Final Report Summary - AVIAN GENOMICS (Avian genomics and ecological speciation)
Summary description of the project objectives:
This joint exchange programme aims to continue and refine our research programme on the genetics and genomics of ecological speciation, using birds as model systems. This includes creating a reference genome sequence assembly for our main avian study species, using de novo next-generation sequencing (NGS) techniques. We also use population genomics approaches and follow up with association mapping. In particular, we will gather genome-wide molecular evidence to confirm or refute the occurrence of sympatric speciation in avian radiations, and initiate the search for genetic regions that are under selection, in order to determine the genetic bases of adaptation and ultimately speciation. We aim to identify the genes underlying the evolution of bill size/shape. Bill morphology is an important trait in resource-driven bird diversification, and therefore the establishment of the links between phenotype-fitness-genotype will advance significantly our understanding of the speciation process in birds. Our project is primarily focussing on Nesospiza on Tristan da Cunha and Serinus finches on Sao Tomé, but we have also expanded our programme to also include evolutionary genetics studies of Acrocephalus warblers in Europe and continental and island Zosterops white-eyes in the Pacific, as well as the conservation genetics of Angolan range restricted birds and of Lagonosticta finches endemic to West Africa. These additions to the programme have largely been formed during this first exchange period, and complement our initial aims.
In the programme, we exchange the expertise of each participating organisation to enhance their scientific standard. The programme allows us to achieve mutual benefits from exchanging expertise on novel laboratory innovations and bioinformatics, to increase each lab’s efficiency by exchanging experience and sharing available infrastructure and to evaluate the genetics of ecological speciation. Our creative gatherings seed new ideas and collaborations. For example, during the 2012 stay of Martim Melo in the University of Cape Town, novel avenues to further expand the collaboration between South Africa and Europe were discussed. As a result, a new collaborative project between Martim Melo, Peter Ryan and his colleagues at the University of Cape Town, and Angolan partners – always under the general theme of genomics of avian speciation – was launched. This project looks at the processes driving speciation in the little known, but very important, centres of bird endemism in Angola.
Our main scientific aims can be summarized as (i) create reference genome sequence assemblies for three bird species; (ii) gather genome-wide molecular evidence to confirm or refute the occurrence of sympatric speciation in two avian radiations; (iii) search for genetic regions that are under selection, in order to determine the genetic basis of adaptation and ultimately speciation; (iv) and conservation genomics and population differentiation in birds.
The research is divided in seven tasks: (i) workshop and review of avian genomics; (ii) research on applying Illumina Hiseq 2000 sequencing; (iii) workshop and research on de novo sequence assembly; (iv) research on sequencing a large set of individuals using the RAD sequencing technique; (v) workshop and research on detecting polymorphisms and molecular signs of selection; (vi) workshop and research on the genetic bases of adaptation and speciation; and (vii) fieldwork to gather ecological data.
Description of the work performed since the beginning of the project:
(i) We have initiated and completed several scientific papers (see publication list). (ii) We have been applying Illumina Hiseq 2000 sequencing in several subprojects, which also includes building sequencing libraries in the local laboratories at Lund University and University of Pretoria. (iii) We have been collaborating on the de novo sequence assembly in the Tristan da Cunha Nesospiza bunting. We have also conducted a draft genome of Zosterops lateralis, an ecological model white-eye species, and will soon initiate similar work on an Acrocephalus warbler (A. arundinaceus). We have generated large-scale transcriptomic sequence data that is used to annotate the Nesospiza reference genome. (iv) We are conducting research on sequencing a large set of individuals using the RAD sequencing technique. We have now RAD data for Nesospiza buntings, Serinus finches, Acrocephalus warblers and Zosterops white-eyes. (v) We are now collaborating on detecting polymorphisms and will start looking for molecular signs of selection in this data. We have also gathered gene expression data from eight Nesospiza individuals in order to conduct differential gene expression analyses in Nesospiza individuals with key phenotype differences (variation in bill size). (vi) We have not yet started our research on the genetic bases of adaptation and speciation. (vii) We have gathered high quality ecological data on the Tristan Nesospiza buntings and Sao Tomé Serinus finches. In addition to these tasks we have conducted conservation genetics work of rare Angolan birds and of endemic Lagonosticta finches in West Africa.
