Quote of the Month

"If a man has learnt to know a thing in itself, and in its relation to surrounding phenomena, he has got from a University what it is its proper duty to teach." - Thomas Carlyle (1866).

Introduction


Welcome to the Eckert Lab located in the Department of Biology at Virginia Commonwealth University. We are a plant evolutionary genomics lab. Research topics range from the dissection of adaptive plant phenotypes into their genetic components to inferences of genome-wide patterns of polymorphism, divergence and natural selection. Current focal points of research are:

Genetic Architecture of Adaptation

How do woody plants adapt to their environments? What are the genes that facilitate this process? How are these genes organized within the genomes of woody plants? We try to answer these questions using a variety of approaches ranging from population genetic surveys of natural populations to association genetic dissection of complex phenotypes. The unifying theme underlying all of these approaches is the discovery of the genetic basis of adaptive plant phenotypes.

Statistical Methods and Adaptation

Standing patterns of genetic diversity result from the interplay of several population genetic processes, such as natural selection, genetic drift and migration. When methods developed to identify these processes are used in a hypothesis testing framework, however, they do not often exhaustively divide the sample space into mutually incompatible outcomes; so that rejection of one hypothesis, a null hypothesis for example, does not necessarily imply that the alternative is true or even likely. The reason is that several different processes can individually, as well as jointly, result in the same patterns. It is prudent, therefore, to utilize a range of methods that each examines different aspects of the standing patterns of genetic diversity. Recently we have begun collaborating with Rodney Dyer and his lab to examine the use of his measure of conditional genetic covariance, in combination with high-throughput SNP genotyping data, to infer patterns of natural selection across genomes.

Phylogeography and Adaptation

The woody plant flora of North America is composed of a fascinating diversity of species. We use a variety of phylogeographic, biogeographic and phylogenetic approaches with which to understand the origin and diversification of species comprising this flora. Our approaches tend to be hypothesis driven where multiple competing hypotheses are proposed and the best one(s) is/are chosen using some form of statistical model selection. This is also important because divergence history confounds the ability to identify adaptive genetic variants.

Below you will find news and events. Links to specific lab personnel are listed on the left. You can find personal webpages by clicking on the picture of the person.

News in the Lab

There is always something exciting happening in the Eckert lab.

05-Apr-2017: Brandon Lind has published his first paper about the polygenic basis of local adaptation across populations of whitebark pine (Pinus albicaulis) located in the Lake Tahoe Basin. Check it out at Molecular Ecology.

01-Apr-2017: Dr. Justin Bagley has started as the newest postdoctoral scholar in the Eckert lab.

27-Nov-2016: Madison Glackin, an undergraduate researcher in the lab, recently was selected to participate in the Panama Avian Field Ecology Study Abroad course at VCU. Congratulations, Madison!

Spring 2013 Update (02/16/2013)


River art
    
The semester began with attendance at the Plant and Animal Genome Conference XXI, which was held in San Diego, California. We presented some initial data about the flowering dogwood (Cornus florida L.) genome, met a number of wonderful new people, and caught up with old friends. After returning from San Diego, classes at VCU started. This semester I am co-teaching BIOL 691: Genomics and Phylogenetics with Dr. Maria Rivera and BIOL 693: Ecological Genomics. Grant season was also upon lab, with two NSF preliminary proposals and a Jeffress Memorial Trust grant application being submitted in January alone. More submissions are also in the works, as the NSF IOS PGRP is due in March.
Beautiful colors
     The students in the lab have also been busy. Brandon has started to generate genome-wide data for his two focal species: Jeffrey pine (Pinus jeffreyi Balf.) and sugar pine (P. lambertiana Douglas). In addition, Brandon, Erin, and Camille have been preparing multiplexed RADseq libraries for sequencing of foxtail pine (P. balfouriana Grev. & Balf.) megagametophyte arrays. Undergraduate research projects are also moving along well. Erin is busily examining genomic regions in lodgepole pine (P. contorta Douglas) that are physically linked to those identified by Parchman et al. (2012, Molecular Ecology 21: 2991-3005) as associated with cone serotiny. Camille has immersed herself in the RADseq library constructions for foxtail pine, and Ryan has busily been working on simulations of gene trees and species trees where the species are experiencing gene flow, demographic changes, and natural selection. It definitely is an exciting time in the lab!
Richmond at night
    Several papers have been published, are in review, or are on the verge of submission. The opinion piece about landscape genomics for forest trees has finally been accepted at Tree Genetics and Genomes, while several papers addressing adaptive evolution in various Pinus species and gene expression associations are in review. On the horizon are papers about the ecological genetics of sugar pine, the effects of sulfate deposition on red spruce (Picea rubens Sarg.) populations, and a new method for detection of putatively adaptive genomic regions.
    The next several months will be busy, but please do not hesitate to contact me with inquires about joining the lab. Happy spring semester!