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.

Spring 2014 (01/29/2014)


A single-tree linkage map


The spring semester has finally begun. Members of the lab are off and running on their respective projects. Grants are being applied for and papers are being written. Life could not be better.

Chris has begun his sample collections for his NSF funded postdoctoral fellowship and has already contributed to several projects in the lab. These projects range from production of genotype data from RADseq libraries to analysis of data for linkage map construction to association genetics of dispersal traits for gypsy moths. 
 
Brandon is busily preparing for his qualifying exam and defense of his dissertation proposal. In his spare time he is working on spatial patterns of seedling occurrences at Teakettle.

Ethan is busily adjusting to graduate school, preparing his thesis project, and starting analysis of phenotype data for his thesis about the genetic architecture of water-use efficiency in foxtail pine. 

Erin is doing just about everything, but is working especially hard on getting the RADseq libraries for gypsy moth prepared. This is also Erin's last full semester. She is off to a MD/Ph.D. program at Virginia Tech later in the year. We are all happy for her, but will be lost for awhile.

Quercus-Umbellularia woodlands in the hills of Napa, CA
As for me, I drink coffee in my office and watch all of these hard working young folk put me to shame.

As usual, the Eckert lab is looking for graduate students, especailly MS students interested in genomics or ecological genetics. Please contact me if you are interested. Funding for VCU M.S. students is quite reasonable.

Fall is in the Air (08/26/2013)




3.4 MY old pine
After a wonderful summer with my beautiful daughters (see pictures), I am back into the swing of things in Richmond. The Fall semester of 2013 has started off with a growing lab. Two new members have joined the Eckert lab: Chris Friedline (NSF Postdoctoral Fellow) and Ethan Harwood (VCU M.S. student). Chris will be tackling questions related to fire adaptation among southeastern pines. He obtained three years worth of funding through a NSF Postdoctoral Research Fellowship in Biology. Ethan will be mapping quantitative trait loci related to water use efficiency for foxtail pine (Pinus balfouriana). This work is occurring in collaboration with Dr. Patricia Maloney and utilizes a large-scale linkage map for this species currently being generated from next-generation sequencing data.
Sunset at Glacier Point
Sunset at Glacier Point
In other news, Brandon Lind has been working hard to finish up his field sampling at the Teakettle Experimental Forest. He also managed to collect a few foxtail pine samples on recent hike across the Sierra Nevada crest.  These samples will help assess local allele frequencies for QTLs discovered by Ethan. In addition, more than a few papers are finally being finished, so please stay tuned for a whole slew of published research from this lab.

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!

Fall 2012 Update (11/12/2012)

Gottingen, Germany

  
The Eckert Laboratory has received its first official funding. The New Phytologist Trust kindly awarded funds to promote research and undergraduate training in plant science. Thank you.

In addition, members of the Eckert Laboratory have been  involved with the following: teaching Evolutionary Theory, a NESCent working group on the emerging field of geogenomics, massively parallel DNA extractions (e.g. over 1200 DNA extractions of sugar and Jeffrey pine for Brandon Lind's Ph.D. dissertation) and, in a collaboration with the Rivera and Dyer laboratories, an investigation into the genome of flowering dogwood and several pine species. The laboratory is also preparing to implement genotype-by-sequencing (GBS) for several projects.

Fall colors near Blacksburg, VA
I would also like to welcome three new undergraduate researchers to the lab, all of whom are starting during the Spring 2013 semester: Erin Hobson, Ryan Lovitza and Camille Ayyash. Their projects range from searches for the signatures of natural selection in conifer genomes (Hobson), to optimization of GBS in non-model tree species (Ayyash), to the effect of natural selection and historical demography on the inference of species trees from a set of genes trees (Lovitza). Next semester will be very busy.

As usual, the laboratory is also looking for qualified undergraduate, graduate (M.S. and Ph.D.) and postdoctoral researchers. Funding is currently available for computational projects leading to a M.S. degree in Biology. If you are interested in any of these options, please visit the following website.
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