Welcome to CaveCrawler
CaveCrawler is a reactive web interface for bioinformatic analysis of data in the Mexican tetra (Astyanax mexicanus), an emerging evolutionary model organism.
CaveCrawler consists of 4 modules: a Gene Search page for querying data about specific genes, a Transcription page for finding genes whose transcriptional levels differ between samples, a Population Genetics page for investigating statistics on diversity and selection, and a GO Term Info page for identifying and obtaining information on GO terms-of-interest.
Finally, there is the Data Sources module, which describes the publications from which each dataset was obtained, as well as the dates for Ensembl and UniProt-derived information.
To request that new data be integrated into CaveCrawler, please email Heath Blackmon at hblackmon@bio.tamu.edu or Alex Keene at akeene@bio.tamu.edu
To cite CaveCrawler, please cite our paper, currently available on BioRXiv: 'CaveCrawler: An interactive analysis suite for cavefish bioinformatics'
CaveCrawler Data Sources
1. Herman, A., Brandvain, Y., Weagley, J., Jeffery, W. R., Keene, A. C., Kono, T., Bilandzija, H., Borowsky, R., Espinasa, L., O'Quin, K., Ornelas-Garcia, C. P., Yoshizawa, M., Carlson, B., Maldonado, E., Gross, J. B., Cartwright, R. A., Rohner, N., Warren, W. C., and McGaugh, S. E. (2018) The role of gene flow in rapid and repeated evolution of cave related traits in Mexican tetra, Astyanax mexicanus. Molecular ecology, 27, 4397-4416.Description:
Fst, Pi, Dxy, and Tajima's D calculated using whole genomes sequenced from fin clips of wild-caught Pachon (N= 9; collected in 2013), Tinaja (N = 10; collected in 2002 and 2009), Molino (N = 9; collected in 1994 and 2004), Rascon (N = 6; collected in 2013), Rio Choy (N = 9; collected in 2013). Filters were applied to SNPs and indels to remove low confidence calls. Due to high heterozygosity in all individuals, the authors excluded all SNP/ indel sites where 100% of individuals were heterozygous. See publication for more details on sequencing and read filtration. All data was mapped to Astyanax mexicanus 1.02 assembly, Ensembl 93 release.
2. Moran, R.L., Jaggard, J.B., Roback, E.Y., Kenzior, A., Rohner, N., Kowalko, J.E., Ornelas-Garcia, P., McGaugh, S.E. and Keene, A.C. (2022) Hybridization underlies localized trait evolution in cavefish. iScience
Description:
The authors calculated Dxy and Fst for Chica cave fish from two pools: Pool 1 (n = 5; referred as Chica1 in tables) 91m from entry to cave and Pool 2 (n = 14; referred as Chica2 in tables) 10m further into cave relative to Pool 1.
The authors calculated Dxy for Rascon-Pachon, Rascon-Tinaja. Pachon, Tinaja, and Rascon short-read files from Herman et. al 2018 were downloaded from SRA. 1 Rascon and 2 Tinaja individuals were excluded from D-statistic calculations due to recent hybrid ancestry, and additional samples were added to bring the final sample sizes up to Tinaja = 10, Pachon = 9, and Rascon = 8.
Filters were applied to SNPs and indels to remove low confidence calls. See publication for more details on sequencing and read filtration, as well as the websites from which gene information was derived. All data was mapped to Astyanax mexicanus 1.02 assembly, Ensembl 93 release.
3. Bradic, M., Beerli, P., Garcia-de Leon, F.J., Esquivel-Bobadilla, S. and Borowsky, R.L. (2012) Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus). BMC evolutionary biology, 12, 1-17.
Description:
Geographic coordinates of 11 cave (Pachon, Yerbaniz, Japonis, Arroyo, Tinaja, Curva, Toro, Chica, Molino, Caballo Moro) and 10 surface populations (Subterraneo, Rio Frio, Arroyo Sarco, Chamal, Rio Meco, Rio Tantaon, Rio Florido, Rio Tampaon, Nacimiento del Rio Santa Clara, San Rafael Los Castros, Rio Subterraneo Valley) were identified. These coordinates were used, in conjunction with the Google Maps coordinates for the Rascon and Rio Choy surface populations (accessed December 2021), to generate the map on the Home module.
4. Mack, K.L., Jaggard, J.B., Persons, J.L., Roback, E.Y., Passow, C.N., Stanhope, B.A., Ferrufino, E., Tsuchiya, D., Smith, S.E. and Slaughter, B.D. (2021) Repeated evolution of circadian clock dysregulation in cavefish populations. PLoS genetics, 17, e1009642.
Description:
Lab-born Molino, Pachon, Tinaja, and Rio Choy fish were reared on a 14:10 light:dark cycle. At 30 dpf, 6 whole organisms from each population were sampled for RNAseq at 6 time points (144 samples total; average of 14,197,772 reads per sample). Genes were considered rhythmic if their JTK_cycle 24 hr periodicity was below an FDR cutoff of 5%. logFC (calculated for Molino-Rio Choy, Pachon-Rio Choy, and Tinaja-Rio Choy) reflects the average change in expression across all 6 timepoints. All data was mapped to Astyanax mexicanus 1.02 assembly, Ensembl 93 release.
5. McGaugh, S.E., Passow, C.N., Jaggard, J.B., Stahl, B.A. and Keene, A.C. (2020) Unique transcriptional signatures of sleep loss across independently evolved cavefish populations. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 334, 497-510.
Description:
Tinaja, Molino, Pachon, and Rio Choy fish were raised on 14:10 hr light-dark cycle. At 29 dpf, fry were sleep deprived by shaking in Erlenmeyer flasks at random intervals < 60 seconds apart throughout a period of 10 hours during the night. Control fish were housed under identical conditions but were not shaken. At 30 dpf, 6 whole fish per population (Tinaja, Pachon, Molino, and Rio Choy) and experimental group (sleep-deprived and control) were sampled for RNA-seq. The logFC in response to sleep deprivation was calculated for 17,187 genes in each population. Genes were labeled as differentially expressed if the Benjamini-Hochberg adjusted p-value was less than 0.05. All data was re-mapped to Astyanax mexicanus 3 assembly (GCA_023375975.1)
6. Warren, W.C., Boggs, T.E., Borowsky, R., Carlson, B.M., Ferrufino, E., Gross, J.B., Hillier, L., Hu, Z., Keene, A.C. and Kenzior, A. (2021) A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution. Nature communications, 12, 1-12.
Description:
The authors of this study created a fully-annotated surface fish genome assembly. The genome assembly from this study was acquired for CaveCrawler using Ensembl Genome Browser, release 106.
7. The UniProt Consortium. (2020) UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Research, 49, D480-D489.
Description:
All Mexican tetra Gene Ontology information was obtained from UniProtKB (Feb. 2 2021 release) using the following search phrase:
organism: 'Astyanax mexicanus (Blind cave fish) (Astyanax fasciatus mexicanus) [7994]' AND proteome:up000018467