Marine evolution during global change – establishing new model
species for ecogenomic research
Human impacts cause rapid changes of marine environments and a burning issue is if
populations and species can adapt to these changes. With 10-year research council funding
we study rapid evolution, involving population adaptation and speciation of marine
Amcomprehensive genomics, transcriptomics, proteomics and metabolomics methodology
and developing multi-generation culturing for a set of model species is urgent to support
research on the molecular mechanisms involved.
Draft executive summary
Today human activities impact all environments. The oceans, earlier protected by their
enormous sizes, are undergoing dramatic changes that fundamentally impact on marine
ecosystems and the diversity of species found there. Following environmental change,
organisms will either survive through adaptation or disappear (move or become extinct).
Today we are not able to predict under what circumstances a population is able to adapt to an
environmental change, or what genetic and metabolic features of organisms make them more
or less likely to adapt. The main goals of the Linnaeus Centre for Marine Evolutionary
Biology at the University of Gothenburg (www.cemeb.science.gu.se) are to study
mechanisms of adaptation and rapid evolutionary change in marine species. We do this by
investigating the adaptation of marine organisms to a young and perturbed marine
environment (the Baltic Sea), by experimental studies of larval development in distorted
conditions, and by analysing recent and ongoing processes of rapid evolution. We use
advanced molecular tools along with population genetic, ecological and physiological
approaches and focus on ecologically relevant organisms. For the majority of these, however,
the complete genomes sequence and gene maps are lacking, and gene-expression patterns and
gene functions have not yet been characterized and this currently limits our research, as well
as the marine research world-wide. The lack of genome and transcriptome information
seriously impedes our possibilities to understand evolution at the molecular level and restricts
our possibilities to interpret sequence data scattered over the genome. In addition, few noncommercial marine organisms are maintained in culture, with the consequence that
inheritance patterns of ecologically and physiologically important traits are lacking.
The main goal of this project is to develop six ecologically important marine model species
into useful tools for marine evolutionary biology and environmental research by ways of:
» Sequencing complete genomes for gene identification, annotation, population
genomics and studies of hybridization and introgression
» Characterizing gene expression (transcriptomics), protein expression, interaction and
localisation (proteomics, GFP tagging and microscopy) and physiological pathways
(metabolomics)
Establish multiple generation culturing and cross-breed lines and populations for gene
mapping and characterization of gene function, establish gene knock-down or knock –in
technologies
Tentative list of target species (will be reduced to 6 species).
General criteria for choice of target species should be: ecologically important, possible to
culture and manipulate in the laboratory, not (to our knowledge) targeted in any other ongoing
genome sequencing initiative world-wide....
Amphiura filiformis (brittlestar) can reach high densities with several thousand in just a few
square meters. It lives burrowed in mud, a habit that makes it a keystone species in
bioturbation. It suspension feeds with usually 2-3 arms emerging into the water column. It
thus experiences frequent sub lethal predation (it is as a major food source for flatfish and
crayfish). Regeneration of lost arms is essential for survival and A. filiformis possesses
exceptional regenerative abilities and is also employed as a model for regeneration research. It
is easy to culture larval stages to settlement and we have an expanding EST collection and
many other molecular tools.
Balanus improvisus (barnacle). Main fouling organism and potential source for
biotechnological research (superglue). Distributed over salinities from 5-35‰. Culturing
technology already established that provide larvae all year round. Important test-organism for
antifouling research and as useful for ecological research.
Debaryomyces hansenii (The marine fungus) (genome size 13 Mb)
Yeasts are unicellular basidiomycetous and ascomycetous fungi that have been isolated from
different marine sources, e.g. seawater, marine deposits, seaweeds, fish, marine mammals and
sea birds. Ecological studies provide evidence for the contribution of these marine mycota to
productivity and transformation activities in the sea. The yeast species Debaryomyces
hansenii has been isolated from most types of marine niches. This yeast exhibits an
exceptionally wide stress tolerance, and it can thrive in environments of 4M NaCl. D.
hansenii is also highly tolerant to daily and seasonal changes in conditions and can be
presumed to have efficient regulatory circuits that handle environmental challenges. The
study of D. hansenii will yield fascinating insights into evolutionary adaptation for growth
and survival under extreme and varying conditions and provides a unique window into the
molecular biology of response-physiologies for stress tolerance in marine waters. The genome
of D. hansenii has been sequenced (finished in 2004), and efficient transformations systems
have recently been developed. This species is thus a great system for transferring/testing
molecular information on salt-tolerance from the well-studied non-marine S. cerevisiae. The
information on gene-by-salt interactions of D. hansenii genes opens up for highly resolved
population genomics studies on local populations of this marine fungus along the Swedish
salinity gradient.
Fucus vesiculosus (bladderwrak) and F. radicans. Foundation species in northern Atlantic
(F. radicans endemic to the Baltic Sea) providing shelter and food for fish-larvae and
invertebrate grazers (Råberg et al. 2007 Est Coast Shelf Sci). Population genetic data showing
substantial population genetic structuring with genetic differentiation down to a scale of tens
of meters. Generation time 2 years or more, but robust to treatment and easy to cross-breed
and culture, tolerant to salinities between 5-35‰. Baltic populations show varying degrees of
clonality (else separate sexes). The two species are extremely closely related - separate a few
thousand years ago inside the Baltic Sea (Pereyra et al. 2008 BMC Evol Biol) - hence opportunities
for studying mechanisms and rate of evolution of species-specific traits (such as temperature
tolerance Lago-Leston et al. 2010 Mar Biol) over short periods of time. Candidate for pair-genome
comparisons.
