Building genomic resources for the safeguard and improvement of farmed native tilapia species in East Africa
Lead Research Organisation:
Earlham Institute
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
Fisheries in East Africa (Tanzania, Malawi) are endangered due to stocking of foreign tilapi niloticus). Little is known of the impact of economically important native species due to their inherent potential, little is being done to yield for local industrial fisheries, or to leverage widespread tilapia breeds. There is a pressing need to safeguard the academics in Tanzania, Malawi, Kenya and tilapia species. We will also investigate the i genetic diversity of indigenous species
Planned Impact
unavailable
Organisations
- Earlham Institute (Lead Research Organisation)
- University of Dodoma (Collaboration)
- University College London (Collaboration)
- WorldFish (Collaboration)
- University of Basel (Collaboration)
- University of York (Collaboration)
- BANGOR UNIVERSITY (Collaboration)
- South Eastern Kenya University (Collaboration)
- University of Hull (Collaboration)
- University of Dar es Salaam (Collaboration)
- Broad Institute (Collaboration)
Publications
Blackwell T
(2020)
Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species
in Molecular Ecology
| Description | We generated draft genome assemblies for 9 Oreochromis species and a sister species (Oreochromis mossambicus, O. shiranus, O. leucostictus, O. urolepis, O. rukwaensis, O. esculentus, O. aureus, O. amphimelas, and Alcolapia grahami). We generated low coverage sequencing for population genetics analyses for 600 individuals from 29 Oreochromis species across Tanzania and East Africa. We successfully demonstrate the use of the low cost genotyping platform in discriminating species and identifying interspecific hybrids. We also characterized the genetic diversity of 192 individuals using a SNP array designed to discriminate Oreochromis species. We successfully demonstrate the use of the low cost genotyping platform in discriminating species and identifying interspecific hybrids. We generated RNA-Seq data for transcriptome annotation of 4 of the Oreochromis species. We collected a total of 1200 pictures of tilapia and curated them for use in developing automated species identification based on image recognition algorithms. We have discovered that exotic tilapia strains have been widely stocked into natural water bodies across Tanzania. In many cases, these seem to be replacing unique native strains of tilapias. In some cases, the exotics have hybridised with the natives, leading to genetic swamping. These hybrids can be hard to identify other than using molecular genetic methods. Where the exotics have replaced the natives, are many of the genes of the native strains still 'hidden' in the genome of the invasive species? Species comparisons identify strong signatures of genetic mixing between species at both the population and individual level. We further report a novel Oreochromis species from the Ruaha basin, previously identified as a population of O. rukwaensis. We have also found that a lot of strains being reared for fish farming (and used to stock natural waters) are not the fast-growing Nile Tilapia that the farmers think, but are actually 'contaminated' with 2 other species that grow to smaller sizes. Also native strains have sometimes gained access to the breeding ponds from inflowing streams, and have hybridised with the exotics, which have then been stocked in completely different parts of the country, which have different native strains. |
| Exploitation Route | The sequencing helped complement a sNP array previously funded by a BBSRC/NERC award. We are able to distinguish pure Tilapia lines. and data can be used by stakeholders academics and fisheries officers and aquaculture centre in Tanzania to improve biosecurity measures. Unique native tilapia strains may hold precious genes for disease resistance or environmental tolerances valuable for future generation of fish farmers. These are being threatened by poor stocking and fish farming practice, which are not even bringing superior strains to local farmers. We have brought this to the attention of government, academic and private sector stakeholders in Tanzania and are helping to develop policies to improve breeding and stocking practices and to conserve remaining native strains. We have brought our results to the attention of government, academic and private sector stakeholders in Tanzania and are helping to develop policies to improve breeding and stocking practices and to conserve remaining native strains. Our methods and results could be used more widely within Africa, where native tilapia strains are still found in the wild. We recently obtained funding from BBSRC for additional development of bioinformatic and genomic tools for tilapia and a charity grant (JRS Biodiuversity Foundation) to further develop the smartphone App, increase stakeholder engagement with data collection and deposit our data in the public domain. The latter project has expanded our geographic coverage to Kenya, in collaboration with the National Museums of Kenya (NMK). |
| Sectors | Agriculture Food and Drink Communities and Social Services/Policy Environment Government Democracy and Justice |
