1
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Nguyen AK, Schall PZ, Kidd JM. A map of canine sequence variation relative to a Greenland wolf outgroup. Mamm Genome 2024:10.1007/s00335-024-10056-1. [PMID: 39088040 DOI: 10.1007/s00335-024-10056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024]
Abstract
For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e., canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples and breed relationships revealed by principal component analysis are not affected by the choice of reference genome. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves.
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Affiliation(s)
- Anthony K Nguyen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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2
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Hennelly LM, Sarwar G, Fatima H, Werhahn G, Abbas FI, Khan AM, Mahmood T, Kachel S, Kubanychbekov Z, Waseem MT, Zahra Naqvi R, Hamid A, Abbas Y, Aisha H, Waseem M, Farooq M, Sacks BN. Genomic analysis of wolves from Pakistan clarifies boundaries among three divergent wolf lineages. J Hered 2024; 115:339-348. [PMID: 37897187 DOI: 10.1093/jhered/esad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/26/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023] Open
Abstract
Among the three main divergent lineages of gray wolf (Canis lupus), the Holarctic lineage is the most widespread and best studied, particularly in North America and Europe. Less is known about Tibetan (also called Himalayan) and Indian wolf lineages in southern Asia, especially in areas surrounding Pakistan where all three lineages are thought to meet. Given the endangered status of the Indian wolf in neighboring India and unclear southwestern boundary of the Tibetan wolf range, we conducted mitochondrial and genome-wide sequencing of wolves from Pakistan and Kyrgyzstan. Sequences of the mitochondrial D-loop region of 81 wolves from Pakistan indicated contact zones between Holarctic and Indian lineages across the northern and western mountains of Pakistan. Reduced-representation genome sequencing of eight wolves indicated an east-to-west cline of Indian to Holarctic ancestry, consistent with a contact zone between these two lineages in Pakistan. The western boundary of the Tibetan lineage corresponded to the Ladakh region of India's Himalayas with a narrow zone of admixture spanning this boundary from the Karakoram Mountains of northern Pakistan into Ladakh, India. Our results highlight the conservation significance of Pakistan's wolf populations, especially the remaining populations in Sindh and Southern Punjab that represent the highly endangered Indian lineage.
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Affiliation(s)
- Lauren M Hennelly
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA, United States
| | - Ghulam Sarwar
- Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Hira Fatima
- Department of Zoology, University of Education, Lahore, Pakistan
| | - Geraldine Werhahn
- IUCN SCC Canid Specialist Group, Oxford, United Kingdom
- Wildlife Conservation Research Unit, Zoology, University of Oxford, Tubney, United Kingdom
| | | | - Abdul M Khan
- Institute of Zoology, University of the Punjab, Lahore, Pakistan
| | - Tariq Mahmood
- Department of Zoology, Wildlife and Fisheries, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | | | | | - Muhammad T Waseem
- Zoological Science Division, Pakistan Museum of Natural History, Islamabad, Pakistan
| | - Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Abdul Hamid
- Department of Zoology, Wildlife and Fisheries, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Yasir Abbas
- Central Karakoram National Park, Skardu, Pakistan
| | - Hamera Aisha
- World Wildlife Fund, Pakistan, Islamabad, Pakistan
| | | | - Muhammad Farooq
- Department of Zoology, Wildlife and Fisheries, PMAS Arid Agriculture University, Rawalpindi, Pakistan
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, Davis, CA, United States
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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3
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Bozlak E, Pokharel K, Weldenegodguad M, Paasivaara A, Stammler F, Røed KH, Kantanen J, Wallner B. Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies. Ecol Evol 2024; 14:e11573. [PMID: 38863721 PMCID: PMC11164974 DOI: 10.1002/ece3.11573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/13/2024] Open
Abstract
Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species (Rangifer tarandus). It has survived the Holocene thanks to its immense adaptability and successful coexistence with humans in different forms of hunting and herding cultures. Here, we examine the paternal and maternal history of Rangifer based on robust Y-chromosomal and mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest reindeer, Svalbard reindeer, Alaska tundra caribou, and woodland caribou. We first assembled Y-chromosomal contigs, representing 1.3 Mb of single-copy Y regions. Based on 545 Y-chromosomal and 458 mtDNA SNPs defined in 55 males, maximum parsimony trees were created. We observed two well separated clades in both phylogenies: the "EuroBeringian clade" formed by animals from Arctic Islands, Eurasia, and a few from North America and the "North American clade" formed only by caribou from North America. The time calibrated Y tree revealed an expansion and dispersal of lineages across continents after the Last Glacial Maximum. We show for the first time unique paternal lineages in Svalbard reindeer and Finnish forest reindeer and reveal a circumscribed Y haplogroup in Fennoscandian tundra reindeer. The Y chromosome in domesticated reindeer is markedly diverse indicating that several male lineages have undergone domestication and less intensive selection on males. This study places R. tarandus onto the list of species with resolved Y and mtDNA phylogenies and builds the basis for studies of the distribution and origin of paternal and maternal lineages in the future.
