Crossing the divide: population genomics of adaptation to salinity in a model protist.
Lead Research Organisation:
University of Liverpool
Department Name: Institute of Integrative Biology
Abstract
Single celled organisms (microbes) are extremely important to the health and function of global ecosystems. In particular, marine microbes assure the production of about 50% of the planetary oxygen, thus are as important as the world's rainforests, and fuel the marine food web, thereby maintaining the fisheries that are essential to mankind. It is clearly important to understand the dynamics of marine microbial populations-for example, to know the sizes and boundaries of microbial populations, the factors that determine these populations, and what environmental features affect dispersal between areas. However, becase of their small size it is almost impossible to directly track marine microbes in the natural environment and study these parameters and this aspect of their ecology and evolution remains understudied.
Rather, because free-living marine microbes are assumed to have broad distributions and large population sizes, and there are a lack of obvious barriers to dispersal in most seas, there is the common assumption that marine microbial populations are widespread and also genetically diverse and homogeneous over large distances. However, this model of population structure is too simplistic: recent studies have discovered that marine microbes have complex population structures, for example, determined by the ocean currents. In many marine species, especially well-studied groups such as fish, there is evidence that the environment (e.g. salinity) has a strong effect upon what constitutes a distinct population, particularly by selecting for a specific amount and type of genetic diversity present. Such adaptation to the environment can prevent individuals from successfully moving elsewhere (i.e. to an environment that they are not suited to) and conversely prevent immigration by individuals from other areas that have different environments. Hence, understanding population adaptation to the enviroment is crucial to predict response to disturbance and future environment change. Indeed, the question of "how efficient is the environment in selecting for certain types of genetic diversity (i.e. driving population adaptation)?" has not been studied for any species of marine microbe: this represents a fundamental gap in our knowledge.
We propose to collect samples of the free-living, marine microbe, Oxyrrhis marina, across the North Sea-Baltic Sea transition zone, where salinity changes along a 500 km transect from saline (~32 psu) conditions to brackish water (<10 psu). We selected this region as environmental gradients are an efficient means of studying adaptative divergence and also because salinity is one of the most important abiotic drivers for evolution in the oceans: many studies have revealed strong genetic differences between marine fish populations in the North Sea and the Baltic Sea, as well as a typical reduction in genetic diversity in Baltic Sea populations. By sequencing our samples at a large number of genes (350), we can quantify how the amount and type of genetic diversity changes along this environmental gradient. Not only do these data allow us to determine the potential for marine microbes have specific population boundaries, but they indicate how marine microbial populations, and even how specific regions of DNA, can be directly affected by the environment conditions. This will provide a better understanding of the dynamics and evolutionary mechanisms of marine microbial populations, and their capacity to withstand environment change.
Rather, because free-living marine microbes are assumed to have broad distributions and large population sizes, and there are a lack of obvious barriers to dispersal in most seas, there is the common assumption that marine microbial populations are widespread and also genetically diverse and homogeneous over large distances. However, this model of population structure is too simplistic: recent studies have discovered that marine microbes have complex population structures, for example, determined by the ocean currents. In many marine species, especially well-studied groups such as fish, there is evidence that the environment (e.g. salinity) has a strong effect upon what constitutes a distinct population, particularly by selecting for a specific amount and type of genetic diversity present. Such adaptation to the environment can prevent individuals from successfully moving elsewhere (i.e. to an environment that they are not suited to) and conversely prevent immigration by individuals from other areas that have different environments. Hence, understanding population adaptation to the enviroment is crucial to predict response to disturbance and future environment change. Indeed, the question of "how efficient is the environment in selecting for certain types of genetic diversity (i.e. driving population adaptation)?" has not been studied for any species of marine microbe: this represents a fundamental gap in our knowledge.
We propose to collect samples of the free-living, marine microbe, Oxyrrhis marina, across the North Sea-Baltic Sea transition zone, where salinity changes along a 500 km transect from saline (~32 psu) conditions to brackish water (<10 psu). We selected this region as environmental gradients are an efficient means of studying adaptative divergence and also because salinity is one of the most important abiotic drivers for evolution in the oceans: many studies have revealed strong genetic differences between marine fish populations in the North Sea and the Baltic Sea, as well as a typical reduction in genetic diversity in Baltic Sea populations. By sequencing our samples at a large number of genes (350), we can quantify how the amount and type of genetic diversity changes along this environmental gradient. Not only do these data allow us to determine the potential for marine microbes have specific population boundaries, but they indicate how marine microbial populations, and even how specific regions of DNA, can be directly affected by the environment conditions. This will provide a better understanding of the dynamics and evolutionary mechanisms of marine microbial populations, and their capacity to withstand environment change.