| Description | Our findings have been discussed at a number of meetings in Tanzania and Malawi. The importance of zoned aquaculture and screening of farmed strains has been agreed at a high-level meeting of stakeholders in Tanzania in Zanzibar in September 2016. The Malawi Government obtained funding from the World Bank to undertake a survey of the Lake Malawi catchment (including the Tanzanian sector) to check for establishment of exotic species, reinforcing its commitment to excluding exotic species from its waters. We attended a workshop at the Sokoine University of Agriculture at Morogoro, Tanzania in January 2017 to discuss issues around stocking of exotic species and the use of mixed strains in aquaculture, as well as providing training in strain identification, attended by senior government officials, as well researchers, local fishery officers and private sector representatives. Representatives of a private sector fish farming company organised a follow-up workshop for over 120 fishfarmers in the Mbeya region at which it was resolved to promote the use of native strains in the lake Malawi catchment. The Tanzanian Fisheries Research Institute has instituted a programme of culturing native strains at Kyela, so they can be used to stock cages in the lake. In 2018, we participated in a workshop in Dar Es Salaam, attended by researchers and stakeholders including government officials and fish farmers which resulted in the production of a Policy Document in relation to zoned aquaculture. This was accepted by the Permanent Secretary for the Fisheries Sector at the Ministry of Livestock and Fisheries in an interview with national newspaper. We also continually disseminate our research findings with the general public and fellow scientists through public engagement activities e.g. science festivals and conferences on molecular evolution e.g. SMBE and aquaculture e.g. International Symposium on Genomics in Aquaculture. |
| First Year Of Impact | 2016 |
| Sector | Agriculture, Food and Drink,Communities and Social Services/Policy,Education |
| Impact Types | Societal Economic Policy & public services |
| Description | Ensuring pedigree of aquaculture broodstock |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Identification of commercial and governmental fish hatchery broodstock as mixed (hybrid) stocks rather than pure Nile tilapia (as currently marketed) resulted in: - Raising awareness of issues of biosecurity, importance of correct species identification - Practice change in separating fish farm stocks from local water bodies - Practice change in growing wild-caught stocks to maturity for species ID to ensure pure breeding lines |
| Description | Species selection for fish farming (zonal aquaculture) |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Ongoing engagement around biodiversity preservation led to policy change in the stocking of native rather than exotic species. Working with industry - local company Rofacol who organised a workshop emphasising benefits of farming native species for >120 farmers and stakeholders in Kyela. |
| Description | Zanzibar Declaration |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | International partners on the 'Zanzibar Declaration' as a policy briefing outcome from the AgriFose workshop, and commitment to the establishment of a National Aquaculture Development Centre (NADC) in Tanzania |
| Description | GCRF Impact Acceleration Account |
| Amount | £10,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2016 |
| End | 03/2017 |
| Description | GCRF Impact Acceleration Account (IAA) |
| Amount | £217,594 (GBP) |
| Funding ID | BB/GCRF/IAA-05 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2016 |
| End | 03/2017 |
| Description | Global Challenge Research Fund: Data and Resources |
| Amount | £164,268 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2016 |
| End | 07/2017 |
| Description | Grand Challenges Research Fund (GCRF) Data & Resources (EI) - extension |
| Amount | £160,963 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 07/2018 |
| Description | Open call - Mapping for Conservation of Native Tilapia Resources in East Africa |
| Amount | £12,461 (GBP) |
| Organisation | JRS Biodiversity Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 09/2017 |
| End | 09/2020 |
| Description | Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. |
| Organisation | Bangor University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators. |
| Collaborator Contribution | Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection. |
| Impact | Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published. |
| Start Year | 2017 |
| Description | Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. |
| Organisation | University of Dar es Salaam |
| Country | Tanzania, United Republic of |
| Sector | Academic/University |
| PI Contribution | Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators. |
| Collaborator Contribution | Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection. |
| Impact | Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published. |
| Start Year | 2017 |
| Description | Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. |
| Organisation | University of Dodoma |
| Country | Tanzania, United Republic of |
| Sector | Academic/University |
| PI Contribution | Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators. |
| Collaborator Contribution | Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection. |
| Impact | Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published. |
| Start Year | 2017 |
