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Tancredi D, Cardinali I. Being a Dog: A Review of the Domestication Process. Genes (Basel) 2023; 14:genes14050992. [PMID: 37239352 DOI: 10.3390/genes14050992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A "multiphase" view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev's foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny.
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Affiliation(s)
- Domenico Tancredi
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
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2
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Population genetics of the African wolf (Canis lupaster) across its range: first evidence of hybridization with domestic dogs in Africa. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00059-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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3
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Sarabia C, Salado I, Cornellas A, Fernández-Gil A, Vilà C, Leonard JA. Towards high–throughput analyses of fecal samples from wildlife. ANIMAL BIODIVERSITY AND CONSERVATION 2020. [DOI: 10.32800/abc.2020.43.0271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
High–throughput sequencing offers new possibilities in molecular ecology and conservation studies. However, its potential has not yet become fully exploited for noninvasive studies of free–ranging animals, such as those based on feces. High–throughput sequencing allows sequencing of short DNA fragments and could allow simultaneous genotyping of a very large number of samples and markers at a low cost. The application of high throughput genotyping to fecal samples from wildlife has been hindered by several labor–intensive steps. We evaluate alternative protocols which could allow higher throughput for two of these steps: sample collection and DNA extraction. Two different field sampling and seven different DNA extraction methods are tested here on grey wolf (Canis lupus) feces. There was high variation in genotyping success rates. The field sampling method based on surface swabbing performed much worse than the extraction from a fecal fragment. In addition, there is a lot of room for improvement in the DNA extraction step. Optimization of protocols can lead to very much more efficient, cheaper and higher throughput noninvasive monitoring. Selection of appropriate markers is still of paramount importance to increase genotyping success.
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Affiliation(s)
- C. Sarabia
- Estación Biológica de Doñana (EBD–CSIC), Seville, Spain
| | - I. Salado
- Estación Biológica de Doñana (EBD–CSIC), Seville, Spain
| | - A. Cornellas
- Estación Biológica de Doñana (EBD–CSIC), Seville, Spain
| | | | - C. Vilà
- Estación Biológica de Doñana (EBD–CSIC), Seville, Spain
| | - J. A. Leonard
- Estación Biológica de Doñana (EBD–CSIC), Seville, Spain
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4
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Y-chromosome genetic diversity of Bos indicus cattle in close proximity to the centre of domestication. Sci Rep 2020; 10:9992. [PMID: 32561783 PMCID: PMC7305206 DOI: 10.1038/s41598-020-66133-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/11/2020] [Indexed: 02/08/2023] Open
Abstract
Y-chromosome genetic diversity in and around its domestication origin and a better understanding of indicine-specific microsatellite alleles are imperative concerns but less -targeted. We analysed Y-chromosome markers in 301 bulls representing 19 native Indian cattle (Bos indicus) and identified new alleles and haplotypes. Compared to other indicine studies, the high Y-haplotype diversity found in Indian cattle supports the hypothesis of greater genetic variability across the centre of origin decreasing along migratory routes with increasing distance. Hence, a considerable paternal genetic diversity of Indian cattle appears to have been lost in transboundary commercial indicine breeds. The Khillar and Gir are the most diversified populations where the first tends to be the well-differentiated traditional breed carrying strikingly distinct Y-lineages with typical BM861-158 bp allele, characteristics of taurine cattle, while retaining standard indicine lineages for all other markers. Geographical distribution found to be an unreliable predictor of parental variation, and Y-lineages seemed closely related to Indian breed function/utility. The comprehensive Y-chromosome information will be useful to examine the demographic expansion/spread of Bos indicus lineages from close proximity to the domestication centre across different countries worldwide and such diversity should be preserved through effective management and conservation programs.
