Information for SMARTech Record
Title* – Supplemental Dataset
Creator(s)* - Chinar Patil, graduate student, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332;
Description* - There are a total of 9 data tables attached. Table 1-1 is a list of species that were sequenced. Table 2-1 is a list of genes and gene enrichments. Table 2-2 is a list of genes enriched in disease datasets. Table 2-3 is a list of differentially expressed genes and enrichments. Table 2-4 is a list of genes and gene enrichments. Table 3-1 is a list of genes and gene enrichments. Table 3-2 is Allele-specific expression results from MBASED. Table 3-3 has genes set enrichments resulting from the sign test. Table 3-4 has Four population comparisons with significantly negative f4 statistics.
Abstract* - . Evolutionary radiations characterized by a range of natural phenotypic variants between genetically closely related species are a great model to study the origin and genetic mechanisms underlying phenotypic diversity. I use one such model, cichlids from Lake Malawi to understand the basis of complex behavior evolution. Lake Malawi cichlids are broadly divided into rock dwelling and sand dwelling lineages based on the habitat they colonize in the lake. Within this split on the basis of habitat comes a wide range of behavioral differences that define rock dweller and sand dweller cichlids. Within the sand dweller lineage, males build species specific bowers to attract females in seasonal leks. The tables included here describe the species involved, the divergent genes and the transcriptional patterns that differentiate the genes. 
Subject/Keywords* - Evolution, Genomics, cis-regulation, Malawi Cichlids
Date data were made publically available - 5 Nov 2018
Sponsorship - 
Publications related to dataset - York RA†, Patil C†, Abdilleh K, Johnson ZV, Conte MA, Genner MJ, McGrath PT, Fraser HB, Fernald HB, Streelman JT (2018) Behavior-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes , Proceedings of the National Academy of Sciences Nov 2018, 201810140; DOI: 10.1073/pnas.1810140115







Information for README file
Name of contact person – Chinar Patil
Email and phone number for contact person: chinar@gatech.edu 7703357422
Format of data files - Microsoft Excel datasheets
Location where data were collected – Data were generated and analysed at the Georgia Institute of Technology, Atlanta Georgia. 
Time period during which data were collected - between 2012-08-01  and 2018-10-31
File Information - In addition to this readme file, there are a total of 9 tables as described below:  
Table 1.1 : List of Malawi species sequenced : This table contains a list of the species that were sequenced. 
Table 2-1 : Enrichment test for Rock-Sand Variants : This table contains a list of the genes defined as divergent between rock-sand. This sheet also includes gene set enrichment analysis, each tab with enrichment tabs for different categories.  
Table 2-2 :Rock Sand Genes present in SFARI db, Neurcristopathy db and CNEs : This table has 4 tabs, each with genes also found in publicly available disease datasets. 
Table 2-3 Differentially Expressed Genes in Rock Sand F1 males : This table contains differentially expressed genes between rock and sand. This sheet also includes gene set enrichment analysis, each tab with enrichment tabs for different categories.  
Table 2-4 Rock Sand intersect Pit Castle divergence : This table contains genes that are common between the rock-sand and pit-castle divergence. This sheet also includes gene set enrichment analysis, each tab with enrichment tabs for different categories.  
Table 3-1 Pit Castle divergent genes, enrichment test : This table contains a list of the genes defined as divergent between pit-castle. This sheet also includes gene set enrichment analysis, each tab with enrichment tabs for different categories.  
Table 3-2 Allele-specific expression results from MBASED : This table contains a list of genes that show Allele Specific expression between diggging and building alleles. 
Table 3-3 Gene set enrichments resulting from the sign test : This table contains genes that show concordant bias and pathway enrichment for these genes. 
Table 3-4 Four population comparisons with significantly negative f4 statistics : This table shows the significance values of the f4 test. 


Software – Gene set enrichment in Tables 2-1, 2-3, 2-4 and 3-1 was performed using http://geneanalytics.genecards.org/

Date dataset was last modified : October 31, 2018
Related materials - 
Data source -