| Description | Evolution of cis-regulatory activity associated with rapid phenotypic diversity |
| Organisation | University of Basel |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | To further analyse gene regulatory network evolution associated with traits of cichlid phenotypic diversity, we 1. developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. characterised and compared the tissue-specific activity of regulatory regions in representative species of the great lake radiations. This can then be carried over |
| Collaborator Contribution | Our collaborators include Domino Joyce (University of Hull) and Walter Salzburger (University of Basel) that provided live fish and tissues to isolate cells for ATAC-Seq. |
| Impact | We have: 1. Developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. Carried out a single lane of Hi-Seq sequencing of 20 ATAC and genomic DNA control libraries to test the protocol Since the protocol has been largely optimised, we are now preparing libraries for more tissue samples and species for higher-coverage sequencing. |
| Start Year | 2017 |
| Description | Evolution of cis-regulatory activity associated with rapid phenotypic diversity |
| Organisation | University of Hull |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | To further analyse gene regulatory network evolution associated with traits of cichlid phenotypic diversity, we 1. developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. characterised and compared the tissue-specific activity of regulatory regions in representative species of the great lake radiations. This can then be carried over |
| Collaborator Contribution | Our collaborators include Domino Joyce (University of Hull) and Walter Salzburger (University of Basel) that provided live fish and tissues to isolate cells for ATAC-Seq. |
| Impact | We have: 1. Developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. Carried out a single lane of Hi-Seq sequencing of 20 ATAC and genomic DNA control libraries to test the protocol Since the protocol has been largely optimised, we are now preparing libraries for more tissue samples and species for higher-coverage sequencing. |
| Start Year | 2017 |
| Description | Genetic basis of adaptation to extreme environments: insights from the genome of Alcolapia grahami |
| Organisation | University College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Sequencing of A. grahami genome with short and long read technology and transcriptome sequencing |
| Collaborator Contribution | Our collaborators Julia Day and Kanchon Dasmahapatra are able to source live Alcolapia and preserved fish samples for sequencing. As such we have used O. amphimelas for whole genome and transcriptome sequencing. |
| Impact | O. amphimelas DNA/RNA is currently being extracted for genome and transcriptome sequencing. For the purpose of this collaboration, we are also improving the Alcolapia genome assembly for chromosome level contiguity. Our collaborators are interested in carrying out functional testing of interesting candidate genes in Alcolapia that may be important in their adaptations. Julia Day and Lewis White recently travelled to Tanzania, bringing back live Alcolapia to the UK to set up experimental stocks for functional testing. As such, Lewis White has succcesfully carried out gene knock-outs and rescue in Alcolapia that will be useful for future functional validations. |
| Start Year | 2017 |
| Description | Genetic basis of adaptation to extreme environments: insights from the genome of Alcolapia grahami |
| Organisation | University of York |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Sequencing of A. grahami genome with short and long read technology and transcriptome sequencing |
| Collaborator Contribution | Our collaborators Julia Day and Kanchon Dasmahapatra are able to source live Alcolapia and preserved fish samples for sequencing. As such we have used O. amphimelas for whole genome and transcriptome sequencing. |
| Impact | O. amphimelas DNA/RNA is currently being extracted for genome and transcriptome sequencing. For the purpose of this collaboration, we are also improving the Alcolapia genome assembly for chromosome level contiguity. Our collaborators are interested in carrying out functional testing of interesting candidate genes in Alcolapia that may be important in their adaptations. Julia Day and Lewis White recently travelled to Tanzania, bringing back live Alcolapia to the UK to set up experimental stocks for functional testing. As such, Lewis White has succcesfully carried out gene knock-outs and rescue in Alcolapia that will be useful for future functional validations. |
| Start Year | 2017 |
| Description | Genetic basis of adaptation to extreme environments: insights from the genome of the soda tilapia (Alcolapia grahami) |
| Organisation | South Eastern Kenya University |
| Country | Kenya |
| Sector | Academic/University |
| PI Contribution | Full expenses for Geraldine Kavembe (SEKU) to sample Alcolapia tissue samples from Lake Magadi, Kenya. This included sampling equipment/reagents, travel, accomodation and subsistance. |
| Collaborator Contribution | Dr Geraldine Kavembe (SEKU) contributed in the: 1. Organisation and permits for sampling in Lake Magadi by dealing with the appropriate fisherie officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection 5. Sample shipping |
