Research Projects at the Rand Lab & Current Funding

 

The projects conducted in our lab focus on three main lines research in evolutionary genetics: the evolution of mitochondrial genomes, evolution in response of thermal stress, and the ecological genomics of barnacles.

 

Active Funded Research 

 

  • NIH General Medicine, 2R01GM067862-13, "Nuclear-Mitochondrial Fitness Interactions in Drosophila", $1,447,953, 4/01/17 – 3/31/20, Dr. David Rand, PI

  • NIH General Medicine, 2R01GM067862-09 "Nuclear-Mitochondrial Fitness Interactions in Drosophila", $1,351,682, 8/01/12-7/31/17, Dr. David Rand, PI., Dr.Zhijin Wu, co-PI

  • NSF IGERT: Reverse Ecology: Computational Integration of Genomes, Organisms, and Environments, DGE 0966060, $2,900,000; 9/2010 - 8/2017, Dr. David Rand, PI.

  • NIH General Medicine, 1P20GM109035-01, “Center for Biomedical Research Excellence: Center for Computational Biology of Human Disease”, $11,521,659, 6/1/2016-2/28/21, Dr. David Rand, PI.

Completed Funded Research (Selected Grants)

 

  • DEANS Award, Division of Biology and Medicine, Brown University, “Mechanisms for Nutrient Modulation of Mitochondrial Dynamics and Metabolism”, $80,000, 7/1/2015-6/30/2016, Dr. Phillip Gruppuso, Dr. David Rand, co-PIs.

  • NIH National Institute on Aging, 1R01AG027849, "Mitochondrial Genetics of Aging in Drosophila", $1,614,000, 10/01/09 – 9/30/2015, Dr. David Rand, PI.

  • NSF Population Biology, DEB 0343464, "Genetic architecture of thermal selection in Drosophila" Collaborative Research Award with George Gilchirst at William and Mary 3/01/2004–-/28/2007, $536,000 ($281,000 to Brown University)

  • NSF Population Biology, DEB 9707676 "Evolutionary dynamics of mitochondrial DNA"; Dr. David Rand, PI, 9/1997-8/2000, $210,000

  • NSF Population Biology, BSR-9527709, "Molecular Ecological Genetics of the Acorn Barnacle", Dr. David Rand, PI; Dr. Mark Bertness Co-PI, 3/1996-2/1999, $215,000

Mito-Nuclear coevolution and its fitness

 

The mitochondrion is the powerhouse of the eukaryotic cell, consuming 90% of the oxygen we breathe and generating 90% of the energy we need to stay alive. This organelle evolved from a symbiotic association between two divergent microbes that began about 2 billion years ago. Modern day mitochondria house small, circular genomes that have been shaped by reductive evolution through gene loss and transfer to the nuclear genome. As a result, mitochondrial function depends critically on cross talk between hundreds of nuclear-encoded genes and the three-dozen genes encoded in the mitochondrial genome. Thus “mitonuclear” interactions provide rich material for the study of co-evolution and the dissection of metabolic diseases. We are approaching these problems from several angles:

 

1) The molecular bases of evolutionary change in mitochondrial genes and genomes
2) The fitness consequences of variation in nuclear-mitochondrial interactions
3) The mitochondrial genetics of aging. For this work we use Drosophila as a model system

 

Molecular Evolution of mtDNA: DNA sequencing surveys of synonymous and amino acid replacement changes in protein coding genes reveal that mtDNA evolution is not consistent with neutral models of DNA evolution, showing an excess of low frequency amino acid variation consistent with the action of purifying selection. Recent progress with the Drosophila Species Genome Projects has allowed us to mine mtDNA and nuclear gene sequences from the 12 new genome projects, spanning 50 million years of divergence. Comparisons of these protein sequences reveal significant functional variation among the five enzyme complexes of the electron transport chain that generates cellular energy. Future work will involve computational modeling of amino acid substitutions in defined protein structures and functional assays of the genetic interactions governing enzyme activity of these five enzyme complexes.

