Photo of reindeer and reindeer calves in a herd outdoors.
Photo: Leonie Duris

Analysis of runs of homozygosity in reindeer to infer past demographic events and inbreeding levels

Page reviewed:  28/10/2025

Reindeer husbandry, an essential part of Sámi culture in northern Scandinavia, faces multiple challenges that may be creating a "perfect storm" to the sustainability of reindeer populations. Understanding the genetic health and adaptive potential of reindeer populations then becomes crucial.

Background

Reindeer husbandry, an essential part of Sámi culture in northern Scandinavia, faces multiple challenges including climate change, competing land use, and increased predation pressure. These pressures may be creating a "perfect storm" that threatens the sustainability of reindeer populations. In this context, understanding the genetic health and adaptive potential of reindeer populations is crucial.

One key indicator of genetic health is the presence and pattern of runs of homozygosity (ROH) in the genome, which can reveal information about past demographic events and inbreeding levels. ROH are continuous stretches of homozygous genotypes that are inherited from parents sharing common ancestors. The length and frequency of these segments can help track changes in effective population size over time and identify potential genetic vulnerabilities.

The project is part of EQUIP where the causes of losses of reindeer calves from calf marking to slaughter are investigated.

Goal(s)

  1. To estimate the effective population size in reindeer over the past 2000 years using samples collected in Sweden.
  2. To find and describe patterns of ROH that might affect inbreeding.

Project description

Implementation

The data has been collected, and the genotyping is ready. The project requires analysis using bioinformatics and available software for genetic analysis. The recommended period of work is the first half of 2026.

Method

DNA has been extracted from 10 reindeer from four reindeer herding communities in Sweden. The samples have been sequenced by the SciLife Lab using illumina NovaSeq X 2x150bp. Your task will be to analyse ROH and infer historical population sizes.

Specifications

Suitable for students in veterinary or animal science with a strong interest in bioinformatics and genetics, or a student with a background in bioinformatics.

References

Browning, S. R., & Browning, B. L. (2010). High-resolution detection of identity by descent in unrelated individuals. The American Journal of Human Genetics, 86(4), 526-539.

Corbin, L. J., Liu, A. Y. H., Bishop, S. C., & Woolliams, J. A. (2012). Estimation of historical effective population size using linkage disequilibria with marker data. Journal of Animal Breeding and Genetics, 129(4), 257-270.

Chang, C. C., Chow, C. C., Tellier, L. C., Vattikuti, S., Purcell, S. M., & Lee, J. J. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience, 4(1), s13742-015.

Li, H., & Durbin, R. (2011). Inference of human population history from individual whole-genome sequences. Nature, 475(7357), 493-496.

Magi, A., Tattini, L., Palombo, F., Benelli, M., Gialluisi, A., Giusti, B., ... & Pippucci, T. (2014). H 3 m 2: detection of runs of homozygosity from whole-exome sequencing data. Bioinformatics, 30(20), 2852-2859.

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