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Salvatori V, Godinho R, Braschi C, Boitani L, Ciucci P. High levels of recent wolf × dog introgressive hybridization in agricultural landscapes of central Italy. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1313-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Abstract
Levels and patterns of genetic diversity can provide insights into a population’s history. In species with sex chromosomes, differences between genomic regions with unique inheritance patterns can be used to distinguish between different sets of possible demographic and selective events. This review introduces the differences in population history for sex chromosomes and autosomes, provides the expectations for genetic diversity across the genome under different evolutionary scenarios, and gives an introductory description for how deviations in these expectations are calculated and can be interpreted. Predominantly, diversity on the sex chromosomes has been used to explore and address three research areas: 1) Mating patterns and sex-biased variance in reproductive success, 2) signatures of selection, and 3) evidence for modes of speciation and introgression. After introducing the theory, this review catalogs recent studies of genetic diversity on the sex chromosomes across species within the major research areas that sex chromosomes are typically applied to, arguing that there are broad similarities not only between male-heterogametic (XX/XY) and female-heterogametic (ZZ/ZW) sex determination systems but also any mating system with reduced recombination in a sex-determining region. Further, general patterns of reduced diversity in nonrecombining regions are shared across plants and animals. There are unique patterns across populations with vastly different patterns of mating and speciation, but these do not tend to cluster by taxa or sex determination system.
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Affiliation(s)
- Melissa A Wilson Sayres
- School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University
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7
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Long C, Lankford L, Kumar P, Grahn R, Borjesson DL, Farmer D, Wang A. Isolation and characterization of canine placenta-derived mesenchymal stromal cells for the treatment of neurological disorders in dogs. Cytometry A 2017; 93:82-92. [DOI: 10.1002/cyto.a.23171] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/19/2017] [Accepted: 06/27/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Connor Long
- Surgical Bioengineering Laboratory, Department of Surgery; University of California, Davis School of Medicine; Sacramento California
| | - Lee Lankford
- Surgical Bioengineering Laboratory, Department of Surgery; University of California, Davis School of Medicine; Sacramento California
| | - Priyadarsini Kumar
- Surgical Bioengineering Laboratory, Department of Surgery; University of California, Davis School of Medicine; Sacramento California
| | - Robert Grahn
- Veterinary Genetics Laboratory; University of California; Davis California
| | - Dori L. Borjesson
- Veterinary Institute for Regenerative Cures and Department of Pathology, Microbiology, Immunology; University of California, Davis School of Veterinary Medicine; Davis California
| | - Diana Farmer
- Surgical Bioengineering Laboratory, Department of Surgery; University of California, Davis School of Medicine; Sacramento California
| | - Aijun Wang
- Surgical Bioengineering Laboratory, Department of Surgery; University of California, Davis School of Medicine; Sacramento California
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Pires AE, Amorim IR, Borges C, Simões F, Teixeira T, Quaresma A, Petrucci‐Fonseca F, Matos J. New insights into the genetic composition and phylogenetic relationship of wolves and dogs in the Iberian Peninsula. Ecol Evol 2017; 7:4404-4418. [PMID: 28649351 PMCID: PMC5478058 DOI: 10.1002/ece3.2949] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 02/17/2017] [Accepted: 03/05/2017] [Indexed: 12/26/2022] Open
Abstract
This study investigates the gene pool of Portuguese autochthonous dog breeds and their wild counterpart, the Iberian wolf subspecies (Canis lupus signatus), using standard molecular markers. A combination of paternal and maternal molecular markers was used to investigate the genetic composition, genetic differentiation and genetic relationship of native Portuguese dogs and the Iberian wolf. A total of 196 unrelated dogs, including breed and village dogs from Portugal, and other dogs from Spain and North Africa, and 56 Iberian wolves (wild and captive) were analyzed for nuclear markers, namely Y chromosome SNPs, Y chromosome STR loci, autosomal STR loci, and a mitochondrial fragment of the control region I. Our data reveal new variants for the molecular markers and confirm significant genetic differentiation between Iberian wolf and native domestic dogs from Portugal. Based on our sampling, no signs of recent introgression between the two subspecies were detected. Y chromosome data do not reveal genetic differentiation among the analyzed dog breeds, suggesting they share the same patrilineal origin. Moreover, the genetic distinctiveness of the Iberian wolf from other wolf populations is further confirmed with the description of new mtDNA variants for this endemism. Our research also discloses new molecular markers for wolf and dog subspecies assignment, which might become particularly relevant in the case of forensic or noninvasive genetic studies. The Iberian wolf represents a relic of the once widespread wolf population in Europe and our study reveals that it is a reservoir of unique genetic diversity of the grey wolf, Canis lupus. These results stress the need for conservation plans that will guarantee the sustainability of this threatened top predator in Iberia.
