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Antibiotic resistance in Vibrio cholerae El Tor strains isolated during cholera complications in Siberia and the Far East of Russia.

https://arctichealth.org/en/permalink/ahliterature308315
Source
Infect Genet Evol. 2020 03; 78:104096
Publication Type
Journal Article
Date
03-2020
Author
A S Gladkikh
S I Feranchuk
A S Ponomareva
N O Bochalgin
L V Mironova
Author Affiliation
Irkutsk antiplague research institute of Rospotrebnadzor, 78, Trillisser str., Irkutsk 664047, Russia. Electronic address: angladkikh@gmail.com.
Source
Infect Genet Evol. 2020 03; 78:104096
Date
03-2020
Language
English
Publication Type
Journal Article
Keywords
Anti-Bacterial Agents - pharmacology
Cholera - epidemiology - microbiology
Disease Outbreaks
Drug Resistance, Microbial
Humans
Phenotype
Phylogeny
Polymorphism, Single Nucleotide
Russia
Vibrio cholerae - classification - drug effects - genetics
Whole Genome Sequencing - methods
Abstract
Currently, the spread of antimicrobial resistance (AMR) is a global trend and poses a severe threat to public health. The causative agent of cholera, a severe infectious disease with pandemic expansion, becomes more and more resistant to a wider range of drugs with every coming year. The Vibrio cholerae genome is highly flexible and adaptive; the acquisition of the SXT mobile element with a cluster of antibiotic resistance genes on it has marked a new stage in the adaptive evolution of the pathogen. The territory of Siberia and the Russian Far East is free of cholera; however, in the 1970s and 1990s a number of infection importation cases and acute outbreaks associated with the cholera importation were reported. The aim of this study was to describe the phenotypic characteristics and genetic determinants of AMR in V. cholerae strains isolated during epidemic complications in Siberia and the Far East of Russia, as well as to clarify the origin of the strains. The present research comprises analysis of nine V. cholerae El Tor strains isolated from patients and water sources during epidemic complications in Siberia and the Russian Far East in the 1990s. Here, we compared the phenotypic manifestations of antibiotic resistance among strains, harbored the resistance patterns in genomes; we also determined the structure, the type of SXT elements, and the mobilome profile based on the accepted classification. We identified that strains that caused outbreaks in Vladivostok and Yuzhno-Sakhalinsk in 1999 had ICEVchCHN4210 type SXT element with deletion of some loci. The research shows that the integration of the genome, SNP and the mobilome, associated with antibiotic resistance, analyses is necessary to understand the cholera epidemiology, it also helps to establish the origin of strains. The study of resistance determinants features allowed to make a conclusion about the heterogeneity of V. cholerae strains that were isolated during outbreaks in Vladivostok and Yuzhno-Sakhalinsk in 1999.
PubMed ID
31689544 View in PubMed
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An unusual case of Erysipelothrix rhusiopathiae prosthetic joint infection from the Canadian Arctic: whole genome sequencing unable to identify a zoonotic source.

https://arctichealth.org/en/permalink/ahliterature299701
Source
BMC Infect Dis. 2019 Mar 25; 19(1):282
Publication Type
Case Reports
Journal Article
Date
Mar-25-2019
Author
Michael Groeschel
Taya Forde
Shannon Turvey
A Mark Joffe
Catherine Hui
Prenilla Naidu
Fabien Mavrot
Susan Kutz
Ameeta E Singh
Author Affiliation
Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada. michael.groeschel@cls.ab.ca.
Source
BMC Infect Dis. 2019 Mar 25; 19(1):282
Date
Mar-25-2019
Language
English
Publication Type
Case Reports
Journal Article
Keywords
Aged
Animals
Animals, Wild - microbiology
Arctic Regions
Arthritis, Infectious - transmission
Canada
Erysipelothrix
Erysipelothrix Infections - microbiology - transmission
Female
Humans
Knee Prosthesis - microbiology
Prosthesis-Related Infections - microbiology - transmission
Whole Genome Sequencing
Zoonoses - microbiology - transmission
Abstract
Erysipelothrix rhusiopathiae is a zoonotic pathogen that causes erysipeloid and is most frequently associated with exposure to domestic swine. Infection of native and prosthetic joints is a rarely reported manifestation.
We describe a case of E. rhusiopathiae prosthetic joint infection in a woman with a history of exposure to wild animals in the Canadian Arctic. Patient management involved a 1-stage surgical revision exchange with an antibiotic impregnated cement spacer and 6 weeks of intravenous penicillin G followed by 6?weeks of oral amoxicillin. Ten previously reported cases of E. rhusiopathiae joint infection are reviewed. Recent increases in mortality due to infection with this organism among host animal populations in the Canadian Arctic have generated concern regarding a potential increase in human infections. However, whole genome sequencing (WGS) of the organism was unable to identify a zoonotic origin for this case.
Consideration should be given to E. rhusiopathiae as a cause of joint infections if the appropriate epidemiologic and host risk factors exist. Expanded use of WGS in other potential animal hosts and environmental sources may provide important epidemiologic information in determining the source of human infections.
PubMed ID
30909869 View in PubMed
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Bifidobacterium Bacteremia: Clinical Characteristics and a Genomic Approach To Assess Pathogenicity.

