FY2010 Ecology and Evolution Unit

Ecology and Evolution Unit

Independent New Investigator: Alexander Sergeyevich Mikheyev
Research Theme: Understanding the interplay between genes and the environment

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Abstract

The scope of our research covers many subjects related to evolutionary biology. Over the past year, we continued our primary work on the evolutionary fate of horizontally transferred genes in bdelloid rotifers, but have also commenced several additional research directions. One project deals with the evolutionary puzzle of ultra-conservation, whereby apparently inessential elements persist in the genomes of distantly related species, apparently unchanged. Another project deals with the evolutionary genomics of adaptation to new habitats by an invasive species. Yet another project examines how the network structure of group interactions affects social stability and performance in a massively multiplayer online game.

In addition to the permanent staff of the unit, visiting students have played major roles, spearheading two independent research projects, one on population genetics of an endangered butterfly species, and another on testing coalescent theory using whole genome sequencing of experimentally evolved yeast populations. In addition to the students, an ongoing collaboration with a University of Maryland scientist has focused on understanding the proteomes of local snake venoms, specifically the Okinawa habu and hime habu.

1. Staff

  • Dr. Yutaka Watanabe, Researcher
  • Dr. Denise Brooks, Researcher
  • Ms. Man Ying Tin, Technician 
  • Ms. Hitomi Shinzato, Administrative Assistant

2. Collaborations

Nothing to report

3. Activities and Findings

Overview

 In just over a year at OIST our unit has initiated a number of new research directions. Much time was spent developing novel molecular techniques and testing them. We have also started to work with a new model system (yeast), which has involved some trial and error. In the end, many gigabases of sequence data have been gathered in the course of the year. However, much of these data are still being analyzed, and can only be summarized briefly at this point.

3.1 Evolution of Horizontally Transferred Genes

 One of our main goals was to understand the evolutionary fates of horizontally transferred genes in bdelloid rotifers, which are unique among animals in acquiring genes from other kingdoms of life. To this end, we sequenced a draft bdelloid genome, and are mapping several closely related relatives to this reference. Ultimately, we will use these genomes to infer what kind of selection acts on these genes, and try to estimate the rate at which they are introduced and are lost.

3.2 Evolutionary Genomics of Biological Invasions

 Biological invasions provide an opportunity to study evolution in action, placing species into novel habitats on a large scale. Using repeated introductions of the unusual, facultatively clonal little fire ant, we hope to understand how social insects evolve, and what role evolution plays in biological invasions. This species is a widespread invader, with a facultatively clonal reproductive system. These two characteristics allow us to directly examine genetic changes that have occurred during the invasion process. The founding queen clone can be found alongside novel queen clones that have arisen through sexual reproduction in the time since introduction. Since most invasions, regionally and globally, occur via   single queen clones, replicate invasions allow us to "replay the tape of evolution" and look for generalities. We are currently sequencing the genomes of individuals that have founded populations in new geographical regions, and their sexually produced progeny to understand how selection acts on invasive species.

3.3. Social Evolution in Online Communities

 Analysis of data from social networking sites allows new ways to study diverse aspects of human psychology and social interactions. There has been increasing interest in the scientific potential of online virtual worlds, such as World of Warcraft (WoW), as a means to study social interactions.  Because WoW is a massively multiplayer online role-playing fantasy game with more than 10 million subscribers, it is possible to quantitatively record the interactions of millions of users engaged in a complex range of interactions with other players, from functioning economies to political alliances. In particular, WoW enables players to form alliances where players compete against the virtual environment and against each other to gain in-game wealth and achievements. We are using the social groups of WoW, the “guilds”, as models to explore the evolution and persistence of social groups in a non-kin context largely devoid of normative pressures such as socio-economic class, religious beliefs, or cultural background.

3.4. Understanding the Existence of Highly Conserved Yet Dispensable Genomic Regions

 Comparative genomics, made possible by recent advances in sequencing, revealed the existence of numerous sequences, often non-protein coding, conserved at the nucleotide level across distantly related taxa. Although such ultra-conserved sequences are predicted to experience strong stabilizing selection, their functions remain largely unknown. Curiously, in some cases, experimental deletion of ultra-conserved regions has had no obvious phenotypic consequences. To understand this phenomenon, we examined the HMRa2 locus of the budding yeast Saccharomyces cerevisiae. This gene shows 100% conservation at nucleotide level for 360bp among 5 different species in genus Saccharomyces. However, previous studies showed that deletion  of HMRa2 has no phenotypic consequences under laboratory conditions. HMRa2 acts as a donor sequence during mating-type switching, which occurs through a gene conversion event. We constructed a series of HMRa2 mutants, ranging from complete deletion of the locus to a range of more subtle changes, and analyzed how those sequence modifications affect at mating-type switching. Our preliminary results suggest that these mutants do not differ in fitness (growth rate). We will continue to investigate how HMRa2 remain conserved over long periods of evolutionary time, despite a lack of obvious function or fitness effect.

