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


Document Type


File Format


Viewing Instructions

See attached Allenolfea_Analysis_Pipeline file for information.

Publication Date



Utah State University


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)

Award Number

IPA-17-0-0006 and Contract No. W913E5-16-C-0001

Award Title

Genetics of Wetland Plants

Scientfic Names

Allenrolfea occidentalis




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.




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

Allenrolfea_Analysis_Pipeline.html (4460 kB)
MD5: 0449a6e13d4900332707705ee8d2766d

Allenrolfea_Analysis_Pipeline.pdf (2944 kB)
MD5: 50c0a41e7bf16a7301fe08f6817f505b

xaa_Allenr.fastq.zip (1143926 kB)
MD5: 99ba662ed19f999d861d0cb976633123

xab_Allenr.fastq.zip (1149335 kB)
MD5: cd9b94985af91880350e240d7cc4625b

xac_Allenr.fastq.zip (1128055 kB)
MD5: 818f8ee9fdfc0909189119b1f717ea62

xad_Allenr.fastq.zip (1160807 kB)
MD5: 0ba7e81c323db36102de28a15436cf81

xae_Allenr.fastq.zip (1139783 kB)
MD5: 3483c9d1ef8a12edad399acff024c80f

xaf_Allenr.fastq.zip (1142724 kB)
MD5: cdc254ec09e05ee2e4c3406451434509

xag_Allenr.fastq.zip (1144032 kB)
MD5: 2a3ca0e1464faddbec17bc0a608f3b7a

xah_Allenr.fastq.zip (1115322 kB)
MD5: 3c3bf7d2adc712d5602a2fdbd7d604da

xai_Allenr.fastq.zip (1117033 kB)
MD5: 82cdf959f38af0c5875c0ee202af02a5

xaj_Allenr.fastq.zip (1121162 kB)
MD5: 4af0cd80866510922c5e8a1236461305

xak_Allenr.fastq.zip (1139683 kB)
MD5: 96066010d3c02571669fff27fbb45774

xal_Allenr.fastq.zip (1140374 kB)
MD5: f550a2126e3edbd930abda33c5e31edb

xam_Allenr.fastq.zip (1126446 kB)
MD5: 07bd26f3206872cba2fb3836e62a8c5d

xan_Allenr.fastq.zip (360324 kB)
MD5: c5d1842bff879b4d88ce2b28a99a3fa6