Description of the main results:
Generating massive amount of sequencing data and building reference genome de novo for Nesospiza and Zosterops. Conducting comparative analyses of this data against the main passerine model species, the zebra finch. Successful set up of Illumina sequencing libraries locally in Lund and Pretoria. Generating large-scale transcriptomic data that is now used to annotate the Nesospiza reference genome. Differential gene expression analyses in Nesospiza individuals with key phenotype differences initiated. Successful sequencing and genotyping using RAD sequencing of a large set of individuals that will now be used to analyse population differences (in Nesospiza, Serinus, Acrocephalus and Zosterops) and genotype-phenotype analyses using data from the Nesospiza hybrid zone that is present on one of the Tristan da Cunha islands. We have initiated conservation genetics work of Angolan birds and of Lagonosticta finches endemic to West Africa. We are now using our results to confirm or refute the occurrence of sympatric speciation in avian radiations. Our main result is that in the Neospiza/Serinus system there is mainly divergence in allopatry – a result that was possible to reach due to analyses of large scale genomic data (RAD-tag sequencing) generated during this project. In the Tristan finch system we have recently found genetic regions that are under selection, and this is now helping us understanding the biological, physiological and cellular functions of the genes in these regions in order to determine the genetic bases of adaptation and ultimately speciation.
Impact:
Our programme and partnership is positioned at the forefront of evolutionary research and has a very high potential for high scientific impact. Several lines of the research are expected to produce results with the quality and broad implications required for submission to the top scientific journals; and some manuscripts are now published in well-ranked journals (see the uploaded publication list). A very important component of the scientific process is analysing data and writing papers for international journals and the partnership has provided added value.
A priority area of the framework programme is sustainable development and global change. In order to achieve this main objective, it is important to understanding the processes generating biodiversity. Our current research agenda and its results have high potentials for main impact in this context and to contribute to research excellence and European competitiveness.
The genetics of speciation and the speciation process are of fundamental importance in evolutionary and conservation biology, and is also of high international interest and importance. Yet many central questions remain unresolved because theoretical models have failed to incorporate the genomic and ecological complexities of natural populations, whereas empirical advances have been restricted for methodological reasons. By applying research on several complementary study systems and by using recently developed molecular genetic tools our programme has been able to deepen our understanding on speciation and differentiation. We have been setting up collaboration between senior and junior researchers, some with long-standing experience in field biology and/or laboratory work, and use state-of-the-art molecular techniques (Illumina HighSeq and RAD sequencing). Our results have revealed important insights in the genetics of speciation and we hope it will have impact in the scientific community in the area of collaboration.
Contact Details:
Bengt Hansson
Lund University
Email: bengt.hansson[at]biol.lu.se
This joint exchange programme aims to continue and refine our research programme on the genetics and genomics of ecological speciation, using birds as model systems. This includes creating a reference genome sequence assembly for our main avian study species, using de novo next-generation sequencing (NGS) techniques. We also use population genomics approaches and follow up with association mapping. In particular, we will gather genome-wide molecular evidence to confirm or refute the occurrence of sympatric speciation in avian radiations, and initiate the search for genetic regions that are under selection, in order to determine the genetic bases of adaptation and ultimately speciation. We aim to identify the genes underlying the evolution of bill size/shape. Bill morphology is an important trait in resource-driven bird diversification, and therefore the establishment of the links between phenotype-fitness-genotype will advance significantly our understanding of the speciation process in birds. Our project is primarily focussing on Nesospiza on Tristan da Cunha and Serinus finches on Sao Tomé, but we have also expanded our programme to also include evolutionary genetics studies of Acrocephalus warblers in Europe and continental and island Zosterops white-eyes in the Pacific, as well as the conservation genetics of Angolan range restricted birds and of Lagonosticta finches endemic to West Africa. These additions to the programme have largely been formed during this first exchange period, and complement our initial aims.
In the programme, we exchange the expertise of each participating organisation to enhance their scientific standard. The programme allows us to achieve mutual benefits from exchanging expertise on novel laboratory innovations and bioinformatics, to increase each lab’s efficiency by exchanging experience and sharing available infrastructure and to evaluate the genetics of ecological speciation. Our creative gatherings seed new ideas and collaborations. For example, during the 2012 stay of Martim Melo in the University of Cape Town, novel avenues to further expand the collaboration between South Africa and Europe were discussed. As a result, a new collaborative project between Martim Melo, Peter Ryan and his colleagues at the University of Cape Town, and Angolan partners – always under the general theme of genomics of avian speciation – was launched. This project looks at the processes driving speciation in the little known, but very important, centres of bird endemism in Angola.
Our main scientific aims can be summarized as (i) create reference genome sequence assemblies for three bird species; (ii) gather genome-wide molecular evidence to confirm or refute the occurrence of sympatric speciation in two avian radiations; (iii) search for genetic regions that are under selection, in order to determine the genetic basis of adaptation and ultimately speciation; (iv) and conservation genomics and population differentiation in birds.