3.5. Proteomics of Okinawan Snake Venoms (in collaboration with Dr. Steven Aird)

Commonly, we think of snake venoms as cocktails of toxic proteins that damage their prey’s tissues. However, snakes use a range of strategies to immobilize their prey, for example, inducing rapid hypotension. Given their ability to regulate vertebrate homeostasis, snake venoms contain compounds with potential medical applications. We are investigating the venom composition of two local snakes, the Okinawan habu (Trimeresurus flavoviridis) and hime habu (Ovophis okinavensis), using a combination of 2D gel electrophoresis and RNA-seq/mass spectrometry.

3.6. Population Genetics of an Endangered Butterfly (Melanie Smee)

Anthropogenic habitat fragmentation has created barriers to gene flow in many species, and is one of the major proposed reasons for the decline in some of them. The vulnerable marsh fritillary butterfly, Euphydryas aurinia, is protected in both the UK and Europe and is declining dramatically across both regions. In the course of just two months, we developed a set of microsatellite markers that can be used for population genetics in this species, and have analysed population genetic structure of UK and Continental population. These data will be used to inform conservation management decisions for this species, and to examine how adaptation to host plant use affects gene flow between geographically stratified populations.

3.7. Testing Coalescent Theory Using Experimental Evolution in Yeast (Roxana Capper)

Experimental evolution, together with next-generation sequencing, is perhaps the most powerful tool we have available to study the function and organization of eukaryotic genomes. Yeast are particularly suitable for this purpose, given their short generation times and the wide range of genomic manipulation techniques available for their study. We have evolved yeast populations for several hundred generations, splitting populations at pre-determined rates. The evolved yeast genomes were later sequenced. We will use these data to test whether population-based models of evolution, which are typically used with single-gene data, scale to the whole genome.

4. Publications

4.1 Journals

Brooks, D. D., Chan, R., Starks, E. R., Grayston, S. J. & Jones, M. D. Ectomycorrhizal hyphae structure components of the soil bacterial community for decreased phosphatase production. FEMS Microbiol Ecol 76, 245-255, doi:10.1111/j.1574-6941.2011.01060.x (2011).

Foucaud, J., Orivel, J., Loiseau, A., Delabie, J. H. C., Jourdan, H., Konghouleux, D., Vonshak, M., Tindo, M., Mercier, J. L., Fresneau, D., Mikissa, J. B., McGlynn, T., Mikheyev, A. S., Oettler, J. & Estoup, A. Worldwide invasion by the little fire ant: routes of introduction and eco-evolutionary pathways. Evolutionary Applications 3, 363-374, doi:Doi 10.1111/J.1752-4571.2010.00119.X (2010).

Mikheyev, A. S., Mueller, U. G. & Abbot, P. Comparative Dating of Attine Ant and Lepiotaceous Cultivar Phylogenies Reveals Coevolutionary Synchrony and Discord. American Naturalist 175, E126-E133, doi:Doi 10.1086/652472 (2010).

Mikheyev, A. S., Vo, T., Wee, B., Singer, M. C. & Parmesan, C. Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances. PLoS ONE 5, e11212-e11212 (2010).

Mueller UG, M. A., Hong E, Sena R, Warren DL, Solomon SE, Ishaka HD, Cooper M, Miller JL, Shaer KA, and Juenger TE Evolution of cold-tolerant fungal symbionts permits winter fungiculture by leafcutter ants at the northern frontier of a tropical ant-fungus symbiosis. Proceedings of the National Academy of Sciences, doi:10.1073/pnas.1015806108 (2011).

Mueller UG, M. A., Solomon SE and Cooper M. Frontier mutualism: Co-evolutionary patterns at the northern range limit of the leafcutter ant-fungus symbiosis. Proceedings of the Royal Society B, doi:10.1098/rspb.2011.0125 (2011).

Watanabe, Y., Numata, K., Murata, S., Osada, Y., Saito, R., Nakaoka, H., Yamamoto, N., Watanabe, K., Kato, H., Abe, K. & Kiyosawa, H. Genome-wide analysis of expression modes and DNA methylation status at sense-antisense transcript loci in mouse. Genomics 96, 333-341, doi:DOI 10.1016/j.ygeno.2010.08.007 (2010).

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

Mikheyev, A. Evolutionary consequences of horizontal gene transfer in bdelloid rotifers, Division of EcoScience Ewha Womans University, Mar 25, 2011

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

Nothing to report