Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent inFicedulaFlycatcher Genome Sequences

Abstract

Individual inbreeding and historical demography can be estimated by analyzing runs of homozygosity (ROH), which are indicative of chromosomal segments of identity by descent (IBD). Such analyses have so far been rare in natural populations due to limited genomic resources. We analyzed ROH in whole genome sequences from 287 Ficedula flycatchers representing four species, with the objectives of evaluating the causes of genome-wide variation in the abundance of ROH and inferring historical demography. ROH were clearly more abundant in genomic regions with low recombination rate. However, this pattern was substantially weaker when ROH were mapped using genetic rather than physical single nucleotide polymorphism (SNP) coordinates in the genome. Empirical results and simulations suggest that high ROH abundance in regions of low recombination was partly caused by increased power to detect the very long IBD segments typical of regions with a low recombination rate. Simulations also showed that hard selective sweeps (but not soft sweeps or background selection) likely contributed to variation in the abundance of ROH across the genome. Comparisons of the abundance of ROH among several study populations indicated that the Spanish pied flycatcher population had the smallest historical effective population size (N e ) for this species, and that a putatively recently founded island (Baltic) population had the smallest historical N e among the collared flycatchers. Analysis of pairwise IBD in Baltic collared flycatchers indicated that this population was founded ,60 generations ago. This study provides a rare genomic glimpse into demographic history and the mechanisms underlying the genome-wide distribution of ROH.

Importance of infection of haemosporidia blood parasites during different life history stages for long‐term reproductive fitness of collared flycatchers

“…Furthermore, comparing parasite transmission information with the phylogenetic history of the parasite lineages can provide insights in to how new lineages may have arisen. And indeed, the collared flycatchers breeding range has expanded (Kardos et al 2017) giving the birds opportunity to make contact with vectors carrying novel parasites and potentially causing them to diverge (Jones et al 2018). 1A).…”

Recent advances in conservation and population genomics data analysis

“…Differences in historical N e among populations can be qualitatively inferred by analyzing the abundance of ROH. The abundance of very short ROH is informative of N e in distant history, while long ROH is informative of more recent N e (Kardos, Qvarnström, & Ellegren, 2017; Kirin et al., 2010; Pemberton et al., 2012). A limitation of this approach is that it is only qualitative and requires data on multiple populations to be informative.…”

“…A limitation of this approach for most natural populations is that it requires a minimum of approximately 100 individuals and the genetic mapping locations (i.e., on a linkage map) of at least several hundred thousand SNPs (Browning & Browning, 2015). However, the approach has great potential to infer recent demographic history (i.e., to test for and quantify recent population bottlenecks and expansions) in natural populations where it would be difficult or impossible to evaluate recent N e otherwise (Kardos et al., 2017). …”

A model‐based approach to characterize individual inbreeding at both global and local genomic scales

“…ROH are indeed most often interpreted as homozygous‐by‐descent (HBD) or autozygous segments, that is, made up of pairs of haplotypes that were inherited from a common ancestor without recombination (and mutation) in neither of them via two different genealogical paths. Assessing the distribution of ROH within individual genomes has thus become popular to characterize inbreeding in a wide range of model species including humans (Kirin et al., ; McQuillan et al., ; Pemberton et al., ), livestock (Bosse et al., ; Ferenčaković et al., ) or wild populations (Kardos, Qvarnstrom, & Ellegren, ). ROH also allow to distinguish between recent and more ancient inbreeding (Kirin et al., ; Pemberton et al., ; Purfield, Berry, McParland, & Bradley, ) as HBD segments tracing back to more remote ancestors are expected to be shorter because of a higher number of historical recombination events (Thompson, ).…”

“…Broman and Weber () proposed a formal statistical approach to assess the actual HBD status of the ROH they identified by accounting for population allele frequencies and genotyping error rates. Elaborating on this earlier work, likelihood‐based approaches were further developed allowing in particular to compute a LOD score to assess the strength of evidence in favour of autozygosity of genomic windows through the genome, the size of the window being previously optimized (e.g., Kardos et al., ; Pemberton et al., ; Wang, Haynes, Barany, & Ott, ). Alongside these window‐based approaches, Leutenegger et al.…”