Data from: Functional and population genomic divergence within and between two species of killifish adapted to different osmotic niches

 

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Title Velvet_Reference_protein_matching.txt
Downloaded 34 times
Description Sequences of our reference based on the Lucania parva velvet assembly (kmer=25) with a total of 24,781 contigs, combining 1,657 contigs from the L. goodei assembly (all unique contigs over 200bp) with L. parva contigs that had blast matches to any of the following: 1) related teleost proteomes (Atlantic killifish: Fundulus heteroclitus, Japanese medaka: Oryzia latipes, three-spined stickleback: Gasterosteus aculeatus), 2) Fundulus ESTs on the microarray, or 3) target genes of interest (osmoregulation and vision related genes). Blast results from blastX searches against the uniprot proteomes were retained only if contigs had only 1-2 protein matches per species (blast score > 100) to avoid inclusion of contigs that were misassembled from multiple genes.
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Title Popoolation_Fst_all
Downloaded 18 times
Description Results from Fst calculation in Popoolation2 (Kofler et al. 2011). We calculated allele frequencies and Fst between all populations, using a minimum coverage of 8 reads per population (to exclude SNPs from transcripts expressed at low frequency), a pool size of 10, and a sliding window of 50bp. Columns show Fst for populations listed at top (for given 50bp SNP window), last column is average of all L. goodei and all L. parva comparisons. Contigs match velvet reference names. L. goodei populations: Upper Bridge (Wakulla River, Florida) and Everglades (26-Mile Bend, Florida). Freshwater L. parva populations: Pecos (Pecos River, Texas), Lower Bridge (Wakulla River, Florida), Delks (Delk's Bluff, Oklawaha River, Florida). Saltwater L. parva populations: Indian River (Atlantic Ocean, Florida Coast), St. Mark’s (Gulf of Mexico, Florida Coast), Bolivar Peninsula (Galveston Bay, Texas Coast).
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Title Annotated_gene_universe_Lucania
Downloaded 10 times
Description List of annotations for all Lucania reference contigs using blastX and human proteome. Gene universe used in GO enrichment analyses.
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Title Goodei_Parva_Outliers
Downloaded 8 times
Description List of annotations for outliers between species (L. goodei vs. L. parva) using blastX and human proteome. Target gene file used in GO enrichment analyses.
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Title Goodei_outliers
Downloaded 6 times
Description List of annotations for outliers within L. goodei (Upper Bridge vs. Everglades) using blastX and human proteome. Target gene file used in GO enrichment analyses.
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Title SWSW_outliers
Downloaded 9 times
Description List of annotations for outliers within L. parva between geographically distant saltwater populations (Indian River and Bolivar Peninsula) using blastX and human proteome. Target gene file used in GO enrichment analyses. These outliers were removed from all freshwater-saltwater drainage analyses.
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Title Parva_outliers1Drain_SWrem
Downloaded 13 times
Description List of annotations for outliers between freshwater-saltwater drainages in L. parva using blastX and human proteome. Outliers in at least one drainage (and not present in saltwater-saltwater outliers). Target gene file used in GO enrichment analyses.
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Title Parva_outliers2-3Drainages
Downloaded 7 times
Description List of annotations for outliers between freshwater-saltwater drainages in L. parva using blastX and human proteome. Outliers present in two to three drainages shown (and not present in saltwater-saltwater outliers). Target gene file used in GO enrichment analyses.
Download Parva_outliers2-3Drainages.txt (21.79 Kb)
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Title Infinium Chip Souce Sequences
Downloaded 31 times
Description Source sequences for Illumina Infinium Bead Chip custom designed for Lucania. 4,545 SNPs from 454 contigs (assembled using Newbler). Contains 1,679 candidate SNPs segregating between species, 1,497 SNPs segregating between Everglades and Upper Bridge L. goodei, 1,369 SNPs segregating between Florida Atlantic saltwater and Texas Gulf freshwater L. parva).
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Title Infinuim_Chip_annotations
Downloaded 8 times
Description Annonations for Infinium contigs using BlastX against human proteome. Used in GO Enrichment analyses.
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Title Infinium_Parva_Goodei_Fst
Downloaded 12 times
Description Fst calculations between 33 L. goodei and 39 L. parva genotyped on the Infinium Chip. Calculations done in hierfstat in R.
Download Infinium_Parva_Goodei_Fst.txt (72.99 Kb)
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Title InfiniumFWSW_fst
Downloaded 10 times
Description Fst calculations between all freshwater and all saltwater L. parva (18 freshwater, 21 saltwater individuals: Florida Atlantic = 5 fresh, 6 salt; Florida Gulf = 8 fresh, 7 salt; Texas Gulf = 5 fresh, 8 salt) genotyped on the Infinium Chip. Calculations done in hierfstat in R.
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When using this data, please cite the original publication:

Kozak GM, Brennan RS, Berdan EL, Fuller RC, Whitehead A (2013) Functional and population genomic divergence within and between two species of killifish adapted to different osmotic niches. Evolution 68(1): 63–80. http://dx.doi.org/10.1111/evo.12265

Additionally, please cite the Dryad data package:

Kozak GM, Brennan RS, Berdan EL, Fuller RC, Whitehead A (2013) Data from: Functional and population genomic divergence within and between two species of killifish adapted to different osmotic niches. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.hv75h
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