Date: 23 May, 2018

Dataset Title: Xantusia vigilis ddRADseq fastq files

Dataset Creators: Iris A Holmes, Ivan V Monagan Jr., Michael F Westphal, Alison R Davis Rabosky

Dataset Contact: Iris Holmes, iholmes@umich.edu

Funding: This study was supported by startup funds from the University of Michigan to ARDR and from the U.S. Bureau of Land Management to MFW and ARDR


Key Points:
- We generated RADseq data on night lizards from the genus Xantusia, particularly Xantusia vigilis from central California

- We prepared the genetic libraries based on the ddRAD protocol from Peterson et al. 2012 (https://doi.org/10.1371/journal.pone.0037135)


Research Overview:
We generated these data from desert night lizards, Xantusia vigilis, from populations in central California. We performed phylogeographic analyses based on these data. 


Methodology:
We used a double digest Restriction-Associated Sequencing protocol to prepare reduced-representation DNA sequencing library. The DNA fragments were sequenced on an Illumina HiSeq 2500 platform at the University of Michigan Sequencing Core, using 200 base-pair, paired-end reads. The sequencing core used proprietary Illumina software to process sequencing platform output into two .fastq per individual, one with forward reads and one with reverse reads. We provide the unedited fastq files, which can be opened with a text editor or platforms, such as GLOGG (https://glogg.bonnefon.org/), designed specifically for large and complex files.


Files contained here:
The files are gzipped and in fastq formatting. Each sampled individual has one file with forward reads and one with reverse reads:

