Multivariate evolution in replicated adaptive radiations: pattern, process and the role of the environment.
Lead Research Organisation:
University of Nottingham
Department Name: Sch of Biology
Abstract
The studies of ecology and evolution are closely related. Ecologists seek to understand the environmental factors that explain the distribution and abundance of species, while evolutionary biologists investigate the process of natural selection and the evolution that results, by examination of adaptation in phenotypes and genotypes. It is curious in these times of environmental change that one of the biggest gaps in our understanding of the natural world falls exactly at the intersection between ecology and evolution: we know less than we should about how the environment shapes the evolution of biodiversity. Although it is generally understood that the environment is the cause of adaptation, the links between them have seldom been explicitly explored. Many ecological studies do not consider how the environmental variation that they measure affects evolution, while many studies of evolution measure selection or adaptation without considering their environmental causes, concentrating instead on the consequences for evolution of what is genetically possible.
Explicit study of the involvement of the environment in evolution has the potential to fuel a paradigm shift in our comprehension of fundamental evolutionary patterns. For example: (i) Divergence. Evolution has resulted in abundant diversity in the natural world, but the extent of this divergence within related groups of organisms is often circumscribed. Are these limits, on the kind of organisms that evolve, a consequence of what is genetically possible, or do they result from similarities in the environments to which the organisms are exposed? (ii) Convergence. Within the greater divergence, organisms have often apparently converged on similar evolutionary solutions, suggesting that evolutionary outcomes are to some extent repeatable. Is the repeated evolution of similar organisms in different places the result of genetic biases or environmental determinants? If the latter, do similar organisms always evolve in similar environments, or can different environments favour the same outcome of organismal form? Vice versa, do similar environmental combinations always result in essentially the same organism, or are there different evolutionary solutions to similar environmental problems? (iii) Novelty. Although similar organisms in different places often converge on repeated evolutionary solutions, evolution also occasionally comes up with solutions that are different from the general pattern, by dint of developing, or having lost, some distinguishing feature or combination of features. Is such evolutionary novelty the result of particularly unusual environments?
Most previous studies of how the environment affects evolution have measured only a single, or small number of aspects of both the organism and the environment, but thorough answers to the questions we pose require a more comprehensive understanding of multiple different aspects of organism and environment, and of how they interact and affect other. Our approach requires the use of recently developed multivariate statistical methods that allow the simultaneous analysis of many organismal traits and many environmental variables.
Adaptive radiation is the differentiation of an ancestral species into divergent new populations or species. The abundance of variation in both environment and biodiversity make adaptive radiations the perfect natural laboratories to address our questions. We will use data from replicated adaptive radiations of three-spined stickleback fish in Scotland, Iceland, western Canada and Alaska in order to answer our questions and achieve a comprehensive understanding of how the environment affects evolution. Three-spined stickleback are originally marine fish that have invaded freshwater throughout the northern hemisphere since the last ice age. Freshwater stickleback can occupy contrasting environments and exhibit great phenotypic variation, providing a perfect system for our study.
Explicit study of the involvement of the environment in evolution has the potential to fuel a paradigm shift in our comprehension of fundamental evolutionary patterns. For example: (i) Divergence. Evolution has resulted in abundant diversity in the natural world, but the extent of this divergence within related groups of organisms is often circumscribed. Are these limits, on the kind of organisms that evolve, a consequence of what is genetically possible, or do they result from similarities in the environments to which the organisms are exposed? (ii) Convergence. Within the greater divergence, organisms have often apparently converged on similar evolutionary solutions, suggesting that evolutionary outcomes are to some extent repeatable. Is the repeated evolution of similar organisms in different places the result of genetic biases or environmental determinants? If the latter, do similar organisms always evolve in similar environments, or can different environments favour the same outcome of organismal form? Vice versa, do similar environmental combinations always result in essentially the same organism, or are there different evolutionary solutions to similar environmental problems? (iii) Novelty. Although similar organisms in different places often converge on repeated evolutionary solutions, evolution also occasionally comes up with solutions that are different from the general pattern, by dint of developing, or having lost, some distinguishing feature or combination of features. Is such evolutionary novelty the result of particularly unusual environments?
