strains' growth rate (total biomass and surface area) when grown on a set menu with access to a particular diet. We then assessed whether the growth rate of strains increased on a buffet menu with access to all diets. Our findings show that the growth rate of P. polycephalum is generally higher on diets containing more carbohydrates than protein and that total calories negatively affect the growth rate. Three-way interactions between mitochondrial, nuclear haplotypes and dietary P:C ratios affected the strains' surface area of growth but not biomass. Intriguingly, strains did not increase their surface area and biomass when they had access to all diets on the buffet menu. Our findings have broad implications for our understanding of the effect of mitonuclear interactions on trait expression across diverse eukaryotic lineages.
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Affiliation(s)
- Venkatesh Nagarajan‐Radha
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental SciencesThe University of SydneyCamperdownNew South WalesAustralia
| | - Natalie Cordina
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental SciencesThe University of SydneyCamperdownNew South WalesAustralia
| | - Madeleine Beekman
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental SciencesThe University of SydneyCamperdownNew South WalesAustralia
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2
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Marques JF, Ali H, Varbanov BM, Finkel M, Veen HM, van der Meer SLM, Valles-Sanclemente S, Muthusubramanian N, Beekman M, Haider N, Terhal BM, DiCarlo L. All-Microwave Leakage Reduction Units for Quantum Error Correction with Superconducting Transmon Qubits. Phys Rev Lett 2023; 130:250602. [PMID: 37418741 DOI: 10.1103/physrevlett.130.250602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/24/2023] [Indexed: 07/09/2023]
Abstract
Minimizing leakage from computational states is a challenge when using many-level systems like superconducting quantum circuits as qubits. We realize and extend the quantum-hardware-efficient, all-microwave leakage reduction unit (LRU) for transmons in a circuit QED architecture proposed by Battistel et al. This LRU effectively reduces leakage in the second- and third-excited transmon states with up to 99% efficacy in 220 ns, with minimum impact on the qubit subspace. As a first application in the context of quantum error correction, we show how multiple simultaneous LRUs can reduce the error detection rate and suppress leakage buildup within 1% in data and ancilla qubits over 50 cycles of a weight-2 stabilizer measurement.
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Affiliation(s)
- J F Marques
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - H Ali
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - B M Varbanov
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - M Finkel
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - H M Veen
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - S L M van der Meer
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - S Valles-Sanclemente
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - N Muthusubramanian
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - M Beekman
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Netherlands Organisation for Applied Scientific Research (TNO), P.O. Box 96864, 2509 JG The Hague, Netherlands
| | - N Haider
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Netherlands Organisation for Applied Scientific Research (TNO), P.O. Box 96864, 2509 JG The Hague, Netherlands
| | - B M Terhal
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- EEMCS Department, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - L DiCarlo
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
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3
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Nagarajan-Radha V, Beekman M. G × G × E effect on phenotype expression in a non-conventional model organism, the unicellular slime mould Physarum polycephalum. Biol Lett 2023; 19:20220494. [PMID: 36789533 PMCID: PMC9929494 DOI: 10.1098/rsbl.2022.0494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/26/2023] [Indexed: 02/16/2023] Open
Abstract
In metazoans, the expression of key phenotypic traits is sensitive to two- and three-way interactions between variation in mitochondrial DNA, nuclear DNA and the external environment. Whether gene-by-environment interactions affect phenotypes in single-celled eukaryotes is poorly studied, except in a few species of yeast and fungi. We developed a genetic panel of the unicellular slime mould, Physarum polycephalum containing strains differing in mitochondrial and nuclear DNA haplotypes. The panel also included two strains harbouring a selfishly replicating mitochondrial-fusion (mF) plasmid that could affect phenotype expression. We assayed movement and growth rate differences among the strains across two temperature regimes: 24° and 28°C. We found that the slime mould's growth rate, but not movement, is affected by G × G × E interactions. Predictably, mtDNA × nDNA interactions significantly affected both traits. The inter-trait correlation across the strains in each temperature regime was positive. Surprisingly, the mF plasmid had no negative effects on our chosen traits. Our study is the first to demonstrate genetic regulation of phenotype expression in a unicellular slime mould. The genetic effect on phenotypes manifests via epistatic interactions with the thermal environment, thus shedding new light on the role of G × G × E interactions in trait evolution in protists.
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Affiliation(s)
- Venkatesh Nagarajan-Radha
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental Sciences, University of Sydney, Sydney NSW, 2006, Australia
| | - Madeleine Beekman
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental Sciences, University of Sydney, Sydney NSW, 2006, Australia
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4
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van Holstein Y, van den Berkmortel P, Trompet S, van Heemst D, Van den Bos F, Roemeling-van Rhijn M, De Glas N, Beekman M, Slagboom P, Portielje J, Mooijaart S, Van Munster B. The association of blood biomarkers with outcomes in older patients with solid tumors: a systematic review. J Geriatr Oncol 2022. [DOI: 10.1016/s1879-4068(22)00286-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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Bizzarri D, Reinders MJT, Beekman M, Slagboom PE, van den Akker EB. MiMIR: R-shiny application to infer risk factors and endpoints from Nightingale Health's 1H-NMR Metabolomics data. Bioinformatics 2022; 38:3847-3849. [PMID: 35695757 PMCID: PMC9344846 DOI: 10.1093/bioinformatics/btac388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION 1H-NMR metabolomics is rapidly becoming a standard resource in large epidemiological studies to acquire metabolic profiles in large numbers of samples in a relatively low-priced and standardized manner. Concomitantly, metabolomics-based models are increasingly developed that capture disease risk or clinical risk factors. These developments raise the need for user-friendly toolbox to inspect new 1H-NMR metabolomics data and project a wide array of previously established risk models. RESULTS We present MiMIR (Metabolomics-based Models for Imputing Risk), a graphical user interface that provides an intuitive framework for ad-hoc statistical analysis of Nightingale Health's 1H-NMR metabolomics data and allows for the projection and calibration of 24 pre-trained metabolomics-based models, without any pre-required programming knowledge. AVAILABILITY The R-shiny package is available in CRAN or downloadable at https://github.com/DanieleBizzarri/MiMIR, together with an extensive user manual (also available as Supplementary Documents to the paper). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- D Bizzarri
- Molecular Epidemiology, LUMC, Leiden, The Netherlands.,Leiden Computational Biology Center, LUMC, Leiden, The Netherlands
| | - M J T Reinders
- Leiden Computational Biology Center, LUMC, Leiden, The Netherlands.,Delft Bioinformatics Lab, TU Delft, Delft, The Netherlands
| | - M Beekman
- Molecular Epidemiology, LUMC, Leiden, The Netherlands
| | - P E Slagboom
- Molecular Epidemiology, LUMC, Leiden, The Netherlands.,Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - E B van den Akker
- Molecular Epidemiology, LUMC, Leiden, The Netherlands.,Leiden Computational Biology Center, LUMC, Leiden, The Netherlands.,Delft Bioinformatics Lab, TU Delft, Delft, The Netherlands
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6
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Van Vliet N, Bos M, Thesing C, Chaker L, Pietzner M, Houtman E, Neville M, Li-Gao R, Trompet S, Mustafa R, Ahmadizar F, Beekman M, Bot M, Budde K, Christodoulides C, Dehghan A, Delles C, Elliott P, Evangelou M, Gao H, Ghanbari M, Van Herwaarden A, Ikram M, Jaeger M, Jukema J, Karaman I, Karpe F, Kloppenburg M, Meessen J, Meulenbelt I, Milaneschi Y, Mooijaart S, Mook-Kanamori D, Netea M, Netea-Maier R, Peeters R, Penninx B, Sattar N, Slagboom P, Suchiman H, Völzke H, Van Dijk KW, Noordam R. Higher thyroid stimulating hormone leads to cardiovascular disease and an unfavorable lipid profile: EVidence from multi-cohort Mendelian randomization and metabolomic profiling. Atherosclerosis 2021. [DOI: 10.1016/j.atherosclerosis.2021.06.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Oldroyd BP, Yagound B, Allsopp MH, Holmes MJ, Buchmann G, Zayed A, Beekman M. Adaptive, caste-specific changes to recombination rates in a thelytokous honeybee population. Proc Biol Sci 2021; 288:20210729. [PMID: 34102886 PMCID: PMC8187994 DOI: 10.1098/rspb.2021.0729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/13/2021] [Indexed: 11/12/2022] Open
Abstract
The ability to clone oneself has clear benefits-no need for mate hunting or dilution of one's genome in offspring. It is therefore unsurprising that some populations of haplo-diploid social insects have evolved thelytokous parthenogenesis-the virgin birth of a female. But thelytokous parthenogenesis has a downside: the loss of heterozygosity (LoH) as a consequence of genetic recombination. LoH in haplo-diploid insects can be highly deleterious because female sex determination often relies on heterozygosity at sex-determining loci. The two female castes of the Cape honeybee, Apis mellifera capensis, differ in their mode of reproduction. While workers always reproduce thelytokously, queens always mate and reproduce sexually. For workers, it is important to reduce the frequency of recombination so as to not produce offspring that are homozygous. Here, we ask whether recombination rates differ between Cape workers and Cape queens that we experimentally manipulated to reproduce thelytokously. We tested our hypothesis that Cape workers have evolved mechanisms that restrain genetic recombination, whereas queens have no need for such mechanisms because they reproduce sexually. Using a combination of microsatellite genotyping and whole-genome sequencing we find that a reduction in recombination is confined to workers only.
