Periodic Reporting for period 1 - FRUITFUL (On the evolution of fleshy fruits: An integrative test to assess the relative role of intrinsic and extrinsic factors in shaping fruit type)
Periodo di rendicontazione: 2019-06-01 al 2022-05-31
A trip to a grocery store exposes us to an outstanding diversity of fruits. While this variety was influenced by human selection during plant domestication, it mainly reflects strategies of seed dispersal that evolved over millions of years. Despite the huge variation in fruit color, shape, and size, common patterns can still be identified, especially the repeated evolution of fleshy fruits (e.g. olives, apples, tomatoes). Though this pattern is well observed, we are still exploring the role of different factors and their selective pressures. These can be intrinsic, as evolution of inherited genes determining fruit traits, or extrinsic, as the environment.
FRUITFUL dissected the evolution of fleshy fruits in the olive family (Oleaceae). Within its ca. 700 species, multiple lineages independently evolved fleshy fruits and species live in a variety of environments. Through this project, we built a new phylogenetic framework of Oleaceae, and updated the taxonomy of several of its lineages, we identified independent transitions to fleshy fruit within the family and estimated the historical biogeography of the groups within the family.
With a new phylogeny for Oleaceae, based on cytoplasmic and nuclear information, we showed that the five tribes (Myxopyreae, Fontanesieae, Forthythieae, Jasmineae and Oleeae) are well supported and monophyletic, with Jasmineae clearly sister to Oleeae. We also show that the four Oleeae subtribes (Schreberinae, Ligustrinae, Fraxininae, Oleinae) are well defined.
The phylogenetic framework in Oleaceae was further revised by updates to the taxonomy of the Notelaea and Schreberinae clades. For Notelaea, we re-circumscribed the genus and updated species names. For the Schreberinae tribe, we proposed a complete incorporation of Comoranthus species into Schrebera.
Using the updated phylogenetic framework and a database of fruit types, we showed that the ancestral state for fruit type in Oleaceae is a dry, dehiscent fruit (i.e. a dry fruit that opens when mature). We also found that several transitions towards fleshy, indehiscent fruits happened throughout the family's evolutionary history. Further, we showed that the intermediate state between a dry, dehiscent fruit, and a fleshy, indehiscent one, is a dry, indehiscent fruit. This means that anatomically-speaking, fruits first change their dehiscence (from dehiscent to indehiscent), and then change the state of their fruit wall (from dry to fleshy).
Finally, the biogeography of some Oleaceae’s clades is very complex, with groups succeeding to reach far-away regions in the world. For instance, we showed that species of the Notelaea clade are distributed today in very segregated parts of the world as Australasia, the Hawaiian Islands, Macaronesia, and the Mediterranean Region. This group originated most likely in Eurasia during the Early Miocene, and to reach some of the farther regions they most likely had birds as dispersers for their fleshy fruits.
FRUITFUL dissected the evolution of fleshy fruits in the olive family (Oleaceae). Within its ca. 700 species, multiple lineages independently evolved fleshy fruits and species live in a variety of environments. Through this project, we built a new phylogenetic framework of Oleaceae, and updated the taxonomy of several of its lineages, we identified independent transitions to fleshy fruit within the family and estimated the historical biogeography of the groups within the family.
With a new phylogeny for Oleaceae, based on cytoplasmic and nuclear information, we showed that the five tribes (Myxopyreae, Fontanesieae, Forthythieae, Jasmineae and Oleeae) are well supported and monophyletic, with Jasmineae clearly sister to Oleeae. We also show that the four Oleeae subtribes (Schreberinae, Ligustrinae, Fraxininae, Oleinae) are well defined.
The phylogenetic framework in Oleaceae was further revised by updates to the taxonomy of the Notelaea and Schreberinae clades. For Notelaea, we re-circumscribed the genus and updated species names. For the Schreberinae tribe, we proposed a complete incorporation of Comoranthus species into Schrebera.
Using the updated phylogenetic framework and a database of fruit types, we showed that the ancestral state for fruit type in Oleaceae is a dry, dehiscent fruit (i.e. a dry fruit that opens when mature). We also found that several transitions towards fleshy, indehiscent fruits happened throughout the family's evolutionary history. Further, we showed that the intermediate state between a dry, dehiscent fruit, and a fleshy, indehiscent one, is a dry, indehiscent fruit. This means that anatomically-speaking, fruits first change their dehiscence (from dehiscent to indehiscent), and then change the state of their fruit wall (from dry to fleshy).
Finally, the biogeography of some Oleaceae’s clades is very complex, with groups succeeding to reach far-away regions in the world. For instance, we showed that species of the Notelaea clade are distributed today in very segregated parts of the world as Australasia, the Hawaiian Islands, Macaronesia, and the Mediterranean Region. This group originated most likely in Eurasia during the Early Miocene, and to reach some of the farther regions they most likely had birds as dispersers for their fleshy fruits.
For the work performed under FRUITFUL, nearly 100 species were newly sampled and sequenced to build a new phylogenetic framework of Oleaceae and update its taxonomy. We used the collections of herbaria and botanic gardens in France, Germany, and the United Kingdom, and gathered dry and fresh leaf samples. We then extracted and purified the genomic DNAs of those samples (nuclear, chloroplastic, and mitochondrial).
