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Branch CL, Jahner JP, Kozlovsky DY, Parchman TL, Pravosudov VV. Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees ( Poecile gambeli). ROYAL SOCIETY OPEN SCIENCE 2017; 4:170057. [PMID: 28405402 PMCID: PMC5383859 DOI: 10.1098/rsos.170057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/16/2017] [Indexed: 06/07/2023]
Abstract
Montane habitats are characterized by predictably rapid heterogeneity along elevational gradients and are useful for investigating the consequences of environmental heterogeneity for local adaptation and population genetic structure. Food-caching mountain chickadees inhabit a continuous elevation gradient in the Sierra Nevada, and birds living at harsher, high elevations have better spatial memory ability and exhibit differences in male song structure and female mate preference compared to birds inhabiting milder, low elevations. While high elevation birds breed, on average, two weeks later than low elevation birds, the extent of gene flow between elevations is unknown. Despite phenotypic variation and indirect evidence for local adaptation, population genetic analyses based on 18 073 single nucleotide polymorphisms across three transects of high and low elevation populations provided no evidence for genetic differentiation. Analyses based on individual genotypes revealed no patterns of clustering, pairwise estimates of genetic differentiation (FST, Nei's D) were very low, and AMOVA revealed no evidence for genetic variation structured by transect or by low and high elevation sites within transects. In addition, we found no consistent evidence for strong parallel allele frequency divergence between low and high elevation sites within the three transects. Large elevation-related phenotypic variation may be maintained by strong selection despite gene flow and future work should focus on the mechanisms underlying such variation.
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202
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Vendrami DLJ, Telesca L, Weigand H, Weiss M, Fawcett K, Lehman K, Clark MS, Leese F, McMinn C, Moore H, Hoffman JI. RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160548. [PMID: 28386419 PMCID: PMC5367306 DOI: 10.1098/rsos.160548] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/04/2017] [Indexed: 05/07/2023]
Abstract
The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations.
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Affiliation(s)
- David L. J. Vendrami
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
| | - Luca Telesca
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, Cambridgeshire, CB2 3EQ, UK
| | - Hannah Weigand
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Universitaetsstrasse 5, 45141 Essen, Germany
| | - Martina Weiss
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Universitaetsstrasse 5, 45141 Essen, Germany
| | - Katie Fawcett
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
| | - Katrin Lehman
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
| | - M. S. Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Florian Leese
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Universitaetsstrasse 5, 45141 Essen, Germany
| | - Carrie McMinn
- Agri-Food and Biosciences Institute, Fisheries and Aquatic Ecosystems, 18a Newforge Lane, Belfast BT9 5PX, UK
| | - Heather Moore
- Agri-Food and Biosciences Institute, Fisheries and Aquatic Ecosystems, 18a Newforge Lane, Belfast BT9 5PX, UK
| | - Joseph I. Hoffman
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
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203
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Vendrami DLJ, Telesca L, Weigand H, Weiss M, Fawcett K, Lehman K, Clark MS, Leese F, McMinn C, Moore H, Hoffman JI. RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160548. [PMID: 28386419 DOI: 10.5061/dryad.mk860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/04/2017] [Indexed: 05/23/2023]
Abstract
The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations.