The research is divided in seven tasks: (i) workshop and review of avian genomics; (ii) research on applying Illumina Hiseq 2000 sequencing; (iii) workshop and research on de novo sequence assembly; (iv) research on sequencing a large set of individuals using the RAD sequencing technique; (v) workshop and research on detecting polymorphisms and molecular signs of selection; (vi) workshop and research on the genetic bases of adaptation and speciation; and (vii) fieldwork to gather ecological data.
Description of the work performed since the beginning of the project:
(i) We have initiated and completed several scientific papers (see publication list). (ii) We have been applying Illumina Hiseq 2000 sequencing in several subprojects, which also includes building sequencing libraries in the local laboratories at Lund University and University of Pretoria. (iii) We have been collaborating on the de novo sequence assembly in the Tristan da Cunha Nesospiza bunting. We have also conducted a draft genome of Zosterops lateralis, an ecological model white-eye species, and will soon initiate similar work on an Acrocephalus warbler (A. arundinaceus). We have generated large-scale transcriptomic sequence data that is used to annotate the Nesospiza reference genome. (iv) We are conducting research on sequencing a large set of individuals using the RAD sequencing technique. We have now RAD data for Nesospiza buntings, Serinus finches, Acrocephalus warblers and Zosterops white-eyes. (v) We are now collaborating on detecting polymorphisms and will start looking for molecular signs of selection in this data. We have also gathered gene expression data from eight Nesospiza individuals in order to conduct differential gene expression analyses in Nesospiza individuals with key phenotype differences (variation in bill size). (vi) We have not yet started our research on the genetic bases of adaptation and speciation. (vii) We have gathered high quality ecological data on the Tristan Nesospiza buntings and Sao Tomé Serinus finches. In addition to these tasks we have conducted conservation genetics work of rare Angolan birds and of endemic Lagonosticta finches in West Africa.
Description of the main results:
Generating massive amount of sequencing data and building reference genome de novo for Nesospiza and Zosterops. Conducting comparative analyses of this data against the main passerine model species, the zebra finch. Successful set up of Illumina sequencing libraries locally in Lund and Pretoria. Generating large-scale transcriptomic data that is now used to annotate the Nesospiza reference genome. Differential gene expression analyses in Nesospiza individuals with key phenotype differences initiated. Successful sequencing and genotyping using RAD sequencing of a large set of individuals that will now be used to analyse population differences (in Nesospiza, Serinus, Acrocephalus and Zosterops) and genotype-phenotype analyses using data from the Nesospiza hybrid zone that is present on one of the Tristan da Cunha islands. We have initiated conservation genetics work of Angolan birds and of Lagonosticta finches endemic to West Africa. We are now using our results to confirm or refute the occurrence of sympatric speciation in avian radiations. Our main result is that in the Neospiza/Serinus system there is mainly divergence in allopatry – a result that was possible to reach due to analyses of large scale genomic data (RAD-tag sequencing) generated during this project. In the Tristan finch system we have recently found genetic regions that are under selection, and this is now helping us understanding the biological, physiological and cellular functions of the genes in these regions in order to determine the genetic bases of adaptation and ultimately speciation.
Impact:
Our programme and partnership is positioned at the forefront of evolutionary research and has a very high potential for high scientific impact. Several lines of the research are expected to produce results with the quality and broad implications required for submission to the top scientific journals; and some manuscripts are now published in well-ranked journals (see the uploaded publication list). A very important component of the scientific process is analysing data and writing papers for international journals and the partnership has provided added value.
A priority area of the framework programme is sustainable development and global change. In order to achieve this main objective, it is important to understanding the processes generating biodiversity. Our current research agenda and its results have high potentials for main impact in this context and to contribute to research excellence and European competitiveness.
The genetics of speciation and the speciation process are of fundamental importance in evolutionary and conservation biology, and is also of high international interest and importance. Yet many central questions remain unresolved because theoretical models have failed to incorporate the genomic and ecological complexities of natural populations, whereas empirical advances have been restricted for methodological reasons. By applying research on several complementary study systems and by using recently developed molecular genetic tools our programme has been able to deepen our understanding on speciation and differentiation. We have been setting up collaboration between senior and junior researchers, some with long-standing experience in field biology and/or laboratory work, and use state-of-the-art molecular techniques (Illumina HighSeq and RAD sequencing). Our results have revealed important insights in the genetics of speciation and we hope it will have impact in the scientific community in the area of collaboration.
Contact Details:
Bengt Hansson
Lund University
Email: bengt.hansson[at]biol.lu.se