Yesterday 1st February 2018, we welcomed Andrew to our lab! Welcome!
Andrew undertook his PhD in evolutionary biology at Imperial College London, on the evolution of annual killifish (Austrolebias) and other Cyprinodontiformes. He then undertook several Postdoctoral Research Fellows in plant genomics at Royal Botanic Gardens, Kew, working on hazelnut production in Turkey, demographic history of the sea campion, Silene uniflora and analyzing genomic data fora range of projects on Madagascan plants (including some palms!).
He will be here in Montpellier for 2 years and will work on the comparative phylogeography of several co distributed rain forest plant species (Annonaceae and palms) across Central Africa, part of the AFRODYN project.
Next stop: Cameroon for some field work and hands on discussions about rain forest evolution!
Check out one of his intresting papers from his PhD:
Helmstetter, A.J., Papadopulos, A.S., Igea, J., Van Dooren, T.J., Leroi, A.M., & Savolainen, V. (2016) Viviparity stimulates diversification in an order of fish. Nature communications, 7, 11271.
Our paper introducing our new R package called ConR: Conservation with R is out in Ecology and Evolution.
ConR allows people to undertake preliminary conservation assessments for hundreds of taxa at a time. The package was specifically aimed to use IUCN criteria, in particular criteria needed for category B assessments. It is particularity suited to analyse large scale datasets containing many taxa, for example at country or even continental level. The output (tabular and graphical) provides an overview of threatened versus non threatened species, useful for identifying taxa or areas of conservation importance. In parralelel, ConR can be used to generated all the needed parameters to undertake full IUCN assessments, for example within the framework of Red Listing workshops or for monographic studies.
However, ConR output should not be taken as final IUCN ready assessments.
This package was mainly implemented by Gilles Daudy in R. The package comes with a complete and detail tutorial.
This article is a direct output of the RAINBIO project. The article is OPEN ACCESS
Below an example of one graphical output from ConR.
Dauby, G., Stévart, T., Droissart, V., Cosiaux, A., Deblauwe, V., Simo-Droissart, M., Sosef, M.S.M., Lowry II, P.P., Schatz, G.E., Gereau, R.E., & Couvreur, T.L.P. (2017) ConR: an R package to assist large scale multi-species preliminary conservation assessments using distribution data. Ecology and Evolution, 7, 11292–11303
Research Area and Project Description: This postdoc is part of the project “Central AFrican Rain fOrests: past DYNamics and future resilience” (AFRODYN), funded by the French ANR. AFRODYN aims to understand the evolutionary dynamics of central African rain forests using a multispecies approach and an unprecedented DNA sequence dataset for African plant species. The overall objectives of AFRODYN are to 1) test different hypotheses of Central African rain forests dynamics in the past within and between species using a statistical comparative phylogeographic approach and 2) infer the potential resilience of this ecosystem to future climate change. Specifically, the post doc will be in charge of analyzing a large dataset of ~800 exons (ca. 200 kpb) captured for over 600 individuals of six different plant species (palms and Annonaceae) sampled across central Africa. This dataset is partly already available and no lab work is required. Finally, the postdoc is expected to contribute ideas and concepts to the project and lead at least two high-quality papers in this research area, contribute to the project’s public outreach, as well as collaborate with other team members, including students and sharing skills.
Ariane Cosiaux, our international volunteer based in Yaoundé, has been Red Listing all African palms this last year. Today, her first article was published in the Biodiversity Data Journal under its new Species Conservation Profile section. We published the IUCN conservation assessment of Eremospatha dransfieldii, a rattan species growing in West Africa (Ghana and Ivory Coast). This species was assessed as "EN" meaning endangered, the second highest threat level, just after CR or critically endangered. Data gathered around this species (including its distribution, field observations and ongoing and future threats) suggests that its future will be in peril if nothing is done to stop deforestation and agriculture extension in the areas where it grows. Recently a total of 8 African rattan species were also included on the official IUCN Red List, one of them even being CR. Soon, the rest of the African palm species will be published too.
Red Listing is a central part of biodiversity conservation as this list is the only authoritative list governments, companies and project funders turn too when taking decisions about the impact a project has on biodiversity. As one one the co authors of this recent paper said: A species doesn't exist unless it has a conservation status (Lauren Gardiner).
Cosiaux A, Gardiner L, Ouattara D, Stauffer F, Sonké B, Couvreur TLP (2017) An endangered West African rattan palm: Eremospatha dransfieldii. Biodiversity Data Journal 5: e11176. https://doi.org/10.3897/BDJ.5.e11176
We had our last RAINBIO meeting from 5th-9th December 2016 in Aix-en-Provence. RAINBIO started back in 2013 (funded by the CESAB call of the FRB) with the aim of synthesizing plant distribution data from tropical Africa. The RAINBIO publications is now available and open access here and the database is available here.
Several articles are in the pipe line, including a new R package that undertakes batch preliminary IUCN conservation assessments. More details will be available soon. We are now in the process of looking for extra funding to continue RAINBIO (2.0) and generate an online African distribution data platform.
On Thursday 24th of November 2016, Foulques Couvreur (FLS Production) and I organized an "avant première" of the award winning short documentary "Raphia: tree of life" (follow link for full movie) under my scientific supervision. This documentary and event is one of the outputs of the RAPHIA project. The event was attended by over 100 people (family, friends and colleagues), at the Vendôme cinema in Brussels. An excellent Q&A session followed the projection during which the public got acquainted with the RAPHIA project, Raphia palms, Africa and the technical difficulties of droning!
This movie is complementary to a second documentary that is due early december 2016 ("à l'échelle du Raphia"; "on Raphia and Man" (29 mins, directed by Joseph Fumtim & Thomas Couvreur, IRD).
Made a short video on the AFRODYN project. Images taken from several field trips during the project. Drone images from FLS production.
On Saturday 12th of November 2016, we travelled to the wonderful region of Oku (North West Cameroon) to project "à l'échelle du Raphia" ("On Raphia and Man"). The documentary relates the importance of the African Raphia palms and follows a team of researchers investigating the biodiversity, uses and economic importance of its species across Cameroon. We were accompanied by Philippe Le Gall (Entomologist, IRD), Joseph Fumtim (co producer, IRD), Suzanne Mogue (PhD Student, Université de Yaoundé 1) and Ariane Cosiaux (International Volunteer, IRD).
We were received by the Fon (king) of Oku, His Majesty Senteih II and the prince Shey Wilfred Mbunda as well as numerous other notables of the region.
The official version of the documentary will be available by end November.
This project was funded by IRD and Agropolis International as part of the RAPHIA project.
Our article detailing the RAINBIO mega dataset is out!
With this article we publish one of the largest datasets of tropical African plant distributions to date. It contains over 600k unique georeferenced plant occurrences for over 22k plant species. Manual and automatic specimen checking was undertaken by the RAINBIO consortium. This article is published within the framework of the RAINBIO project, funded by FRB, CESAB calls.
Link to the project web page here where you can download the database!
Our new study focused on two central African understory palm species of the genus Podococcus. Using species distribution modeling in the past and the present combined with over 100 plastomes sequenced using NGS we found a strong correlation between climatically stable areas for the species and high unique genetic diversity. Read more here. www.sciencedirect.com/science/article/pii/S1055790316301981
Congrats to Adama for his third PhD article!