| Impact | Tissue samples from A. grahami have been sequenced to include: 1. Whole genome sequencing using short Illumina and Nanopore reads (10x Chromium pending). We currently have a whole genome assembly based on the short reads that is currently being supplemented with the long read data. 2. RNA-Seq of gill and liver for genome annotation and gene expression analyses. Both will be published. Also, Tarang Mehta hosted a year in industry student (Nicole Forrester) at the Earlham Institute where she extracted RNA, prepared cDNA libraries and sequenced the trnascriptomes of Alcolapia and other tilapia tissue samples. |
| Start Year | 2017 |
| Description | Tanzania Fieldwork - Lake Rukwa |
| Organisation | University of Dar es Salaam |
| Country | Tanzania, United Republic of |
| Sector | Academic/University |
| PI Contribution | Support and funding to carry out fieldwork in the south of Tanzania, Lake Rukwa where two species of tilapia are of economic and food sustainability interest. Genetic anaylses of such samples can have wider benefits to discover traits of interest for aquaculture (fish-farming) practices. This also include training for local fisheries officers in best practices for certain fish-farming techniques. |
| Collaborator Contribution | Two collaborators (Levinus Leonard and Edaward Moto) contibuted to the organisation of the field trip, liaising with the fisheries officers and sample/reagent aquirement as per required for the fieldwork. Their expertise and knoweldge of the area was pivotal for successful acquisition of samples. Also, Alexandra Tyers (uni of Bangor) accompanied for sample dissection techniques and held a valid export licence to ship samples to the UK for research purposes. |
| Impact | Research samples acquired from this fieldwork have been sequenced and are currently being analysed with other data sets; research impacts will include publications, oral/poster presentation at conferences, press releases and public engagement activities via workshops/media. |
| Start Year | 2016 |
| Description | Tanzania Fieldwork - Lake Rukwa |
| Organisation | University of Dodoma |
| Country | Tanzania, United Republic of |
| Sector | Academic/University |
| PI Contribution | Support and funding to carry out fieldwork in the south of Tanzania, Lake Rukwa where two species of tilapia are of economic and food sustainability interest. Genetic anaylses of such samples can have wider benefits to discover traits of interest for aquaculture (fish-farming) practices. This also include training for local fisheries officers in best practices for certain fish-farming techniques. |
| Collaborator Contribution | Two collaborators (Levinus Leonard and Edaward Moto) contibuted to the organisation of the field trip, liaising with the fisheries officers and sample/reagent aquirement as per required for the fieldwork. Their expertise and knoweldge of the area was pivotal for successful acquisition of samples. Also, Alexandra Tyers (uni of Bangor) accompanied for sample dissection techniques and held a valid export licence to ship samples to the UK for research purposes. |
| Impact | Research samples acquired from this fieldwork have been sequenced and are currently being analysed with other data sets; research impacts will include publications, oral/poster presentation at conferences, press releases and public engagement activities via workshops/media. |
| Start Year | 2016 |
| Description | The 200 mammals project: sequencing genomes by a novel cost-effective method, yielding a high resolution annotation of the human genome. |
| Organisation | Broad Institute |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | Part of the consortium which is analysing the data. |
| Collaborator Contribution | Proposal submitted to NHGRI and funded |
| Impact | In combination with the ~50 already existing high quality placental mammalian assemblies, the project produced the sequence of one placental mammal per family for a total of 150 species. The new assembly method: DISCOVAR de novo, was used to allow the production of a good quality novel genome assembly using only a single sequencing library type. |
| Start Year | 2016 |
| Description | Tilapia for sustainable fish production while maintaining Biodiversity |
| Organisation | Worldfish |
| Country | Malaysia |
| Sector | Charity/Non Profit |
| PI Contribution | F. Di Palma is a research partner in the new CGIAR research program on fish agri-food systems. |
| Collaborator Contribution | J. Benzie from WorldFish is a research partner on Earlham BBSRC Core Strategic programme "Genomics for Food Security" for the Natural diversity and adaptation in aquaculture research activities. |
| Impact | Partnership yielded activities in Core strategic programmes and training workshops and further partnerships.I t is multidisciplinary including genomics, informatics, breeding expertise, Fisheries officers from tanzania, Ministry of aquaculture and Life stocks in Tanzania, further academic institutions in Tanzania Uk and Sweden, ecology, and environmental policy as well as disease resistance. |
| Start Year | 2016 |
