Institution: Senckenberg Gesellschaft für Naturforschung

TBG group members

  • Axel Janke
  • Stefan Prost

Affiliated

  • Sven Winter
  • Raphael Coimbra
  • Fritjof Lammers

Geneflow in speciation

TBG project summary

We are interested in evolution and speciation processes of mammals and how to read these from genomic data using methods developed for comparative genomics. These methods are developed by others, but also want to understand their limits and combine them to a user-friendly bioinformatics pipelines to make gene-flow analyses more economic.

One focus is gene flow between species. This will tell us how, why and to what extend does gene flow influence/enhance speciation and biodiversity.

We study this on a number of groups where we have evidence for gene flow or where we expect to find it. To date we have found substantial geneflow in all taxa that we studied (bear, kangaroos, whale), but only limited one in giraffe.

Group expertise / Methods

We sequence mammalian species de novo using data generated with the 10x Genomics Chromium platform. The assembly uses SuperNova2. Tests of the program tigmint, showed no significant improvement, therefore we limit our assemblies to SuperNova2. The reference-based genomes were generated by mapping the reads against the closest de novo assembly using the standard pipeline of BWA, samtools and picard. Repeatmasking was done with RepeatMasker (with RepBase and Dfam databases for mammals) and gene annotation is performed using Braker2. ProteinOrtho identifies orthologes. Demographic analyses were based on diploid genomes (generated using samtools) and PSMC. Gene flow analyses were carried out using the ABBA-BABA test implemented in ANGSD.