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Affiliation(s)
- Benjamin P. Oldroyd
- Behaviour, Ecology and Evolution (BEE) Laboratory, University of Sydney, Macleay Building A12, NSW 2006, Australia
- Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany
| | - Boris Yagound
- Behaviour, Ecology and Evolution (BEE) Laboratory, University of Sydney, Macleay Building A12, NSW 2006, Australia
| | - Michael H. Allsopp
- Michael H Allsopp, Honeybee Research Section, ARC-Plant Protection Research Institute, Stellenbosch 7600, South Africa
| | - Michael J. Holmes
- Behaviour, Ecology and Evolution (BEE) Laboratory, University of Sydney, Macleay Building A12, NSW 2006, Australia
| | - Gabrielle Buchmann
- Behaviour, Ecology and Evolution (BEE) Laboratory, University of Sydney, Macleay Building A12, NSW 2006, Australia
| | - Amro Zayed
- Department of Biology, Faculty of Science, York University, Toronto, Ontario M3J 1P3, Canada
| | - Madeleine Beekman
- Behaviour, Ecology and Evolution (BEE) Laboratory, University of Sydney, Macleay Building A12, NSW 2006, Australia
- Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany
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8
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Negîrneac V, Ali H, Muthusubramanian N, Battistel F, Sagastizabal R, Moreira MS, Marques JF, Vlothuizen WJ, Beekman M, Zachariadis C, Haider N, Bruno A, DiCarlo L. High-Fidelity Controlled-Z Gate with Maximal Intermediate Leakage Operating at the Speed Limit in a Superconducting Quantum Processor. Phys Rev Lett 2021; 126:220502. [PMID: 34152182 DOI: 10.1103/physrevlett.126.220502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 04/06/2021] [Indexed: 06/13/2023]
Abstract
Simple tuneup of fast two-qubit gates is essential for the scaling of quantum processors. We introduce the sudden variant (SNZ) of the net zero scheme realizing controlled-Z (CZ) gates by flux control of transmon frequency. SNZ CZ gates realized in a multitransmon processor operate at the speed limit of transverse coupling between computational and noncomputational states by maximizing intermediate leakage. Beyond speed, the key advantage of SNZ is tuneup simplicity, owing to the regular structure of conditional phase and leakage as a function of two control parameters. SNZ is compatible with scalable schemes for quantum error correction and adaptable to generalized conditional-phase gates useful in intermediate-scale applications.
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Affiliation(s)
- V Negîrneac
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - H Ali
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - N Muthusubramanian
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - F Battistel
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - R Sagastizabal
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - M S Moreira
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - J F Marques
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - W J Vlothuizen
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Netherlands Organisation for Applied Scientific Research (TNO), P.O. Box 96864, 2509 JG The Hague, Netherlands
| | - M Beekman
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Netherlands Organisation for Applied Scientific Research (TNO), P.O. Box 96864, 2509 JG The Hague, Netherlands
| | - C Zachariadis
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - N Haider
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Netherlands Organisation for Applied Scientific Research (TNO), P.O. Box 96864, 2509 JG The Hague, Netherlands
| | - A Bruno
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
| | - L DiCarlo
- QuTech, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, P.O. Box 5046, 2600 GA Delft, Netherlands
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Norton AM, Remnant EJ, Tom J, Buchmann G, Blacquiere T, Beekman M. Adaptation to vector-based transmission in a honeybee virus. J Anim Ecol 2021; 90:2254-2267. [PMID: 33844844 DOI: 10.1111/1365-2656.13493] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 04/06/2021] [Indexed: 11/27/2022]
Abstract
Global pollinator declines as a result of emerging infectious diseases are of major concern. Managed honeybees Apis mellifera are susceptible to numerous parasites and pathogens, many of which appear to be transmissible to sympatric non-Apis taxa. The ectoparasitic mite Varroa destructor is considered to be the most significant threat to honeybees due to its role in vectoring RNA viruses, particularly Deformed wing virus (DWV). Vector transmission of DWV has resulted in the accumulation of high viral loads in honeybees and is often associated with colony death. DWV has two main genotypes, A and B. DWV-A was more prevalent during the initial phase of V. destructor establishment. In recent years, the global prevalence of DWV-B has increased, suggesting that DWV-B is better adapted to vector transmission than DWV-A. We aimed to determine the role vector transmission plays in DWV genotype prevalence at a colony level. We experimentally increased or decreased the number of V. destructor mites in honeybee colonies, and tracked DWV-A and DWV-B loads over a period of 10 months. Our results show that the two DWV genotypes differ in their response to mite numbers. DWV-A accumulation in honeybees was positively correlated with mite numbers yet DWV-A was largely undetected in the absence of the mite. In contrast, colonies had high loads of DWV-B even when mite numbers were low. DWV-B loads persisted in miticide-treated colonies, indicating that this genotype has a competitive advantage over DWV-A irrespective of mite numbers. Our findings suggest that the global increase in DWV-B prevalence is not driven by selective pressure by the vector. Rather, DWV-B is able to persist in colonies at higher viral loads relative to DWV-A in the presence and absence of V. destructor. The interplay between V. destructor and DWV genotypes within honeybee colonies may have broad consequences upon viral diversity in sympatric taxa as a result of spillover.
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Affiliation(s)
- Amanda M Norton
- Behaviour, Ecology and Evolution (BEE) Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Emily J Remnant
- Behaviour, Ecology and Evolution (BEE) Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Jolanda Tom
- Wageningen University and Research, Wageningen, The Netherlands
| | - Gabriele Buchmann
- Behaviour, Ecology and Evolution (BEE) Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | | | - Madeleine Beekman
- Behaviour, Ecology and Evolution (BEE) Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.,Wissenschaftskolleg zu Berlin, Berlin, Germany
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Bos M, Van Vliet N, Beekman M, Slagboom P, Vernooij M, Van Der Grond J, Van Der Lugt A, Ahmadizar F, Ghanbari M, Ikram M, Van Heemst D, Bos D, Kavousi M. Circulating levels of metabolic biomarkers of site-specific and sex-specific arterial calcification in the multi-cohort BBMRI setting. Eur Heart J 2020. [DOI: 10.1093/ehjci/ehaa946.1339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background/Introduction
Increasing evidence shows that greater arterial calcification leads to an elevated risk of atherosclerotic cardiovascular disease. Risk factors and prognosis of arterial calcification seems to vary per site and between women and men. However, the underlying biological mechanisms of site-specific calcification and the associated sex differences are largely unknown. Within the BBMRI framework, we performed a multi-cohort study on the associations of the circulating levels of metabolic biomarkers with arterial calcification at various sites among women and men.
Purpose
To examine the associations of the circulating levels of metabolic biomarkers with coronary artery (CAC), aortic arch (AAC) and the aortic valve (AVC) calcifications among women and men.