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Affiliation(s)
- Elif Bozlak
- Department of Biomedical Sciences, Institute of Animal Breeding and GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
- Vienna Graduate School of Population GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
| | | | | | | | | | - Knut H. Røed
- Department of Preclinical Sciences and PathologyNorwegian University of Life SciencesÅsNorway
| | | | - Barbara Wallner
- Department of Biomedical Sciences, Institute of Animal Breeding and GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
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4
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Smeds L, Huson LSA, Ellegren H. Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration. Evol Appl 2024; 17:e13652. [PMID: 38333557 PMCID: PMC10848878 DOI: 10.1111/eva.13652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
When populations decrease in size and may become isolated, genomic erosion by loss of diversity from genetic drift and accumulation of deleterious mutations is likely an inevitable consequence. In such cases, immigration (genetic rescue) is necessary to restore levels of genetic diversity and counteract inbreeding depression. Recent work in conservation genomics has studied these processes focusing on the genetic diversity of single nucleotide polymorphisms. In contrast, our knowledge about structural genomic variation (insertions, deletions, duplications and inversions) in endangered species is limited. We analysed whole-genome, short-read sequences from 212 wolves from the inbred Scandinavian population and from neighbouring populations in Finland and Russia, and detected >35,000 structural variants (SVs) after stringent quality and genotype frequency filtering; >26,000 high-confidence variants remained after manual curation. The majority of variants were shorter than 1 kb, with a distinct peak in the length distribution of deletions at 190 bp, corresponding to insertion events of SINE/tRNA-Lys elements. The site frequency spectrum of SVs in protein-coding regions was significantly shifted towards rare alleles compared to putatively neutral variants, consistent with purifying selection. The realized genetic load of SVs in protein-coding regions increased with inbreeding levels in the Scandinavian population, but immigration provided a genetic rescue effect by lowering the load and reintroducing ancestral alleles at loci fixed for derived SVs. Our study shows that structural variation comprises a common type of in part deleterious mutations in endangered species and that establishing gene flow is necessary to mitigate the negative consequences of loss of diversity.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Lars S. A. Huson
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
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5
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Smeds L, Ellegren H. From high masked to high realized genetic load in inbred Scandinavian wolves. Mol Ecol 2022; 32:1567-1580. [PMID: 36458895 DOI: 10.1111/mec.16802] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
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.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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6
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Viluma A, Flagstad Ø, Åkesson M, Wikenros C, Sand H, Wabakken P, Ellegren H. Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population. Genome Res 2022; 32:449-458. [PMID: 35135873 PMCID: PMC8896455 DOI: 10.1101/gr.276070.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022]
Abstract
Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%–24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.