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Affiliation(s)
- Ana Elisabete Pires
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
| | - Isabel R. Amorim
- Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Universidade dos AçoresFaculdade de Ciências Agrárias e do AmbienteAçoresPortugal
| | - Carla Borges
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
| | - Fernanda Simões
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
| | - Tatiana Teixeira
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
| | - Andreia Quaresma
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
| | - Francisco Petrucci‐Fonseca
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
| | - José Matos
- Biotechnology and Genetic Resources UnitNational Institute of Agrarian and Veterinary Research, I.P. (INIAV)OeirasPortugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c)Faculty of SciencesUniversity of LisbonLisbonPortugal
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Iacolina L, Brajković V, Canu A, Šprem N, Cubric-Curik V, Fontanesi L, Saarma U, Apollonio M, Scandura M. Novel Y-chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations. Anim Genet 2016; 47:682-690. [PMID: 27558303 DOI: 10.1111/age.12483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2016] [Indexed: 11/27/2022]
Abstract
Y-chromosome markers are important tools for studying male-specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non-human mammals is often hampered by the lack of Y-specific polymorphic markers. We identified new male-specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5-10 alleles per locus), falling in one duplicated and two single-copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (HD = 0.904 ± 0.011 and HD = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (FST = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y-chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.
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Affiliation(s)
- L Iacolina
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy. .,Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, Aalborg, 9000, Denmark.
| | - V Brajković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - A Canu
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
| | - N Šprem
- Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - V Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - L Fontanesi
- Division of Animal Science, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, I-40127, Italy
| | - U Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - M Apollonio
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
| | - M Scandura
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
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10
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Polymorphisms in ERAP1 and ERAP2 are shared by Caninae and segregate within and between random- and pure-breeds of dogs. Vet Immunol Immunopathol 2016; 179:46-57. [PMID: 27590425 DOI: 10.1016/j.vetimm.2016.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 01/01/2023]
Abstract
Specific polymorphisms in the endoplasmic reticulum amino peptidase genes ERAP1 and ERAP2, when present with certain MHC class receptor types, have been associated with increased risk for specific cancers, infectious diseases and autoimmune disorders in humans. This increased risk has been linked to distinct polymorphisms in both ERAPs and MHC class I receptors that affect the way cell-generated peptides are screened for antigenicity. The incidence of cancer, infectious disease and autoimmune disorders differ greatly among pure breeds of dogs as it does in humans and it is possible that this heightened susceptibility is also due to specific polymorphisms in ERAP1 and ERAP2. In order to determine if such polymorphisms exist, the ERAP1 and ERAP2 genes of 10 dogs of nine diverse breeds were sequenced and SNPs causing synonymous or non-synonymous amino acid changes, deletions or insertions were identified. Eight ERAP1 and 10 ERAP2 SNPs were used to create a Sequenom MassARRAY iPLEX based test panel which defined 24 ERAP1, 36 ERAP2 and 128 ERAP1/2 haplotypes. The prevalence of these haplotypes was then measured among dog, wolf, coyote, jackal and red fox populations. Some haplotypes were species specific, while others were shared across species, especially between dog, wolf, coyote and jackal. The prevalence of these haplotypes was then compared among various canid populations, and in particular between various populations of random- and pure-bred dogs. Human-directed positive selection has led to loss of ERAP diversity and segregation of certain haplotypes among various dog breeds. A phylogenetic tree generated from 45 of the most common ERAP1/2 haplotypes demonstrated three distinct clades, all of which were rooted with haplotypes either shared among species or specific to contemporary dogs, coyote and wolf.