Fitness Consequences of Mitonuclear Interactions in Drosophila: We examine the functional genomics of joint mitonuclear interactions by placing alternative mtDNAs onto defined nuclear genetic backgrounds. Typical experiments involve population cage competition experiments, or specific chromosome inheritance assays where we can measure the evolutionary fitness of genotypes carrying different combinations of nuclear and mitochondrial genomes. We use genetic crosses to construct strains of flies carrying their own mtDNA on a native set of chromosomes (the “home team”) and compare these to a strain of flies carrying a foreign mtDNA on the same set of nuclear chromosomes (the “away team”). The rich genetics of Drosophila offers many ways to manipulate mitonuclear genotypes for functional analysis of whole animals or enzyme activities. Recent studies have identified a specific gene on chromosome 2 that shows strong epistatic interactions with particular mtDNA genotypes. These experiments seek to dissect the genetic interactions underlying metabolic diseases.

Prof. Rand discusses findings at the 2016 Evolution meeting. Austin TX, USA

Mitochondrial Genetics of Aging: A leading hypothesis for the cause of aging is the production of reactive oxygen species in the mitochondria. We are testing this hypothesis using genetic manipulations of nuclear-mitochondrial interactions. We have shown that alternative mtDNAs alter the patterns of aging in a nuclear-background dependent manner. We have further shown that mitochondrial genotype alters the longevity-extending effects of dietary restriction, and that hypomorphic mutations of insulin signaling (chico) can rescue this mitochondrial defect.

 

Thermal Tolerance of Drosophila

 

We have conducted thermal selection experiments that have altered the genetically based thermal tolerance of Drosophila. Through continuous culture at different temperatures, or selective breeding of temperature resistant vs. temperature sensitive flies, we have constructed genetically differentiated strains of Drosophila. Using genomic scans of molecular markers, we have identified a gene region that is responsible for part of this phenotype. We are in the process of fine-scale mapping and mutant analysis to identify the gene involved. Our current candidate gene region also shows latitudinal variation in allele frequency, suggesting that this gene plays a general role in adaptation to different climates.

Ecological and Evolutionary Genetics of Barnacles

 

We use barnacles as a system to study adaptation to environmetal heterogenety. These inhabitants of the intertidal have a well studied and easily manipulated ecology. This, combined with a charaterisitc planktonic life stage with high dispersal and a sesile adult stage, makes barnacles ideal systems to study adaptations to ecological heterogenetity.  

 

 

MPI - GPI Dynamics: We have shown that barnacles from different tidal heights in the intertidal zone are genetically differentiated for key enzymes of glycolysis. Alternative homozygotes of the Mpi and Gpi allozyme loci show significant tidal-height zonation, with Mpi exhibiting strong zonation in Maine and Gpi showing zonation in Rhode Island. Survivorship experiments with the substrates of these enzymes (mannose and glucose, or different plankton) indicate that genotype zonation is mediated by the combined effect of thermal stress and the availability of these sugars in the diet. Sequence analyses of the Mpi locus have identified the specific amino acid change that causes the enzyme polymorphism and sequence polymorphism surveys indicate that balancing selection has operated at this locus.

 

 

A Genome for Semibalanus: We use next generation sequencing technology to develop a complete draft genome of the northern accorn barnacle. We have conducted a pool-seq analyses on populations from 3 locations in Maine, Rhode Island, and England. We identified  >335,000 high quality SNPs (excluding singletons). Some of these SNPs have high Fst values among population comparisons.

 

We are currently working on improving the quality of our draft genome for studies on ecological adaptation. 

 

 

Distribution of FST values. Of interest are the many of loci with FST values outside the 1% tail of this distribution (black vertical line in Figure), indicating excessive allelic differentiation between the three populations. Figure from Flight and Rand 2012, Integr Comp Biol, Vol 52 - Issue 3 (http://icb.oxfordjournals.org/content/52/3/418.full.pdf)