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Affiliation(s)
- David L J Vendrami
- Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany
| | - Luca Telesca
- Department of Earth Sciences , University of Cambridge , Downing Street, Cambridge, Cambridgeshire, CB2 3EQ , UK
| | - Hannah Weigand
- Faculty of Biology, Aquatic Ecosystem Research , University of Duisburg-Essen , Universitaetsstrasse 5, 45141 Essen , Germany
| | - Martina Weiss
- Faculty of Biology, Aquatic Ecosystem Research , University of Duisburg-Essen , Universitaetsstrasse 5, 45141 Essen , Germany
| | - Katie Fawcett
- Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany
| | - Katrin Lehman
- Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany
| | - M S Clark
- British Antarctic Survey , Natural Environment Research Council , High Cross, Madingley Road, Cambridge CB3 0ET , UK
| | - Florian Leese
- Faculty of Biology, Aquatic Ecosystem Research , University of Duisburg-Essen , Universitaetsstrasse 5, 45141 Essen , Germany
| | - Carrie McMinn
- Agri-Food and Biosciences Institute , Fisheries and Aquatic Ecosystems , 18a Newforge Lane, Belfast BT9 5PX , UK
| | - Heather Moore
- Agri-Food and Biosciences Institute , Fisheries and Aquatic Ecosystems , 18a Newforge Lane, Belfast BT9 5PX , UK
| | - Joseph I Hoffman
- Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany
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204
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Gilbert KJ, Whitlock MC. The genetics of adaptation to discrete heterogeneous environments: frequent mutation or large-effect alleles can allow range expansion. J Evol Biol 2017; 30:591-602. [PMID: 27992089 DOI: 10.1111/jeb.13029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/17/2016] [Accepted: 12/05/2016] [Indexed: 01/01/2023]
Abstract
Range expansions are complex evolutionary and ecological processes. From an evolutionary standpoint, a populations' adaptive capacity can determine the success or failure of expansion. Using individual-based simulations, we model range expansion over a two-dimensional, approximately continuous landscape. We investigate the ability of populations to adapt across patchy environmental gradients and examine how the effect sizes of mutations influence the ability to adapt to novel environments during range expansion. We find that genetic architecture and landscape patchiness both have the ability to change the outcome of adaptation and expansion over the landscape. Adaptation to new environments succeeds via many mutations of small effect or few of large effect, but not via the intermediate between these cases. Higher genetic variance contributes to increased ability to adapt, but an alternative route of successful adaptation can proceed from low genetic variance scenarios with alleles of sufficiently large effect. Steeper environmental gradients can prevent adaptation and range expansion on both linear and patchy landscapes. When the landscape is partitioned into local patches with sharp changes in phenotypic optimum, the local magnitude of change between subsequent patches in the environment determines the success of adaptation to new patches during expansion.
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Affiliation(s)
- K J Gilbert
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - M C Whitlock
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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205
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206
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Boulding EG, Rivas MJ, González‐Lavín N, Rolán‐Alvarez E, Galindo J. Size selection by a gape-limited predator of a marine snail: Insights into magic traits for speciation. Ecol Evol 2016; 7:674-688. [PMID: 28116062 PMCID: PMC5243190 DOI: 10.1002/ece3.2659] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/24/2016] [Accepted: 11/05/2016] [Indexed: 12/22/2022] Open
Abstract
The intertidal snail Littorina saxatilis has repeatedly evolved two parallel ecotypes assumed to be wave adapted and predatory shore crab adapted, but the magnitude and targets of predator‐driven selection are unknown. In Spain, a small, wave ecotype with a large aperture from the lower shore and a large, thick‐shelled crab ecotype from the upper shore meet in the mid‐shore and show partial size‐assortative mating. We performed complementary field tethering and laboratory predation experiments; the first set compared the survival of two different size‐classes of the crab ecotype while the second compared the same size‐class of the two ecotypes. In the first set, the large size‐class of the crab ecotype survived significantly better than the small size‐class both on the upper shore and in the laboratory. In the second set, the small size‐class of the crab ecotype survived substantially better than that of the wave ecotype both on the upper shore and in the laboratory. Shell‐breaking predation on tethered snails was almost absent within the lower shore. In the laboratory shore crabs (Pachygrapsus marmoratus) with larger claw heights selected most strongly against the small size‐class of the crab ecotype, whereas those with medium claw heights selected most strongly against the thin‐shelled wave ecotype. Sexual maturity occurred at a much larger size in the crab ecotype than in the wave ecotype. Our results showed that selection on the upper shore for rapid attainment of a size refuge from this gape‐limited predator favors large size, thick shells, and late maturity. Model parameterization showed that size‐selective predation restricted to the upper shore resulted in the evolution of the crab ecotype despite gene flow from the wave ecotype snails living on the lower shore. These results on gape‐limited predation and previous ones showing size‐assortative mating between ecotypes suggest that size may represent a magic trait for the thick‐shelled ecotype.