31BFF_R1.fq.gz fastq file with forward reads
31BFF_R2.fq.gz fastq file with reverse reads
6Af_R1.fq.gz fastq file with forward reads
6Af_R2.fq.gz fastq file with reverse reads
A1M_R1.fq.gz fastq file with forward reads
A1M_R2.fq.gz fastq file with reverse reads
AC1f_R1.fq.gz fastq file with forward reads
AC1f_R2.fq.gz fastq file with reverse reads
AC3_R1.fq.gz fastq file with forward reads
AC3_R2.fq.gz fastq file with reverse reads
AC8_R1.fq.gz fastq file with forward reads
AC8_R2.fq.gz fastq file with reverse reads
AQ1243_R1.fq.gz fastq file with forward reads
AQ1243_R2.fq.gz fastq file with reverse reads
AQ1251_R1.fq.gz fastq file with forward reads
AQ1251_R2.fq.gz fastq file with reverse reads
AQ1258_R1.fq.gz fastq file with forward reads
AQ1258_R2.fq.gz fastq file with reverse reads
AQ1259_R1.fq.gz fastq file with forward reads
AQ1259_R2.fq.gz fastq file with reverse reads
AQ1273_R1.fq.gz fastq file with forward reads
AQ1273_R2.fq.gz fastq file with reverse reads
AQ1276_R1.fq.gz fastq file with forward reads
AQ1276_R2.fq.gz fastq file with reverse reads
AQ1299_R1.fq.gz fastq file with forward reads
AQ1299_R2.fq.gz fastq file with reverse reads
AQ1301_R1.fq.gz fastq file with forward reads
AQ1301_R2.fq.gz fastq file with reverse reads
AQ1302_R1.fq.gz fastq file with forward reads
AQ1302_R2.fq.gz fastq file with reverse reads
AQ1309_R1.fq.gz fastq file with forward reads
AQ1309_R2.fq.gz fastq file with reverse reads
AQ1322_R1.fq.gz fastq file with forward reads
AQ1322_R2.fq.gz fastq file with reverse reads
AQ1323_R1.fq.gz fastq file with forward reads
AQ1323_R2.fq.gz fastq file with reverse reads
Apache11_R1.fq.gz fastq file with forward reads
Apache11_R2.fq.gz fastq file with reverse reads
BALX2F_R1.fq.gz fastq file with forward reads
BALX2F_R2.fq.gz fastq file with reverse reads
BALX3_R1.fq.gz fastq file with forward reads
BALX3_R2.fq.gz fastq file with reverse reads
BALX4M_R1.fq.gz fastq file with forward reads
BALX4M_R2.fq.gz fastq file with reverse reads
BALX4_R1.fq.gz fastq file with forward reads
BALX4_R2.fq.gz fastq file with reverse reads
BALX5F_R1.fq.gz fastq file with forward reads
BALX5F_R2.fq.gz fastq file with reverse reads
CALR2_R1.fq.gz fastq file with forward reads
CALR2_R2.fq.gz fastq file with reverse reads
CALR3_R1.fq.gz fastq file with forward reads
CALR3_R2.fq.gz fastq file with reverse reads
CALR7_R1.fq.gz fastq file with forward reads
CALR7_R2.fq.gz fastq file with reverse reads
CALX2_13_11_R1.fq.gz fastq file with forward reads
CALX2_13_11_R2.fq.gz fastq file with reverse reads
CALX2_13_12_R1.fq.gz fastq file with forward reads
CALX2_13_12_R2.fq.gz fastq file with reverse reads
CALX2_13_15_R1.fq.gz fastq file with forward reads
CALX2_13_15_R2.fq.gz fastq file with reverse reads
CIER1_12_R1.fq.gz fastq file with forward reads
CIER1_12_R2.fq.gz fastq file with reverse reads
CIER1_13_R1.fq.gz fastq file with forward reads
CIER1_13_R2.fq.gz fastq file with reverse reads
CIER1_3_R1.fq.gz fastq file with forward reads
CIER1_3_R2.fq.gz fastq file with reverse reads
CIER2_14_R1.fq.gz fastq file with forward reads
CIER2_14_R2.fq.gz fastq file with reverse reads
CIER2_5_R1.fq.gz fastq file with forward reads
CIER2_5_R2.fq.gz fastq file with reverse reads
CIER2_7_R1.fq.gz fastq file with forward reads
CIER2_7_R2.fq.gz fastq file with reverse reads
CIER3_11_R1.fq.gz fastq file with forward reads
CIER3_11_R2.fq.gz fastq file with reverse reads
CIER3_2_R1.fq.gz fastq file with forward reads
CIER3_2_R2.fq.gz fastq file with reverse reads
CIER3_9_R1.fq.gz fastq file with forward reads
CIER3_9_R2.fq.gz fastq file with reverse reads
CUYX1_R1.fq.gz fastq file with forward reads
CUYX1_R2.fq.gz fastq file with reverse reads
CUYX3_R1.fq.gz fastq file with forward reads
CUYX3_R2.fq.gz fastq file with reverse reads
CUYX5_R1.fq.gz fastq file with forward reads
CUYX5_R2.fq.gz fastq file with reverse reads
CYX2M_R1.fq.gz fastq file with forward reads
CYX2M_R2.fq.gz fastq file with reverse reads
CYX4F_R1.fq.gz fastq file with forward reads
CYX4F_R2.fq.gz fastq file with reverse reads
CYX6F_R1.fq.gz fastq file with forward reads
CYX6F_R2.fq.gz fastq file with reverse reads
CurryXN1_R1.fq.gz fastq file with forward reads
CurryXN1_R2.fq.gz fastq file with reverse reads
CurryXN2_R1.fq.gz fastq file with forward reads
CurryXN2_R2.fq.gz fastq file with reverse reads
CurryXN3_R1.fq.gz fastq file with forward reads
