Replication data and scripts for: Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

This dataset includes the data and scripts supporting the replicability of the paper: Louis M.*, Korlević P.*, Nykänen M.*, Archer F., Berrow S., Brownload A., Lorenzen E. D., O’Brien J., Post K., Racimo F., Rogan E., Rosel P. E., Sinding M.-H. S., van der Es H., Wales N., Fontaine M. C.**, Gaggiotti O. E.**, Foote A. D.** Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters. Nature Communications, in press. (*joint first author ; **joint senior author) Parallel evolution provides among the strongest evidence of the role of natural selection in shaping adaptation to the local environment. Yet, the chronology, mode and tempo of the process of parallel evolution remains broadly debated and discussed in the field of evolutionary biology. In this study, we harness the temporal resolution of paleogenomics to understand the tempo and independence of parallel coastal ecotype adaptation in common bottlenose dolphins (Tursiops truncatus). For this, we generated whole genome re-sequencing data from subfossil dolphins (8,610-5,626 years BP) originating from around the formation time of new coastal habitat and compared them with data from contemporary populations

Code and data used for the study: 'BioDeepTime: a database of biodiversity time series for modern and fossil assemblages'

The repository includes code and data to reproduce the results in the manuscript ‘BioDeepTime: a database of biodiversity time series for modern and fossil assemblages' by Smith et al. (analysis_biodeeptime.zip)

BioDeepTime: database and compilation code

The archive includes copies, compilation code, documentation and temporary data files for the BioDeepTime database. Deposited files: Relational database in SQLite format: biodeeptime_sqlite.zip. Denormalized database in zipped .csv format: biodeeptime_csv.zip Denormalized database in zipped .parquet (v1.0) format: biodeeptime_parquet.zip. Denormalized database in .rds (R version 4.0) format: biodeeptime.rds. Description of tables and columns: biodeeptime.md. Database schema: schema.pdf. Synonymy of sources: Synonymy of sources.xlsx. Change log and known issues: NEWS.md Compilation files: bdt_compilation.zip References in .csv format: references.csv Bchron ages calculated for Neotoma: neotoma_bchron.rds This repository accompanies the study BioDeepTime: a database of biodiversity time series for modern and fossil assemblages by Smith et al. (pending publication) and will be updated after a successful peer-review