Directionality in Genomics and Macroevolution

Papers From This Cluster

Sterner, B., & Elliott, S. (2023). How data governance principles influence participation in biodiversity science. Science as Culture, 1–26.

https://doi.org/10.1080/09505431.2023.2214155

Nuño De La Rosa, L. (2023). Agency in Reproduction. Evolution & Development, ede.12440.

https://doi.org/10.1111/ede.12440

Livnat, A., & Melamed, D. (2023). Evolutionary honing in and mutational replacement: how long-term directed mutational responses to specific environmental pressures are possible. Theory in Biosciences, 142(2), 87–105.

https://doi.org/10.1007/s12064-023-00387-z

Sterner, B., Sen, A., & Witteveen, J. (2022). Consensus and Scientific Classification. Knowledge Organization, 49(4), 236–256.

https://doi.org/10.5771/0943-7444-2022-4-236

Halpern, B. S., Boettiger, C., Dietze, M. C., Gephart, J. A., Gonzalez, P., Grimm, N. B., Groffman, P. M., Gurevitch, J., Hobbie, S. E., Komatsu, K. J., Kroeker, K. J., Lahr, H. J., Lodge, D. M., Lortie, C. J., Lowndes, J. S. S., Micheli, F., Possingham, H. P., Ruckelshaus, M. H., Scarborough, C., … Youngflesh, C. (2023). Priorities for synthesis research in ecology and environmental science. Ecosphere, 14(1).

https://doi.org/10.1002/ecs2.4342

Pollen, A. A., Kilik, U., Lowe, C. B., & Camp, J. G. (2023). Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution. Nature Reviews Genetics.

https://doi.org/10.1038/s41576-022-00568-4

Basanta, S., & Nuño de la Rosa, L. (2023). The female orgasm and the homology concept in evolutionary biology. Journal of Morphology, 284(1).

https://doi.org/10.1002/jmor.21544

Bolotin, E., Melamed, D., & Livnat, A. (2022). Genes that are Used Together are More Likely to be Fused Together in Evolution by Mutational Mechanisms: A Bioinformatic Test of the Used-Fused Hypothesis. Evolutionary Biology.

https://doi.org/10.1007/s11692-022-09579-9

Saelens, J. W., Sweeney, M. I., Viswanathan, G., Xet-Mull, A. M., Jurcic Smith, K. L., Sisk, D. M., Hu, D. D., Cronin, R. M., Hughes, E. J., Brewer, W. J., Coers, J., Champion, M. M., Champion, P. A., Lowe, C. B., Smith, C. M., Lee, S., Stout, J. E., & Tobin, D. M. (2022). An ancestral mycobacterial effector promotes dissemination of infection. Cell, 185(24), 4507-4525.e18.

Data:

  • Genomic sequencing and RNA-seq data are available at NCBI (BioProjects PRJNA540867 and PRJNA872173)
  • Raw and processed mass spectrometry files are archived and available at MassIVE and PRIDE repositories under accession numbers MSV000090143 and PDX036131.
  • Original code is deposited and publicly available on GitHub and Zenodo.
  • DOIs are listed in the Key Resource Table.
  • All other data are available in the main text or supplementary figures.
  • Any additional information required to reanalyze the data reported in this work paper is available from the lead contact upon request.
https://doi.org/10.1016/j.cell.2022.10.019

Mangan, R. J., Alsina, F. C., Mosti, F., Sotelo-Fonseca, J. E., Snellings, D. A., Au, E. H., Carvalho, J., Sathyan, L., Johnson, G. D., Reddy, T. E., Silver, D. L., & Lowe, C. B. (2022). Adaptive sequence divergence forged new neurodevelopmental enhancers in humans. Cell, 185(24), 4587-4603.e23.

Data and code availability:

  • All software written for this manuscript was implemented as a part of Gonomics, an ongoing effort to develop an open-source genomics platform in the Go programming language (golang).
     
  • Raw and analyzed datasets, including browser tracks, sequencing files, multiple alignments, and variant sets used in selection analysis, have been made freely available on our lab website
     
  • Raw and analyzed datasets: www.thekorenlab.org/data;  https://hgwdev.gi.ucsc.edu; www.eva.mpg.de/neandertal/draftneandertal-genome/data.html
     
  • Experimental models:
    • https://support.illumina.com/downloads/bcl2fastqconversion-software-v2-20.html
    • https://github.com/lh3/bwa
    • https://support.10xgenomics.com/
    • https://www.ebi.ac.uk/Tools/phylogeny/simplephylogeny/gonomics
    • https://github.com/vertgenlab/gonomics
    • https://www.graphpad.com
    • http://great.stanford.edu/public/html
    • https://imagej.net/software/fiji
    • https://github.com/ENCODE-DCC/kentUtils
    • https://github.com/lastz/lastz
    • https://bio.tools/multiz
    • https://www.ebi.ac.uk/Tools/msa/muscle/phylotree
    • https://phylotree.hyphy.org
    • https://zzz.bwh.harvard.edu/plink
    • https://www.r-project.org
    • https://github.com/CshlSiepelLab/RPHAST
    • https://satijalab.org/seurat
    • http://pcingola.github.io/SnpEff
https://doi.org/10.1016/j.cell.2022.10.016