https://arctichealth.org/en/permalink/ahliterature290400
Source
J Clin Microbiol. 2017 07; 55(7):2234-2248
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
07-2017
Author
Eirin Esaiassen
Erik Hjerde
Jorunn Pauline Cavanagh
Gunnar Skov Simonsen
Claus Klingenberg
Author Affiliation
Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway eirin.esaiassen@uit.no.
Source
J Clin Microbiol. 2017 07; 55(7):2234-2248
Date
07-2017
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Adult
Aged
Aged, 80 and over
Anti-Bacterial Agents - pharmacology
Bacteremia - microbiology
Bifidobacterium - classification - genetics - isolation & purification - pathogenicity
Female
Genomics
Gram-Positive Bacterial Infections - microbiology
Humans
Infant
Infant, Newborn
Male
Microbial Sensitivity Tests
Middle Aged
Norway
Retrospective Studies
Virulence Factors - genetics
Whole Genome Sequencing
Abstract
Bifidobacteria are commensals that colonize the orogastrointestinal tract and rarely cause invasive human infections. However, an increasing number of bifidobacterial blood culture isolates has lately been observed in Norway. In order to investigate the pathogenicity of the Bifidobacterium species responsible for bacteremia, we studied Bifidobacterium isolates from 15 patients for whom cultures of blood obtained from 2013 to 2015 were positive. We collected clinical data and analyzed phenotypic and genotypic antibiotic susceptibility. All isolates (11 Bifidobacterium longum, 2 B. breve, and 2 B. animalis isolates) were subjected to whole-genome sequencing. The 15 patients were predominantly in the extreme lower or upper age spectrum, many were severely immunocompromised, and 11 of 15 had gastrointestinal tract-related conditions. In two elderly patients, the Bifidobacterium bacteremia caused a sepsis-like picture, interpreted as the cause of death. Most bifidobacterial isolates had low MICs (=0.5 mg/liter) to beta-lactam antibiotics, vancomycin, and clindamycin and relatively high MICs to ciprofloxacin and metronidazole. We performed a pangenomic comparison of invasive and noninvasive B. longum isolates based on 65 sequences available from GenBank and the sequences of 11 blood culture isolates from this study. Functional annotation identified unique genes among both invasive and noninvasive isolates of Bifidobacterium Phylogenetic clusters of invasive isolates were identified for a subset of the B. longum subsp. longum isolates. However, there was no difference in the number of putative virulence genes between invasive and noninvasive isolates. In conclusion, Bifidobacterium has an invasive potential in the immunocompromised host and may cause a sepsis-like picture. Using comparative genomics, we could not delineate specific pathogenicity traits characterizing invasive isolates.
Notes
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PubMed ID
28490487 View in PubMed
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Common and Rare Sequence Variants Influencing Tumor Biomarkers in Blood.

