NAISS
SUPR
NAISS Projects
SUPR
Johannes Bergsten Lab
Dnr:

NAISS 2026/3-677

Type:

NAISS Medium

Principal Investigator:

Johannes Bergsten

Affiliation:

Naturhistoriska riksmuseet

Start Date:

2026-10-12

End Date:

2027-11-01

Primary Classification:

10612: Biological Systematics

Secondary Classification:

10615: Evolutionary Biology

Tertiary Classification:

10608: Zoology

Allocation

Abstract

My Lab works with insect phylogenomics, species delimitation and various evolutionary questions often requiring a phylogenetic tree. We use whole genome sequence data (long and short read), RAD-seq data, transcriptomes or data generated from reduced representation methods. I often have a PhD student and one to three masterstudents at a time working with different phylogenetic projects and with need for computation resources and to store genomic data for their projects. I prefer to from-now-on gather all under one project "Johannes Bergsten Lab" to reduce the number of reporting occassions, which has been difficult to keep up with in the past. This fall starting September 1st 2026 I will take on 2 new Master students both of which will have computation intensive projects and generate substantial new genomic Illumina data. One master student will generate shotgun Illumina short read data (approximately 200 samples) in a Museomics project using older insect specimens from collections to assess the resulting data quality from different time periods (18th to 21st century), from important auctors and from significant historic expeditions that have generated a lot of type material of new species. This project will be heavy on quality assessment, de novo assembly and evaluative statistics, but not predominantly on phylogenetic analyses. The second master student's project will be an analysis-heavy phylogenomic project where the student will produce new shotgun Illumina genomic data for an increased taxon sampling (approximatly 50 new samples) to a large existing 5000+ genes x 150 taxa dataset of world diving beetles and rerun ML (IQ-Tree) and species tree (Astral) analyses in an attempt to resolve remaining outstanding questions in the backbone phylogeny of diving beetles, especially among tribes in the large subfamily Hydroporinae. This will entail de novo genome assembly and gene-fishing to complement the existing orthlogous gene dataset prior to phylogenetic analyses, and likely also post topology testing with four cluster likelihood mapping and sensitivity analyses of results under different models and missing data thresholds. Performing these kinds of analyses with over 100+ taxa and 5000+ genes are computationally demanding. Both master student projects are for one year, 60Hp. In addition to these for HT26-VT27 I have various collaborations that on and off require computation resources.