Most previous studies of how the environment affects evolution have measured only a single, or small number of aspects of both the organism and the environment, but thorough answers to the questions we pose require a more comprehensive understanding of multiple different aspects of organism and environment, and of how they interact and affect other. Our approach requires the use of recently developed multivariate statistical methods that allow the simultaneous analysis of many organismal traits and many environmental variables.
Adaptive radiation is the differentiation of an ancestral species into divergent new populations or species. The abundance of variation in both environment and biodiversity make adaptive radiations the perfect natural laboratories to address our questions. We will use data from replicated adaptive radiations of three-spined stickleback fish in Scotland, Iceland, western Canada and Alaska in order to answer our questions and achieve a comprehensive understanding of how the environment affects evolution. Three-spined stickleback are originally marine fish that have invaded freshwater throughout the northern hemisphere since the last ice age. Freshwater stickleback can occupy contrasting environments and exhibit great phenotypic variation, providing a perfect system for our study.
Planned Impact
The current proposal is for responsive mode, 'blue skies' research. Its principal benefit is 'simply' a better understanding of how the world around us works. We should never underestimate the value of this knowledge in its own right. We envisage the following impacts:
(1) The project will lead to improved excellence in UK research by supporting the NERC mission of promoting high quality basic research in freshwater systems, and by addressing fundamental but empirically unexplored questions about the role of the environment in generating biodiversity at the intra-species level.
(2) Funding will give a PDRA the opportunity to codirect a major international collaborative project, while gaining skills in fieldwork, environmental analysis, geometric morphometrics and quantitative and molecular genetics. The technician employed on the grant will gain skills in fieldwork, fish husbandry, phenotypic analysis techniques and molecular genetics. Funding would also support the career of Alan Crampton, widening his experience and strengthening the development of facilities for stickleback research in Nottingham. Biological material and data collected during the project will be used as the basis for Masters and Honours project theses for years to come.
(3) Part of the project will be carried out in the Western Isles, where ADCM has been engaged in research for five years, and where there is already interest in our research within the community, as a result of contributions that ADCM has made to websites, by giving talks to the local natural history society and donating posters about our research to the local museum and arts centre. We will seek to strengthen these links by: (a) organising a workshop with local conservation bodies (e.g. RSPB, Scottish Natural Heritage, Comann na Mara) and landowners to (i) highlight the astonishing local variation in freshwater and brackish environments, which result in waterbodies on the Hebrides supporting what is certainly one of the best examples of adaptive radiation among temperate freshwater fishes. (ii) Discuss our research and identify how it might contribute to conservation policy and land management e.g. by helping to identify evolutionary significant units. (b) Developing activities that promote our engagement with the local general public such as (i) Website: We will make contributions to the website of a local conservation organisation, Comman na Mara that seeks to promote interest in the importance of local aquatic habitats. We will also enhance our existing group web pages to include more details about our research project and the wider background of adaptive radiation and three-spined sticklebacks. (ii) Posters: We will supplement existing posters that we have supplied for display in the local community centre with others about adaptive radiation and environmental change. (iii) Educational workshops: We will undertake to organise workshops with schoolchldren in the local primary and secondary schools, to be run by the PDRA. These will include similar content to those outlined in 3a (i), but delivered in appropriate ways for schoolchildren.
(4) ADCM has a history of engagement with public interest groups in the Sheffield and Nottingham areas. He has visited local primary schools to give slide shows and given seminars about his research to night school classes. For this project he will undertake to deliver talks to Cafe Scientifique meetings in Nottingham and Sheffield. The PDRA will be encouraged to engage with the public in similar ways. The School of Biology at the University of Nottingham is home for two very active schools outreach programmes (Public Understanding of Science Project and the Open Air Laboratories (OPAL) network), which offer training in outreach. The PDRA will be encouraged to take part in these.
