PhD Code: MARES_13_08:
- Host institute 1: P5 - University of Algarve
- Host institute 2: P11 - Université Pierre et Marrie Curie (UPMC)
- T1 - Future Oceans: temperature changes - hypoxia - acidifation
- T3 - Biological Invasions
- Serrão Ester - firstname.lastname@example.org
- Viard Frédérique - email@example.com
- Dr. Aschwin Engelen: firstname.lastname@example.org Dr. Gareth Pearson: email@example.com both of CCMAR
Introductions of alien species cause fundamental and irreversible changes to natural communities and ecosystems worldwide (Winters et al. 2009; Molnar et al. 2008), affecting ecosystem functioning (Sousa et al. 2009). Europe is a hot-spot for aquatic introductions with around 1000 alien species recorded at present (Gollasch 2008). Alien seaweeds represent one of the largest groups of marine aliens in Europe, and constitute between 20 and 29 % of all alien marine species (Schaffelke et al. 2006; Williams & Smith 2007). Introduction of Invasive Alien Species (IAS) is regarded as a serious threat to European biodiversity and ecosystems as stated in the EU biodiversity strategy to 2020. Moreover, The European Marine Strategy Framework Directive, a legislative framework for an ecosystem-based approach to environmental management, states that “Non-indigenous species introduced by human activities [should be kept] at levels that do not adversely alter the ecosystems”. Alien seaweeds represent one of the largest groups of marine aliens in Europe, and constitute between 20 and 29 % of all alien marine species (Schaffelke et al. 2006; Williams & Smith 2007).In this context, there is an urgent need to put biological invasions into a temporal perspective (i.e. future spread; evolution of invasiveness etc.) even though these may seem a major challenge (Strayer et al. 2006). This is particularly true when considering the mechanisms and speed of acclimation and adaptation of alien species into their new range, an issue which only started to be addressed recently (Keller et al. 2008). Several processes have been proposed, including genetic adaptation by selection on standing genetic variation (Riquet et al. 2013), epigenetic and phenotypic changes, or adaptation through hybridization (Prentis et al. 2008).
The invasive seaweed Sargassum muticum has been shown by both research groups involved in this application to lack genetic variation at microsatellite loci across Europe and America (in contrast to the native range), but has still become one of the most successful marine invaders across habitats over a large geographical range. This suggests the importance of phenotypic and/or epigenetic processes in the evolution of invasiveness. An additional non genetic mechanism could be the co-evolution between seaweeds and specific bacterial communities. The importance of associations between microorganisms and their host is becoming increasingly apparent in shaping the evolutionary paths of both. Phenotypic and/or genetic changes driven by the (abiotic and biotic) environment may thus result in the rapid evolution of invasive species on ecological time scales (Buswell et al. 2011). These mechanisms remain to be investigated in the marine realm, in particular for algae. The main objective of this project is to examine how the processes of acclimation and adaptation influence the success of invasive seaweeds. We will focus on S. muticum as model species, one of the most invasive seaweeds at a worldwide level. This work is supported by the EU SEAS-ERA project INVASIVES, which will guarantee the candidate research funding, international collaboration, mobility and outreach opportunities.
Two specific issues are addressed through the following objectives: 1. To assess the role of genetic vs. epigenetic variation in S. muticum 2. To assess the role of bacterial communities in S. muticum
Task 1: Investigating genetic variation in invasive Sargassum muticum. Recent results, based on microsatellite markers and obtained by collaboration between the two applying research groups, suggest that phenotypic plasticity is responsible for the invasive success of S. muticum, in contrast to all current emphasis on the importance of genetic diversity for the fitness of a species.