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7
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Wang MS, Thakur M, Jhala Y, Wang S, Srinivas Y, Dai SS, Liu ZX, Chen HM, Green RE, Koepfli KP, Shapiro B. OUP accepted manuscript. Genome Biol Evol 2022; 14:6524629. [PMID: 35137061 PMCID: PMC8841465 DOI: 10.1093/gbe/evac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, USA
- Corresponding authors: E-mails: ; ; ;
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, India
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Corresponding authors: E-mails: ; ; ;
| | | | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yellapu Srinivas
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, India
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zheng-Xi Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Hong-Man Chen
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA
- Computer Technologies Laboratory, ITMO University, St. Petersburg, Russia
- Corresponding authors: E-mails: ; ; ;
| | - Beth Shapiro
- Howard Hughes Medical Institute, University of California Santa Cruz, USA
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, USA
- Corresponding authors: E-mails: ; ; ;
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8
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Åkesson M, Flagstad Ø, Aspi J, Kojola I, Liberg O, Wabakken P, Sand H. Genetic signature of immigrants and their effect on genetic diversity in the recently established Scandinavian wolf population. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01423-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractTransboundary connectivity is a key component when conserving and managing animal species that require large areas to maintain viable population sizes. Wolves Canis lupus recolonized the Scandinavian Peninsula in the early 1980s. The population is geographically isolated and relies on immigration to not lose genetic diversity and to maintain long term viability. In this study we address (1) to what extent the genetic diversity among Scandinavian wolves has recovered during 30 years since its foundation in relation to the source populations in Finland and Russia, (2) if immigration has occurred from both Finland and Russia, two countries with very different wolf management and legislative obligations to ensure long term viability of wolves, and (3) if immigrants can be assumed to be unrelated. Using 26 microsatellite loci we found that although the genetic diversity increased among Scandinavian wolves (n = 143), it has not reached the same levels found in Finland (n = 25) or in Russia (n = 19). Low genetic differentiation between Finnish and Russian wolves, complicated our ability to determine the origin of immigrant wolves (n = 20) with respect to nationality. Nevertheless, based on differences in allelic richness and private allelic richness between the two countries, results supported the occurrence of immigration from both countries. A priori assumptions that immigrants are unrelated is non-advisable, since 5.8% of the pair-wise analyzed immigrants were closely related. To maintain long term viability of wolves in Northern Europe, this study highlights the potential and need for management actions that facilitate transboundary dispersal.
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9
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Xiao C, Li J, Xie T, Chen J, Zhang S, Elaksher SH, Jiang F, Jiang Y, Zhang L, Zhang W, Xiang Y, Wu Z, Zhao S, Du X. The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat. Ecol Evol 2021; 11:7779-7795. [PMID: 34188851 PMCID: PMC8216945 DOI: 10.1002/ece3.7611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 02/05/2023] Open
Abstract
The mammalian Y chromosome offers a unique perspective on the male reproduction and paternal evolutionary histories. However, further understanding of the Y chromosome biology for most mammals is hindered by the lack of a Y chromosome assembly. This study presents an integrated in silico strategy for identifying and assembling the goat Y-linked scaffolds using existing data. A total of 11.5 Mb Y-linked sequences were clustered into 33 scaffolds, and 187 protein-coding genes were annotated. We also identified high abundance of repetitive elements. A 5.84 Mb subset was further ordered into an assembly with the evidence from the goat radiation hybrid map (RH map). The existing whole-genome resequencing data of 96 goats (worldwide distribution) were utilized to exploit the paternal relationships among bezoars and domestic goats. Goat paternal lineages were clearly divided into two clades (Y1 and Y2), predating the goat domestication. Demographic history analyses indicated that maternal lineages experienced a bottleneck effect around 2,000 YBP (years before present), after which goats belonging to the A haplogroup spread worldwide from the Near East. As opposed to this, paternal lineages experienced a population decline around the 10,000 YBP. The evidence from the Y chromosome suggests that male goats were not affected by the A haplogroup worldwide transmission, which implies sexually unbalanced contribution to the goat trade and population expansion in post-Neolithic period.
