Final Report Summary - EUROINVADERS (Understanding the evolutionary mechanisms of invasion success: Selective footprints in the genome of an Euro-invader – the raccoon dog (Nyctereutes procyonoides))
It is a worldwide, worrisome phenomenon that faunal endemism is threatened by introduced species populating new habitats, a process that is aided by the growing globalization which makes natural dispersal barriers more permeable. One of the most successful invaders of Europe is the raccoon dog (Nyctereutes procyonoides), a mammal that severely affects endemic biodiversity while thriving in new environments. The species’ peculiar evolutionary history was primarily facilitated by its ability to quickly adapt. While previous research has provided some knowledge of the ecological and environmental conditions the species has adapted to, we lack crucial understanding of the genetic mechanisms that render such a dramatic expansion possible. Moreover, raccoon dogs exhibit a karyotype pattern that is unique amongst mammals and deserves further in depth investigations as it might provide new insights into chromosomal evolution and fundamental knowledge of speciation processes. By synergizing novel molecular technologies with sophisticated analysis tools the study pioneers the field of wildlife population genomics and will provide new, valuable insights into the biology of invasions and speciation. In this project, I conducted a genetic study utilizing modern, next generation sequencing technologies in order to investigate the underlying mechanisms that have facilitated adaptive and speciation processes in raccoon dogs ultimately bringing the study of bio-invasions to a new level.
In a first phase of the project I generated a comprehensive library of all genes expressed in each of three Asian and three European raccoon dogs. By means of sequencing the complete transcriptomes an average of 38 million sequence reads were generated per individual, which allowed reliable identification of single nucleotide polymorphisms in candidate loci selection has acted upon. This enables investigation of population specific patterns of alternative splicing and lastly elucidation of genes that are differentially expressed within varying environments the raccoon dog has adapted to. The generated data are currently analyzed as part of an MSc project.
The second phase of the project aims at attaining a comprehensive picture of the diversification process that ultimately led to various karyotypes being established within a short period of time in different raccoon dog populations. Investigating the different chromosomal arrangements on a nucleotide level for the first time allows identifying genomic regions that might be involved in speciation and diversification processes. This has implications for our perception of the mechanisms associated with speciation, e.g. Robertsonian Translocation, a theory that has been widely accepted amongst biologists as one of the drivers in speciation processes but little is known about the actual genomic architecture allowing this force to act upon. As a first milestone into the direction of generating complete genomes of raccoon dogs of Asian origin, the region where karyotypic variation actually occurs, has been achieved during the second phase of EUROINVADERS, namely the sequencing of expressed genes of Japanese raccoon dogs. Intriguingly, Japan shows a diverse array of karyotypes while the rest of the species distribution remains homogeneous for the number of chromosomes. Consequently, the seven sequenced specimens from Japan provide a first glimpse into the genomic background of diverse karyotypes. Given the complexity and large amount of data generated, powerful computing resources are required to succeed with the project and are currently heavily exploited in the course of the analyses.
While the analyses of the raccoon dog transcriptomes are proceeding and the final publication of the results are anticipated during 2015, two papers in peer reviewed journals have been delivered thus far. One methodological paper (Schwochow et a. 2012) describes the advantages of a particular procedure to preserve RNA from whole blood samples obtained in the field, the method of choice for EUROINVADERS. The second paper (Thalmann et al. 2013) focused not directly on the raccoon dog itself but rather on an evolutionary cousin. In order to comprehend the genetic peculiarities of a species, we are to put the focal species into a phylogenetic perspective and thus have a profound understanding of the evolutionary history of its closest relatives as well. The raccoon dog belongs to the family of Canidae, which also contains man’s best friend – the dog. In a multidisciplinary, collaborative effort we applied laboratory methods, which are of use in EUROINVADERS as well and ancient specimens to derive in a new evolutionary scenario explaining the origin and timing of dog domestication. This is of direct relevance to the project since we use the dog as a reference for our genomic inferences and a comprehensive understanding of the demographic history that shaped the patterns of genetic variation in the dog genome is a pre-requisite to allude to functional changes in the focal species, the raccoon dog. In order to substantiate our new hypothesis of dog domestication Dr. Thalmann is furthermore involved in a follow-up study that will shed more light into the genetic composition of Pleistocene canids. Lastly, broadening the phylogenetic perspective, Dr. Thalmann together with scientists from other fields solved a longstanding mystery in canid evolution – the existence of an African wolf. Altogether, the published and anticipated papers will put the raccoon dog into a new perspective of canid evolution and allow drawing a more accentuated picture of the specie’s evolutionary and adaptive history. Aside from the publication, the results of the two studies as well as preliminary results and the concept of EUROINVADERS have been presented at various occasions including an invited talk at the 2013 meeting of the International Union of Physiological Sciences, Birmingham, England (Thalmann eta l. 2013). Dr. Thalmann was further invited to speak at 10 seminars hosted in five different countries. During the course of the EUROINVADERS Dr. Thalmann assembled an international consortium with the aim of uniting experts of raccoon dog biology in order to promote and establish future research on this critical bioinvader. The collaborative character of the project contributed to the globalization of research both within the European Union and between Europe and Asia by initiating an active and fruitful intellectual exchange.
As part of the career development of the researcher, the mobility opportunities of EUROINVADERS have been exploited for a research stay abroad to advance the bioinformatics skills as well as an MSc was recruited to the project under the supervision of Dr. Thalmann. In summary, the capacities provided by EUROINVADERS allowed the publication of seminal research as well as to help the researcher to advance in his career and develop into an expert in canid evolution and the processes of bio-invasions.