https://arctichealth.org/en/permalink/ahliterature308420
Source
Cancer Epidemiol Biomarkers Prev. 2020 01; 29(1):225-235
Publication Type
Comparative Study
Journal Article
Research Support, N.I.H., Extramural
Date
01-2020
Author
Sigurgeir Olafsson
Kristjan F Alexandersson
Johann G K Gizurarson
Katrin Hauksdottir
Orvar Gunnarsson
Karl Olafsson
Julius Gudmundsson
Simon N Stacey
Gardar Sveinbjornsson
Jona Saemundsdottir
Einar S Bjornsson
Sigurdur Olafsson
Sigurdur Bjornsson
Kjartan B Orvar
Arnor Vikingsson
Arni J Geirsson
Sturla Arinbjarnarson
Gyda Bjornsdottir
Thorgeir E Thorgeirsson
Snaevar Sigurdsson
Gisli H Halldorsson
Olafur T Magnusson
Gisli Masson
Hilma Holm
Ingileif Jonsdottir
Olof Sigurdardottir
Gudmundur I Eyjolfsson
Isleifur Olafsson
Patrick Sulem
Unnur Thorsteinsdottir
Thorvaldur Jonsson
Thorunn Rafnar
Daniel F Gudbjartsson
Kari Stefansson
Author Affiliation
deCODE genetics/AMGEN, Reykjavik, Iceland.
Source
Cancer Epidemiol Biomarkers Prev. 2020 01; 29(1):225-235
Date
01-2020
Language
English
Publication Type
Comparative Study
Journal Article
Research Support, N.I.H., Extramural
Keywords
Adolescent
Adult
Aged
Aged, 80 and over
Biomarkers, Tumor - blood - genetics
Child
Child, Preschool
Female
Gene Frequency
Genome-Wide Association Study
Humans
Iceland - epidemiology
Infant
Infant, Newborn
Male
Middle Aged
Neoplasms - blood - diagnosis - epidemiology - genetics
Polymorphism, Single Nucleotide
Predictive value of tests
Reference Values
Registries - statistics & numerical data
Sequence Analysis, RNA
Whole Genome Sequencing
Young Adult
Abstract
Alpha-fetoprotein (AFP), cancer antigens 15.3, 19.9, and 125, carcinoembryonic antigen, and alkaline phosphatase (ALP) are widely measured in attempts to detect cancer and to monitor treatment response. However, due to lack of sensitivity and specificity, their utility is debated. The serum levels of these markers are affected by a number of nonmalignant factors, including genotype. Thus, it may be possible to improve both sensitivity and specificity by adjusting test results for genetic effects.
We performed genome-wide association studies of serum levels of AFP (N = 22,686), carcinoembryonic antigen (N = 22,309), cancer antigens 15.3 (N = 7,107), 19.9 (N = 9,945), and 125 (N = 9,824), and ALP (N = 162,774). We also examined the correlations between levels of these biomarkers and the presence of cancer, using data from a nationwide cancer registry.
We report a total of 84 associations of 79 sequence variants with levels of the six biomarkers, explaining between 2.3% and 42.3% of the phenotypic variance. Among the 79 variants, 22 are cis (in- or near the gene encoding the biomarker), 18 have minor allele frequency less than 1%, 31 are coding variants, and 7 are associated with gene expression in whole blood. We also find multiple conditions associated with higher biomarker levels.
Our results provide insights into the genetic contribution to diversity in concentration of tumor biomarkers in blood.
Genetic correction of biomarker values could improve prediction algorithms and decision-making based on these biomarkers.
PubMed ID
31666285 View in PubMed
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Comparison of routine field epidemiology and whole genome sequencing to identify tuberculosis transmission in a remote setting.

https://arctichealth.org/en/permalink/ahliterature307061
Source
Epidemiol Infect. 2020 02 04; 148:e15
Publication Type
Comparative Study
Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't
Date
02-04-2020
Author
J L Guthrie
L Strudwick
B Roberts
M Allen
J McFadzen
D Roth
D Jorgensen
M Rodrigues
P Tang
B Hanley
J Johnston
V J Cook
J L Gardy
Author Affiliation
School of Population and Public Health, University of British Columbia, Vancouver, Canada.
Source
Epidemiol Infect. 2020 02 04; 148:e15
Date
02-04-2020
Language
English
Publication Type
Comparative Study
Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Contact Tracing - methods
Disease Transmission, Infectious
Genotype
Humans
Molecular Epidemiology - methods
Molecular Typing - methods
Mycobacterium - classification - genetics - isolation & purification
Tuberculosis - epidemiology - transmission
Whole Genome Sequencing - methods
Yukon Territory - epidemiology
Abstract
Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005-2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.
PubMed ID
32014080 View in PubMed
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Complete genome of Sulfitobacter sp. BSw21498 isolated from seawater of Arctic Kongsfjorden.

