Final Report Summary - REHYSTRIX (Evolutionary response of two African Rodent species (Hystrix sp) to climate changes: the study of the past as an estimate of the future)
The project “Evolutionary response of two African rodent species (Hystrix sp) to climate changes: studying the past to estimate the future” was granted to Emiliano Trucchi in the call FP7-PEOPLE-IEF-2009 and it was carried out between 01/02/2011 and 31/01/2013 at the Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, under the supervision of Prof Nils Christian Stenseth.
One of the main objectives of this study was the implementation of novel methodologies to extensively use Next-Generation Sequencing data in population genetics and phylogeography. In particular, one of this NGS method, the sequencing of restriction-associated DNA fragments (RADseq), was explored and further developed during the course of the project. We can refer to the implementation of this method as the most important achievement during the Marie Curie Fellowship. In fact, reduced-complexity approaches in genome typing as RADseq have been indicated as the most promising methodology for genomic analysis at population level. In the last two years they rapidly became the workhorse in population genetics giving the possibility of screening hundred thousand loci across multiple individuals in non-model species. Thanks to the great support of the host institution (CEES, University of Oslo), the method was quickly implemented and further developed concerning the wet lab work and the following bioinformatic analysis. On one side, I was then able to produce a whole-genome population-level dataset for the two species under investigation as the main molecular dataset in the project and, on the other hand, it placed me in an unique condition of advanced experience in the field thus opening the way to many collaborations and networking. The training in this NGS method was enriched by a course attended at the University of Lund, Sweden, on the bioinformatic analysis of the RADseq data held by prominent experts in the field, Julian Catchen and William Cresko, University of Oregon, Eugene, USA, and by an internal course on python scripting attended at CEES, University of Oslo, and taught by Dr Karin Lagesen. The training received allowed me to set a RADseq platform at the host institution that has been accessed by internal and external researchers thus further increasing the opportunities for collaborations. A complete list of the scientific projects that are currently using our platform is available on the webpage http://www.mn.uio.no/cees/english/research/groups/rad/ and international collaborations have been set with the CSM-CNRS in France, IASMA in Italy, University of Roma Tor Vergata in Italy. I had also the opportunity to give a wet lab course at CEES on December 2012 where more than 20 PhD student and postdoc signed in. Following the interest raised by this course, I have been invited as main teacher in the course on RADseq arranged by the Nordic School of Biosystematics (ForBio http://www.forbio.uio.no/) that will be held on June and October 2013 at the University of Oslo. Further networking and collaborations in other scientific projects are expected as an outcome of this event. Both courses totally fulfill the overall scope of the Marie Curie Fellowship that is to spread the acquired knowledge and to build collaborative networks.
A challenging aspect of this project was the analysis of museum samples in order to complete the modern sample data. The two species investigated in this study have a very broad geographical distribution as they occur all over the African continent. A direct sampling of extant population was not feasible time- and cost-wise. To this regard, museum collections could represent a valid alternative when they possess specimens coming from the whole area of distribution of the target species. The down side of this approach can be the difficulty in being granted access to the collection for destructive molecular analyses, and the more complex protocol for DNA analysis. The poor state of preservation of the DNA (low quality and quantity) makes the use of museum samples in NGS protocols not really straightforward. We were granted access to several collections and we performed standard molecular analysis on more than 50 museum specimens. However, the implementation on these sample of the chosen NGS method (RADseq) was not cost-effective. We then used these samples for standard mitochondrial molecular marker analyses gaining extremely useful information on the extent and the spatial pattern of the genetic diversity in the African porcupines.
The other main objective of this project was the study of the most advanced methods for modeling species distribution according to ecological variables (Ecological Niche Modeling) in present and past climatic scenarios. This can be considered as necessary tool for completing high-quality phylogeographic analyses. Thanks to the good training received in the Species Distribution Modeling course, attended at the Centre for Macroecology, Evolution and Climate, University of Copenhagen, and the following collaboration with an expert in the field, Prof. David Nogues-Bravo, University of Copenhagen, we produced models of the distributions of the two porcupine species according to the present climatic conditions and we projected these models on past climatic scenarios (five time-slices: 126K, 42K, 30K, 21K, and 6K years ago). This overview on the past distribution allowed us to formulate different hypotheses about the evolutionary dynamics of the two species. These hypotheses have then been tested through molecular data. The collaboration with Prof. Nogues-Bravo and his research group was built in the meanwhile of this Marie Curie Fellowship and is still ongoing, thus giving us the opportunity to further improve our results.
