Periodic Reporting for period 1 - GLDAFRICA (GLOBAL BIODIVERSITY LEGUME ASSESSMENTS IN AFRICA: WEST CENTRAL AFRICA AS A CASE STUDY)
Período documentado: 2015-10-15 hasta 2017-10-14
Tropical rain forests are one of the most biologically diverse habitats on the planet. Yet their description and the understanding of their evolutionary history are far from complete. Because of their role as global biodiversity repositories, there is an increasing and pressing need to assess global biodiversity changes in tropical rainforests. West Central Africa represents the area of greatest biodiversity richness in tropical Africa and has the highest percentage of untouched pristine forest in all of Africa and Madagascar. West Central African biodiversity not only faces the challenges linked to climate change, but also human pressure with the highest population growth rates in the world. This project contributes to the ongoing Global Legume Diversity Assessment programme aiming at improving our understanding of biodiversity loss using legumes, the third largest family of angiosperms, as a proxy. The project focusses on subfamily Detarioideae, which are the dominant tree components of West Central African forests, and thus an ideal exemplar clade for the proposed study. The project aimed to produce a phylogenetic framework that will serve as basis for studying the diversification and the evolutionary history of Detarioideae.
Our GLDAFRICA project has lasted two years, from October 2015. We have developed a whole research program with three main objectives outlined in the MSCF proposal:
1) investigate the evolutionary-conservation patterns in West Central Africa
2) enrol the fellow in a training program to become a XXIst century evolutionary researcher
3) boost the fellow’s research publications and profile to increase his future professional options.
Training received:
The fellow had a meeting with his advisor and GLDAFRICA collaborators and we designed a strategy to learn and use effectively a high-throughput sequencing (HTS). He has attended to the following courses:
- Phylogenomics Summer School 2016, Maynooth University.
- Introducción a las Técnicas de Next Generation Sequencing, URJC.
- Seminario de Introducción al uso de la supercomputación aplicado a la Bioinformática, Fundación Centro de Supercomputación de CYL.
- Curso Práctico de Iniciación al uso de la Supercomputación aplicado al Análisis de datos RNA-Seq, Fundación Centro de Supercomputación de CYL.
- Hyb-Seq Workshop, RBG Kew.
- Filogenias y Genealogías de DNA, UB.
- He has also received training to improve his skills in project management, student supervision and grant applications, from the supervisor Felix Forest at the host institution.
Additional funding obtained:
Although our project GLDAFRICA was fully funded by EU, the supervisor encouraged the fellow to apply to other funding sources, both as a training exercise and with the idea that securing additional funding would allow the expansion of the proposed data gathering objectives, i.e. further genera could be sampled. The fellow applied for and was successful in obtaining funds from RGB Kew.
Work performed:
* Taxon sampling. With access to the extensive RBG Kew collections, we obtained leaf samples for DNA extractions. All samples and DNA extracts at RBG Kew follow and comply with the Nagoya Protocol.
* Bait design. We decided to use targeted enrichment as methodology to obtain DNA sequence data for a complete genus-level phylogeny of Detarioideae.
* Laboratory Work. Laboratory work was performed during a 1.5 months period in cooperation with our colleagues from ULB (Belgium).
* Preliminary analyses. Of the 325 samples sequenced, good quality DNA sequences were obtained for 296 samples. This is particularly successful given that a large proportion of the samples used were from herbarium specimens and of less good quality.
* IUCN assessments. The fellow compiled a database with distribution records of Detarioideae in West Central Africa. We have run IUCN assessments for part of those, in particular for the Daniellia clade that has been the subject of a MSc project supervised by the Fellow. We plan to use BIOMOD to model the diversity patterns of Detarioideae in West Central Africa.