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Affiliation(s)
- Changyi Xiao
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Jingjin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Tanghui Xie
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Jianhai Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- Institutes for Systems GeneticsFrontiers Science Center for Disease‐related Molecular NetworkWest China HospitalSichuan UniversityChengduChina
| | - Sijia Zhang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Salma Hassan Elaksher
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- Genetics and Genetic Engineering DepartmentFaculty of AgricultureBenha UniversityMoshtohorEgypt
| | - Fan Jiang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yaoxin Jiang
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Lu Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Wei Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Yue Xiang
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Zhenyang Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
- College of Agroforestry Engineering and PlanningTongren UniversityTongrenChina
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
| | - Xiaoyong Du
- College of InformaticsHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Agricultural Animal Genetics, Breeding and ReproductionMinistry of EducationCollege of Animal Science and Veterinary MedicineHuazhong Agricultural UniversityWuhanChina
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10
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Smeds L, Aspi J, Berglund J, Kojola I, Tirronen K, Ellegren H. Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations. Evol Appl 2021; 14:721-734. [PMID: 33767747 PMCID: PMC7980305 DOI: 10.1111/eva.13151] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 01/02/2023] Open
Abstract
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.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | - Jouni Aspi
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | - Jonas Berglund
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke)RovaniemiFinland
| | - Konstantin Tirronen
- Institute of BiologyKarelian Research Centre of the Russian Academy of SciencePetrozavodskRussian Federation
| | - Hans Ellegren
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
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11
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Martínez-Pacheco M, Tenorio M, Almonte L, Fajardo V, Godínez A, Fernández D, Cornejo-Páramo P, Díaz-Barba K, Halbert J, Liechti A, Székely T, Urrutia AO, Cortez D. Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals. Genome Biol Evol 2020; 12:2015-2028. [PMID: 32790864 PMCID: PMC7674692 DOI: 10.1093/gbe/evaa173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Placental mammals present 180 million-year-old Y chromosomes that have retained a handful of dosage-sensitive genes. However, the expression evolution of Y-linked genes across placental groups has remained largely unexplored. Here, we expanded the number of Y gametolog sequences by analyzing ten additional species from previously unexplored groups. We detected seven remarkably conserved genes across 25 placental species with known Y repertoires. We then used RNA-seq data from 17 placental mammals to unveil the expression evolution of XY gametologs. We found that Y gametologs followed, on average, a 3-fold expression loss and that X gametologs also experienced some expression reduction, particularly in primates. Y gametologs gained testis specificity through an accelerated expression decay in somatic tissues. Moreover, despite the substantial expression decay of Y genes, the combined expression of XY gametologs in males is higher than that of both X gametologs in females. Finally, our work describes several features of the Y chromosome in the last common mammalian ancestor.
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Affiliation(s)
| | | | - Laura Almonte
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | - Alan Godínez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | | | | | - Jean Halbert
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Tamas Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Araxi O Urrutia
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom.,Ecology Institute, UNAM, Mexico
| | - Diego Cortez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
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12
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Galeta P, Lázničková-Galetová M, Sablin M, Germonpré M. Morphological evidence for early dog domestication in the European Pleistocene: New evidence from a randomization approach to group differences. Anat Rec (Hoboken) 2020; 304:42-62. [PMID: 32869467 DOI: 10.1002/ar.24500] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022]
Abstract
The antiquity of the wolf/dog domestication has been recently pushed back in time from the Late Upper Paleolithic (~14,000 years ago) to the Early Upper Paleolithic (EUP; ~36,000 years ago). Some authors questioned this early dog domestication claiming that the putative (EUP) Paleolithic dogs fall within the morphological range of recent wolves. In this study, we reanalyzed a data set of large canid skulls using unbalanced- and balanced-randomized discriminant analyses to assess whether the putative Paleolithic dogs are morphologically unique or whether they represent a subsample of the wolf morpho-population. We evaluated morphological differences between 96 specimens of the 4 a priori reference groups (8 putative Paleolithic dogs, 41 recent northern dogs, 7 Pleistocene wolves, and 40 recent northern wolves) using discriminant analysis based on 5 ln-transformed raw and allometrically size-adjusted cranial measurements. Putative Paleolithic dogs are classified with high accuracies (87.5 and 100.0%, cross-validated) and randomization experiment suggests that these classification rates cannot be exclusively explained by the small and uneven sample sizes of reference groups. It indicates that putative Upper Paleolithic dogs may represent a discrete canid group with morphological signs of domestication (a relatively shorter skull and wider palate and braincase) that distinguish them from sympatric Pleistocene wolves. The present results add evidence to the view that these specimens could represent incipient Paleolithic dogs that were involved in daily activities of European Upper Paleolithic forager groups.