(1) The project will lead to improved excellence in UK research by supporting the NERC mission of promoting high quality basic research in freshwater systems, and by addressing fundamental but empirically unexplored questions about the role of the environment in generating biodiversity at the intra-species level.
(2) Funding will give a PDRA the opportunity to codirect a major international collaborative project, while gaining skills in fieldwork, environmental analysis, geometric morphometrics and quantitative and molecular genetics. The technician employed on the grant will gain skills in fieldwork, fish husbandry, phenotypic analysis techniques and molecular genetics. Funding would also support the career of Alan Crampton, widening his experience and strengthening the development of facilities for stickleback research in Nottingham. Biological material and data collected during the project will be used as the basis for Masters and Honours project theses for years to come.
(3) Part of the project will be carried out in the Western Isles, where ADCM has been engaged in research for five years, and where there is already interest in our research within the community, as a result of contributions that ADCM has made to websites, by giving talks to the local natural history society and donating posters about our research to the local museum and arts centre. We will seek to strengthen these links by: (a) organising a workshop with local conservation bodies (e.g. RSPB, Scottish Natural Heritage, Comann na Mara) and landowners to (i) highlight the astonishing local variation in freshwater and brackish environments, which result in waterbodies on the Hebrides supporting what is certainly one of the best examples of adaptive radiation among temperate freshwater fishes. (ii) Discuss our research and identify how it might contribute to conservation policy and land management e.g. by helping to identify evolutionary significant units. (b) Developing activities that promote our engagement with the local general public such as (i) Website: We will make contributions to the website of a local conservation organisation, Comman na Mara that seeks to promote interest in the importance of local aquatic habitats. We will also enhance our existing group web pages to include more details about our research project and the wider background of adaptive radiation and three-spined sticklebacks. (ii) Posters: We will supplement existing posters that we have supplied for display in the local community centre with others about adaptive radiation and environmental change. (iii) Educational workshops: We will undertake to organise workshops with schoolchldren in the local primary and secondary schools, to be run by the PDRA. These will include similar content to those outlined in 3a (i), but delivered in appropriate ways for schoolchildren.
(4) ADCM has a history of engagement with public interest groups in the Sheffield and Nottingham areas. He has visited local primary schools to give slide shows and given seminars about his research to night school classes. For this project he will undertake to deliver talks to Cafe Scientifique meetings in Nottingham and Sheffield. The PDRA will be encouraged to engage with the public in similar ways. The School of Biology at the University of Nottingham is home for two very active schools outreach programmes (Public Understanding of Science Project and the Open Air Laboratories (OPAL) network), which offer training in outreach. The PDRA will be encouraged to take part in these.
Organisations
- University of Nottingham (Lead Research Organisation)
- University of British Columbia (Collaboration, Project Partner)
- State University of New York (Collaboration)
- Holar University College (Collaboration, Project Partner)
- Stony Brook University (Project Partner)
- University of Calgary (Project Partner)
Publications
Dean LL
(2023)
On the Origins of Phenotypic Parallelism in Benthic and Limnetic Stickleback.
in Molecular biology and evolution
Dean LL
(2019)
Admixture between Ancient Lineages, Selection, and the Formation of Sympatric Stickleback Species-Pairs.
in Molecular biology and evolution
Dean LL
(2019)
Internal embryonic development in a non-copulatory, egg-laying teleost, the three-spined stickleback, Gasterosteus aculeatus.
in Scientific reports
Haenel Q
(2019)
Predictable genome-wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fish.
in Evolution letters
MacColl AD
(2014)
Inappropriate analysis does not reveal the ecological causes of evolution of stickleback armour: a critique of Spence et al. 2013.
