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Conservation genomics in inbred Scandinavian wolves using bioinformatic methods
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.ORCID iD: 0000-0002-8415-9259
2024 (English)Doctoral thesis, comprehensive summary (Other academic)
Description
Abstract [en]

With the recent and unprecedented progress in retrieving DNA sequence information from a large number of individuals of any species, conservation genetic research has entered a new phase. Specifically, it has become possible to study how genomes of endangered species respond to reductions in population size. Using genomic and bioinformatic approaches, in this thesis I investigate the contemporary Scandinavian wolf population founded 40 years ago by only three individuals, after the original population had been extirpated some decades earlier. The origin of the founders has been the subject of controversy, so I aimed to trace their origin using first male-specific Y chromosome sequences, and then whole-genome sequence data. I compared Scandinavian wolves to wolves from the nearby Finnish-Russian population as well as to publicly available wolf and dog samples from around the northern hemisphere, and found that the Scandinavian founders shared Y-haplotypes only with Finnish wolves. Consistent with this observation, when assessing population structure on the genomic scale, founders clustered with Finnish and Russian wolves, and an admixture analysis showed no other ancestries, nor traces of introgression from dogs. 

Small populations tend to have less genetic variation than larger populations, which might reduce their adaptive potential and increase the risk for extinction. A common measure used to investigate the genetic health of small populations is the genetic load, which is the fitness reduction of individuals due to accumulation of deleterious variants. I assessed the genetic load in Scandinavian wolves, divided into the components masked load (comprised of deleterious mutations in heterozygous state) and realized load (comprised of deleterious mutations in homozygous state), using both putatively deleterious single nucleotides and structural variants. I found that the realized load increased with every generation of inbreeding but was alleviated after genetic rescue events when new immigrants entered the population. Finally, I searched for the genetic basis of cryptorchidism, a testis condition that results in lowered fertility and is thought to be related to inbreeding depression. The trait is likely highly polygenic and the fact that only one significant association (to a region on the X chromosome) was found can be explained by that the number of available samples was very low, as is inevitable for small populations. 

In conclusion, this thesis explores the origin and the genetic health status of a small and recently founded natural population, and gives insights into how patterns of genetic load are affected by inbreeding and genetic rescue.  

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2024. , p. 65
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 2351
Keywords [en]
conservation genomics, Canis lupus, bioinformatics, Y chromosome, admixture, genetic load, structural variation, GWAS
National Category
Evolutionary Biology
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
URN: urn:nbn:se:uu:diva-517653ISBN: 978-91-513-1998-8 (print)OAI: oai:DiVA.org:uu-517653DiVA, id: diva2:1820127
Public defence
2024-02-16, Zootissalen, EBC, Villavägen 9, Uppsala, 10:00 (English)
Opponent
Supervisors
Available from: 2024-01-24 Created: 2023-12-15 Last updated: 2024-01-24
List of papers
1. The evolutionary history of grey wolf Y chromosomes
Open this publication in new window or tab >>The evolutionary history of grey wolf Y chromosomes
2019 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 9, p. 2173-2191Article in journal (Refereed) Published
Abstract [en]

Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male-specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified approximate to 1,500 Y-linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019
Keywords
bioinfomatics, phyloinfomatics, conservation genetics, haplotypes, population genomics, Y chromosome
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-389874 (URN)10.1111/mec.15054 (DOI)000471073000005 ()30788868 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2019-07-31 Created: 2019-07-31 Last updated: 2023-12-15Bibliographically approved
2. Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations
Open this publication in new window or tab >>Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations
Show others...
2021 (English)In: Evolutionary Applications, E-ISSN 1752-4571, Vol. 14, no 3, p. 721-734Article in journal (Refereed) Published
Abstract [en]

Hybridization and admixture can threaten the genetic integrity of populations and be of particular concern to endangered species. Hybridization between grey wolves and dogs has been documented in many wolf populations worldwide and is a prominent example of human-mediated hybridization between a domesticated species and its wild relative. We analysed whole-genome sequences from >200 wolves and >100 dogs to study admixture in Fennoscandian wolf populations. A principal component analysis of genetic variation and Admixture showed that wolves and dogs were well-separated, without evidence for introgression. Analyses of local ancestry revealed that wolves had <1% mixed ancestry, levels comparable to the degree of mixed ancestry in many dogs, and likely not resulting from recent wolf-dog hybridization. We also show that the founders of the Scandinavian wolf population were genetically inseparable from Finnish and Russian Karelian wolves, pointing at the geographical origin of contemporary Scandinavian wolves. Moreover, we found Scandinavian-born animals among wolves sampled in Finland, demonstrating bidirectional gene flow between the Scandinavian Peninsula and eastern countries. The low incidence of admixture between wolves and dogs in Fennoscandia may be explained by the fact that feral dogs are rare in this part of Europe and that careful monitoring and management act to remove hybrids before they backcross into wolf populations.

Place, publisher, year, edition, pages
John Wiley & SonsWILEY, 2021
Keywords
admixture, conservation genomics, grey wolf, hybridization, introgression
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-450533 (URN)10.1111/eva.13151 (DOI)000587448300001 ()33767747 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council
Available from: 2021-08-16 Created: 2021-08-16 Last updated: 2024-01-15Bibliographically approved
3. From high masked to high realized genetic load in inbred Scandinavian wolves
Open this publication in new window or tab >>From high masked to high realized genetic load in inbred Scandinavian wolves
2023 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 32, no 7, p. 1567-1580Article in journal (Refereed) Published
Abstract [en]

When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious mutations will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for the highly inbred Scandinavian wolf (Canis lupus) population, founded by only three wolves in the 1980s and suffering from inbreeding depression. We used functional annotation and evolutionary conservation scores to study deleterious variation in a total of 209 genomes from both the Scandinavian and neighbouring wolf populations in northern Europe. The masked load (deleterious mutations in heterozygote state) was highest in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles, fixation of deleterious variants and a significant increase in the per-individual realized load (deleterious mutations in homozygote state; an increase by 45% in protein-coding genes) over five generations of inbreeding. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and thereby shifting deleterious alleles from homozygous into heterozygote genotypes. However, in the absence of permanent connectivity to Finnish and Russian populations, inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the magnitude of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
conservation genetics, deleterious mutations, genetic load
National Category
Evolutionary Biology Genetics
Identifiers
urn:nbn:se:uu:diva-501377 (URN)10.1111/mec.16802 (DOI)000897947900001 ()36458895 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation, 2014-0044Swedish Research Council, 2013-8271
Available from: 2023-05-09 Created: 2023-05-09 Last updated: 2023-12-15Bibliographically approved
4. Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration
Open this publication in new window or tab >>Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration
(English)Manuscript (preprint) (Other academic)
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-517640 (URN)
Available from: 2023-12-11 Created: 2023-12-11 Last updated: 2023-12-15
5. A scan for the genetic basis of cryptorchidism in inbred Scandinavian wolves using GWAS and haplotype analysis
Open this publication in new window or tab >>A scan for the genetic basis of cryptorchidism in inbred Scandinavian wolves using GWAS and haplotype analysis
(English)Manuscript (preprint) (Other academic)
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-517643 (URN)
Available from: 2023-12-11 Created: 2023-12-11 Last updated: 2023-12-15

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