https://arctichealth.org/en/permalink/ahliterature311435
Source
Mar Genomics. 2020 Oct; 53:100769
Publication Type
Journal Article
Date
Oct-2020
Author
Yin-Xin Zeng
Yi-He Zhang
Hui-Rong Li
Wei Luo
Author Affiliation
Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, People's Republic of China. Electronic address: yxzeng@yahoo.com.
Source
Mar Genomics. 2020 Oct; 53:100769
Date
Oct-2020
Language
English
Publication Type
Journal Article
Keywords
Genome, Bacterial
Rhodobacteraceae - genetics
Seawater - microbiology
Svalbard
Whole Genome Sequencing
Abstract
The genus Sulfitobacter has been mostly found in marine and hypersaline environments. Members of this genus were observed to be associated with marine microalgae by inducing cell death of algae and degrading of algae-derived dimethylsulfoniopropionate (DMSP). Here we reported the complete genome sequence of strain Sulfitobacter sp. BSw21498 isolated from seawater of Kongsfjorden, an Arctic fjord in Svalbard. The strain contained a circular chromosome of 3,097,372 bp with G+C content of 58.55 mol% and a plasmid of 147,547 bp with G+C content of 56.53 mol%. In particular, a gene for DMSP lyase DddL was found in the genome, rendering Sulfitobacter sp. strain BSw21498 one of the Rhodobacterales bacteria equipped with the potential for DMSP degradation.
PubMed ID
32229098 View in PubMed
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Complete mitochondrial genome of the white char Salvelinus albus (Salmoniformes, Salmonidae).

https://arctichealth.org/en/permalink/ahliterature289352
Source
Mitochondrial DNA A DNA Mapp Seq Anal. 2016 09; 27(5):3753-4
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
09-2016
Author
Evgeniy S Balakirev
Valery A Parensky
Mikhail Yu Kovalev
Francisco J Ayala
Author Affiliation
a Department of Ecology and Evolutionary Biology , University of California , Irvine , CA , United States of America .
Source
Mitochondrial DNA A DNA Mapp Seq Anal. 2016 09; 27(5):3753-4
Date
09-2016
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
DNA, Mitochondrial - genetics
Fish Proteins - genetics
Genome, Mitochondrial
Phylogeny
Salmonidae - genetics
Whole Genome Sequencing
Abstract
The complete mitochondrial genome was sequenced in two individuals of white char Salvelinus albus. The genome sequences are 16?653?bp in size, and the gene arrangement, composition, and size are very similar to the salmonid fish genomes published previously. The low level of sequence divergence detected between the genome of S. albus and the GenBank complete mitochondrial genomes of the Northern Dolly Varden char S. malma (KJ746618) and the Arctic char S. alpinus (AF154851) may likely be due to recent divergence of the species and/or historical hybridization and interspecific replacement of mtDNA.
PubMed ID
26358825 View in PubMed
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Detection and genetic characterisation of porcine circovirus 3 from pigs in Sweden.

https://arctichealth.org/en/permalink/ahliterature295159
Source
Virus Genes. 2018 Jun; 54(3):466-469
Publication Type
Journal Article
Date
Jun-2018
Author
Xingyu Ye
Mikael Berg
Caroline Fossum
Per Wallgren
Anne-Lie Blomström
Author Affiliation
Guangyuan Center for Animal Disease Control and Prevention, Guangyuan, 628017, China.
Source
Virus Genes. 2018 Jun; 54(3):466-469
Date
Jun-2018
Language
English
Publication Type
Journal Article
Keywords
Animals
Circoviridae Infections - veterinary - virology
Circovirus - classification - genetics - isolation & purification
Genome, Viral
Phylogeny
Polymerase Chain Reaction - veterinary
Sweden
Swine
Swine Diseases - virology
Viral Proteins - genetics
Whole Genome Sequencing
Abstract
Porcine circovirus 3 (PCV3) is a newly detected circovirus belonging to the family Circoviridae with a circular ssDNA genome of 2000 bp that encodes two proteins-the replicase protein and the capsid protein. PCV3 was discovered for the first time in the US in 2016. After this initial discovery, PCV3 was detected in other parts of the world such as in China, South Korea, Italy and Poland. In this study, 49 tissue samples from Swedish pig herds were screened for PCV3 using PCR and 10 samples were positive and one was uncertain. The entire PCV3 genome and a mini PCV-like virus (MPCLV) were obtained from one of these samples. These two viruses showed a high sequence identity to PCV3 viruses from other countries as well as to MPCLV from the US. However, the sequence identity to PCV1 and 2 was only 31-48% on amino acid level. This is the first detection and complete genetic characterisation of PCV3 in Swedish pigs. It is also interesting to note that one of the positive samples was collected in 1993, showing that PCV3 has been present for a long time.
Notes
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PubMed ID
29564688 View in PubMed
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Discovery of Novel Sequences in 1,000 Swedish Genomes.