| Description | Agriculture for Food Security (AgriFose) STAKEHOLDERS WORKSHOP ON TILAPIA AQUACULTURE IN TANZANIA |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Workshop to look at: Genetic improvement in aquaculture and its impact around the world by WorldFish; Aquaculture development in Africa: the case of Malawi by WorldFish (Malawi); Tilapia and its endemism in Africa: challenges and opportunities; Experiences of small scale fish farmers in Tanzania: case studies by TAFIRI; Aquaculture Policy in Tanzania by Director of Aquaculture Tanzania; Aquaculture research and technology transfer; Potential species/strains for breeding program in Tanzania; Aquaculture entrepreneur-researcher interaction in Tanzania: challenges and opportunities by SUA; The status of aquaculture breeding programs in Africa and lessons from Malaysia by UDSM; Tilapia aquaculture development strategy in Tanzania and possible collaborations (Remarks on way forward from TAFIRI, UDSM, SUA, Bangor, Earlham, SLU, WorldFish, Aquaculture Department -MALF) |
| Year(s) Of Engagement Activity | 2016 |
| Description | Conference Poster - Aquaculture Europe |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Poster on Evolution of tissue-specific modular regulatory networks in tilapia and East African cichlids - enabled engagement with fellow researchers in aquaculture as well as advancement of associated technologies. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Conference poster: Examining genetic diversity and traits under selection in several aquaculture-relevant tilapia species |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Poster presentation on work on examining genetic diversity and traits under selection in several aquaculture-relevant tilapia species at Genome Science conference, Nottingham, UK. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Genomic characterisation of wild tilapia populations |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The presentation took place as part of a workshop organised in Bogota (Colombia) between UK and Colombia scientific Institutions. The audience was composed of UK and Colombia university lecturers, Colombian industry partners. The presentation helped raising the international profile of Wilfried Haerty, Federica Di Palma and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Host Year in Industry Project |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | Tarang hosted a Year in Industry student who selected his project on the 'Genetic basis of adaptation to extreme environments: insights from the genome of soda tilapia (Alcolapia grahami)'. This project offered a great opportunity for an undergraduate student, Nicole Forrester, to learn about cutting edge wet- and dry- lab techniques associated with the study of an important model system for evolution, genetic diversity and aquaculture practices. Nicole found the whole experience very insightful and thoroughly enjoyed it, as such, she selected a simialr themed project for her PhD Thesis. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Hosting and Training of PhD students from Tanzania |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | We hosted three PhD students at Earlham Institute for up to one month - the visit helped to develop their understanding and technical ability in several key genomic areas; this includes DNA/RNA extraction protocols, library preparation protocols, sequencing technologies and subsequent bioinformatics data analysis techniques. All of this was beneficial for developing current and future aquaculture projects. Also, by undertaking a course on Population Variation Genetics hosted at Earlham Institute in May, the students felt better prepared to carry out RAD data analysis (as part of their PhD) as well as other associated techniques, like phylogenetic analysis. Details: Names: Levinus Leonard Christer Nyinondi Redempta Kajungiro Institutions: University of Dar Es Salaam and University of Dodoma, Tanzania Dates: Levinus - 27/04/2017 to 28/05/2017 Christer and Redempta - 20/05/2017 to 28/05/2017 |
| Year(s) Of Engagement Activity | 2017 |
| Description | Inside EI 2019: Preserving Tilapia biodiversity (poster) |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Around 100 people attended the 'Inside EI' open day; there were several talks and informal discussions on our work at poster sessions. As a result, there was increased interest in several of the research areas, including our work on fish. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/open-day-2019#Programme-7 |
| Description | Internal Seminar on 'Evolution of regulatory networks associated with traits of cichlid phenotypic diversity' |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Earlham Institute Internal Seminar (also open to NBI colleagues) on the 'Evolution of regulatory networks associated with traits of cichlid phenotypic diversity'. There was a round of questions and discussion afterwards. |
| Year(s) Of Engagement Activity | 2020 |
| Description | International Conference Poster Presentation: Evolution of tissue-specific regulatory programs in cichlids. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the Cold Spring Harbour Biology of Genomes conference was selected on abstract submission. The poster was presented in front of university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Tarang Metha, Luca Penso Dolfin, Tomasz Wrzesinski, Will Nash, Padhmanand Sudhakar, Wilfried Haerty, Tamas Korcsmaros, Federica Di Palma and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invasive species threat to native tilapia biodiversity |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Invasive species threat to native tilapia biodiversity |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/newsroom/invasive-species-threat-newly-discovered-native-tilapia-biodivers... |