Methods
We included a total of 1,114 participants from the population-based Rotterdam Study and 390 from the Leiden Longevity Study. Study populations were comparable concerning study characteristics. Blood samples were used to determine a wide range of plasma metabolic biomarkers by proton nuclear magnetic resonance (NMR). Participants underwent non-contrast computed tomography to quantify the volume of CAC, AAC, and AVC. Linear regression modelling adjusted for relevant covariates was used to assess the associations of 166 metabolic biomarkers with CAC, AAC, and AVC. Correction for multiple testing was based on 33 independent metabolic biomarkers (p-value 0.05/33 = 1.5 x 10–3).
Results
Mean (standard deviation - SD) age was 69.5 (6.8) and 780 (52.0%) of the study population were women. One SD increase in concentration of a1-acid glycoprotein, was associated with a 0.10 SD (standard error (SE) = 0.03) increase in AAC (p-value = 9.5x10–4) in the overall population (Figure 1). When we stratified our analyses based on sex, this association was mainly driven by men [beta (SE) per SD: 0.12 (0.05), p-value = 0.007]. Moreover, an SD increase in acetate was associated with a 0.14 SD (SE = 0.04) decrease in CAC (p-value 1.7x10–4) in women but not in men [beta (SE) per SD: −0.04 (0.03), p-value = 0.22] (Figure 1).
Conclusion(s)
Higher levels of circulating glycoproteins were associated with increased AAC in men. Moreover, lower levels of circulating acetate were associated with increased CAC in women. These results provide evidence for location-specific differences and sex-specific effects in the underlying biological mechanisms of atherosclerosis. Our findings carry the potential to contribute to the early detection of individuals at increased risk for developing atherosclerotic cardiovascular disease and to a better understanding of disease etiology.
Figure 1
Funding Acknowledgement
Type of funding source: Public grant(s) – National budget only. Main funding source(s): This work was performed within the framework of the BBMRI Metabolomics Consortium funded by BBMRI-NL, a research infrastructure financed by the Dutch government through Netherlands Organisation for Scientific Research (NWO) (Grant Nos. 184.021.007 and 184033111). MK was supported by VENI grant (91616079) from The Netherlands Organization for Health Research and Development (ZonMw).
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Affiliation(s)
- M.M Bos
- Erasmus University Medical Centre, Department of Epidemiology, Rotterdam, Netherlands (The)
| | - N.A Van Vliet
- Leiden University Medical Center, Section of Gerontology and Geriatrics, Department of Internal medicine, Leiden, Netherlands (The)
| | - M Beekman
- Leiden University Medical Center, Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden, Netherlands (The)
| | - P.E Slagboom
- Leiden University Medical Center, Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden, Netherlands (The)
| | - M Vernooij
- Erasmus University Medical Centre, Department of Radiology & Nuclear Medicine, Rotterdam, Netherlands (The)
| | - J Van Der Grond
- Leiden University Medical Center, Department of Radiology, Leiden, Netherlands (The)
| | - A Van Der Lugt
- Erasmus University Medical Centre, Department of Radiology & Nuclear Medicine, Rotterdam, Netherlands (The)
| | - F Ahmadizar
- Erasmus University Medical Centre, Department of Epidemiology, Rotterdam, Netherlands (The)
| | - M Ghanbari
- Erasmus University Medical Centre, Department of Epidemiology, Rotterdam, Netherlands (The)
| | - M.A Ikram
- Erasmus University Medical Centre, Department of Epidemiology, Rotterdam, Netherlands (The)
| | - D Van Heemst
- Leiden University Medical Center, Section of Gerontology and Geriatrics, Department of Internal medicine, Leiden, Netherlands (The)
| | - D Bos
- Erasmus University Medical Centre, Department of Radiology & Nuclear Medicine, Rotterdam, Netherlands (The)
| | - M Kavousi
- Erasmus University Medical Centre, Department of Epidemiology, Rotterdam, Netherlands (The)
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Smith NMA, Yagound B, Remnant EJ, Foster CSP, Buchmann G, Allsopp MH, Kent CF, Zayed A, Rose SA, Lo K, Ashe A, Harpur BA, Beekman M, Oldroyd BP. Paternally-biased gene expression follows kin-selected predictions in female honey bee embryos. Mol Ecol 2020; 29:1523-1533. [PMID: 32220095 DOI: 10.1111/mec.15419] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/01/2020] [Accepted: 03/12/2020] [Indexed: 11/30/2022]
Abstract
The Kinship Theory of Genomic Imprinting (KTGI) posits that, in species where females mate with multiple males, there is selection for a male to enhance the reproductive success of his offspring at the expense of other males and his mating partner. Reciprocal crosses between honey bee subspecies show parent-of-origin effects for reproductive traits, suggesting that males modify the expression of genes related to female function in their female offspring. This effect is likely to be greater in the Cape honey bee (Apis mellifera capensis), because a male's daughters have the unique ability to produce female offspring that can develop into reproductive workers or the next queen without mating. We generated reciprocal crosses between Capensis and another subspecies and used RNA-seq to identify transcripts that are over- or underexpressed in the embryos, depending on the parental origin of the gene. As predicted, 21 genes showed expression bias towards the Capensis father's allele in colonies with a Capensis father, with no such bias in the reciprocal cross. A further six genes showed a consistent bias towards expression of the father's allele across all eight colonies examined, regardless of the direction of the cross. Consistent with predictions of the KTGI, six of the 21 genes are associated with female reproduction. No gene consistently showed overexpression of the maternal allele.
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Affiliation(s)
- Nicholas M A Smith
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Boris Yagound
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Charles S P Foster
- Evolutionary and Integrative Zoology Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Gabriele Buchmann
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Michael H Allsopp
- Honey Bee Research Section, ARC-Plant Protection Research Institute, Stellenbosch, South Africa
| | - Clement F Kent
- Department of Biology, Faculty of Science, York University, Toronto, ON, Canada
| | - Amro Zayed
- Department of Biology, Faculty of Science, York University, Toronto, ON, Canada
| | - Stephen A Rose
- Department of Biology, Faculty of Science, York University, Toronto, ON, Canada
| | - Kitty Lo
- Statistics Research Group, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Alyson Ashe
- Molecular Biosciences, The University of Sydney, Sydney, NSW, Australia
| | - Brock A Harpur
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
| | - Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Laboratory, The University of Sydney, Sydney, NSW, Australia
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Norton AM, Remnant EJ, Buchmann G, Beekman M. Accumulation and Competition Amongst Deformed Wing Virus Genotypes in Naïve Australian Honeybees Provides Insight Into the Increasing Global Prevalence of Genotype B. Front Microbiol 2020; 11:620. [PMID: 32328051 PMCID: PMC7160646 DOI: 10.3389/fmicb.2020.00620] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/19/2020] [Indexed: 12/27/2022] Open
Abstract
Honeybee colony deaths are often attributed to the ectoparasitic mite Varroa destructor and deformed wing virus (DWV), vectored by the mite. In the presence of V. destructor both main genotypes (DWV-A and DWV-B) have been correlated with colony loss. Studies show that DWV-B is the most prevalent genotype in the United Kingdom and Europe. More recently DWV-B has increased in prevalence in the United States. The increasing prevalence of DWV-B at the expense of DWV-A suggests that competition exists between the genotypes. Competition may be due to disparities in virulence between genotypes, differences in fitness, such as rate of replication, or a combination of factors. In this study we investigated if DWV genotypes differ in their rate of accumulation in Australian honeybees naïve to both V. destructor and DWV, and if viral load was associated with mortality in honeybee pupae. We singly and co-infected pupae with DWV-A, DWV-B, and a recombinant strain isolated from a V. destructor tolerant bee population. We monitored viral accumulation throughout pupation, up to 192 h post-injection. We found significant differences in accumulation, where DWV-A accumulated to significantly lower loads than DWV-B and the DWV-recombinant. We also found evidence of competition, where DWV-B loads were significantly reduced in the presence of DWV-A, but still accumulated to the highest loads overall. In contrast to previous studies, we found significant differences in virulence between pupae injected with DWV-A and DWV-B. The average mortality associated with DWV-B (0.4% ± 0.33 SE) and DWV-recombinant (2.2% ± 0.83 SE) injection were significantly less than observed for DWV-A (11% ± 1.2 SE). Our results suggest that a higher proportion of DWV-B infected pupae will emerge into adults, compared to DWV-A. Overall, our data suggest that low mortality in pupae and the ability of DWV-B to accumulate to higher loads relative to DWV-A even during co-infection may favor vector transmission by V. destructor, and may thus be contributing factors to the increasing prevalence of DWV-B globally.