Taking benefit of new high-throughput sequencing technologies, we will first do an in-depth investigation of genetic variation on the success of S. muticum along its latitudinal gradient in Europe. This will be done first by carrying out a genome scan approach to increase the likelihood to observe genetic variants as compared to microsatellites. Rad-Seq technologies will be chosen as it allows for genome-scale population genetics with or without a reference genome. 96 specimens collected along two latitudinal gradients located in the two main regions of introduction (Europe and North-Amercia) will be tagged and analyzed through a Rad-seq method to look for polymorphic SNPs. The library production and the sequencing will be done by a private company. Such a genome scan approach, increases the likelihood to observe genetic variants as compared to microsatellites. Then SNP polymorphism will be analyzed at population level (40 individuals per population; 12 localities) along the latitudinal cline using a BeadExpress method or similar technologies available at the time of the study. The required genotyping will be carried out by a private company. For both approaches the PhD student will be in charge of the molecular preparation of samples and the bioinformatic analyses. The hands-on work for this task will take place at the Station Biologique de Roscoff (France) under the supervision of Dr. Frédérique Viard, where the analyses will be collaborative work between the two research teams. The aims of the data analyses are two-fold: to delineate population units based on neutral markers divergence and to delineate groups under divergent selection (i.e. Funk et al. 2012). In addition, an exploratory work of epigenetic mechanisms will be carried out. Epigenetic patterns will be examined across tissue types (holdfast, vegetative and reproductive tissue), across latitudes and from temperature experiments. One epigenetic mechanism candidate, the extent and patterns of cytosine methylation, will be screened using the methylation-sensitive amplified polymorphism (MSAP) technique. The MSAP method enables the identification of methylation-based epi-allelic markers in wild populations of non-model plants in absence of detailed genomic information. Other epigenetic mechanisms will be explored if, cytosine methylation is not relevant in the study species. This task will be carried out at the University of Algarve in the MAREE research group in Faro (Portugal).
Task 2: The role of associated bacterial communities in adaptation and evolution. Seaweeds have an abundant and diverse associated microbial community with species or even location specific components. This microbial community is involved for instance in morphogenesis (as in the case of Ulva spp; REF) and production of biologically active compounds. The PhD candidate will 1) characterize the bacterial community associated with S. muticum across latitudes along European coasts, 2) assess bacterial community differentiation across tissue types in the south, central and north of its European distribution and 3) assess seasonal dynamics in associated bacterial communities and 4) investigate effects of experimental temperature manipulations by next generation sequencing of 16S rDNA, a reference marker for bacterial community analyses. Approximately 6000 sequences per sample will be generated resulting in a DNA database of an estimated total of 600000 sequences. This will enable the identification of the core microbial community of S. muticum, as well as to assess shifts in the microbial assemblages according to regions/environment along the latitudinal gradient of colonization. The candidate will be in charge of sampling, DNA extraction, amplification and data analysis with the exception of the next generation sequencing which will be outsourced. All these activities will take place at the University of Algarve, Faro, Portugal.
- Buswell et al. (2011). J. Ecol. 99: 214-224
- Funk et al. (2012) Trends in Ecology & Evolution 27:489-496.
- Gollasch (2008). Helgol Mar Res 60: 84–89
- Keller & Taylor (2008). Ecol Lett 11: 852-866
- Molnar et al. (2008). Front Ecol Environ 6: 485-492
- Prentis et al. (2008). Trends in Plant Science 13: 288-294.
- Riquet et al. (2013) Molecular Ecology 22:1003-1018.
- Schaffelke et al. (2006). Journal of Applied Phycology 18: 529-541
- Sousa et al. (2009). Biol Invasions 11: 2367-2385
- Strayer et al. (2006) Trends in Ecology and Evolution 21:646-651.
- Williams & Smith (2007). Annu. Rev. Ecol. Evol. Syst. 38:327–59
- Winter et al. (2009). PNAS 106: 21721-21725
We expect that the proposed project would lead to 4 publications for the thesis of the candidate on innovative insights on invasive seaweeds with the application of next generation sequencing approaches and associated bioinformatic techniques. Invasive species studies are mainly used to study the invasive problems associated to them and seldomly used to study underlying mechanisms and as models to elucidate evolutionary aspects as is proposed here. The PhD candidate will be embedded in research in 2 top marine institutes and an European project (INVASIVES) and promote the education of the candidate in trans-disciplinary research that covers ecology, genomics, microbiology and bioinformatics. The candidate will participate in public outreach events of both host locations and present work at local and international scientific meetings. The project Invasives will have a web- and facebook page in which the candidate will participate actively as part of the outreach to the general public.
Putative Thesis structure:
- Chpt 1 Acclimation and adaptation of invaders: a review.
- Chpt 2 Cryptic differentiation of an invader across latitudes invaded regions revealed by Rad-Seq.
- Chpt 2 Single nucleotide differentiation of an invader across its entire distribution range.
- Chpt 3 Epigenetic mechanisms of an invader with minimal genetic differentiation to be successful across environmental gradients (latitudes).
- Chpt 4 Adaprive potential of marine invasive species linked to associated microbiome composition across space and time.
- Chpt 5 General discussion