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Affiliation(s)
- Elizabeth G. Boulding
- Integrative BiologyUniversity of GuelphGuelphONCanada
- Departamento de Bioquímica, Genética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- ECIMAT, Estación de Ciencias Mariñas de TorallaUniversidade de VigoVigoSpain
| | - María José Rivas
- Departamento de Bioquímica, Genética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- ECIMAT, Estación de Ciencias Mariñas de TorallaUniversidade de VigoVigoSpain
| | - Nerea González‐Lavín
- Departamento de Bioquímica, Genética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- ECIMAT, Estación de Ciencias Mariñas de TorallaUniversidade de VigoVigoSpain
| | - Emilio Rolán‐Alvarez
- Departamento de Bioquímica, Genética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- ECIMAT, Estación de Ciencias Mariñas de TorallaUniversidade de VigoVigoSpain
| | - Juan Galindo
- Departamento de Bioquímica, Genética e InmunologíaFacultad de BiologíaUniversidade de VigoVigoSpain
- ECIMAT, Estación de Ciencias Mariñas de TorallaUniversidade de VigoVigoSpain
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207
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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208
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Dennenmoser S, Vamosi SM, Nolte AW, Rogers SM. Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq. Mol Ecol 2016; 26:25-42. [DOI: 10.1111/mec.13805] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/29/2016] [Accepted: 08/11/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Stefan Dennenmoser
- Max-Planck Institute for Evolutionary Biology; August Thienemann Strasse 2 24306 Plön Germany
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
| | - Steven M. Vamosi
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
| | - Arne W. Nolte
- Max-Planck Institute for Evolutionary Biology; August Thienemann Strasse 2 24306 Plön Germany
- Institute for Biology; Carl von Ossietzky University Oldenburg; Carl von Ossietzky Str. 9-11 26111 Oldenburg Germany
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary AB Canada T2N 1N4
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209
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Gante HF, Matschiner M, Malmstrøm M, Jakobsen KS, Jentoft S, Salzburger W. Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika. Mol Ecol 2016; 25:6143-6161. [DOI: 10.1111/mec.13767] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/30/2016] [Accepted: 07/11/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Hugo F. Gante
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
| | - Michael Matschiner
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Martin Malmstrøm
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Kjetill S. Jakobsen
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
| | - Sissel Jentoft
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
- Department of Natural Sciences University of Agder 4604 Kristiansand Norway
| | - Walter Salzburger
- Zoological Institute University of Basel Vesalgasse 1 4051 Basel Switzerland
- Department of Biosciences CEES (Centre for Ecological and Evolutionary Synthesis) University of Oslo 0316 Oslo Norway
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210
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Rahn AK, Krassmann J, Tsobanidis K, MacColl ADC, Bakker TCM. Strong neutral genetic differentiation in a host, but not in its parasite. INFECTION GENETICS AND EVOLUTION 2016; 44:261-271. [PMID: 27421211 DOI: 10.1016/j.meegid.2016.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 11/28/2022]
Abstract
The genetic diversity and population structure of a parasite with a complex life cycle generally depends on the dispersal by its most motile host. Given that high gene flow is assumed to hinder local adaptation, this can impose significant constraints on a parasite's potential to adapt to local environmental conditions, intermediate host populations, and ultimately to host-parasite coevolution. Here, we aimed to examine the population genetic basis for local host-parasite interactions between the eye fluke Diplostomum lineage 6, a digenean trematode with a multi-host life cycle (including a snail, a fish, and a bird) and its second intermediate host, the three-spined stickleback Gasterosteus aculeatus L. We developed the first microsatellite primers for D. lineage 6 and used them together with published stickleback markers to analyse host and parasite population structures in 19 freshwater lakes, which differ in their local environmental characteristics regarding water chemistry and Diplostomum abundance. Our analyses suggest that one parasite population successfully infects a range of genetically differentiated stickleback populations. The lack of neutral genetic differentiation in D. lineage 6, which could be attributed to the motility of the parasite's definitive host as well as its life cycle characteristics, makes local host-parasite co-adaptations seem more likely on a larger geographical scale than among the lakes of our study site. Our study provides a suitable background for future studies in this system and the first microsatellite primers for a widespread fish parasite.
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Affiliation(s)
- Anna K Rahn
- Institute for Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany.
| | - Johannes Krassmann
- Institute for Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany
| | - Kostas Tsobanidis
- Institute for Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany
| | - Andrew D C MacColl
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Theo C M Bakker
- Institute for Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany
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