https://arctichealth.org/en/permalink/ahliterature308839
Source
Mol Biol Evol. 2020 Jan 01; 37(1):18-30
Publication Type
Journal Article
Date
Jan-01-2020
Author
Jesper Eisfeldt
Gustaf Mårtensson
Adam Ameur
Daniel Nilsson
Anna Lindstrand
Author Affiliation
Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden.
Source
Mol Biol Evol. 2020 Jan 01; 37(1):18-30
Date
Jan-01-2020
Language
English
Publication Type
Journal Article
Keywords
Animals
Genetic Variation
Genome, Human
Humans
Pan troglodytes - genetics
Sweden
Whole Genome Sequencing
Abstract
Novel sequences (NSs), not present in the human reference genome, are abundant and remain largely unexplored. Here, we utilize de novo assembly to study NS in 1,000 Swedish individuals first sequenced as part of the SweGen project revealing a total of 46 Mb in 61,044 distinct contigs of sequences not present in GRCh38. The contigs were aligned to recently published catalogs of Icelandic and Pan-African NSs, as well as the chimpanzee genome, revealing a great diversity of shared sequences. Analyzing the positioning of NS across the chimpanzee genome, we find that 2,807 NS align confidently within 143 chimpanzee orthologs of human genes. Aligning the whole genome sequencing data to the chimpanzee genome, we discover ancestral NS common throughout the Swedish population. The NSs were searched for repeats and repeat elements: revealing a majority of repetitive sequence (56%), and enrichment of simple repeats (28%) and satellites (15%). Lastly, we align the unmappable reads of a subset of the thousand genomes data to our collection of NS, as well as the previously published Pan-African NS: revealing that both the Swedish and Pan-African NS are widespread, and that the Swedish NSs are largely a subset of the Pan-African NS. Overall, these results highlight the importance of creating a more diverse reference genome and illustrate that significant amounts of the NS may be of ancestral origin.
Notes
CommentIn: Mol Biol Evol. 2020 Jan 1;37(1):306 PMID 31880781
PubMed ID
31560401 View in PubMed
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Draft genome of the reindeer (Rangifer tarandus).

https://arctichealth.org/en/permalink/ahliterature294194
Source
Gigascience. 2017 12 01; 6(12):1-5
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
12-01-2017
Author
Zhipeng Li
Zeshan Lin
Hengxing Ba
Lei Chen
Yongzhi Yang
Kun Wang
Qiang Qiu
Wen Wang
Guangyu Li
Author Affiliation
Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, No. 4899, Juye Street, Jingyue District, Changchun, Jilin province, 130112, P.R. China.
Source
Gigascience. 2017 12 01; 6(12):1-5
Date
12-01-2017
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
Female
Genome Size
Genomic Library
Genomics
Molecular Sequence Annotation
Reindeer - genetics
Species Specificity
Whole Genome Sequencing
Abstract
The reindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and it is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer, as well as males, regularly grow cranial appendages (antlers, the defining characteristics of cervids). Moreover, reindeer milk contains more protein and less lactose than bovids' milk. A high-quality reference genome of this species will assist efforts to elucidate these and other important features in the reindeer.
We obtained 615 Gb (Gigabase) of usable sequences by filtering the low-quality reads of the raw data generated from the Illumina Hiseq 4000 platform, and a 2.64-Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21 555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1339 snRNA, and 863 tRNA sequences in the genome of R. tarandus. The divergence time between R. tarandus and ancestors of Bos taurus and Capra hircus is estimated to be about 29.5 million years ago.
Our results provide the first high-quality reference genome for the reindeer and a valuable resource for studying the evolution, domestication, and other unusual characteristics of the reindeer.
Notes
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