The qGen (quantitative genetics) experiment investigates the heritability of traits in Echinacea angustifolia.
The qGen dataset includes survival and fitness measures for 4468 seedlings planted in the main common garden experimental plot (exPt1) in 2003. The qGen dataset has two files: 1. qGenExpPedigreeSprouts.csv and 2. qGenExpAnnualFitness.csv, see explanation below.
1) qGenExpPedigreeSprouts.csv contains the pedigree and seedling data (3,751 records). This file will not be updated:
cgPlaId: common garden plant Id (numeric)
tray: seedling tray (numeric)
cohort: cohort category based on germination (numeric)
plug: plug identification number (numeric)
lds1: living during seedling stage 1 / 1 = yes, 0 = no (binary)
lds2: living during seedling stage 2 / 1 = yes, 0 = no (binary)
lds3: living during seedling stage 3 / 1 = yes, 0 = no (binary)
dam: dam identification / maternal plant cgPlaId (numeric)
damFam: dam family identification (numeric)
damSite: dam site of origin (text)
sire: sire identification / paternal plant cgPlaId (numeric)
sireFam: sire family identification (numeric)
sireSite: sire site of origin (text)
emmr: common garden location coordinate / easting or row coordinate in mm (numeric)
nmmp: common garden location coordinate / northing or position coordinate in mm (numeric)
2) qGenExpAnnualFitness.csv will remain the most up to date link to the qGen dataset. This file contains the annual survival, flowering, head count, and achene count data:
cgPlaId: common garden plant Id (numeric)
measureYr: measure year / year plant was observed (numeric)
ld: living during observation year / 1 = yes, 0 = no (binary)
fl: flowering during observation year / 1 = yes, 0 = no (binary)
hdCt: head count / if flowering, count of heads per plant for observation year; not including “dud” heads (numeric)
achCt: achene count / count of achenes per plant for observation year (numeric)
*NOTE* here is an explanation for negative numbers in acheneCt: We use “-9999” as code for “missing data” in the achCt field for each head. If the plant had multiple heads & a count was missing for one of the heads, -9999 was summed together with the good achene count(s). So far, we don’t have any instances where more than one head has a missing achene count per plant; but if we do, I’ll make a note of it. So if hdCt > 1 & acheneCt < 0 adding 9999 to acheneCt will give you the acheneCt for the heads that are not missing data.
The key field ‘cgPlaId’ links the two files. Records in qGenExpPedigreeSprouts.csv with null cgPlaId’s represent plants that did not survive to be planted in the common garden.
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02/21/2020 GK
Here is a link to an updated qGen annual survey dataset with annual survival, flowering, & head count data through 2019 and achene count data through 2017 (47,243 records).
qGenExpAnnualFitness.csv will remain the most up to date link to the qGen dataset.
qGenExpAnnualFitness20200221.csv is a permanent link to this version of the dataset.
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04/10/2019 GK
Here is a link to an updated qGen annual survey dataset with annual survival, flowering, head count, and achene count data through 2017 (41,685 records).
qGenExpAnnualFitness20190410.csv is a permanent link to this version of the dataset.
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04/07/2019 GK
Here is a link to an updated qGen annual survey dataset with annual survival, flowering, head count, and achene count data through 2017 (41,685 records). Two things to note: Achenes lost at time of harvest are not included in the achene count for 2016 & 2017. We may be missing achene counts for up to 11 heads harvested in 2016 (with gBagId’s = “EA” & “EB”). I need to explore more!
qGenExpAnnualFitness20190406.csv is a permanent link to this version of the dataset.
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01/18/2017 GK
Here is a link to an updated qGen annual survey dataset with annual survival, flowering, and head count data through 2016 and achene count data through 2014 (38,906 records).
qGenExpAnnualFitness20170118.csv is a permanent link to this version of the dataset.
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12/22/2015 GK
Here is a link to an updated qGen annual survey dataset with annual survival, flowering, and head count data through 2015 and achene count data through 2014 (36,127 records). Two things to note: there are fewer records than posted in the past because within-site and unknown crosses have been removed (newExpNm = ‘qGen_a’ are included while ‘qGen_b’ are not). Also, to be consistent with the CORE dataset, questionable heads (those that were noted as gone or crisp before flowering) were not counted in hdCt.
qGenExpAnnualFitness20151222.csv is a permanent link to this version of the dataset.
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02/14/2015 GK
Here is a link to an updated qGen annual survey dataset with annual survival, flowering, and head count data through 2014 and achene count data through 2012 (42,852 records).
qGenExpAnnualFitness20150214.csv is a permanent link to this version of the dataset.
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02/11/2015 GK
Here is a link to an updated qGen annual survey dataset with annual survival, flowering, and head count data through 2014 and achene count data through 2010 (42,852 records). I hope to include achene counts for 2011 & 2012 ASAP!:
qGenExpAnnualFitness20150211.csv is a permanent link to this version of the dataset.
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01/27/2014 GK
Here is a link to an updated qGen annual survey dataset. ‘qGenAnnualSurveyJan2014.csv’ contains annual survival, flowering, and head count data through 2013 and achene count data through 2010 (39,281 records):
qGen Annual Survey January 2014 is a permanent link to this version of the dataset.
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04/25/2013 GK
Here is a link to an updated qGen annual survey dataset. Updates are based on two scenarios that were identified in the dataset posted in January: 1. problem: plants reappear after they are not found and assumed dead, solution: plants are assumed to be living in years when they weren’t found if they were found living in subsequent years, 2. problem: crisp heads not included in head count have achene counts, solution: regardless of the status of the head at the time of measuring, if achene count is greater than 0, head will be included in head count.
qGen Annual Survey April 2013 is a permanent link to this version of the dataset.
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01/07/2013 GK
Here are links to the qGen dataset that was updated for Ruth:
qGen Annual Survey is a permanent link to this version of the dataset.
qGen Pedigree Sprouts is a permanent link to this version of the dataset (this file has been renamed qGenExpPedigreeSprouts.csv).