Planned Impact
We have indentified 4 main groups of beneficiaries: (1) academic colleagues, (2) the investigators on this project - Dr PC Watts and Dr CD Lowe, (3) our existing network of non-biologist collaborators, and (4) local community science and education groups.
1. Please see the section "Academic Beneficiaries" for details.
2. Our particular focus here is the researcher Co-I Dr Lowe. As an early career scientist and emerging expert in the field of protist evolutionary biology, Dr Lowe stands to gain much essential training and experience in bioinformatic analysis from this work. In addition, the papers generated by this project will provide Dr Lowe with a platform from which to generate fellowship applications and thus establish himself as a leading independent scientist. Of course, Dr Watts will benefit through the continued development of Oxyrrhis as a multidisciplinary model, additional bioinformatics collaboration/training with Liverpool CGR and the generation of high-impact scientific papers and development of additional new grants.
3. The impact objectives with regard to group 3 (above) will be achieved through an extension of our existing research impact activities. As part of our current NERC research grant (NE/F005237/1) on Oxyrrhis marina we have contacted an extensive network of people across Europe who have collaborated with us to collect environmental samples (from which we have isolated O. marina). The majority of our collaborators are non-biologists, who have been enthused at the propsect of helping with fundamental scientific research, and accordingly we disseminate our project outcomes to, and receive feedback from, this network via a 6 monthly newsletter. As the proposed project is related to our current research and will utilise some of the samples, we will use this same mechanism to continue to communicate our research output to this non-specialist audience.
4. As a research group we are strongly committed to the research impact agenda, and while there are no direct commercial private sector beneficiaries to our current research on protist genome diversity, we actively pursue knowledge exchange activities in the local community. For example, past impact activities related to research output have included a "DNA forensics for kids" day-long workshop in conjunction with the world museum Liverpool, and a marine biology and conservation workshop for Merseyside 6th form colleges that was held at the Liverpool Guild of Students (BAckChat 2008: Marine Environments. BA Festival of Science, Liverpool). Finally, members of our research group are actively involved with promoting the research impact agenda within our institute. For example, Dr Watts has provided interviews for radio and newspapers, and Dr Lowe was a panel member on the Institute of Integrative Biology's entry to the BBSRC impact with excellence competition (2009-2010) and is the post-doctoral representative on the Institute's research impact committee. Particularly with regard to primary research a focus has been made on integrating our research within the local community (via schools, museums, and local community groups). For the proposed project, these existing networks will be employed to engage with local community. Specifically, we will contribute to the British Science Association's Merseyside annual meeting (in Nov 2012).
1. Please see the section "Academic Beneficiaries" for details.
2. Our particular focus here is the researcher Co-I Dr Lowe. As an early career scientist and emerging expert in the field of protist evolutionary biology, Dr Lowe stands to gain much essential training and experience in bioinformatic analysis from this work. In addition, the papers generated by this project will provide Dr Lowe with a platform from which to generate fellowship applications and thus establish himself as a leading independent scientist. Of course, Dr Watts will benefit through the continued development of Oxyrrhis as a multidisciplinary model, additional bioinformatics collaboration/training with Liverpool CGR and the generation of high-impact scientific papers and development of additional new grants.
3. The impact objectives with regard to group 3 (above) will be achieved through an extension of our existing research impact activities. As part of our current NERC research grant (NE/F005237/1) on Oxyrrhis marina we have contacted an extensive network of people across Europe who have collaborated with us to collect environmental samples (from which we have isolated O. marina). The majority of our collaborators are non-biologists, who have been enthused at the propsect of helping with fundamental scientific research, and accordingly we disseminate our project outcomes to, and receive feedback from, this network via a 6 monthly newsletter. As the proposed project is related to our current research and will utilise some of the samples, we will use this same mechanism to continue to communicate our research output to this non-specialist audience.
4. As a research group we are strongly committed to the research impact agenda, and while there are no direct commercial private sector beneficiaries to our current research on protist genome diversity, we actively pursue knowledge exchange activities in the local community. For example, past impact activities related to research output have included a "DNA forensics for kids" day-long workshop in conjunction with the world museum Liverpool, and a marine biology and conservation workshop for Merseyside 6th form colleges that was held at the Liverpool Guild of Students (BAckChat 2008: Marine Environments. BA Festival of Science, Liverpool). Finally, members of our research group are actively involved with promoting the research impact agenda within our institute. For example, Dr Watts has provided interviews for radio and newspapers, and Dr Lowe was a panel member on the Institute of Integrative Biology's entry to the BBSRC impact with excellence competition (2009-2010) and is the post-doctoral representative on the Institute's research impact committee. Particularly with regard to primary research a focus has been made on integrating our research within the local community (via schools, museums, and local community groups). For the proposed project, these existing networks will be employed to engage with local community. Specifically, we will contribute to the British Science Association's Merseyside annual meeting (in Nov 2012).