Dissemination of results:
During GLDAFRICA one of our objectives was to engage with our colleagues and share our findings. The Fellow participated and gave oral communications at the following venues:
States of the World's Plants Symposium (Kew, 2016)
UK Plant Evolution Meeting (Cambridge, 2016)
European Conference of Tropical Ecology (Brussels, 2017)
XIX International Botanical Congress (Shenzhen, China)
The Fellow also co-organized a symposium on Legume phylogenomics, IBC in Shenzhen (China) in July 2017.
The Fellow also had the opportunity to participate in activities of public engagement at RBG Kew. In particular during the 2016 Kew Science Festival, he was heavily involved in several planned activities during two of the three days of the event.
On publications we have published three papers:
One under the broad Legume Phylogeny Working Group that proposed a new subfamily classification for the Legumes; Taxon (IF 2.45).
A biogeographic and evolutionary study of subfamily Detarioideae which is directly related to GLDAFRICA’s objectives; New Phytologist (IF 7.33).
The third published paper is on the phylogenetics of genus Macrolobium (currently in press, International Journal of Plant Science, IF 1.748).
The Fellow has also submitted two additional papers:
A new biogeographic model that includes Antarctica in the area definition (submitted, J. of Biogeography, IF 4.25).
A study on the evolutionary patterns within the Brownea clade (submitted, Mol. Phylogenetics and Evolution, IF 4.42).
There are a few more additional papers that are close to submission:
A new tribal classification for subfamily Detarioideae.
A paper on the biogeography of Daniellia (a genus under study in GLDAFRICA).
A paper with the hybrid capture design and Anthonotha phylogenomics with collaborators Dario Ojeda, Sandra Cervantes (Oulu University, Finland) and Olivier Hardy (ULB, Belgium).
A paper of the phylogenomics and evolution of Detarioideae.
A paper on the evolutionary origin and conservation of African biomes in which Detarioideae are dominant.
All the results published until now and that we plan to publish in the coming year show clear trends: 1) the Fellow’s presentations have been a success and he has been invited to prestigious conferences since he became a MSCF; 2) his research is published in increasingly higher impact factor journals; 3) his research has moved from a more descriptive taxonomic view to an evolutionary and conservationist approach, aspects that are more relevant and of interest to a broader spectrum the scientific community and society.
1) investigate the evolutionary-conservation patterns in West Central Africa
2) enrol the fellow in a training program to become a XXIst century evolutionary researcher
3) boost the fellow’s research publications and profile to increase his future professional options.
Training received:
The fellow had a meeting with his advisor and GLDAFRICA collaborators and we designed a strategy to learn and use effectively a high-throughput sequencing (HTS). He has attended to the following courses:
- Phylogenomics Summer School 2016, Maynooth University.
- Introducción a las Técnicas de Next Generation Sequencing, URJC.
- Seminario de Introducción al uso de la supercomputación aplicado a la Bioinformática, Fundación Centro de Supercomputación de CYL.
- Curso Práctico de Iniciación al uso de la Supercomputación aplicado al Análisis de datos RNA-Seq, Fundación Centro de Supercomputación de CYL.
- Hyb-Seq Workshop, RBG Kew.
- Filogenias y Genealogías de DNA, UB.
- He has also received training to improve his skills in project management, student supervision and grant applications, from the supervisor Felix Forest at the host institution.
Additional funding obtained:
Although our project GLDAFRICA was fully funded by EU, the supervisor encouraged the fellow to apply to other funding sources, both as a training exercise and with the idea that securing additional funding would allow the expansion of the proposed data gathering objectives, i.e. further genera could be sampled. The fellow applied for and was successful in obtaining funds from RGB Kew.
Work performed:
* Taxon sampling. With access to the extensive RBG Kew collections, we obtained leaf samples for DNA extractions. All samples and DNA extracts at RBG Kew follow and comply with the Nagoya Protocol.
* Bait design. We decided to use targeted enrichment as methodology to obtain DNA sequence data for a complete genus-level phylogeny of Detarioideae.
