Directionality in Genomics and Macroevolution

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).

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

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.

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.

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

Nelson, A. N., Dennis, M., Mangold, J. F., Li, K., Saha, P. T., Cronin, K., Cross, K. A., Kumar, A., Mangan, R. J., Shaw, G. M., Bar, K. J., Haynes, B., Moody, A. M., Munir Alam, S., Pollara, J., Hudgens, M. G., Van Rompay, K. K. A., De Paris, K., & Permar, S. R. (2022). Leveraging antigenic seniority for maternal vaccination to prevent mother-to-child transmission of HIV-1. Npj Vaccines, 7(1), 87.

Data: The datasets generated and/or analyzed during the current study are available from the corresponding author on reasonable request. All sequences have been deposited in GenBank with accession numbers: OM686910-OM686980 for pre-ART Env sequences, and OM906830-OM906850 for post-ART sequences.

Al-Ashhab, A., Marmen, S., Schweitzer-Natan, O., Bolotin, E., Patil, H., Viner-Mozzini, D., Aharonovich, D., Hershberg, R., Minz, D., Carmeli, S., Cytryn, E., Sukenik, A., & Sher, D. (2022). Freshwater microbial metagenomes sampled across different water body characteristics, space and time in Israel. Scientific Data, 9(1), 652.

Data: The raw, unprocessed Illumina sequencing reads (fastq files) for all metagenomes are available from the NCBI Sequence Read Archive (PRJNA497963 and PRJNA488159). All sample accession numbers 11 - 28, 33 - 55, 58 - 73, sample date/location, and library concentration and intensity for each metagenome can be found in Supplementary Table 2. The first 11 - 28 and third 58 - 73 datasets (Tables 1 and 3) were deposited under NCBI project number PRJNA497963, Supplementary Table 2). The second 33 - 55 dataset (Table 2) was deposited under NCBI project number PRJNA488159 (Supplementary Table 2). All various environmental measurements (EC, oxygen, temperature, Ammonia, total phosphorus, NO2, NO3, pH, photosynthetic pigments and toxin concentrations) (Supplementary Table 1) and samples metadata file (Supplementary Table 2). We note that not all data are available for every sample. Data pertinent to a specific dataset (e.g. Microcystis concentrations in dataset 2) are marked as “-“ in Supplementary Table 2 when not collected. Other missing data are marked as “NA”.

Wucherpfennig, J. I., Howes, T. R., Au, J. N., Au, E. H., Roberts Kingman, G. A., Brady, S. D., Herbert, A. L., Reimchen, T. E., Bell, M. A., Lowe, C. B., Dalziel, A. C., & Kingsley, D. M. (2022). Evolution of stickleback spines through independent cis-regulatory changes at HOXDB. Nature Ecology & Evolution.

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