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Affiliation(s)
- Amanda M. Norton
- Behaviour, Ecology and Evolution (BEE) Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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13
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Abstract
Hamilton's theory of inclusive fitness provides a framework for understanding the evolution of social behaviour between kin, including parental and alloparental care. Brood parasitism is a reproductive tactic in which parasites exploit the care of other individuals of the same species (conspecific parasitism) or different species (interspecific parasitism) to rear their brood. Here, drawing from examples in birds and social insects, we identify two insights into brood parasitism that stem from inclusive fitness theory. First, the kin structure within nests, or between neighbouring nests, can create a niche space favouring the evolution of conspecific parasitism. For example, low average relatedness within social insect nests can increase selection for reproductive cheats. Likewise, high average relatedness between adjacent nests of some birds can increase a female's tolerance of parasitism by her neighbour. Second, intrabrood conflict will be high in parasitized broods, from the perspective of both parasite and host young, relative to unparasitized broods. We also discuss offspring recognition by hosts as an example of discrimination in a kin-selected social behaviour. We conclude that the inclusive fitness framework is instructive for understanding aspects of brood parasite and host evolution. In turn, brood parasites present some unique opportunities to test the predictions of inclusive fitness theory. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.
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Affiliation(s)
- Ros Gloag
- School of Life and Environmental Sciences, University of Sydney , Sydney, 2006 , Australia
| | - Madeleine Beekman
- School of Life and Environmental Sciences, University of Sydney , Sydney, 2006 , Australia
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Remnant EJ, Mather N, Gillard TL, Yagound B, Beekman M. Direct transmission by injection affects competition among RNA viruses in honeybees. Proc Biol Sci 2020; 286:20182452. [PMID: 30963951 DOI: 10.1098/rspb.2018.2452] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The arrival of the ectoparasitic mite Varroa destructor on the western honeybee Apis mellifera saw a change in the diversity and prevalence of honeybee RNA viruses. One virus in particular, deformed wing virus (DWV) has become closely associated with V. destructor, leading many to conclude that V. destructor has affected viral virulence by changing the mode of transmission. While DWV is normally transmitted via feeding and faeces, V. destructor transmits viruses by direct injection. This change could have resulted in higher viral prevalence causing increased damage to the bees. Here we test the effect of a change in the mode of transmission on the composition and levels of honeybee RNA viruses in the absence of V. destructor. We find a rapid increase in levels of two viruses, sacbrood virus (SBV) and black queen cell virus (BQCV) after direct injection of viral extracts into honeybee pupae. In pupae injected with high levels of DWV extracted from symptomatic adult bees, DWV levels rapidly decline in the presence of SBV and BQCV. Further, we observe high mortality in honeybee pupae when injected with SBV and BQCV, whereas injecting pupae with high levels of DWV results in near 100% survival. Our results suggest a different explanation for the observed association between V. destructor and DWV. Instead of V. destructor causing an increase in DWV virulence, we hypothesize that direct virus inoculation, such as that mediated by a vector, quickly eliminates the most virulent honeybee viruses resulting in an association with less virulent viruses such as DWV.
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Affiliation(s)
- Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales , Australia
| | - Niklas Mather
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales , Australia
| | - Thomas L Gillard
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales , Australia
| | - Boris Yagound
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales , Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney , Sydney, New South Wales , Australia
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15
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van der Poort EKJ, Gunn DA, Beekman M, Griffiths CEM, Slagboom PE, van Heemst D, Noordam R. Basal cell carcinoma genetic susceptibility increases the rate of skin ageing: a Mendelian randomization study. J Eur Acad Dermatol Venereol 2019; 34:97-100. [PMID: 31419349 DOI: 10.1111/jdv.15880] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/07/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Onset of basal cell carcinoma (BCC) is connected to skin ageing, but it is unclear whether higher BCC genetic susceptibility drives skin ageing. OBJECTIVES To investigate whether loci increasing genetic susceptibility to BCC also drive multiple features of skin ageing, independently of confounding factors, using Mendelian randomization. METHODS A Mendelian randomization study was conducted in older adults from the Leiden Longevity Study (N = 604). A total of 25 BCC loci, selected based on a published genome-wide association study on BCC (P-value < 5 × 10-8 ), were used as genetic instruments for the calculation of a standardized (mean = 0, SD = 1) weighted BCC genetic risk score. Based on facial photographs, we determined perceived age, and skin wrinkling and pigmented spot grading. RESULTS A higher BCC genetic risk score was associated with a higher perceived age (adjusted for chronological age and sex) of 0.88 years (95% CI: 0.44, 1.31; P-value = 7.1e-5 ), greater wrinkling by 0.14 grades (95% CI: 0.05, 0.23; P-value = 2.3e-3 ), and greater pigmented spots by 0.17 grades (95% CI: 0.08, 0.25; P-value = 1.1e-4 ). These findings were weakened but still present after exclusion of gene variants in MC1R and IRF4 which have potential pleiotropic effects. CONCLUSIONS Mechanisms influenced by genetic loci increasing susceptibility to BCC also drive skin ageing suggesting shared biology and shared targets for interventions.
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Affiliation(s)
- E K J van der Poort
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - D A Gunn
- Colworth Science Park, Unilever Research and Development, Sharnbrook, Bedfordshire, UK
| | - M Beekman
- Department of Biomedical Data Sciences, Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - C E M Griffiths
- Dermatology Centre, Salford Royal Hospital, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - P E Slagboom
- Department of Biomedical Data Sciences, Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - D van Heemst
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - R Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
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16
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Beekman M, Oldroyd BP. Conflict and major transitions - why we need true queens. Curr Opin Insect Sci 2019; 34:73-79. [PMID: 31247422 DOI: 10.1016/j.cois.2019.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/18/2019] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
In contrast to human societies, where kings and queens can be sources of conflict, we argue that the morphologically distinct queens of insect colonies are central to the minimization of conflict within their societies. Thus, the evolution of irreversible queen and worker castes represents a major transition in social evolution. Queens are selected to become better reproducers, and workers are selected to become better workers. The reproductive success of queens and workers are, therefore, inextricably linked. Workers achieve reproductive success by assisting the queen, whereas the queen needs her workers to provide her with the wherewithal to raise her brood. The tighter the mutual dependence, the lower conflict, and the larger insect societies can become. As the queen becomes a better breeder, workers are selected to become better at raising their siblings. Yet, nothing in nature is ever free of conflict and with the evolution of a true worker caste a new set of conflicts arises. Multiple mating by queens in particular opens the door to a new set of conflicts. Ironically, multiple mating can only evolve once within-colony conflict is reduced by evolving a true worker caste.