CurryXN3_R2.fq.gz fastq file with reverse reads
CurryXN4_R1.fq.gz fastq file with forward reads
CurryXN4_R2.fq.gz fastq file with reverse reads
DCX1_R1.fq.gz fastq file with forward reads
DCX1_R2.fq.gz fastq file with reverse reads
DCX2_R1.fq.gz fastq file with forward reads
DCX2_R2.fq.gz fastq file with reverse reads
GRIS2_12_R1.fq.gz fastq file with forward reads
GRIS2_12_R2.fq.gz fastq file with reverse reads
GRIS2_F_1_R1.fq.gz fastq file with forward reads
GRIS2_F_1_R2.fq.gz fastq file with reverse reads
GRIS2_U_4_R1.fq.gz fastq file with forward reads
GRIS2_U_4_R2.fq.gz fastq file with reverse reads
GRIS4_2_R1.fq.gz fastq file with forward reads
GRIS4_2_R2.fq.gz fastq file with reverse reads
Gris3_13_R1.fq.gz fastq file with forward reads
Gris3_13_R2.fq.gz fastq file with reverse reads
Gris3_14_R1.fq.gz fastq file with forward reads
Gris3_14_R2.fq.gz fastq file with reverse reads
Gris3_22_R1.fq.gz fastq file with forward reads
Gris3_22_R2.fq.gz fastq file with reverse reads
Gris4_15_R1.fq.gz fastq file with forward reads
Gris4_15_R2.fq.gz fastq file with reverse reads
Gris4_17_R1.fq.gz fastq file with forward reads
Gris4_17_R2.fq.gz fastq file with reverse reads
Gris4_5_R1.fq.gz fastq file with forward reads
Gris4_5_R2.fq.gz fastq file with reverse reads
MTD1_R1.fq.gz fastq file with forward reads
MTD1_R2.fq.gz fastq file with reverse reads
MTD2_R1.fq.gz fastq file with forward reads
MTD2_R2.fq.gz fastq file with reverse reads
MTD5_R1.fq.gz fastq file with forward reads
MTD5_R2.fq.gz fastq file with reverse reads
MVZ232669_R1.fq.gz fastq file with forward reads
MVZ232669_R2.fq.gz fastq file with reverse reads
MVZ232719_R1.fq.gz fastq file with forward reads
MVZ232719_R2.fq.gz fastq file with reverse reads
MVZ232720_R1.fq.gz fastq file with forward reads
MVZ232720_R2.fq.gz fastq file with reverse reads
N2_N4_2_R1.fq.gz fastq file with forward reads
N2_N4_2_R2.fq.gz fastq file with reverse reads
N4_10_9A_R1.fq.gz fastq file with forward reads
N4_10_9A_R2.fq.gz fastq file with reverse reads
N4_8_R1.fq.gz fastq file with forward reads
N4_8_R2.fq.gz fastq file with reverse reads
PINNXBG1_R1.fq.gz fastq file with forward reads
PINNXBG1_R2.fq.gz fastq file with reverse reads
PINNXFC1_R1.fq.gz fastq file with forward reads
PINNXFC1_R2.fq.gz fastq file with reverse reads
PINNXFC2_R1.fq.gz fastq file with forward reads
PINNXFC2_R2.fq.gz fastq file with reverse reads
PINNXFC3_R1.fq.gz fastq file with forward reads
PINNXFC3_R2.fq.gz fastq file with reverse reads
PINNXFC5_R1.fq.gz fastq file with forward reads
PINNXFC5_R2.fq.gz fastq file with reverse reads
PINNXFC6_R1.fq.gz fastq file with forward reads
PINNXFC6_R2.fq.gz fastq file with reverse reads
PINNXNW1_R1.fq.gz fastq file with forward reads
PINNXNW1_R2.fq.gz fastq file with reverse reads
PINNXOP1_R1.fq.gz fastq file with forward reads
PINNXOP1_R2.fq.gz fastq file with reverse reads
PINNXOP3_R1.fq.gz fastq file with forward reads
PINNXOP3_R2.fq.gz fastq file with reverse reads
PINNXOP4_R1.fq.gz fastq file with forward reads
PINNXOP4_R2.fq.gz fastq file with reverse reads
PINNXSC11_R1.fq.gz fastq file with forward reads
PINNXSC11_R2.fq.gz fastq file with reverse reads
PINNXSC13_R1.fq.gz fastq file with forward reads
PINNXSC13_R2.fq.gz fastq file with reverse reads
PINNXSC1_R1.fq.gz fastq file with forward reads
PINNXSC1_R2.fq.gz fastq file with reverse reads
PINNXSC2_R1.fq.gz fastq file with forward reads
PINNXSC2_R2.fq.gz fastq file with reverse reads
PINNXSC4_R1.fq.gz fastq file with forward reads
PINNXSC4_R2.fq.gz fastq file with reverse reads
PINNXSC9_R1.fq.gz fastq file with forward reads
PINNXSC9_R2.fq.gz fastq file with reverse reads
PINNXWS1_R1.fq.gz fastq file with forward reads
PINNXWS1_R2.fq.gz fastq file with reverse reads
PINNXWS2_R1.fq.gz fastq file with forward reads
PINNXWS2_R2.fq.gz fastq file with reverse reads
PINNXWS3_R1.fq.gz fastq file with forward reads
PINNXWS3_R2.fq.gz fastq file with reverse reads
QTX1M_R1.fq.gz fastq file with forward reads
QTX1M_R2.fq.gz fastq file with reverse reads
QTX4F_R1.fq.gz fastq file with forward reads
QTX4F_R2.fq.gz fastq file with reverse reads
QTX5F_R1.fq.gz fastq file with forward reads
QTX5F_R2.fq.gz fastq file with reverse reads
QUATX2.1_R1.fq.gz fastq file with forward reads
QUATX2.1_R2.fq.gz fastq file with reverse reads
QUATX2.2_R1.fq.gz fastq file with forward reads
QUATX2.2_R2.fq.gz fastq file with reverse reads
