I am Praveen Nadukkalam Ravindran , a PhD student in the Faculty of Computer Science, Dalhousie university. I am supervised by Dr. Robert G. Beiko (FCS, Dalhousie) and Dr. Ian R. Bradbury (DFO) . My project aims at building algorithms for effective assembly of de novo loci and population genetics inferences from RAD-seq data. We have built a parameter search module to identify the best set of parameter values for the ustacks program provided by STACKS, a widely used pipeline for processing restriction-enzyme based DNA sequence data. As part of the project, a noval method using sequence similarity is also developed for identifying paralogous sequences from the de novo assembled loci. Currently, I am focussing on developing methods for faster processing of these RAD-seq data with much reduced computational requirements, enabling effective analyses of such data with limited resources.
Co-supervised by Dr Ian Bradbury and Dr Paul Bentzen, my PhD project focusses on the role genomic architecture in the evolution of migratory behaviours in Northwest Atlantic cod. Local adaptation and ecotype divergence between life-history strategies are important determinants of cod population structure and have been linked to genomic structural features such as large chromosomal inversions. These inversions may harbour important adaptive or life-history genes and changes in their frequency may have implications for the recovery of the Northern cod. I am using a whole-genome resequencing approach to genotype telemetry fish and examining the relationship between chromosomal inversions and different migration phenotypes. Once this relationship is better understood, I aim to examine temporal changes in the frequency of inversion genotypes and associated life-history genes by genotyping historical samples from the time of the 1992 Northern cod collapse. This comparison will provide insight to important questions such as the role of fisheries induced evolution in the Northern cod collapse, as well as whether the apparent recovery is being fuelled by immigration or local recruitment. Broadly, I am interested in the application of genomics to wildlife conservation and management. Outside of the lab I am also a keen scuba diver and drummer.
Memorial University of Newfoundland
I am a MSc student, co-supervised by Dr. Ian Bradbury and Dr. Ian Fleming. I am characterizing the presence and magnitude of recent adaptive divergence (rapid evolution) in an introduced population of Atlantic salmon (Salmo salar) in Rocky River on the Avalon Peninsula of Newfoundland. This was done by conducting reciprocal transplant experiments with F1 purebred and hybrid offspring at both Rocky River, and the parental population at the nearby Little Salmonier River. I also examined the potential for rapid evolution with genomics by analyzing and comparing three types of molecular data: microsatellites, single nucleotide polymorphisms (SNPs), and restriction enzyme-associated DNA sequencing (RAD-seq) SNPs. Overall, reciprocal transplants warranted little evidence of rapid evolution between the population, although there is speculation that outbreeding depression may exist. Genomically, the two SNP data sets had higher resolution in detecting rapid evolution than microsatellites, and a second group unique to Rocky River was discovered, likely due to hybridization with landlocked, resident salmon in the watershed.
Biology Department Dalhousie University
As a MSc student, co-supervised by Dr. Ian Bradbury and Dr. Paul Bentzen, my research will focus on improving understanding of indirect genetic impacts of wild-farm interactions. Indirect genetic impacts may led to reduced population size, increased genetic drift, and/or lowered adaptive capacity. Small populations or populations experiencing declines in abundance may be more susceptible to these genetic impacts than large, stable populations. To enable quantification of future impacts, a genomic baseline for wild Atlantic salmon populations within Placentia Bay, Newfoundland will be generated, effective population size of wild populations will be estimated, and genomic tools for the identification of Norwegian farm escapees and hybrids will be developed. Through this project I will also explore the power of large genomic datasets to detect changes in the character and abundance of wild populations differing in size over various periods of time using simulation studies.
Biology Department Dalhousie University
I am a MSc student co-supervised by Dr. Ian Bradbury and Dr. Paul Bentzen. My research is to determine the direct impacts of aquaculture salmon escapes breeding with wild salmon populations. One method I am using is measuring changes in body shape using geometric morphometrics of different pure and hybrid groups identified using diagnostic with single nucleotide polymorphism panels. Using the shape and genomic data allows the comparison of shape differences between levels of hybridization and introgression. Measuring shape change with between wild, farm, and hybrid salmon is a means of measuring fitness; this will aid in efforts to understand, and monitor the ongoing impact of salmon aquaculture on wild salmon populations in the Northwest Atlantic.
There are currently no undergraduate students in the lab.