Data Set Release Disclaimer

The following lists links to a variety of data sets used in publications coming out of the Eckert lab. When possible they are grouped by publication. Feel free to use the data as needed. We only ask that you acknowledge the source of the data - either the original publication or this site.

Saturday, February 16, 2013

BAC annotations for loblolly pine (Pinus taeda L.)

A set of seven BACs from loblolly pine were annotated using MAKER in the following publication:
Figure 1: Eckert and Dyer (2012)

Eckert, A. J. and R. J. Dyer. 2012. Defining the landscape of adaptive genetic diversity. Molecular Ecology 21: 2836-2838. (commentary).

Annotations were performed, because these BACs contained homologous sequences to those of lodgepole pine (Pinus contorta) that were associated with cone serotiny (see Parchman et al. 2012).

MAKER outfiles can be obtained here.

Local adaptation for Bolander pine (Pinus contorta subsp. bolanderi)

Figure 1: Eckert et al. (2012)
Data for the following publication can be obtained here:

Eckert, A. J., H. Shahi, S. L. Datwyler, and D. B. Neale. 2012. Spatially variable natural selection and the divergence between parapatric subspecies of lodgepole pine (Pinus contorta, Pinaceae). American Journal of Botany 99: 1323-1334.

Data are given as FASTA formatted DNA sequence files. Each file contains the complete data for a single locus. There are 21 files upon which the analysis presented in the previously mentioned publication are based. More information about these loci can be obtained by reading the original publication. Please cite this publication if you use these data.

FASTA formatted files can be obtained here.

Sample information can be obtained here.

Friday, January 27, 2012

Landscape genomic data for loblolly pine (Pinus taeda L.)

During my tenure in the Neale Lab, we examined landscape level correlations between climate and SNP allele frequencies in two papers:

Eckert et al. (2010). Figure 1 from the 2010 Genetics paper.
(1) Eckert, A. J., A. D. Bower, S. C. González-Martínez, J. L. Wegrzyn, G. Coop and D. B. Neale. 2010. Back to nature: Ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Molecular Ecology 19: 3789-3805.

(2) Eckert, A. J., J. van Heerwaarden, J. L. Wegrzyn, C. D. Nelson, J. Ross-Ibarra, S. C. González-Martínez and D. B. Neale. 2010. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185: 969-982.

Data for these papers can be downloaded using the link below. Please remember to cite the papers listed above if you use these data.

Data for both papers are available: here. Due to changes by Google, these will now appear as Google Documents. I have included a short ReadMe file that broadly describes the data. More information can be obtained in the papers or by contacting me (aeckert2@vcu.edu).

Sunday, November 13, 2011

Loblolly pine linkage map


Eckert et al.: Figure 6. Linkage map with outliers
The linkage map described in several publications out of the Neale Lab can be found by following the links provided here. This map has played a part in at least three publications by Andrew J. Eckert:

(1) Eckert, A. J., J. van Heerwaarden, J. L. Wegrzyn, C. D. Nelson, J. Ross-Ibarra, S. C. González-Martínez and D. B. Neale. 2010. Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185: 969-982.
(2) Eckert, A. J., A. D. Bower, S. C. González-Martínez, J. L. Wegrzyn, G. Coop and D. B. Neale. 2010. Back to nature: Ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Molecular Ecology 19: 3789-3805.
(3) Eckert, A. J., J. L. Wegrzyn, W. P. Cumbie, B. Goldfarb, D. A. Huber, V. Tolstikov, O. Fiehn, and D. B. Neale. 2012. Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome. New Phytologist 193: 890-902.

The map is available as an Excel file by clicking here. The file contains map information for the latest round of linkage mapping, as well as nucleotide diversity and divergence summaries for loci containing these markers.

If you use this map, please cite the first publication and its accession number for the TreeGenes CMap database (TG091). More information about the SNP markers residing on the map can be found using the DiversiTree database.

Sunday, October 30, 2011

Eckert et al.: Distribution of deleterious fitness effects in soft pines

Eckert et al.: Figure 1. Focal species.
The following links are for DNA sequence alignments (*.fasta, UNIX encoded text) used to infer the distribution of deleterious fitness effects across 11 species of soft pines. They were used in the following publications:

(1) Eckert, A. J., A. D. Bower, K. D. Jermstad, J. L. Wegrzyn, B. J. Knauss, J. V. Syring, and D. B. Neale. Multilocus analyses reveal little evidence for lineage wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus).

(2) DeGiorgio, M., J. Syring, A. J. Eckert, A. I. Liston, R. Cronn, D. B. Neale, and N. A. Rosenberg. An empirical evaluation of species tree inference strategies using a multilocus dataset from North American pines.

At a minimum, the first paper needs to be cited if you use the data. Please read the documentation carefully before you use these data, as the papers listed above used only parts of the data.

DNA sequence alignments (not functional yet)
Documentation (not functional yet)

Eckert et al.: Metabolomics in loblolly pine, New Phytologist

Eckert et al.: Figure 1. Population structure.
These data were part of a study trying to associate genotypes at single nucleotide polymorphisms (SNPs) to concentrations of primary metabolites. The data are given as a set of Excel files.


These also appeared in a supplemental file of the primary paper. If you use these data, please acknowledge the following publication: Eckert, A. J., J. L. Wegrzyn, W. P. Cumbie, B. Goldfarb, D. A. Huber, V. Tolstikov, O. Fiehn, and D. B. Neale. 2012. Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome. New Phytologist 193: 890-902.