Idothea spp. The isopod genus Idotea contains about 25 species of small, littoral crustaceans,
mainly from temperate marine waters. In many areas, e.g. northern Europe, Idotea spp. are
important herbivores and are also important as food for many fish species. In the Baltic Sea
Idotea balthica is regarded as a key species and forms an important link between primary
production and higher trophic levels.
Species within Idotea have short generation times (ca 2 months) and are very easy to culture.
The natural environment of most Idotea spp. is easily reproduced in laboratory experiments
and even field manipulations are possible. Idotea species have dimorphic sexes and the
brooded offspring have direct development with no planktonic stages. This makes Idotea
species ideal marine model organisms for evolutionary studies where phenotypic plasticity
and response to selection can be estimated using common-garden and breeding experiments.
The recent and dramatic history of the Baltic Sea offers a unique testbed for studies of
evolution to environmental change. The three species of Idotea that have invaded the Baltic
Sea may offer key information about evolutionary history, evolutionary potential for
environmental change, and the role of phenotypic plasticity. No genetic resources yet
available.
Littorina saxatilis (periwinkle snail). Rocky-shore key-species in N Atlantic. Repeated
development of local adaptation to different shore environments over spatial scales of tens of
meters (Johannesson et al. 1995 PNAS). Comprehensively assessed for population genetic
structure, ecology and behaviour (eg. Panova et al 2006 Mol Ecol). Nuclear and mitochondrial
based species phylogeny including well-defined ecotypes is in pipeline. One of the most
promising marine models for studies of micro-evolution, including mechanisms of speciation
(Quesada et al. 2006 Evolution; Butlin et al. 2009 Phil. Trans. R. Soc.; Johannesson et al. 2010 Phil. Trans. R.
Soc. B.). Generation time 6 months and a direct development. Some in-house knowledge of
multiple generation culturing and cross-breeding.
Pomatoceros lamarckii /triqueter are widespread biofouling organisms on both man-made
marine structures and biological structures such as shellfish carapaces and shells. They have
economic impacts such as requiring regular removal from oil rigs, vent pipes, boats, and
marine-based renewable energy producing structures, as well as reducing the economic value
of commercial shellfish produce or even its viability and survival (e.g. mussel fouling in
aquaculture. They are widespread, easily accessible, and intertidal, and so tolerate a wide
array of conditions (temperature, salinity) permitting the examination of the biological effects
of such treatments in live material.
Their natural spawning time is supposed to be around July/August/September. With a culture
facility they could be kept at optimal light and temperature settings plus food so that they
think they are in permanent early summer, so that the proportion of worms with ripe gametes
is maximized. Polychaetes increasingly used in Evo-Devo and some genomic tools are
already available (e.g. Takahashi et al. 2009 BMC Evolutionary Biology;
McDougall C, et al. 2008 Parasite)
Pomatoschistus minutus (sand goby) A small marine fish with male care of the offspring.
Important model in evolutionary behavioural ecology, in particular mating and reproduction
systems are extensively studied. It is common along all the coasts of northern Europe. Adult
fish are easy to catch, easy keep in the lab and they breed willingly in aquaria. It is yet
unknown how easy or difficult they are to culture, but initial lab breeding attempts will soon
commence. They most challenging step will no doubt be to raise fish fry into juvenile fish.
The first aim is to establish a common garden experiment to compare fish from the Swedish
west coast to fish from the Baltic Sea. Given that their behaviour is particularly well-studied
in these two parts of their distribution, a further aim is to link behavioural differences to
particular genes as well as gene expression, thus allowing us to study genotypic and
phenotypic adaptations to the lower salinity of the Baltic Sea. Several fish genomes already
available, which will be useful in this work.
Shipworm – important commercial for underwater wood constructions (ships, pilings and
dykes). There is also a considerable interest in this species amongst marine archaeologists
who wish to protect ancient wrecks from being attacked and damaged. It’s unique feature is
being able to utilize cellulose and decompose it into glucose, (with symbiotic bacteria) and for
this reason interesting in a biotechnological aspect. Relatively large mollusc with extremely
short generation time (weeks) and easy to culture (in pieces of wood).
We have 3 options here:
Teredo navalis a short-term brooder, so larval feeding is needed. Generation time?
Nototeredo norvagica a broadcast spawner so larval feeding needed. Generation time?
Both are around Sweden.
Lyrodus pedicellatus is starting to turn up in the UK but not in Sweden yet (as far as we
know). It is wide-spread in warmer waters further south. It has a short breeding cycle and is a
batch brooder so might be able to get several generations/year.
Strongylocentrotus droebachiensis is common throughout the region and has the added
advantage of also having a “circum-arctic” distribution, which means it is also found along
the eastern seaboard of North America. We already have a large EST collection in
collaboration with our colleagues in Kiel. S. droebachiensis is used widely for population
genetic studies and is also an important commercial species being “ranched” in Norway and is
some areas of North America. We have easy access to two contrasting populations and it is
easy to keep and culture in the lab. The sister species S. pupuratus has the genome available.
Zoarces viviparous (eelpout). Interesting model in ecotoxicological studies (cf Lars Förlin’s
project) of selection from antropogenic contamination. Direct development – probably easy to
culture.