RLB5221_R1.fq.gz fastq file with forward reads
RLB5221_R2.fq.gz fastq file with reverse reads
RT2_R1.fq.gz fastq file with forward reads
RT2_R2.fq.gz fastq file with reverse reads
RTF8_R1.fq.gz fastq file with forward reads
RTF8_R2.fq.gz fastq file with reverse reads
SE4_14_R1.fq.gz fastq file with forward reads
SE4_14_R2.fq.gz fastq file with reverse reads
SE4_15_R1.fq.gz fastq file with forward reads
SE4_15_R2.fq.gz fastq file with reverse reads
SE4_6_R1.fq.gz fastq file with forward reads
SE4_6_R2.fq.gz fastq file with reverse reads
SE4_7_R1.fq.gz fastq file with forward reads
SE4_7_R2.fq.gz fastq file with reverse reads
SE4_9_R1.fq.gz fastq file with forward reads
SE4_9_R2.fq.gz fastq file with reverse reads
SW17_R1.fq.gz fastq file with forward reads
SW17_R2.fq.gz fastq file with reverse reads
SW18_R1.fq.gz fastq file with forward reads
SW18_R2.fq.gz fastq file with reverse reads
TC1002_R1.fq.gz fastq file with forward reads
TC1002_R2.fq.gz fastq file with reverse reads
TC1003_R1.fq.gz fastq file with forward reads
TC1003_R2.fq.gz fastq file with reverse reads
TC1006_R1.fq.gz fastq file with forward reads
TC1006_R2.fq.gz fastq file with reverse reads
TC2081_R1.fq.gz fastq file with forward reads
TC2081_R2.fq.gz fastq file with reverse reads
TUM1_15_R1.fq.gz fastq file with forward reads
TUM1_15_R2.fq.gz fastq file with reverse reads
TUM1_16_R1.fq.gz fastq file with forward reads
TUM1_16_R2.fq.gz fastq file with reverse reads
TUM1_21_R1.fq.gz fastq file with forward reads
TUM1_21_R2.fq.gz fastq file with reverse reads
WW1492_R1.fq.gz fastq file with forward reads
WW1492_R2.fq.gz fastq file with reverse reads
WW1494_R1.fq.gz fastq file with forward reads
WW1494_R2.fq.gz fastq file with reverse reads
WW1496_R1.fq.gz fastq file with forward reads
WW1496_R2.fq.gz fastq file with reverse reads
WW1497_R1.fq.gz fastq file with forward reads
WW1497_R2.fq.gz fastq file with reverse reads
WW1510_R1.fq.gz fastq file with forward reads
WW1510_R2.fq.gz fastq file with reverse reads
WW1538_R1.fq.gz fastq file with forward reads
WW1538_R2.fq.gz fastq file with reverse reads
WW1540_R1.fq.gz fastq file with forward reads
WW1540_R2.fq.gz fastq file with reverse reads
WW1545_R1.fq.gz fastq file with forward reads
WW1545_R2.fq.gz fastq file with reverse reads
WW1567_R1.fq.gz fastq file with forward reads
WW1567_R2.fq.gz fastq file with reverse reads
WW1583_R1.fq.gz fastq file with forward reads
WW1583_R2.fq.gz fastq file with reverse reads
WW1620_R1.fq.gz fastq file with forward reads
WW1620_R2.fq.gz fastq file with reverse reads
WW1629_R1.fq.gz fastq file with forward reads
WW1629_R2.fq.gz fastq file with reverse reads
Xawi_R1.fq.gz fastq file with forward reads
Xawi_R2.fq.gz fastq file with reverse reads
Xe004_R1.fq.gz fastq file with forward reads
Xe004_R2.fq.gz fastq file with reverse reads
Xe005_R1.fq.gz fastq file with forward reads
Xe005_R2.fq.gz fastq file with reverse reads
Xg27_R1.fq.gz fastq file with forward reads
Xg27_R2.fq.gz fastq file with reverse reads
Xg29_R1.fq.gz fastq file with forward reads
Xg29_R2.fq.gz fastq file with reverse reads
Xg9_R1.fq.gz fastq file with forward reads
Xg9_R2.fq.gz fastq file with reverse reads
XrBO6M_R1.fq.gz fastq file with forward reads
XrBO6M_R2.fq.gz fastq file with reverse reads
XrES43_R1.fq.gz fastq file with forward reads
XrES43_R2.fq.gz fastq file with reverse reads
XrHN257_R1.fq.gz fastq file with forward reads
XrHN257_R2.fq.gz fastq file with reverse reads
Xs13_R1.fq.gz fastq file with forward reads
Xs13_R2.fq.gz fastq file with reverse reads
Xs17_R1.fq.gz fastq file with forward reads
Xs17_R2.fq.gz fastq file with reverse reads


Related publication(s): 
These data are associated with Chapter 3 (titled "Parsing Variance by Marker Type: Testing Biogeographic Hypotheses and Differential Contribution of Historical Processes to Population Structure in a Desert Lizard") in the dissertation "When Does Gene Flow Stop? A Mechanistic Approach to the Formation of Phylogeographic Breaks in Nature," by Iris Holmes. The dissertation is deposited in Deep Blue. 



Use and Access: 
This data set is made available under a Creative Commons Public Domain license (CC0 1.0).


To Cite Data: 
Holmes, I., Monagan Jr., I., Westphal, M., Davis Rabosky, A. Xantusia vigilis ddRADseq fastq files [Data set]. University of Michigan - Deep Blue. https://doi.org/10.7302/mep1-5124