* Laboratory Work. Laboratory work was performed during a 1.5 months period in cooperation with our colleagues from ULB (Belgium).
* Preliminary analyses. Of the 325 samples sequenced, good quality DNA sequences were obtained for 296 samples. This is particularly successful given that a large proportion of the samples used were from herbarium specimens and of less good quality.
* IUCN assessments. The fellow compiled a database with distribution records of Detarioideae in West Central Africa. We have run IUCN assessments for part of those, in particular for the Daniellia clade that has been the subject of a MSc project supervised by the Fellow. We plan to use BIOMOD to model the diversity patterns of Detarioideae in West Central Africa.
Dissemination of results:
During GLDAFRICA one of our objectives was to engage with our colleagues and share our findings. The Fellow participated and gave oral communications at the following venues:
States of the World's Plants Symposium (Kew, 2016)
UK Plant Evolution Meeting (Cambridge, 2016)
European Conference of Tropical Ecology (Brussels, 2017)
XIX International Botanical Congress (Shenzhen, China)
The Fellow also co-organized a symposium on Legume phylogenomics, IBC in Shenzhen (China) in July 2017.
The Fellow also had the opportunity to participate in activities of public engagement at RBG Kew. In particular during the 2016 Kew Science Festival, he was heavily involved in several planned activities during two of the three days of the event.
On publications we have published three papers:
One under the broad Legume Phylogeny Working Group that proposed a new subfamily classification for the Legumes; Taxon (IF 2.45).
A biogeographic and evolutionary study of subfamily Detarioideae which is directly related to GLDAFRICA’s objectives; New Phytologist (IF 7.33).
The third published paper is on the phylogenetics of genus Macrolobium (currently in press, International Journal of Plant Science, IF 1.748).
The Fellow has also submitted two additional papers:
A new biogeographic model that includes Antarctica in the area definition (submitted, J. of Biogeography, IF 4.25).
A study on the evolutionary patterns within the Brownea clade (submitted, Mol. Phylogenetics and Evolution, IF 4.42).
There are a few more additional papers that are close to submission:
A new tribal classification for subfamily Detarioideae.
A paper on the biogeography of Daniellia (a genus under study in GLDAFRICA).
A paper with the hybrid capture design and Anthonotha phylogenomics with collaborators Dario Ojeda, Sandra Cervantes (Oulu University, Finland) and Olivier Hardy (ULB, Belgium).
A paper of the phylogenomics and evolution of Detarioideae.
A paper on the evolutionary origin and conservation of African biomes in which Detarioideae are dominant.
All the results published until now and that we plan to publish in the coming year show clear trends: 1) the Fellow’s presentations have been a success and he has been invited to prestigious conferences since he became a MSCF; 2) his research is published in increasingly higher impact factor journals; 3) his research has moved from a more descriptive taxonomic view to an evolutionary and conservationist approach, aspects that are more relevant and of interest to a broader spectrum the scientific community and society.
- The MSCF project GLDAFRICA has developed cutting edge phylogenomic approaches for the Legume family, with special focus on West Central Africa conservation. Our papers will be among the first ones exploring relationships for a group of such importance as Detarioideae in Africa using phylogenomic tools.
- GLDAFRICA has already produced a new biogeographical model that we are proposing for a more general use, i.e. highlighting the importance of Antarctica in shaping the world diversity in geological times. This work is currently under review in Journal of Biogeography.
- GLDAFRICA will represent an advance in our knowledge of African diversity evolution, which would allow us to suggest better informed initiatives to preserve those forests considering the current climate change.
- GLDAFRICA has already produced a new biogeographical model that we are proposing for a more general use, i.e. highlighting the importance of Antarctica in shaping the world diversity in geological times. This work is currently under review in Journal of Biogeography.
- GLDAFRICA will represent an advance in our knowledge of African diversity evolution, which would allow us to suggest better informed initiatives to preserve those forests considering the current climate change.