The molecular dataset including mitochondrial and nuclear (whole-genome) data obtained from modern and museum samples has been then used together with the species distribution models for the past climatic conditions to understand the past evolutionary dynamics of the African porcupines following the Late-Pleistocene/Holocene major climatic shifts. The overall geographic pattern of the genetic diversity closely match those of other savannah-dwellers: East-West main differentiation can be identified in the crested porcupine mainly living north of the Equator while a more homogenous population characterizes the cape porcupine inhabiting the South portion of the African continent. The oscillation between glacial and interglacial periods together with the alternation of wet and dry conditions on the African continent fostered the diversification in the crested species: the alternation of tropical rainforest, savannah and desert certainly played a major role. In particular, the alternate openings of the Saharan waterways and the peculiar orography of Eastern Africa (Ethiopia and the Rift valley) can be identified as the main drivers of the porcupines diversity. Our results can be used to forecast the distribution of porcupines under future climatic scenarios and can help predicting the effect of the ongoing global warming on this species and, more generally, on savannah ecosystem.
Two scientific papers presenting the results of this project and a paper dealing with the methodological improvements are currently under preparation and will be submitted soon to highly-rated journals. The first two are currently in preparation: a general one fully describing African porcupines response to past climatic shifts “What makes a species and what does not: a genomic and historic perspective on African porcupines diversification” and a close-up on the ecological and evolutionary prerequisites of the successful colonization of a new area: “The (historical) background of the alien (species) matters: high genomic diversity in the crested porcupine successful invasive population.” The methodological paper is at a final stage of preparation and it is focused on the use of RADseq data in inferring past demography. In the meanwhile, the results have been (and will be) presented at international conferences (11th African Small Mammal Symposium, UNISWA, Kwaluseni, Swaziland, 3-8/07/2011, SIBE workshop, Ferrara, Italy, 15-16/12/2012, abstract for a talk or poster submitted to ESEB Conference 2013, Lisbon, Portugal, 19-24/08/2013).
Contacts:
Emiliano Trucchi
Centre for Ecological and Evolutionary Synthesis (CEES)
Department of Biology - University of Oslo
PO Box 1066 Blindern, N-0316 Oslo, NORWAY
Phone: +47-228-55-065, Email: emiliano.trucchi@bio.uio.no Web: www.emilianotrucchi.it
One of the main objectives of this study was the implementation of novel methodologies to extensively use Next-Generation Sequencing data in population genetics and phylogeography. In particular, one of this NGS method, the sequencing of restriction-associated DNA fragments (RADseq), was explored and further developed during the course of the project. We can refer to the implementation of this method as the most important achievement during the Marie Curie Fellowship. In fact, reduced-complexity approaches in genome typing as RADseq have been indicated as the most promising methodology for genomic analysis at population level. In the last two years they rapidly became the workhorse in population genetics giving the possibility of screening hundred thousand loci across multiple individuals in non-model species. Thanks to the great support of the host institution (CEES, University of Oslo), the method was quickly implemented and further developed concerning the wet lab work and the following bioinformatic analysis. On one side, I was then able to produce a whole-genome population-level dataset for the two species under investigation as the main molecular dataset in the project and, on the other hand, it placed me in an unique condition of advanced experience in the field thus opening the way to many collaborations and networking. The training in this NGS method was enriched by a course attended at the University of Lund, Sweden, on the bioinformatic analysis of the RADseq data held by prominent experts in the field, Julian Catchen and William Cresko, University of Oregon, Eugene, USA, and by an internal course on python scripting attended at CEES, University of Oslo, and taught by Dr Karin Lagesen. The training received allowed me to set a RADseq platform at the host institution that has been accessed by internal and external researchers thus further increasing the opportunities for collaborations. A complete list of the scientific projects that are currently using our platform is available on the webpage http://www.mn.uio.no/cees/english/research/groups/rad/ and international collaborations have been set with the CSM-CNRS in France, IASMA in Italy, University of Roma Tor Vergata in Italy. I had also the opportunity to give a wet lab course at CEES on December 2012 where more than 20 PhD student and postdoc signed in. Following the interest raised by this course, I have been invited as main teacher in the course on RADseq arranged by the Nordic School of Biosystematics (ForBio http://www.forbio.uio.no/) that will be held on June and October 2013 at the University of Oslo. Further networking and collaborations in other scientific projects are expected as an outcome of this event. Both courses totally fulfill the overall scope of the Marie Curie Fellowship that is to spread the acquired knowledge and to build collaborative networks.