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Affiliation(s)
- Madeleine Beekman
- Behaviour and Genetics of Social Insects Lab, School of Life and Environmental Sciences A12, University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Lab, School of Life and Environmental Sciences A12, University of Sydney, Sydney, NSW 2006, Australia
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17
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Gao C, Liu C, Schenz D, Li X, Zhang Z, Jusup M, Wang Z, Beekman M, Nakagaki T. Does being multi-headed make you better at solving problems? A survey of Physarum-based models and computations. Phys Life Rev 2019; 29:1-26. [DOI: 10.1016/j.plrev.2018.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/25/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022]
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18
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Smith‐Ferguson J, Beekman M. Can't see the colony for the bees: behavioural perspectives of biological individuality. Biol Rev Camb Philos Soc 2019; 94:1935-1946. [DOI: 10.1111/brv.12542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Jules Smith‐Ferguson
- School of Life and Environmental SciencesUniversity of Sydney Sydney New South Wales 2006 Australia
| | - Madeleine Beekman
- School of Life and Environmental SciencesUniversity of Sydney Sydney New South Wales 2006 Australia
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19
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Beekman M, Thompson M, Jusup M. Ectothermic vertebrates are too cool to care: a response to comments on Beekman et al. Behav Ecol 2019. [DOI: 10.1093/beheco/arz071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Madeleine Beekman
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Michael Thompson
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Marko Jusup
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
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20
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Affiliation(s)
- Madeleine Beekman
- School of Life and Environmental Sciences, The University of Sydney, Sydney NSW, Australia
| | - Michael Thompson
- School of Life and Environmental Sciences, The University of Sydney, Sydney NSW, Australia
| | - Marko Jusup
- World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama, Japan
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21
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Beekman M, Oldroyd BP. Different bees, different needs: how nest-site requirements have shaped the decision-making processes in homeless honeybees ( Apis spp.). Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0010. [PMID: 29581395 DOI: 10.1098/rstb.2017.0010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2017] [Indexed: 11/12/2022] Open
Abstract
During reproductive swarming, a honeybee swarm needs to decide on a new nest site and then move to the chosen site collectively. Most studies of swarming and nest-site selection are based on one species, Apis mellifera Natural colonies of A. mellifera live in tree cavities. The quality of the cavity is critical to the survival of a swarm. Other honeybee species nest in the open, and have less strict nest-site requirements, such as the open-nesting dwarf honeybee Apis floreaApis florea builds a nest comprised of a single comb suspended from a twig. For a cavity-nesting species, there is only a limited number of potential nest sites that can be located by a swarm, because suitable sites are scarce. By contrast, for an open-nesting species, there is an abundance of equally suitable twigs. While the decision-making process of cavity-nesting bees is geared towards selecting the best site possible, open-nesting species need to coordinate collective movement towards areas with potential nest sites. Here, we argue that the nest-site selection processes of A. florea and A. mellifera have been shaped by each species' specific nest-site requirements. Both species use the same behavioural algorithm, tuned to allow each species to solve their species-specific problem.This article is part of the theme issue 'Collective movement ecology'.
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Affiliation(s)
- Madeleine Beekman
- Behaviour and Genetics of Social Insects Lab, School of Life and Environmental Sciences A12, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Lab, School of Life and Environmental Sciences A12, University of Sydney, Sydney, New South Wales 2006, Australia
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22
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Aanen D, Beekman M, Kokko H. Weird sex: the underappreciated diversity of sexual reproduction. Philos Trans R Soc Lond B Biol Sci 2018; 371:rstb.2016.0262. [PMID: 27619706 DOI: 10.1098/rstb.2016.0262] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2016] [Indexed: 11/12/2022] Open
Affiliation(s)
- Duur Aanen
- Plant Sciences Group, Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands
| | - Madeleine Beekman
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Hanna Kokko
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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23
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Latty T, Holmes MJ, Makinson JC, Beekman M. Argentine ants ( Linepithema humile) use adaptable transportation networks to track changes in resource quality. ACTA ACUST UNITED AC 2017; 220:686-694. [PMID: 28202653 DOI: 10.1242/jeb.144238] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/30/2016] [Indexed: 11/20/2022]
Abstract
Transportation networks play a crucial role in human and animal societies. For a transportation network to be efficient, it must have adequate capacity to meet traffic demand. Network design becomes increasingly difficult in situations where traffic demand can change unexpectedly. In humans, network design is often constrained by path dependency because it is difficult to move a road once it is built. A similar issue theoretically faces pheromone-trail-laying social insects; once a trail has been laid, positive feedback makes re-routing difficult because new trails cannot compete with continually reinforced pre-existing trails. In the present study, we examined the response of Argentine ant colonies and their trail networks to variable environments where resources differ in quality and change unexpectedly. We found that Argentine ant colonies effectively tracked changes in food quality such that colonies allocated the highest proportion of foragers to the most rewarding feeder. Ant colonies maximised access to high concentration feeders by building additional trails and routes connecting the nest to the feeder. Trail networks appeared to form via a pruning process in which lower traffic trails were gradually removed from the network. At the same time, we observed several instances where new trails appear to have been built to accommodate a surge in demand. The combination of trail building when traffic demand is high and trail pruning when traffic demand is low results in a demand-driven network formation system that allows ants to monopolise multiple dynamic resources.
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Affiliation(s)
- Tanya Latty
- Faculty of Agriculture and Environment, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Michael J Holmes
- Behaviour and Genetics of Social Insects Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - James C Makinson
- Department of Biological and Experimental Psychology, School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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24
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Remnant EJ, Shi M, Buchmann G, Blacquière T, Holmes EC, Beekman M, Ashe A. A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations. J Virol 2017; 91:e00158-17. [PMID: 28515299 PMCID: PMC5533899 DOI: 10.1128/jvi.00158-17] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/26/2017] [Indexed: 01/16/2023] Open
Abstract
Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management.IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales Collapsing Varroa-infected colonies are often overwhelmed with high levels of picornaviruses. To examine the underlying viral diversity in honey bees, we employed viral metatranscriptomics analyses on three geographically diverse Varroa-resistant populations from Europe, Africa, and the Pacific. We describe seven novel viruses from a range of diverse viral families, including two viruses that are present in all three locations. In honey bees, small RNA sequences indicate that these viruses are processed by Dicer and the RNA interference pathway, whereas Varroa mites produce strikingly novel small RNA patterns. This work increases the number and diversity of known honey bee viruses and will ultimately contribute to improved disease management in our most important agricultural pollinator.
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Affiliation(s)
- Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Mang Shi
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Gabriele Buchmann
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
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25
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Affiliation(s)
- Joshua R. Christie
- School of Life and Environmental Sciences The University of Sydney Sydney NSW 2006 Australia
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich 8057 Switzerland
| | - Madeleine Beekman
- School of Life and Environmental Sciences The University of Sydney Sydney NSW 2006 Australia
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26
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Abstract
Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes-specifically their organization into host cells and their uniparental (maternal) inheritance-enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller's ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes-despite their asexual mode of reproduction-can readily undergo adaptive evolution.
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Affiliation(s)
- Joshua R Christie
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Madeleine Beekman
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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27
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Stephens RE, Beekman M, Gloag R. The upside of recognition error? Artificially aggregated colonies of the stingless bee Tetragonula carbonaria tolerate high rates of worker drift. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Beekman M, Nieuwenhuis B, Ortiz-Barrientos D, Evans JP. Sexual selection in hermaphrodites, sperm and broadcast spawners, plants and fungi. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150541. [PMID: 27619704 PMCID: PMC5031625 DOI: 10.1098/rstb.2015.0541] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/12/2022] Open
Abstract
Darwin was the first to recognize that sexual selection is a strong evolutionary force. Exaggerated traits allow same-sex individuals to compete over access to mates and provide a mechanism by which mates are selected. It is relatively easy to appreciate how inter- and intrasexual selection work in organisms with the sensory capabilities to perceive physical or behavioural traits that signal mate quality or mate compatibility, and to assess the relative quality of competitors. It is therefore not surprising that most studies of sexual selection have focused on animals with separate sexes and obvious adaptations that function in the context of reproductive competition. Yet, many sexual organisms are both male and female at the same time, often lack sexual dimorphism and never come into direct contact at mating. How does sexual selection act in such species, and what can we learn from them? Here, we address these questions by exploring the potential for sexual selection in simultaneous hermaphrodites, sperm- and broadcast spawners, plants and fungi. Our review reveals a range of mechanisms of sexual selection, operating primarily after gametes have been released, which are common in many of these groups and also quite possibly in more familiar (internally fertilizing and sexually dimorphic) organisms.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Madeleine Beekman
- School of Life and Environmental Sciences, University of Sydney, 2006 New South Wales, Australia
| | - Bart Nieuwenhuis
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | | | - Jonathan P Evans
- Centre for Evolutionary Biology, School of Animal Biology, University of Western Australia, 6009 Western Australia, Australia
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Remnant EJ, Ashe A, Young PE, Buchmann G, Beekman M, Allsopp MH, Suter CM, Drewell RA, Oldroyd BP. Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation. BMC Genomics 2016; 17:226. [PMID: 26969617 PMCID: PMC4788913 DOI: 10.1186/s12864-016-2506-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/19/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Intersexual genomic conflict sometimes leads to unequal expression of paternal and maternal alleles in offspring, resulting in parent-of-origin effects. In honey bees reciprocal crosses can show strong parent-of-origin effects, supporting theoretical predictions that genomic imprinting occurs in this species. Mechanisms behind imprinting in honey bees are unclear but differential DNA methylation in eggs and sperm suggests that DNA methylation could be involved. Nonetheless, because DNA methylation is multifunctional, it is difficult to separate imprinting from other roles of methylation. Here we use a novel approach to investigate parent-of-origin DNA methylation in honey bees. In the subspecies Apis mellifera capensis, reproduction of females occurs either sexually by fertilization of eggs with sperm, or via thelytokous parthenogenesis, producing female embryos derived from two maternal genomes. RESULTS We compared genome-wide methylation patterns of sexually-produced, diploid embryos laid by a queen, with parthenogenetically-produced diploid embryos laid by her daughters. Thelytokous embryos inheriting two maternal genomes had fewer hypermethylated genes compared to fertilized embryos, supporting the prediction that fertilized embryos have increased methylation due to inheritance of a paternal genome. However, bisulfite PCR and sequencing of a differentially methylated gene, Stan (GB18207) showed strong allele-specific methylation that was maintained in both fertilized and thelytokous embryos. For this gene, methylation was associated with haplotype, not parent of origin. CONCLUSIONS The results of our study are consistent with predictions from the kin theory of genomic imprinting. However, our demonstration of allele-specific methylation based on sequence shows that genome-wide differential methylation studies can potentially confound imprinting and allele-specific methylation. It further suggests that methylation patterns are heritable or that specific sequence motifs are targets for methylation in some genes.