| Description | Morogoro workshop on Tilapia Aquaculture |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Workshop looking at opportunities and challenges in Tanzanian tilapia fisheries and aquaculture programme. Programme included: Biodiversity, endemism, and importance/potential of native species to fisheries and aquaculture; Aquaculture initiatives in Tanzania, impact of non-native species stocked in natural water bodies on native species; Tanzanian tilapia species identification and sample collection; The TilapiaMap project and use of smartphone application; Group discussions and feedback on training needs and provision in Tanzania; Tour of facilities at Sokoine University, description of on-going aquaculture projects. |
| Year(s) Of Engagement Activity | 2017 |
| Description | New bioinformatics tool spots hybrid fish that threaten the survival of natural tilapia populations in aquaculture |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News letter describing the development of a cost effective genotyping platform enabling tilapia species discrimination and species identification |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/newsroom/new-bioinformatics-tool-spots-hybrid-fish-threaten-survival-natur... |
| Description | Opportunities and challenges in Tanzanian tilapia fisheries and aquaculture programme |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Workshop 1: Biodiversity, species identification, and stocking of non-native tilapiines, Sokoine University of Agriculture, Morogoro, Tanzania, 16-17 Jan 2017. This workshop raised awareness of potential threats to native Tanzanian Tilapia species by breeding and stocking non-native species in Tanzanian water bodies. We included practical training in the identification of tilapia species, both in the field and from captive breeding facilities, through introduction of the new smartphone app 'TilapiaMap', and featured research seminars addressing issues of hybridisation, and the problems that mixed stocks may present to aquaculture. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Oral Presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation as part of the annual PopGroup meeting |
| Year(s) Of Engagement Activity | 2021 |
| Description | Oral Presentation - Norwich Science Festival |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Around 40 people attended a talk given on "Food for thought" - understanding biodiversity and it's impact on life and health; this sparked extensive questions and discussion afterwards. As a result, the event reported great interest in the area of biodiversity, fish biology and aquaculture (fish-farming). |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://norwichsciencefestival.co.uk/events/food-for-thought/ |
| Description | Oral presentation - Non-human genomes, why bother? |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Oral presentation at the EI Open Day |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - Whole genome sequencing of tilapia species and improved strains WorldFish |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation at the WorldFish Genetic Improvement Program (GIP) Meeting, Edinburgh UK |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation as part of the Biodiversity Genomics Conference |
| Year(s) Of Engagement Activity | 2020 |
| Description | Poster presentation - Evolution of gene regulatory networks controlling traits under natural selection in cichlids |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the volutionary Systems Biology Conference, Wellcome Trust Sanger Centre. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster presentation - Examining genetic diversity and traits under selection in several aquaculture-relevant tilapia species |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Genome Science Conference, Nottingham, UK . The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster presentation - Gene regulatory network evolution in East African lake cichlids |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Evolution 2018 conference, Montpellier. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster presentation - Networks to catch the difference: Construction and analysis of Regulatory Networks applied to East African Lake Cichlids |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Evolutionary Systems Biology conference, Wellcome Trust Sanger Centre. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster presentation - Characterisation of structural variants in the adaptive radiation of East African Lake cichlids |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the SMBE Annual Meeting 2019, Manchester, UK 21-25 July 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the SMBE Annual Meeting 2019, Manchester, UK 21-25 July 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - Gene regulatory network evolution in East African lake cichlids |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation as part of the PopGroup 52, Oxford. The audience included group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - Genomic introgression in Oreochromis tilapias |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the PopGroup53 , Leicester UK |
| Year(s) Of Engagement Activity | 2020 |