Using a genome skimming approach, we sequenced all specimens by producing short sequence reads. We then used these to assemble full chloroplastic genome, mitochondrial genes, and nuclear genes. By combining sequences from those genomic compartments with fossil information we estimated dated phylogenies for groups within Oleaceae.
From this, we identified independent transitions to fleshy fruit within the family. We built a database of fruit types based on reports in the scientific literature, and herbaria records. We used phylogenetic comparative methods implemented in code packages of the R software, to estimate: the ancestral fruit state in Oleaceae, the number of likely transitions between fruit types (dry and fleshy), and to test hypothesis regarding the order of transitions between the characters of dehiscence and fleshiness.
We further used phylogenies of two Oleaceae groups to estimate their historical biogeography. We built a database of species distributions based on herbaria records (mainly from Kew and the Natural History Museum in Paris), the online database "Plants of the World Online" (POWO), and the data available in the Global Biodiversity Information Facility (GBIF) database. We then combined phylogeny and information on species distribution to estimate the biogeographic history.
Alongside all wet lab and dry lab work, we also followed skill training through participation on courses about the Linux environment, computer cluster access, and approaches to handle genomic data in biology, and further developed skills on manuscript writing, project management, and mentoring of students.
Overall, the main results of FRUITFUL were disseminated to the scientific community and the general public. We have published two papers and have a third one accepted for publication, discussing the taxonomy, phylogenetics, and biogeography of Oleaceae. We presented the results of our fruit evolution analysis in a scientific conference during the second year of the action. Beyond those, we participated to four other events to disseminate our results: two invited seminars and two outreach events (the European researcher's night 2021 and the City Nature Challenge 2022, an event that the Museum of Natural History of Toulouse took part and invited local researchers).
Using a genome skimming approach, we sequenced all specimens by producing short sequence reads. We then used these to assemble full chloroplastic genome, mitochondrial genes, and nuclear genes. By combining sequences from those genomic compartments with fossil information we estimated dated phylogenies for groups within Oleaceae.
From this, we identified independent transitions to fleshy fruit within the family. We built a database of fruit types based on reports in the scientific literature, and herbaria records. We used phylogenetic comparative methods implemented in code packages of the R software, to estimate: the ancestral fruit state in Oleaceae, the number of likely transitions between fruit types (dry and fleshy), and to test hypothesis regarding the order of transitions between the characters of dehiscence and fleshiness.
We further used phylogenies of two Oleaceae groups to estimate their historical biogeography. We built a database of species distributions based on herbaria records (mainly from Kew and the Natural History Museum in Paris), the online database "Plants of the World Online" (POWO), and the data available in the Global Biodiversity Information Facility (GBIF) database. We then combined phylogeny and information on species distribution to estimate the biogeographic history.
Alongside all wet lab and dry lab work, we also followed skill training through participation on courses about the Linux environment, computer cluster access, and approaches to handle genomic data in biology, and further developed skills on manuscript writing, project management, and mentoring of students.
Overall, the main results of FRUITFUL were disseminated to the scientific community and the general public. We have published two papers and have a third one accepted for publication, discussing the taxonomy, phylogenetics, and biogeography of Oleaceae. We presented the results of our fruit evolution analysis in a scientific conference during the second year of the action. Beyond those, we participated to four other events to disseminate our results: two invited seminars and two outreach events (the European researcher's night 2021 and the City Nature Challenge 2022, an event that the Museum of Natural History of Toulouse took part and invited local researchers).
The results presented in FRUITFUL have advanced our knowledge on the evolution of the olive family. FRUITFUL presents a new phylogenetic framework for Oleaceae that allows contextualizing the origin and evolution of different traits of interest in the family. Moreover, genomic data generated are a step further to better grasp the genomics of several economically important species in the family, such as olives, ash trees, jasmines and lilacs. While we focused our analyses in a remarkable trait (fruits), FRUITFUL's datasets are potential sources of information on today's questions on topics such as species adaptation to climate change.
The results of this project also have impacts on socio-economic aspects and wider societal implications. Regarding its workforce, this project was led by two researchers, the scientific coordinator, and the experienced researcher. Even though FRUITFUL did not have additional researchers who were recruited specifically to work on it, we have used products and services from at least ten organizations, between research centers, museums, botanic gardens, and companies.
Under the wider societal implication, this project has produced science education materials in two languages, outputs relevant for policy makers, and three scientific publications. Our posters about plant reproduction are now part of the permanent collection of education materials of the Museum of Natural History in Toulouse. Moreover, these materials are available in both French and English. Further, our scientific papers on the phylogenetics and taxonomy of Oleaceae could be used by policy makers: e.g. the description of new species, and information on the types of environments they are found in, are important for conservation lists of threatened species.
The results of this project also have impacts on socio-economic aspects and wider societal implications. Regarding its workforce, this project was led by two researchers, the scientific coordinator, and the experienced researcher. Even though FRUITFUL did not have additional researchers who were recruited specifically to work on it, we have used products and services from at least ten organizations, between research centers, museums, botanic gardens, and companies.
Under the wider societal implication, this project has produced science education materials in two languages, outputs relevant for policy makers, and three scientific publications. Our posters about plant reproduction are now part of the permanent collection of education materials of the Museum of Natural History in Toulouse. Moreover, these materials are available in both French and English. Further, our scientific papers on the phylogenetics and taxonomy of Oleaceae could be used by policy makers: e.g. the description of new species, and information on the types of environments they are found in, are important for conservation lists of threatened species.