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Affiliation(s)
- Patrik Galeta
- Department of Anthropology, University of West Bohemia, Pilsen, Czech Republic
| | - Martina Lázničková-Galetová
- Department of Anthropology, University of West Bohemia, Pilsen, Czech Republic.,The Moravian Museum, Brno, Czech Republic
| | - Mikhail Sablin
- Zoological Institute, Russian Academy of Sciences, Saint-Petersburg, Russia
| | - Mietje Germonpré
- Operational Direction "Earth and History of Life", Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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13
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Deng J, Xie XL, Wang DF, Zhao C, Lv FH, Li X, Yang J, Yu JL, Shen M, Gao L, Yang JQ, Liu MJ, Li WR, Wang YT, Wang F, Li JQ, Hehua EE, Liu YG, Shen ZQ, Ren YL, Liu GJ, Chen ZH, Gorkhali NA, Rushdi HE, Salehian-Dehkordi H, Esmailizadeh A, Nosrati M, Paiva SR, Caetano AR, Štěpánek O, Olsaker I, Weimann C, Erhardt G, Curik I, Kantanen J, Mwacharo JM, Hanotte O, Bruford MW, Ciani E, Periasamy K, Amills M, Lenstra JA, Han JL, Zhang HP, Li L, Li MH. Paternal Origins and Migratory Episodes of Domestic Sheep. Curr Biol 2020; 30:4085-4095.e6. [PMID: 32822607 DOI: 10.1016/j.cub.2020.07.077] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/14/2020] [Accepted: 07/27/2020] [Indexed: 01/22/2023]
Abstract
The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.
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Affiliation(s)
- Juan Deng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Life Science, Hebei University, Baoding 071002, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jia-Lin Yu
- Station for Breeding and Improvement of Animal and Poultry of Changshou District, Chongqing 401220, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi 830001, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi 830001, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashi University, Kashi 844000, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010000, China
| | - EEr Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750000, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650000, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou 256600, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou 256600, China
| | - Guang-Jian Liu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Neena A Gorkhali
- Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council (NARC), Kathmandu, Nepal
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Samuel R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Avenida W5 Norte (Final), Caixa Postal 02372, CEP 70770-917 Brasília, DF, Brazil
| | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Avenida W5 Norte (Final), Caixa Postal 02372, CEP 70770-917 Brasília, DF, Brazil
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Rantirovska 93, 58601, Jihlava, Czech Republic
| | - Ingrid Olsaker
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - Joram M Mwacharo
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia; CTLGH and SRUC, the Roslin Institute Building, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - Olivier Hanotte
- LiveGene, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia; School of Life Sciences, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff CF10 3AX, Wales, United Kingdom; Sustainable Places Research Institute, Cardiff University CF10 3BA, Wales, United Kingdom
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24 Moro, Bari, Italy
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Hong-Ping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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14
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Rando HM, Wadlington WH, Johnson JL, Stutchman JT, Trut LN, Farré M, Kukekova AV. The Red Fox Y-Chromosome in Comparative Context. Genes (Basel) 2019; 10:E409. [PMID: 31142040 PMCID: PMC6627929 DOI: 10.3390/genes10060409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (Feliscatus), dog (Canislupusfamiliaris), and grey wolf (Canislupuslupus), providing the opportunity to examine the red fox (Vulpesvulpes) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific k-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of BCORY2 and UBE1Y than has been reported in related species and fewer copies of SRY than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.
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Affiliation(s)
- Halie M Rando
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - William H Wadlington
- Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031, USA.
| | - Jennifer L Johnson
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Jeremy T Stutchman
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Marta Farré
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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15
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Smeds L, Kojola I, Ellegren H. The evolutionary history of grey wolf Y chromosomes. Mol Ecol 2019; 28:2173-2191. [PMID: 30788868 PMCID: PMC6850511 DOI: 10.1111/mec.15054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/30/2022]
Abstract
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 ≈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.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke), Rovaniemi, Finland
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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