| Description | Presentation - Evolution of regulatory networks controlling adaptive traits in cichlids Network Biology CSHL, NY, USA Mar 19-23 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation at the Network Biology meeting Cold Spring Harbor Laboratory. The audience included group leaders, university lecturers, postdoctoral researchers, graduate students and industry representatives. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation - The role of structural variants in the adaptive radiation of African Cichlids |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentatio at the Genome Informatics 2018 Conference, Hinxton, Cambridge. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation - Genomics applications for conservation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Presentation as part of a training course for the use of genomic resources for species identification delivered to law enforcement officers in Cali, Colombia. The audience included university lecturers, graduate and undergraduate students, conservation organizations, law officers, representatives of the ministry of environment, ministry of justice, |
| Year(s) Of Engagement Activity | 2018 |
| Description | Press Article - Breeding diversity into the future of aquaculture |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press article on breeding diversity into the future of aquaculture featured in the International Aquafeed and Milling & Grain magazines. This article will reach well over 500 people from diverse areas, including policymakers, the general public as well as business/industries. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://issuu.com/international_aquafeed/docs/iaf1801_w1/20 |
| Description | Press Release: Double fish production while preserving biodiversity - can it be done? |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press release on our recent workshop in Tanzania, towards a new resolution to establish National Aquaculture Research and Development Centre (NARDC) in Tanzania could help tackle poverty and undernutrition. This press release was submitted to several media channels/websites, generating far reaching public awareness. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/newsroom/double-fish-production-while-preserving-biodiversity-%E2%80%93-can... |
| Description | Press Release: Double fish production while preserving biodiversity - can it be done? Double fish production while preserving biodiversity - can it be done? |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | The press release aimed to highlight the activities of the Earlham Institute in aquaculture stressing the importance of this industrial sector for food security |
| Year(s) Of Engagement Activity | 2017 |
| Description | Press release: Breeding diversity into the future of aquaculture |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press release on breeding diversity into the future of aquaculture in a popular well-read aquaculture magazine. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://issuu.com/international_aquafeed/docs/iaf1801_w1/20 |
| Description | Scool Visit, Insight into Science Day - Evolution, biodiversity, career development |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | I gave a talk on evolution, biodiversity and career development to three separate groups of 15 A-level pupils (Wymondham College) - this sparked questions and discussion afterwards, and several pupils found this subject area to be the most intersting from all the talks during the day. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Stakeholders Workshop - Tilapia aquaculture in Tanzania and the way forward |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | To develop an aquaculture strategy for Tanzania, 30 scientists representing Tanzanian stakeholders as well as international research organisations met for a three-day workshop in Zanzibar. The main outcome of this workshop was a new collaboration between the Tanzanian government, industry, international scientists and funders that could help double the production of fish in the country by 2025. The National Aquaculture Research and Development Centre (NARDC) aims to improve access to this nutrient-rich resource - especially for women - and to triple the contribution that aquaculture makes to the economy. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Talk at Visegrad Interdisciplinary Signaling workshop, Hungary |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Federica Di Palma gave a talk on "Evolution of tissue-specific regulatory programs in cichlids". In vertebrates, the East African cichlid radiations represent arguably the most dramatic examples of adaptive speciation. In the great lakes Victoria, Malawi and Tanganyika and within the last few million years, one or a few ancestral lineages of haplochromine cichlid fish have given rise to over 1500 species exhibiting an unprecedented diversity of morphological and ecological adaptations. Such explosive phenotypic diversification of East African cichlids is unparalleled among vertebrates and the low protein divergence between species implies the rapid evolution of regulatory regions and networks underlying the traits under selection. Comparative functional genomics, transcriptomics and epigenomics are powerful tools to study the evolution of tissue and species divergence. We recently developed Arboretum, an algorithm to identify modules of co-expressed genes across multiple species in a phylogeny. By integrating inferred modules with