Due to its rapid expansion throughout Europe, the raccoon dog has become a significant, global “problem species” that was used here as a “model” organism to investigate the underlying genetic mechanisms of its invasion success. Such knowledge might ultimately help to develop effective management plans in order to confine the expansion of invading species and protect native fauna and flora. The methods and tools applied in EUROINVADERS and the derived implications are potentially transferable to other invasive species and the quest to find common, uniting feature of these aliens has thus reached another level. In light of evolutionary genetics, this research has contributed to a better understanding of the mechanisms that have shaped the genomes of an invasive species and facilitated its evolutionary success during its relatively young invasion and speciation history.
In a first phase of the project I generated a comprehensive library of all genes expressed in each of three Asian and three European raccoon dogs. By means of sequencing the complete transcriptomes an average of 38 million sequence reads were generated per individual, which allowed reliable identification of single nucleotide polymorphisms in candidate loci selection has acted upon. This enables investigation of population specific patterns of alternative splicing and lastly elucidation of genes that are differentially expressed within varying environments the raccoon dog has adapted to. The generated data are currently analyzed as part of an MSc project.
The second phase of the project aims at attaining a comprehensive picture of the diversification process that ultimately led to various karyotypes being established within a short period of time in different raccoon dog populations. Investigating the different chromosomal arrangements on a nucleotide level for the first time allows identifying genomic regions that might be involved in speciation and diversification processes. This has implications for our perception of the mechanisms associated with speciation, e.g. Robertsonian Translocation, a theory that has been widely accepted amongst biologists as one of the drivers in speciation processes but little is known about the actual genomic architecture allowing this force to act upon. As a first milestone into the direction of generating complete genomes of raccoon dogs of Asian origin, the region where karyotypic variation actually occurs, has been achieved during the second phase of EUROINVADERS, namely the sequencing of expressed genes of Japanese raccoon dogs. Intriguingly, Japan shows a diverse array of karyotypes while the rest of the species distribution remains homogeneous for the number of chromosomes. Consequently, the seven sequenced specimens from Japan provide a first glimpse into the genomic background of diverse karyotypes. Given the complexity and large amount of data generated, powerful computing resources are required to succeed with the project and are currently heavily exploited in the course of the analyses.
While the analyses of the raccoon dog transcriptomes are proceeding and the final publication of the results are anticipated during 2015, two papers in peer reviewed journals have been delivered thus far. One methodological paper (Schwochow et a. 2012) describes the advantages of a particular procedure to preserve RNA from whole blood samples obtained in the field, the method of choice for EUROINVADERS. The second paper (Thalmann et al. 2013) focused not directly on the raccoon dog itself but rather on an evolutionary cousin. In order to comprehend the genetic peculiarities of a species, we are to put the focal species into a phylogenetic perspective and thus have a profound understanding of the evolutionary history of its closest relatives as well. The raccoon dog belongs to the family of Canidae, which also contains man’s best friend – the dog. In a multidisciplinary, collaborative effort we applied laboratory methods, which are of use in EUROINVADERS as well and ancient specimens to derive in a new evolutionary scenario explaining the origin and timing of dog domestication. This is of direct relevance to the project since we use the dog as a reference for our genomic inferences and a comprehensive understanding of the demographic history that shaped the patterns of genetic variation in the dog genome is a pre-requisite to allude to functional changes in the focal species, the raccoon dog. In order to substantiate our new hypothesis of dog domestication Dr. Thalmann is furthermore involved in a follow-up study that will shed more light into the genetic composition of Pleistocene canids. Lastly, broadening the phylogenetic perspective, Dr. Thalmann together with scientists from other fields solved a longstanding mystery in canid evolution – the existence of an African wolf. Altogether, the published and anticipated papers will put the raccoon dog into a new perspective of canid evolution and allow drawing a more accentuated picture of the specie’s evolutionary and adaptive history. Aside from the publication, the results of the two studies as well as preliminary results and the concept of EUROINVADERS have been presented at various occasions including an invited talk at the 2013 meeting of the International Union of Physiological Sciences, Birmingham, England (Thalmann eta l. 2013). Dr. Thalmann was further invited to speak at 10 seminars hosted in five different countries. During the course of the EUROINVADERS Dr. Thalmann assembled an international consortium with the aim of uniting experts of raccoon dog biology in order to promote and establish future research on this critical bioinvader. The collaborative character of the project contributed to the globalization of research both within the European Union and between Europe and Asia by initiating an active and fruitful intellectual exchange.
As part of the career development of the researcher, the mobility opportunities of EUROINVADERS have been exploited for a research stay abroad to advance the bioinformatics skills as well as an MSc was recruited to the project under the supervision of Dr. Thalmann. In summary, the capacities provided by EUROINVADERS allowed the publication of seminal research as well as to help the researcher to advance in his career and develop into an expert in canid evolution and the processes of bio-invasions.
Due to its rapid expansion throughout Europe, the raccoon dog has become a significant, global “problem species” that was used here as a “model” organism to investigate the underlying genetic mechanisms of its invasion success. Such knowledge might ultimately help to develop effective management plans in order to confine the expansion of invading species and protect native fauna and flora. The methods and tools applied in EUROINVADERS and the derived implications are potentially transferable to other invasive species and the quest to find common, uniting feature of these aliens has thus reached another level. In light of evolutionary genetics, this research has contributed to a better understanding of the mechanisms that have shaped the genomes of an invasive species and facilitated its evolutionary success during its relatively young invasion and speciation history.