ADAPT-ENVGENOME · ENVIRONMENTAL ADAPTATION OF THE GENOME: A DAPHNIA MODEL UNDER CULTURAL EUTROPHIATION

ENVIRONMENTAL ADAPTATION OF THE GENOME: A DAPHNIA MODEL UNDER CULTURAL EUTROPHIATION

* Project Objectives: Organisms, including man, play a major role in ecosystem processes. However, little work has examined how man-made environmental changes affect the way organisms evolve and adapt to modified ecosystems. The main goal of ADAPT-ENVGENOME project is to explore the evolutionary mechanisms involved in local adaptation of species to anthropogenic environmental changes. To this end, our project assessed how cultural eutrophication (i.e., nutrient enrichment of freshwater systems by humans) influences evolutionary changes in organisms using a multidisciplinary approach involving paleo-genetics, physiology, and genomics. Particularly, we are interested in genes from pathways involved in the handling of phosphorous (P) by analysing natural populations of the model organism, the water flea, Daphnia pulicaria. The two objectives outlined in the project have been completed: - Objective #1, characterize neutral genetic variation (genotypes) and those under selection from dormant egg bank at different dated layers, and extant populations within each habitat was tackled through Next Generation Sequencing (NGS) technology to get higher genome coverage in detecting both neutral loci and loci under selection. We used the Genotyping-by-Sequencing (GBS) approach to identify Single Nucleotide Polymorphisms (SNPs). DNA from several extant Daphnia clones collected from five lakes in Minnesota (USA) with distinct eutrophication histories (from oligotrophic to hypereutrophic) were compared, including clones at least several centuries old resurrected from deep sediment layers. - Objective #2, find natural lineages evolutionarily adapted to low and high Carbon:Phosphorus [C:P] ratio levels showing differentially-adapted genotypes related to Phosphorous processing pathways, was tackled by laboratory competition experiments, at two different C:P ratios/treatments (high and low P conditions), involving a mixture of several allozyme genotypes/clones from two lakes with different eutrophication and P concentration histories. In addition, juvenile growth rate (JGR) and physiological phosphorus retention/use efficiency from these clones were studied in separate experiments. * Main results achieved, conclusions, and potential impact of the project: - By using the described multidisciplinary approach (i.e., genetics, resurrection ecology, competition experiments, Juvenile Growth Rate [JGR] experiments and physiology), our results (first manuscript submitted) reveal that under competition, Daphnia clones from the lake/population with a more variable history of eutrophication have competitive advantages at both high and low phosphorus feeding supplies (i.e., LoP = Low organic Phosphorus algae, and HoP = High organic Phosphorus algae). In addition, it seems that the same population shows higher phosphorus retention efficiency, but not significant, at both P-levels (i.e., LoP and HoP), which could be indicative of greater adaptation and broader survival range to environments with different phosphorus feeding supplies, probably related to lake trophic history. We observed that the higher variability in phosphorus and carbon retention rates was between clones within populations. On the other hand, the lake/population with disadvantages under a competition environment and almost a constant historical phosphorus upload could have a higher plasticity as indicated by our JGR experiments (i.e., juveniles from clones/population that do not compete well, overall show higher growth rate/fitness at earlier stages of their life cycle). These results were presented at the Evolution Meeting 2013 (Snowbird, Utah, USA). - Genomic approach was performed on clones from five different lakes (with different trophic states) has revealed more than 40,000 SNPs with an approximate proportion of 11% aligned to unique positions on the reference genome (i.e., the sister species Daphnia pulex) and 2.9% aligned to multiple positions (second manuscript submitted), which after applying stringent filtering criteria using bioinformatics pipelines, were reduced to 8,490 highly confident and bi-allelic SNP markers. A total of 908 outlier SNPs were detected that identified 1,705 annotated genes in the D. pulex genome, including 454 SNPs in functional genes. Out of 678 EuKaryotic Orthologous Groups (KOG) that we found from outlier SNPs, 240 were involved mainly in three metabolic (lipid, nucleotide and amino acid metabolism) and four regulatory pathways. The generated SNP resource provides an invaluable tool for future population genomics surveys targeting specific and informative loci/regions for Daphnia. Additionally, a preliminary population genomic and phylogenetic analysis indicates that some evolutionary information could be linked to their eutrophication stage (and other ecological traits), but some spatial correlation could be involved as well. We are still working on these analyses to produce a third manuscript. Overall, the results of this project should shed light on local adaptation at both the population and genomic level to environmental changes, particularly phosphorus contamination in freshwater lakes, and we should be able to detect those genes involved in such adaptation and microevolution. Our findings could have a strong impact on ecosystem management with respect to water pollution, conservation biology and invasive species. Project Website: http://www.ebd.csic.es/quini/IOF_ADAPT-ENVGENOME_Quini.htm. Scientist in charge during Outgoing Phase (1st February 2012 - 31st March 2014): Prof. Lawrence J Weider University of Oklahoma. Biology Department. 730 Van Vleet Oval, 103 Sutton Hall, Norman, OK 73019-6121. United States of America Tel: +(1) 405 325 4766 E-mail: ljweider@ou.edu Internet sites: http://faculty-staff.ou.edu/W/Lawrence.J.Weider-1/; http://www.ou.edu/uobs/weider.html Scientist in charge during Return Phase (1st April 2014 - 31st January 2015): Prof. Andy J Green Donana Biological Station (EBD-CSIC). Department of Wetland Ecology. Isla de La Cartuja, Av. Americo Vespucio, S/N, Seville, 41092. Spain Tel: +(34) 954 23 23 40 E-mail: ajgreen@ebd.csic.es Internet site: http://www.ebd.csic.es/andy/ Marie-Curie Fellow: Dr. Joaquin Munoz Donana Biological Station (EBD-CSIC). Isla de La Cartuja, Av. Americo Vespucio, S/N, Seville, 41092. Spain Tel: (+34) 954 23 23 40 E-mail: quini@ebd.csic.es Internet sites: http://www.ebd.csic.es/quini/QuiniPersonal_E.htm; https://www.researchgate.net/profile/Joaquin_Munoz/publications; http://www.researcherid.com/rid/B-9938-2009

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