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Affiliation(s)
- Emily J. Remnant
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Alyson Ashe
- />School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006 Australia
| | - Paul E. Young
- />Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
- />University of New South Wales, Kensington, NSW 2033 Australia
| | - Gabriele Buchmann
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Madeleine Beekman
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Michael H. Allsopp
- />Honey Bee Research Section, ARC-Plant Protection Research Institute, Private Bag X5017, Stellenbosch, South Africa
| | - Catherine M. Suter
- />Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
- />University of New South Wales, Kensington, NSW 2033 Australia
| | - Robert A. Drewell
- />Biology Department, Clark University, 950 Main Street, Worcester, MA 01610 USA
| | - Benjamin P. Oldroyd
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
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Schürch R, Couvillon MJ, Beekman M. Editorial: Ballroom Biology: Recent Insights into Honey Bee Waggle Dance Communications. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2015.00147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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32
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Beekman M, Latty T. Brainless but Multi-Headed: Decision Making by the Acellular Slime Mould Physarum polycephalum. J Mol Biol 2015; 427:3734-43. [DOI: 10.1016/j.jmb.2015.07.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/02/2015] [Accepted: 07/07/2015] [Indexed: 11/26/2022]
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Christie JR, Schaerf TM, Beekman M. Selection against heteroplasmy explains the evolution of uniparental inheritance of mitochondria. PLoS Genet 2015; 11:e1005112. [PMID: 25880558 PMCID: PMC4400020 DOI: 10.1371/journal.pgen.1005112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/28/2015] [Indexed: 12/03/2022] Open
Abstract
Why are mitochondria almost always inherited from one parent during sexual reproduction? Current explanations for this evolutionary mystery include conflict avoidance between the nuclear and mitochondrial genomes, clearing of deleterious mutations, and optimization of mitochondrial-nuclear coadaptation. Mathematical models, however, fail to show that uniparental inheritance can replace biparental inheritance under any existing hypothesis. Recent empirical evidence indicates that mixing two different but normal mitochondrial haplotypes within a cell (heteroplasmy) can cause cell and organism dysfunction. Using a mathematical model, we test if selection against heteroplasmy can lead to the evolution of uniparental inheritance. When we assume selection against heteroplasmy and mutations are neither advantageous nor deleterious (neutral mutations), uniparental inheritance replaces biparental inheritance for all tested parameter values. When heteroplasmy involves mutations that are advantageous or deleterious (non-neutral mutations), uniparental inheritance can still replace biparental inheritance. We show that uniparental inheritance can evolve with or without pre-existing mating types. Finally, we show that selection against heteroplasmy can explain why some organisms deviate from strict uniparental inheritance. Thus, we suggest that selection against heteroplasmy explains the evolution of uniparental inheritance. Mitochondria contain genes that encode the machinery needed to power cells. Unlike the nuclear genome, the mitochondrial genome is typically inherited from one parent only (uniparental inheritance). The most common explanation for uniparental inheritance is the genomic conflict theory, which states that uniparental inheritance evolved to prevent the spread of ‘selfish’ mitochondria that replicate quickly but produce energy inefficiently. Current explanations have a major problem: when using realistic parameters, mathematical models cannot show that uniparental inheritance can replace biparental inheritance. Clearly, we need a new explanation that fits with standard population-genetic theory. Recent evidence suggests cells may incur a cost when they carry multiple types of mitochondria. Here we show mathematically that uniparental inheritance could have evolved to avoid the costs of maintaining multiple mitochondrial lineages within a cell. Our results explain the long-standing evolutionary mystery of uniparental inheritance and provide insight into the evolution of mating types and binary sexes. Selection against heteroplasmy also has implications for the evolution of the mitochondrial genome because new mitochondrial haplotypes always lead to heteroplasmy before becoming fixed in the population. Thus, selection against heteroplasmy may explain why mtDNA coding-genes have slower substitution rates than analogous genes within the nucleus.
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Affiliation(s)
- Joshua R. Christie
- School of Biological Sciences, The University of Sydney, Sydney, Australia
- Centre for Mathematical Biology, The University of Sydney, Sydney, Australia
- * E-mail:
| | - Timothy M. Schaerf
- School of Biological Sciences, The University of Sydney, Sydney, Australia
- Centre for Mathematical Biology, The University of Sydney, Sydney, Australia
| | - Madeleine Beekman
- School of Biological Sciences, The University of Sydney, Sydney, Australia
- Centre for Mathematical Biology, The University of Sydney, Sydney, Australia
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Beekman M, Makinson JC, Couvillon MJ, Preece K, Schaerf TM. Honeybee linguistics—a comparative analysis of the waggle dance among species of Apis. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Chapman NC, Beekman M, Allsopp MH, Rinderer TE, Lim J, Oxley PR, Oldroyd BP. Inheritance of thelytoky in the honey bee Apis mellifera capensis. Heredity (Edinb) 2015; 114:584-92. [PMID: 25585920 DOI: 10.1038/hdy.2014.127] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/27/2014] [Accepted: 12/03/2014] [Indexed: 01/31/2023] Open
Abstract
Asexual reproduction via thelytokous parthenogenesis is widespread in the Hymenoptera, but its genetic underpinnings have been described only twice. In the wasp Lysiphlebus fabarum and the Cape honey bee Apis mellifera capensis the origin of thelytoky have each been traced to a single recessive locus. In the Cape honey bee it has been argued that thelytoky (th) controls the thelytoky phenotype and that a deletion of 9 bp in the flanking intron downstream of exon 5 (tae) of the gemini gene switches parthenogenesis from arrhenotoky to thelytoky. To further explore the mode of inheritance of thelytoky, we generated reciprocal backcrosses between thelytokous A. m. capensis and the arrhenotokous A. m. scutellata. Ten genetic markers were used to identify 108 thelytokously produced offspring and 225 arrhenotokously produced offspring from 14 colonies. Patterns of appearance of thelytokous parthenogenesis were inconsistent with a single locus, either th or tae, controlling thelytoky. We further show that the 9 bp deletion is present in the arrhenotokous A. m. scutellata population in South Africa, in A. m. intermissa in Morocco and in Africanized bees from Brazil and Texas, USA, where thelytoky has not been reported. Thus the 9 p deletion cannot be the cause of thelytoky. Further, we found two novel tae alleles. One contains the previously described 9 bp deletion and an additional deletion of 7 bp nearby. The second carries a single base insertion with respect to the wild type. Our data are consistent with the putative th locus increasing reproductive capacity.