nucleotide variation, predicted cis regulatory elements and miRNA profiles from five East African Cichlids, we investigated the evolution of tissue-specific gene regulation. Our analyses identified modules with tissue-specific patterns for which we reconstructed the evolutionary gene regulatory networks across the five cichlids species. We report striking cases of rapid network rewiring for genes known to be involved in traits under natural and/or sexual selection such as the visual systems, and more specifically a cone opsin (sws2a) responsible for colour vison of selected cichlid fishes. Furthermore, in-depth analyses of regulons (transcription factor - target interactions, e.g. Egr3) show similar rapid species-specific rewiring. Investigation of these novel interactions in Astatotilapia burtoni, a model species for behaviour evolution, reveal significant enrichment for genes involved in neuronal and brain function. Our unique integrative approach that interrogates the evolution of regulatory networks allowed us to identify the rapid regulatory changes associated with certain traits under selection in cichlids. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Talk: A kaleidoscope of colours, shapes and sustainable plates: diving into cichlid fish diversity |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Around 30 people from age range 5-60 attended a talk on "A kaleidoscope of colours, shapes and sustainable plates: diving into cichlid fish diversity" at the Norwich Science Festival. This sparked widespread questions and discussion afterwards and reported an all-round interest in the work and research carried out at Earlham Institute. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://norwichsciencefestival.co.uk/events/water-day-gallery-stage/ |
| Description | Web article - Aquaculture and tilapia: a fish that may tip the balance. |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Web article to support the WorldFish Press Release 'Genetics roadmap to develop more resilient farmed fish. -SOCIAL MEDIA - Engagement 30, Impressions 9676 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/aquaculture-and-tilapia-fish-may-tip-balance |
| Description | Web article - why should you care about biodiversity? |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Information piece to support the Colombian project. Interview with Jose De Vega. -SOCIAL MEDIA- Engagement 107, Impressions 100738 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/why-you-should-care-about-biodiversity |
| Description | Workshop in Morogoro, Tanzania |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Description: Opportunities and challenges in Tanzania tilapia fisheries and aquaculture workshop, Sokoine University, Morogoro, Tanzania Date: 20th to 24th January 2017 Involved: Federica Di Palma (EI), Tarang Mehta (EI), Graham Etherington (EI), Wilfried Haerty (EI), Antonia Ford (Roehampton Uni), George Turner and Alix Tyers (Bangor University) Key Outcomes/Impact: Presentation, networking and discussion on biodiversity, species identification and stocking of non-native tilapiines. Also involved the rollout of TilapiaMap, a smartphone application for species identification and mapping. We hope that accurate identification and distribution records of tilapia species will reduce potential detrimental effects of invasive species; http://tilapiamap.bangor.ac.uk |
| Year(s) Of Engagement Activity | 2017 |
| Description | Workshop on Genomic Selection in WorldFish Breeding Programs |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The workshop was held to determine strategy and focus with respect to the introduction of genomic selection to the WorldFish breeding programs, and in particular the development of key to tolls to enable this (specifically discussed to date a SNP chip for marker assay). The agenda included: Discussion of WorldFish breeding programs and their goals; of the best strategy to introduce genomic selection to WorldFish breeding programs; on introduction of genomic selection to WorldFish breeding programs focused on selection of specific targets and of next steps and development of a strategy, including specifically that of SNP chip development including a draft workplan. |
| Year(s) Of Engagement Activity | 2017 |
| Description | World Federation of Science Journalists (WFSJ) workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Workshop objectives: Acquire basic knowledge about food security innovation and what is exportable to LMIC. Sharing experiences amongst participants. Workshop themes included: -How crop technology is transforming agriculture around the world -How farmers from developing countries are challenged by these changes, affecting livelihoods, food security and environment -How researchers can better understand the complex human dynamics in agro-ecosystems and design more equitable and sustainable solutions -What is the essential message you want journalists to remember from your talk? Federica Di Palma was asked to concentrate on: -Meat from livestock is the main source of world protein and also source of GHG. What are the challenges for scientists to provide enough protein from livestock while coping with climate change? -The latest livestock (and fisheries) research innovations that suitable to LMICs -How LMICs can feed themselves? -Do we have enough sources to provide protein for the world? |
| Year(s) Of Engagement Activity | 2017 |