Vikram E. Chhatre

Research Projects

Laurentides Wildlife Refuge, Quebec

I use population genomic and computational tools to understand genetic structure of tree populations. Specifically, I am interested in how natural selection and demographic processes affect distribution of genetic variation across a landscape. For example, I am employing genome scans to detect local adaptation to climate in southern range-edge populations of balsam poplar. In another project, I am employing this information to understand adaptive introgression in several species of the genus populus which readily hybridize in zones of contact.

In the past, I have worked with diverse model and non-model taxa such as teak, spruce and pine (population genomics), aphids and treehoppers (evolution of social altruism) and zebrafish (reverse genetics of causal variants). I obtained a PhD in population genetics from Texas A&M (2013) and did postdoctoral research at USDA Forest Service and University of Vermont. Here are some highlights from my research projects.

  1. Adaptive Introgression in a Trispecies Hybrid Complex of Populus
  2. Genetic Divergence in Marginal Populations of Eastern White Pine
  3. Climate Adaptation in Core and Rear-Edge Populations of Balsam Poplar
  4. A Consensus Linkage Map for Loblolly Pine and Slash Pine
  5. Salt Tolerance in Slash Pine on Mississippi Barrier Islands
  6. Genetic structure and association mapping in loblolly pine

Adaptive introgression in poplars

We studied extensive hybridization among the two balsam poplars (P. balsamifera and P. trichocarpa) and the narrowleaf cottonwood (P. angustifolia) along the range-edge populations of these species that meet in the rocky mountains of Colorado and Wyoming. While hybridization in commonplace in the genus Populus, little is known about the dynamics of hybridization in rear edge populations that grow in suboptimal conditions.

Our results based on a genome-wide assay of SNPs suggests presence of a trispecies hybrid complex in this area with bidirectional adaptive introgression in the hybrid individuals. The adaptive introgression was found in areas of the genome involved in redox homeostasis and mechanism of induction of flowering. These findings suggest a role for selection in maintaining parental genomic combinations in hybrids due to the functional advantages they provide. Manuscript under internal review.

Climate adaptation in balsam poplar

In long-lived plants such as forest trees, southern range-edge populations may be particularly vulnerable to changing climate especially if they exist at their current physiological limits; yet may also harbor the adaptive variants to warmer, longer growing seasons that will be needed in the central core of the range to maintain adaptation under future climate. Using range-wide populations of the widely distributed boreal forest tree Populus balsamifera as a model system, we asked how climates shape distribution of standing genetic variation, whether range-edge populations harbor unique genetic variants, and how introgression from closely related taxa is shaping the evolution of rear-edge populations. We employed more than 145,000 single nucleotide polymorphisms (SNPs) developed using Genotyping by Sequencing (GBS) to 486 individuals from 24 range-core and 33 range-edge populations to: (1) quantify population structure across the range; and (2) understand genomic responses to climate-driven selection using several univariate and multivariate methods to detect SNP-environment associations.

Genetic divergence in eastern white pine

Central marginal hypothesis is a long standing topic in conservation biology. The conservation importance of marginal populations has been debated for more than 20 years. In northern Ontario, eastern white pine populations face harsh climatic conditions. Some of these old-growth populations are located towards the ecological range edge and are therefore ideal candidates for studying the interplay of various demographic processes and population genetic forces such as gene flow, drift and natural selection. This can be done by comparing genetic structure of these marginal populations with their counterparts from center of the range distribution. We studied two old growth central, two second growth central and two old growth marginal populations of eastern white pine for genetic diversity, divergence, gene flow, population genetic structure and signatures of natural selection.

Our results showed that ecologically marginal populations of eastern white pine show genetic divergence from and differential selection regimes compared with central populations from Ontario thereby supporting a key prediction of evolutionary theory. Further details are available in the PLoS One publication.


• Chhatre, VE and Rajora, OP (2014) Genetic divergence and signatures of natural selection in a long lived conifer eastern white pine from northern Ontario. PLoS ONE 9(5): e97291

Linkage mapping in southern pines

Genetic linkage map remains an indispensable tool for trait analysis and comparative mapping and may be useful for genome assembly in species without a reference genome. Over the last two decades several linkage map based on a variety of marker systems and different mapping populations have become available. A reference map consisting of SSRs, RFLPs and ESTPs is also available (Echt et al 2011). A consensus linkage map that consolidates all the available markers and populations into a single map is needed.

Four individual maps from two cross pollinated populations, a single tree megagametophyte population and a pseudo back cross population were merged together using a linear programming approach implemented in MergeMap ( Wu et al 2011 ). The resulting consensus map contains 3856 markers mostly SNPs, but also several hundred RFLPs, ESTPs, PAVs and SSRs. This map is expected to become an important resource for the forest genetics community and for comparative mapping and analysis of quantitative traits of economic importance. Read more details in our G3 paper.


• Westbrook JW* and Chhatre VE* et al. (2015) A consensus genetic map of Pinus taeda and Pinus elliottii and the extent of linkage disequilibrium in two genotype-phenotype discovery populations of Pinus taeda. G3: Genes, Genomes and Genetics 5(8):1685-1694 *Authors contributed equally.