The genetic basis of coordinated plasticity across functional units in a Lake Malawi cichlid mapping population
Data files
Dec 26, 2020 version files 1.45 MB
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BS_SL_Corr.tps
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BS.TPS
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CF_Lat_SL_Corr.tps
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CF_Lat.tps
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CF_Vent_SL_Corr.tps
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CF_Vent.tps
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FM_SL_Corr.tps
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FM.TPS
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LOD_Scores_for_Network_Analysis.csv
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PJ_Lat_SL_Corr.tps
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PJ_Lat.TPS
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PJ_Vent_SL_Corr.tps
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PJ_Vent.TPS
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QTL_Map_with_Traits.csv
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Shape_Scores_for_Network_Analysis.csv
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SL.csv
Apr 01, 2021 version files 1.81 MB
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BS_SL_Corr.tps
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BS.TPS
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CF_Lat_SL_Corr.tps
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CF_Lat.tps
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CF_Vent_SL_Corr.tps
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CF_Vent.tps
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FM_SL_Corr.tps
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FM.TPS
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LOD_Scores_for_Network_Analysis.csv
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PJ_Lat_SL_Corr.tps
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PJ_Lat.TPS
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PJ_Vent_SL_Corr.tps
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PJ_Vent.TPS
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QTL_Map_with_Traits.csv
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QTL_Map_with_Traits.xls
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Shape_Scores_for_Network_Analysis.csv
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SL.csv
Abstract
Methods
Full methods can be found in the article in Evolution. In brief, we used a hybrid mapping cross of cichlid fish to assess the genetic basis of diet-induced plasticity. F3 hybrid animals resulting from a cross between a Labeotropheus fuelliborni female and a Tropheops sp. "redcheek" male were split into two diet treatments. These hybrids were then sacrificed, dissected, & analyzed for a variety of phenotypic traits, including both linear & geometric morphometrics. Continuous traits resulting from the geometric morphometric analyses were subjected to a canonical variates analysis, which produced an axis arraying individuals from more plastic animals at each extreme, to less plastic animals near the origin. These values were then used as the basis for a series of QTL analyses aimed at linking plasticity to its underlying genetic basis. Finally, both the trait values and the genetic associations were used in two separate network analyses to determine whether plasticity was correlated across the body at either the morphological or genetic level.
For each trait, I have provided two TPS files - one with the unadjusted landmark coordinates (named: "Trait X.tps"), and one with the allometry-adjusted landmark coordinates (named: "Trait X SL Corr.tps"). I also include the file with the standard length values for each individual ("SL.csv") - these were used in the size standardizations. I have also provided the files used in the network analyses based on shape ("Shape Scores for Network Analysis.csv") and genetics ("LOD Scores for Network Analysis.csv"). These provide the shape scores for each individual for each trait and the LOD scores at every position sampled along the genome for each individual for each trait, respectively. Finally, I have provided the QTL map with all 21 phenotypes that were mapped ("QTL Map with Traits.csv").