in Ecology and evolution
MacColl AD
(2013)
The evolutionary ecology of dwarfism in three-spined sticklebacks.
in The Journal of animal ecology
Magalhaes I
(2019)
Intercontinental genomic parallelism in multiple adaptive radiations
Magalhaes IS
(2021)
Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations.
in Nature ecology & evolution
Magalhaes IS
(2016)
The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland.
in Molecular ecology
Singkam AR
(2018)
Otolith development in wild populations of stickleback: Jones & Hynes method does not apply to most populations.
in Journal of fish biology
| Description | For the first time, we have documented patterns of phenotypic evolution and underlying population genetic patterns across multiple, widely spaced adaptive radiations of a vertebrate animal, in response to environmental variation. Our data demonstrate that genes associated with phenotypic and environmental variation are shared between radiations significantly more than expected by chance, demonstrating on an unprecedented scale the phenomenon of evolutionary parallelism that has been widely debated in evolutionary biology and other areas of science. |
| Exploitation Route | Our findings contribute to a growing understanding of the mechanisms by which biodiversity is generated and will inform the work of a wide community of evolutionary biologists and ecologists. |
| Sectors | Education Environment Culture Heritage Museums and Collections |
| Description | Genomic responses to rapid environmental change: selection, plasticity and adaptation. |
| Amount | £579,369 (GBP) |
| Funding ID | NE/R00935X/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 10/2022 |
| Description | Migratory behaviour and the persistence of ecotypes |
| Amount | £994,876 (GBP) |
| Funding ID | NE/Z504105/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2025 |
| End | 03/2028 |
| Title | Data from: A genetics-based approach confirms immune associations with life history across multiple populations of an aquatic vertebrate (Gasterosteus aculeatus) |
| Description | Understanding how wild immune variation covaries with other traits can reveal how costs and trade-offs shape immune evolution in the wild. Divergent life history strategies may increase or alleviate immune costs, helping shape immune variation in a consistent, testable way. Contrasting hypotheses suggest that shorter life histories may alleviate costs by offsetting them against increased mortality; or increase the effect of costs if immune responses are traded off against development or reproduction. We investigated the evolutionary relationship between life history and immune responses within an island radiation of three-spined stickleback, with discrete populations of varying life histories and parasitism. We sampled two short-lived, two long-lived and an anadromous population using qPCR to quantify current immune profile and RAD-seq data to study the distribution of immune variants within our assay genes and across the genome. Short-lived populations exhibited significantly increased expression of all assay genes, which was accompanied by a strong association with population-level variation in local alleles and divergence in a gene that may be involved in complement pathways. In addition, divergence around the eda gene in anadromous fish is likely associated with increased inflammation. A wider analysis of 15 populations across the island revealed that immune genes across the genome show evidence of having diverged alongside life history strategies. Parasitism and reproductive investment were also important sources of variation for expression, highlighting the caution required when assaying immune responses in the wild. These results provide strong, gene-based support for current hypotheses linking life history and immune variation across multiple populations of a vertebrate model. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.d9065 |
| Title | Data from: Predictable genome-wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fish |
| Description | Genomic studies of parallel (or convergent) evolution often compare multiple populations diverged into two ecologically different habitats to search for loci repeatedly involved in adaptation. Because the shared ancestor of these populations is generally unavailable, the source of the alleles at adaptation loci, and the direction in which their frequencies were shifted during evolution, remain elusive. To shed light on these issues, we here use multiple populations of stickleback fish adapted to two different types of derived freshwater habitats - basic and acidic lakes on the island of North Uist, Outer Hebrides, Scotland - and the present-day proxy of their marine ancestor. In a first step, we combine genome-wide pooled sequencing and targeted individual-level sequencing to demonstrate that ecological and phenotypic parallelism in basic-acidic divergence is reflected by genomic parallelism in dozens of genome regions. Exploiting data from the ancestor, we next show that the acidic populations, residing in ecologically more extreme derived habitats, have adapted by accumulating