Allenrolfea Wetland Genetics Data


The hydrophyte Allenrolfea occidentalis (S. Watson) Kuntze (iodine bush) is a halophytic shrub of the arid southwest that is listed as a facultative wetland (FACW) species on the National Wetland Plant List. This rating means the species is usually a hydrophyte but occasionally is found in uplands. We tested for genetic (ecotypic) differences between plants sampled from wetlands versus uplands. We used genotyping-by-sequencing (ddRAD-seq) to generate data from 133 plants from 30 locations representing both wetland and upland occurrences for over 1300 loci. Analyses indicated that the strongest signal is differences in geographic distribution: samples that are in close geographic proximity tend to be more similar genetically regardless of whether they occur in wetland or upland locations. We detected no effect of habitat on overall genetic structure and we found only two (of the 1381) loci with a positive association between genotype and habitat. We infer that A. occidentalis occurrences near or in wetlands are not influenced by significant differences in genetics, but rather the rating for this species is a function of inadequate knowledge of its frequency of occurrence in wetlands.



Document Type




File Format

.fastq, .txt, .html

Viewing Instructions

See attached Allenolfea_Analysis_Pipeline file for information.

Publication Date



U.S. Army Corps of Engineers

Broad Agency Announcement (BAA) Program and the Engineering Research and Development Center (ERDC) – Cold Regions Research and Engineering Laboratory (CRREL)


Utah State University

Award Number

U.S. Army Corps of Engineers W913E5-16-C-0001; Broad Agency Announcement (BAA) Program and the Engineering Research and Development Center (ERDC) – Cold Regions Research and Engineering Laboratory (CRREL) IPA-17-0-0006

Award Title

Genetics of Wetland Plants

Scientfic Names

Allenrolfea occidentalis

Referenced by

Rowe, C. A., Wolf, P. G., & Lichvar, R. W. (2019). Do Genetic Differences Explain the Ability of an Alkaline Shrub to Grow in Both Uplands and Wetlands? Western North American Naturalist, 79(2), 260–269. https://doi.org/10.3398/064.079.0211




The raw data are in compressed fastq files that have been split for ease of data transfer. Files are xaa_Allenr.fastq.zip though xan.etc. Instructions for unzipping and concatenating are found in the README.Allenrolfea.txt file




Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.



Additional Files

README.Allenrolfea.txt (1 kB)
MD5: 021d2eecebef8139e4553787035495b9

Allenrolfea_Analysis_Pipeline.html (4460 kB)
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Allenrolfea_Analysis_Pipeline.pdf (2944 kB)
MD5: 50c0a41e7bf16a7301fe08f6817f505b

xaa_Allenr.fastq.zip (1143926 kB)
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xab_Allenr.fastq.zip (1149335 kB)
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xad_Allenr.fastq.zip (1160807 kB)
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xak_Allenr.fastq.zip (1139683 kB)
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xal_Allenr.fastq.zip (1140374 kB)
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xam_Allenr.fastq.zip (1126446 kB)
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xan_Allenr.fastq.zip (360324 kB)
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