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Affiliation(s)
- N C Chapman
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences A12, University of Sydney, NSW, Australia
| | - M Beekman
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences A12, University of Sydney, NSW, Australia
| | - M H Allsopp
- ARC-Plant Protection Research Institute, Stellenbosch, South Africa
| | - T E Rinderer
- Honey Bee Breeding, Genetics and Physiology Research Laboratory, USDA-ARS, Baton Rouge, LA, USA
| | - J Lim
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences A12, University of Sydney, NSW, Australia
| | - P R Oxley
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences A12, University of Sydney, NSW, Australia
| | - B P Oldroyd
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences A12, University of Sydney, NSW, Australia
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Beekman M, Dowling DK, Aanen DK. The costs of being male: are there sex-specific effects of uniparental mitochondrial inheritance? Philos Trans R Soc Lond B Biol Sci 2015; 369:20130440. [PMID: 24864311 DOI: 10.1098/rstb.2013.0440] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic cells typically contain numerous mitochondria, each with multiple copies of their own genome, the mtDNA. Uniparental transmission of mitochondria, usually via the mother, prevents the mixing of mtDNA from different individuals. While on the one hand, this should resolve the potential for selection for fast-replicating mtDNA variants that reduce organismal fitness, maternal inheritance will, in theory, come with another set of problems that are specifically relevant to males. Maternal inheritance implies that the mitochondrial genome is never transmitted through males, and thus selection can target only the mtDNA sequence when carried by females. A consequence is that mtDNA mutations that confer male-biased phenotypic expression will be prone to evade selection, and accumulate. Here, we review the evidence from the ecological, evolutionary and medical literature for male specificity of mtDNA mutations affecting fertility, health and ageing. While such effects have been discovered experimentally in the laboratory, their relevance to natural populations--including the human population--remains unclear. We suggest that the existence of male expression-biased mtDNA mutations is likely to be a broad phenomenon, but that these mutations remain cryptic owing to the presence of counter-adapted nuclear compensatory modifier mutations, which offset their deleterious effects.
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Affiliation(s)
- Madeleine Beekman
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Duur K Aanen
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands
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38
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Latty T, Beekman M. Slime moulds use heuristics based on within-patch experience to decide when to leave. J Exp Biol 2015; 218:1175-9. [DOI: 10.1242/jeb.116533] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/11/2015] [Indexed: 11/20/2022]
Abstract
Animals foraging in patchy, non- or slowly-renewing environments must make decisions about how long to remain within a patch. Organisms can use heuristics (‘rules of thumb’) based on available information to decide when to leave the patch. Here we investigate proximate patch departure heuristics in two species of giant, brainless amoeba: the slime moulds Didymium bahiense and Physarum polycephalum. We explicitly tested the importance of information obtained through experience by eliminating chemosensory cues of patch quality. In Physarum polycephalum, patch departure was influenced by the consumption of high, and to a much lesser extent low, quality food items such that engulfing a food item increased patch residency time. Physarum polycephalum also tended to forage for longer in darkened, ‘safe’ patches. In Didymium bahiense, engulfment of either a high or low quality food item increased patch residency irrespective of that food item's quality. Exposure to light had no effect on the patch residency time of D. bahiense. Given that our organisms lack a brain, our results illustrate how the use of simple heuristics can give the impression that individuals make sophisticated foraging decisions.
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Affiliation(s)
- Tanya Latty
- Department of Plant and Food Science, Faculty of Agriculture and the Environment, University of Sydney, NSW, 2015, Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Lab and Centre for Mathematical Biology, School of Biological Sciences A12, University of Sydney, NSW 2006, Australia
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Cabanes G, van Wilgenburg E, Beekman M, Latty T. Ants build transportation networks that optimize cost and efficiency at the expense of robustness. Behav Ecol 2014. [DOI: 10.1093/beheco/aru175] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Guigas B, de Leeuw van Weenen JE, van Leeuwen N, Simonis-Bik AM, van Haeften TW, Nijpels G, Houwing-Duistermaat JJ, Beekman M, Deelen J, Havekes LM, Penninx BWJH, Vogelzangs N, van 't Riet E, Dehghan A, Hofman A, Witteman JC, Uitterlinden AG, Grarup N, Jørgensen T, Witte DR, Lauritzen T, Hansen T, Pedersen O, Hottenga J, Romijn JA, Diamant M, Kramer MHH, Heine RJ, Willemsen G, Dekker JM, Eekhoff EM, Pijl H, de Geus EJ, Slagboom PE, 't Hart LM. Sex-specific effects of naturally occurring variants in the dopamine receptor D2 locus on insulin secretion and type 2 diabetes susceptibility. Diabet Med 2014; 31:1001-8. [PMID: 24724616 DOI: 10.1111/dme.12464] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 01/13/2014] [Accepted: 04/08/2014] [Indexed: 12/21/2022]
Abstract
AIMS Modulation of dopamine receptor D2 (DRD2) activity affects insulin secretion in both rodents and isolated pancreatic β-cells. We hypothesized that single nucleotide polymorphisms in the DRD2/ANKK1 locus may affect susceptibility to type 2 diabetes in humans. METHODS Four potentially functional variants in the coding region of the DRD2/ANKK1 locus (rs1079597, rs6275, rs6277, rs1800497) were genotyped and analysed for type 2 diabetes susceptibility in up to 25 000 people (8148 with type 2 diabetes and 17687 control subjects) from two large independent Dutch cohorts and one Danish cohort. In addition, 340 Dutch subjects underwent a 2-h hyperglycaemic clamp to investigate insulin secretion. Since sexual dimorphic associations related to DRD2 polymorphisms have been previously reported, we also performed a gender-stratified analysis. RESULTS rs1800497 at the DRD2/ANKK1 locus was associated with a significantly increased risk for type 2 diabetes in women (odds ratio 1.14 (1.06-1.23); P = 4.1*10⁴) but not in men (odds ratio 1.00 (95% CI 0.93-1.07); P = 0.92) or the combined group. Although rs1800497 was not associated with insulin secretion, we did find another single nucleotide polymorphism in this locus, rs6275, to be associated with increased first-phase glucose-stimulated insulin secretion in women (P = 5.5*10⁴) but again not in men (P = 0.34). CONCLUSION The present data identify DRD2/ANKK1 as a potential sex-specific type 2 diabetes susceptibility gene.
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Affiliation(s)
- B Guigas
- Department of Molecular Cell Biology, Leiden University Medical Centre, Leiden, The Netherlands; Department of Parasitology, Leiden University Medical Centre, Leiden, The Netherlands
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Aanen DK, Spelbrink JN, Beekman M. What cost mitochondria? The maintenance of functional mitochondrial DNA within and across generations. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130438. [PMID: 24864309 PMCID: PMC4032515 DOI: 10.1098/rstb.2013.0438] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The peculiar biology of mitochondrial DNA (mtDNA) potentially has detrimental consequences for organismal health and lifespan. Typically, eukaryotic cells contain multiple mitochondria, each with multiple mtDNA genomes. The high copy number of mtDNA implies that selection on mtDNA functionality is relaxed. Furthermore, because mtDNA replication is not strictly regulated, within-cell selection may favour mtDNA variants with a replication advantage, but a deleterious effect on cell fitness. The opportunities for selfish mtDNA mutations to spread are restricted by various organism-level adaptations, such as uniparental transmission, germline mtDNA bottlenecks, germline selection and, during somatic growth, regular alternation between fusion and fission of mitochondria. These mechanisms are all hypothesized to maintain functional mtDNA. However, the strength of selection for maintenance of functional mtDNA progressively declines with age, resulting in age-related diseases. Furthermore, organismal adaptations that most probably evolved to restrict the opportunities for selfish mtDNA create secondary problems. Owing to predominantly maternal mtDNA transmission, recombination among mtDNA from different individuals is highly restricted or absent, reducing the scope for repair. Moreover, maternal inheritance precludes selection against mtDNA variants with male-specific effects. We finish by discussing the consequences of life-history differences among taxa with respect to mtDNA evolution and make a case for the use of microorganisms to experimentally manipulate levels of selection.
