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Affiliation(s)
- Reinder Radersma
- Biometris Wageningen University & Research Wageningen The Netherlands
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Montiglio PO, Gotanda KM, Kratochwil CF, Laskowski KL, Farine DR. Hierarchically embedded interaction networks represent a missing link in the study of behavioral and community ecology. Behav Ecol 2020; 31:279-286. [PMID: 32210523 PMCID: PMC7083094 DOI: 10.1093/beheco/arz168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/05/2019] [Accepted: 08/29/2019] [Indexed: 12/19/2022] Open
Abstract
Because genes and phenotypes are embedded within individuals, and individuals within populations, interactions within one level of biological organization are inherently linked to interactors at others. Here, we expand the network paradigm to consider that nodes can be embedded within other nodes, and connections (edges) between nodes at one level of organization form "bridges" for connections between nodes embedded within them. Such hierarchically embedded networks highlight two central properties of biological systems: 1) processes occurring across multiple levels of organization shape connections among biological units at any given level of organization and 2) ecological effects occurring at a given level of organization can propagate up or down to additional levels. Explicitly considering the embedded structure of evolutionary and ecological networks can capture otherwise hidden feedbacks and generate new insights into key biological phenomena, ultimately promoting a broader understanding of interactions in evolutionary theory.
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Affiliation(s)
- P O Montiglio
- Département des Sciences Biologiques, Université du Québec à Montréal, Succursale Centre-ville, Montréal, Québec, Canada
| | - K M Gotanda
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - C F Kratochwil
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
- Zukunftskolleg, University of Konstanz, Konstanz, Konstanz, Germany
| | - K L Laskowski
- Department of Biology, & Ecology of Fishes, Leibniz-Institute of Freshwater Ecology & Inland Fisheries, Berlin, Germany
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
| | - D R Farine
- Department of Collective Behavior, Max Planck Institute of Animal Behavior, Universitätsstraße 10, Konstanz, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
- Edward Grey Institute of Ornithology, Department of Zoology, University of Oxford, Oxford, UK
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Driscoe AL, Nice CC, Busbee RW, Hood GR, Egan SP, Ott JR. Host plant associations and geography interact to shape diversification in a specialist insect herbivore. Mol Ecol 2019; 28:4197-4211. [DOI: 10.1111/mec.15220] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Amanda L. Driscoe
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
| | - Chris C. Nice
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
| | - Robert W. Busbee
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
| | - Glen R. Hood
- Department of Biological Sciences Wayne State University Detroit Michigan
| | - Scott P. Egan
- Department of Biosciences Rice University Houston Texas
| | - James R. Ott
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos Texas
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4
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The role of habitat configuration in shaping social structure: a gap in studies of animal social complexity. Behav Ecol Sociobiol 2019. [DOI: 10.1007/s00265-018-2602-7] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Kim JM, Santure AW, Barton HJ, Quinn JL, Cole EF, Visser ME, Sheldon BC, Groenen MAM, van Oers K, Slate J. A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour. Mol Ecol Resour 2018; 18:877-891. [PMID: 29573186 DOI: 10.1111/1755-0998.12778] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 12/25/2022]
Abstract
High-density SNP microarrays ("SNP chips") are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this article, we describe the development and application of a high-density Affymetrix Axiom chip with around 500,000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per-SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation. The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genomewide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays; (ii) detecting SNPs by more than one pipeline, and in independent data sets, ensures a high proportion of working assays; (iii) allele frequency ascertainment bias is minimized by performing SNP discovery in individuals from multiple populations; and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.
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Affiliation(s)
- J-M Kim
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, Korea
| | - A W Santure
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - H J Barton
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK
| | - J L Quinn
- School of Biological, Earth and Environmental Science (BEES), University College Cork, Cork, Ireland
| | - E F Cole
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | | | - M E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - B C Sheldon
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - M A M Groenen
- Wageningen University and Research - Animal Breeding and Genomics, Wageningen, Netherlands
| | - K van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - J Slate
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK
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Maldonado-Chaparro AA, Montiglio PO, Forstmeier W, Kempenaers B, Farine DR. Linking the fine-scale social environment to mating decisions: a future direction for the study of extra-pair paternity. Biol Rev Camb Philos Soc 2018. [DOI: 10.1111/brv.12408] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Adriana A. Maldonado-Chaparro
- Department of Collective Behaviour, Max Planck Institute for Ornithology; Universitätsstrasse 10; 78457 Konstanz Germany
- Chair of Biodiversity and Collective Behaviour, Department of Biology; University of Konstanz; Universitätsstrasse 10, 78457 Konstanz Germany
| | - Pierre-Olivier Montiglio
- Department of Biology & Redpath Museum; McGill University; 1205 Dr Penfield Avenue, Montreal, Quebec H3A 1B1 Canada
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; 82319 Seewiesen Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; 82319 Seewiesen Germany
| | - Damien R. Farine
- Department of Collective Behaviour, Max Planck Institute for Ornithology; Universitätsstrasse 10; 78457 Konstanz Germany
- Chair of Biodiversity and Collective Behaviour, Department of Biology; University of Konstanz; Universitätsstrasse 10, 78457 Konstanz Germany
- Edward Grey Institute of Field Ornithology, Department of Zoology; University of Oxford; South Parks Road, Oxford OX1 3PS U.K
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