alleles rare in the ancestor, whereas the basic populations have retained alleles common in the ancestor. Genomic responses to selection are thus predictable from the ecological difference of each derived habitat type from the ancestral one. This asymmetric sorting of standing genetic variation at loci important to basic-acidic divergence has further resulted in more numerous selective sweeps in the acidic populations. Finally, our data suggest that the maintenance of standing variation important to adaptive basic-acidic differentiation in marine fish does not require extensive hybridization between the marine and freshwater populations. Overall, our study reveals striking genome-wide determinism in both the loci involved in parallel divergence, and in the direction in which alleles at these loci have been selected. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.4ck2q0m |
| Title | Data from: The ecology of an adaptive radiation of three-spined stickleback from North Uist, Scotland |
| Description | There has been a large focus on the genetics of traits involved in adaptation, but knowledge of the environmental variables leading to adaptive changes is surprisingly poor. Combined use of environmental data with morphological and genomic data should allow us to understand the extent to which patterns of phenotypic and genetic diversity within a species can be explained by the structure of the environment. Here, we analyse the variation of populations of three-spined stickleback from 27 freshwater lakes on North Uist, Scotland, that vary greatly in their environment, to understand how environmental and genetic constraints contribute to phenotypic divergence. We collected 35 individuals per population and 30 abiotic and biotic environmental parameters to characterize variation across lakes and analyse phenotype-environment associations. Additionally, we used RAD sequencing to estimate the genetic relationships among a subset of these populations. We found a large amount of phenotypic variation among populations, most prominently in armour and spine traits. Despite large variation in the abiotic environment, namely in ion composition, depth and dissolved organic Carbon, more phenotypic variation was explained by the biotic variables (presence of predators and density of predator and competitors), than by associated abiotic variables. Genetic structure among populations was partly geographic, with closer populations being more similar. Altogether, our results suggest that differences in body shape among stickleback populations are the result of both canalized genetic and plastic responses to environmental factors, which shape fish morphology in a predictable direction regardless of their genetic starting point. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.rb5s1 |
| Description | Alaska 2015 |
| Organisation | State University of New York |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Contribution of personnel and funding to carry out fieldwork |
| Collaborator Contribution | Support for execution of fieldwork, academic discussions, application for follow-up funding |
| Impact | Successful completion of fieldwork |
| Start Year | 2012 |
| Description | BC 2015 |
| Organisation | University of British Columbia |
| Department | Department of Zoology |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | Contribution of personnel and funding to carry out fieldwork |
| Collaborator Contribution | Support for execution of fieldwork, academic discussions, application for follow-up funding |
| Impact | Successful completion of fieldwork |
| Description | Iceland 2014 |
| Organisation | Holar University College |
| Country | Iceland |
| Sector | Academic/University |
| PI Contribution | Contribution of personnel and funding to carry out fieldwork |
| Collaborator Contribution | Support for execution of fieldwork, academic discussions, application for follow-up funding |
| Impact | Successful completion of fieldwork |
| Start Year | 2013 |
| Description | Crafoord prize giving symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited presentation to the prize-giving symposium for the Crafoord Prize 2023, at the Swedish Royal Academy of Sciences, Stockholm, made to Professor Dolph Schluter by HRH The King of Sweden |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.youtube.com/watch?v=15RqoTNXgfs |
| Description | Public talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Talk led to questions, discussion and increased awareness about our research Improved contact with local community, which aids execution of research |
| Year(s) Of Engagement Activity | 2013 |
| Description | Quekett Microscopical Club |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Presentation about stickleback under the microscope to members of an amateur scientific club |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.facebook.com/events/1013631619924047/?_rdr |
| Description | School visit (Inverness) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | Talk to secondary school children about ecology, evolution and careers in science |
| Year(s) Of Engagement Activity | 2019 |