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Affiliation(s)
- Duur K Aanen
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, PO Box 309, 6700 AH Wageningen, The Netherlands
| | - Johannes N Spelbrink
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, PO Box 9101, 6500 HB Nijmegen, The Netherlands FinMIT Centre of Excellence, BioMediTech and Tampere University Hospital, Pirkanmaa Hospital District, 33014 Tampere, Finland
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Lab, The University of Sydney, Sydney NSW 2006, Australia
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Makinson JC, Schaerf TM, Rattanawannee A, Oldroyd BP, Beekman M. Consensus building in giant Asian honeybee, Apis dorsata, swarms on the move. Anim Behav 2014. [DOI: 10.1016/j.anbehav.2014.04.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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van Leeuwen N, Beekman M, Deelen J, van den Akker EB, de Craen AJM, Slagboom PE, ’t Hart LM. Low mitochondrial DNA content associates with familial longevity: the Leiden Longevity Study. Age (Dordr) 2014; 36:9629. [PMID: 24554339 PMCID: PMC4082602 DOI: 10.1007/s11357-014-9629-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/05/2014] [Indexed: 05/02/2023]
Abstract
Long-lived individuals delay aging and age-related diseases like diabetes, hypertension, and cardiovascular disease. The exact underlying mechanisms are largely unknown, but enhanced mitochondrial biogenesis and preservation of mitochondrial function have been suggested to explain healthy ageing. We investigated whether individuals belonging to long-lived families have altered mitochondrial DNA (mtDNA) content, as a biomarker of mitochondrial biogenesis and measured expression of genes regulating mitochondrial biogenesis. mtDNA and nuclear DNA (nDNA) levels were measured in blood samples from 2,734 participants from the Leiden Longevity Study: 704 nonagenarian siblings, 1,388 of their middle-aged offspring and 642 controls. We confirmed a negative correlation of mtDNA content in blood with age and a higher content in females. The middle-aged offspring had, on average, lower levels of mtDNA than controls and the nonagenarian siblings had an even lower mtDNA content (mtDNA/nDNA ratio = 0.744 ± 0.065, 0.767 ± 0.058 and 0.698 ± 0.074, respectively; p controls-offspring = 3.4 × 10(-12), p controls-nonagenarians = 6.5 × 10(-6)), which was independent of the confounding effects of age and gender. Subsequently, we examined in a subset of the study the expression in blood of two genes regulating mitochondrial biogenesis, YY1 and PGC-1α. We found a positive association of YY1 expression and mtDNA content in controls. The observed absence of such an association in the offspring suggests an altered regulation of mitochondrial biogenesis in the members of long-lived families. In conclusion, in this study, we show that mtDNA content decreases with age and that low mtDNA content is associated with familial longevity. Our data suggest that preservation of mitochondrial function rather than enhancing mitochondrial biogenesis is a characteristic of long-lived families.
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Affiliation(s)
- N. van Leeuwen
- />Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - M. Beekman
- />Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- />Netherlands Consortium for Healthy Ageing, Leiden University Medical Center, Leiden, The Netherlands
| | - J. Deelen
- />Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- />Netherlands Consortium for Healthy Ageing, Leiden University Medical Center, Leiden, The Netherlands
| | - E. B. van den Akker
- />Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- />The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - A. J. M. de Craen
- />Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - P. E. Slagboom
- />Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- />Netherlands Consortium for Healthy Ageing, Leiden University Medical Center, Leiden, The Netherlands
| | - L. M. ’t Hart
- />Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
- />Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
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Holmes MJ, Tan K, Wang Z, Oldroyd BP, Beekman M. Why acquiesce? Worker reproductive parasitism in the Eastern honeybee (Apis cerana
). J Evol Biol 2014; 27:939-49. [DOI: 10.1111/jeb.12366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/24/2014] [Accepted: 03/06/2014] [Indexed: 02/02/2023]
Affiliation(s)
- M. J. Holmes
- Behaviour and Genetics of Social Insects Laboratory; School of Biological Sciences; University of Sydney; Sydney NSW Australia
| | - K. Tan
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Science; Kunming China
- Eastern Bee Research Institute of Yunnan Agricultural University; Kunming China
| | - Z. Wang
- Eastern Bee Research Institute of Yunnan Agricultural University; Kunming China
| | - B. P. Oldroyd
- Behaviour and Genetics of Social Insects Laboratory; School of Biological Sciences; University of Sydney; Sydney NSW Australia
| | - M. Beekman
- Behaviour and Genetics of Social Insects Laboratory; School of Biological Sciences; University of Sydney; Sydney NSW Australia
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Makinson JC, Beekman M. Moving without a purpose: an experimental study of swarm guidance in the Western honey bee, Apis mellifera. ACTA ACUST UNITED AC 2014; 217:2020-7. [PMID: 24675563 DOI: 10.1242/jeb.103283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
During reproductive swarming, honey bee scouts perform two very important functions. Firstly, they find new nesting locations and return to the swarm cluster to communicate their discoveries. Secondly, once the swarm is ready to depart, informed scout bees act as guides, leading the swarm to its final destination. We have previously hypothesised that the two processes, selecting a new nest site and swarm guidance, are tightly linked in honey bees. When swarms can be laissez faire about where they nest, reaching directional consensus prior to lift off seems unnecessary. If, in contrast, it is essential that the swarm reaches a precise location, either directional consensus must be near unanimous prior to swarm departure or only a select subgroup of the scouts guide the swarm. Here, we tested experimentally whether directional consensus is necessary for the successful guidance of swarms of the Western honey bee Apis mellifera by forcing swarms into the air prior to the completion of the decision-making process. Our results show that swarms were unable to guide themselves prior to the swarm reaching the pre-flight buzzing phase of the decision-making process, even when directional consensus was high. We therefore suggest that not all scouts involved in the decision-making process attempt to guide the swarm.
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Affiliation(s)
- James C Makinson
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences, University of Sydney, NSW 2006, Australia Centre for Mathematical Biology, University of Sydney, NSW 2006, Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Lab, School of Biological Sciences, University of Sydney, NSW 2006, Australia Centre for Mathematical Biology, University of Sydney, NSW 2006, Australia
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Roth KM, Beekman M, Allsopp MH, Goudie F, Wossler TC, Oldroyd BP. Cheating workers with large activated ovaries avoid risky foraging. Behav Ecol 2014. [DOI: 10.1093/beheco/aru043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Remnant EJ, Koetz A, Tan K, Hinson E, Beekman M, Oldroyd BP. Reproductive interference between honeybee species in artificial sympatry. Mol Ecol 2014; 23:1096-107. [DOI: 10.1111/mec.12669] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 01/05/2014] [Accepted: 01/10/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Emily J. Remnant
- Behaviour and Genetics of Social Insects Laboratory; School of Biological Sciences A12; University of Sydney; Sydney NSW 2006 Australia
| | - Anna Koetz
- Biosecurity Queensland; Department of Agriculture; Fisheries and Forestry; PO Box 652 Cairns QLD 4870 Australia
| | - Ken Tan
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Science; Kunming Yunnan Province 650223 China
| | - Eloise Hinson
- Behaviour and Genetics of Social Insects Laboratory; School of Biological Sciences A12; University of Sydney; Sydney NSW 2006 Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory; School of Biological Sciences A12; University of Sydney; Sydney NSW 2006 Australia
| | - Benjamin P. Oldroyd
- Behaviour and Genetics of Social Insects Laboratory; School of Biological Sciences A12; University of Sydney; Sydney NSW 2006 Australia
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Abstract
Apis mellifera capensis is unique among honeybees in that unmated workers can produce pseudo-clonal female offspring via thelytokous parthenogenesis. Workers use this ability to compete among themselves and with their queen to be the mother of new queens. Males could therefore enhance their reproductive success by imprinting genes that enhance fertility in their daughter workers. This possibility sets the scene for intragenomic conflict between queens and drones over worker reproductive traits. Here, we show a strong parent-of-origin effect for ovary size (number of ovarioles) in reciprocal crosses between two honeybee subspecies, A. m. capensis and Apis mellifera scutellata. In this cross, workers with an A. m. capensis father had 30% more ovarioles than genotypically matched workers with an A. m. scutellata father. Other traits we measured (worker weight at emergence and the presence/absence of a spermatheca) are influenced more by rearing conditions than by parent-of-origin effects. Our study is the first to show a strong epigenetic (or, less likely, cytoplasmic maternal) effect for a reproductive trait in the honeybee and suggests that a search for parent-of-origin effects in other social insects may be fruitful.
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Affiliation(s)
- Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Laboratory, School of Biological Sciences, University of Sydney, , Sydney, New South Wales 2006, Australia, Honey Bee Research Section, ARC-Plant Protection Research Institute, , Private Bag X5017, Stellenbosch 7599, South Africa, Department of Biology, Harvey Mudd College, , 301 Platt Boulevard, Claremont, CA 91001, USA
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