A challenging aspect of this project was the analysis of museum samples in order to complete the modern sample data. The two species investigated in this study have a very broad geographical distribution as they occur all over the African continent. A direct sampling of extant population was not feasible time- and cost-wise. To this regard, museum collections could represent a valid alternative when they possess specimens coming from the whole area of distribution of the target species. The down side of this approach can be the difficulty in being granted access to the collection for destructive molecular analyses, and the more complex protocol for DNA analysis. The poor state of preservation of the DNA (low quality and quantity) makes the use of museum samples in NGS protocols not really straightforward. We were granted access to several collections and we performed standard molecular analysis on more than 50 museum specimens. However, the implementation on these sample of the chosen NGS method (RADseq) was not cost-effective. We then used these samples for standard mitochondrial molecular marker analyses gaining extremely useful information on the extent and the spatial pattern of the genetic diversity in the African porcupines.
The other main objective of this project was the study of the most advanced methods for modeling species distribution according to ecological variables (Ecological Niche Modeling) in present and past climatic scenarios. This can be considered as necessary tool for completing high-quality phylogeographic analyses. Thanks to the good training received in the Species Distribution Modeling course, attended at the Centre for Macroecology, Evolution and Climate, University of Copenhagen, and the following collaboration with an expert in the field, Prof. David Nogues-Bravo, University of Copenhagen, we produced models of the distributions of the two porcupine species according to the present climatic conditions and we projected these models on past climatic scenarios (five time-slices: 126K, 42K, 30K, 21K, and 6K years ago). This overview on the past distribution allowed us to formulate different hypotheses about the evolutionary dynamics of the two species. These hypotheses have then been tested through molecular data. The collaboration with Prof. Nogues-Bravo and his research group was built in the meanwhile of this Marie Curie Fellowship and is still ongoing, thus giving us the opportunity to further improve our results.
The molecular dataset including mitochondrial and nuclear (whole-genome) data obtained from modern and museum samples has been then used together with the species distribution models for the past climatic conditions to understand the past evolutionary dynamics of the African porcupines following the Late-Pleistocene/Holocene major climatic shifts. The overall geographic pattern of the genetic diversity closely match those of other savannah-dwellers: East-West main differentiation can be identified in the crested porcupine mainly living north of the Equator while a more homogenous population characterizes the cape porcupine inhabiting the South portion of the African continent. The oscillation between glacial and interglacial periods together with the alternation of wet and dry conditions on the African continent fostered the diversification in the crested species: the alternation of tropical rainforest, savannah and desert certainly played a major role. In particular, the alternate openings of the Saharan waterways and the peculiar orography of Eastern Africa (Ethiopia and the Rift valley) can be identified as the main drivers of the porcupines diversity. Our results can be used to forecast the distribution of porcupines under future climatic scenarios and can help predicting the effect of the ongoing global warming on this species and, more generally, on savannah ecosystem.
Two scientific papers presenting the results of this project and a paper dealing with the methodological improvements are currently under preparation and will be submitted soon to highly-rated journals. The first two are currently in preparation: a general one fully describing African porcupines response to past climatic shifts “What makes a species and what does not: a genomic and historic perspective on African porcupines diversification” and a close-up on the ecological and evolutionary prerequisites of the successful colonization of a new area: “The (historical) background of the alien (species) matters: high genomic diversity in the crested porcupine successful invasive population.” The methodological paper is at a final stage of preparation and it is focused on the use of RADseq data in inferring past demography. In the meanwhile, the results have been (and will be) presented at international conferences (11th African Small Mammal Symposium, UNISWA, Kwaluseni, Swaziland, 3-8/07/2011, SIBE workshop, Ferrara, Italy, 15-16/12/2012, abstract for a talk or poster submitted to ESEB Conference 2013, Lisbon, Portugal, 19-24/08/2013).
Contacts:
Emiliano Trucchi
Centre for Ecological and Evolutionary Synthesis (CEES)
Department of Biology - University of Oslo
PO Box 1066 Blindern, N-0316 Oslo, NORWAY
Phone: +47-228-55-065, Email: emiliano.trucchi@bio.uio.no Web: www.emilianotrucchi.it