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11
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Pedersen NC, Pooch AS, Liu H. A genetic assessment of the English bulldog. Canine Genet Epidemiol 2016; 3:6. [PMID: 27478618 PMCID: PMC4965900 DOI: 10.1186/s40575-016-0036-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/10/2016] [Indexed: 01/16/2023] Open
Abstract
Background This study examines genetic diversity among 102 registered English Bulldogs used for breeding based on maternal and paternal haplotypes, allele frequencies in 33 highly polymorphic short tandem repeat (STR) loci on 25 chromosomes, STR-linked dog leukocyte antigen (DLA) class I and II haplotypes, and the number and size of genome-wide runs of homozygosity (ROH) determined from high density SNP arrays. The objective was to assess whether the breed retains enough genetic diversity to correct the genotypic and phenotypic abnormalities associated with poor health, to allow for the elimination of deleterious recessive mutations, or to make further phenotypic changes in body structure or coat. An additional 37 English bulldogs presented to the UC Davis Veterinary Clinical Services for health problems were also genetically compared with the 102 registered dogs based on the perception that sickly English bulldogs are products of commercial breeders or puppy-mills and genetically different and inferior. Results Four paternal haplotypes, with one occurring in 93 % of dogs, were identified using six Y-short tandem repeat (STR) markers. Three major and two minor matrilines were identified by mitochondrial D-loop sequencing. Heterozygosity was determined from allele frequencies at genomic loci; the average number of alleles per locus was 6.45, with only 2.7 accounting for a majority of the diversity. However, observed and expected heterozygosity values were nearly identical, indicating that the population as a whole was in Hardy-Weinberg equilibrium (HWE). However, internal relatedness (IR) and adjusted IR (IRVD) values demonstrated that a number of individuals were the offspring of parents that were either more inbred or outbred than the population as a whole. The diversity of DLA class I and II haplotypes was low, with only 11 identified DLA class I and nine class II haplotypes. Forty one percent of the breed shared a single DLA class I and 62 % a single class II haplotype. Nineteen percent of the dogs were homozygous for the dominant DLA class I haplotype and 42 % for the dominant DLA class II haplotype. The extensive loss of genetic diversity is most likely the result of a small founder population and artificial genetic bottlenecks occurring in the past. The prominent phenotypic changes characteristic of the breed have also resulted in numerous large runs of homozygosity (ROH) throughout the genome compared to Standard Poodles, which were phenotypically more similar to indigenous-type dogs. Conclusions English bulldogs have very low genetic diversity resulting from a small founder population and artificial genetic bottlenecks. Although some phenotypic and genotypic diversity still exists within the breed, whether it is sufficient to use reverse selection to improve health, select against simple recessive deleterious traits, and/or to accommodate further genotypic/phenotypic manipulations without further decreasing existing genetic diversity is questionable.
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Affiliation(s)
- Niels C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Ashley S Pooch
- School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Hongwei Liu
- Center for Companion Animal Health, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616 USA
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12
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Brown SK, Darwent CM, Wictum EJ, Sacks BN. Using multiple markers to elucidate the ancient, historical and modern relationships among North American Arctic dog breeds. Heredity (Edinb) 2015; 115:488-95. [PMID: 26103948 DOI: 10.1038/hdy.2015.49] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 03/17/2015] [Accepted: 04/28/2015] [Indexed: 11/09/2022] Open
Abstract
Throughout most of the Americas, post-colonial dogs largely erased the genetic signatures of pre-historical dogs. However, the North American Arctic harbors dogs that are potentially descended from pre-historical ancestors, as well as those affected by post-colonial translocations and admixtures. In particular, Inuit dogs from Canada and Greenland are thought to descend from dogs associated with Thule peoples, who relied on them for transportation ca. 1000 years ago. Whether Thule dogs reflected an earlier colonization by Paleoeskimo dogs ca. 4500 years ago is unknown. During the Alaskan Gold Rush, additional sled dogs, possibly of post-colonial derivation, the Alaskan Husky, Malamute and Siberian Husky, were used in the Arctic. The genealogical relationships among and origins of these breeds are unknown. Here we use autosomal, paternal and maternal DNA markers to (1) test the hypothesis that Inuit dogs have retained their indigenous ancestry, (2) characterize their relationship to one another and to other Arctic breeds, and (3) estimate the age of North American indigenous matrilines and patrilines. On the basis of the agreement of all three markers we determined that Inuit dogs have maintained their indigenous nature, and that they likely derive from Thule dogs. In addition, we provide support for previous research that the Inuit dogs from Canada and Greenland dog should not be distinguished as two breeds. The Alaskan Husky displayed evidence of European introgression, in contrast to the Malamute and Siberian Husky, which appear to have maintained most of their ancient Siberian ancestry.
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Affiliation(s)
- S K Brown
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, CA, USA.,Department of Anthropology, University of California, Davis, CA, USA
| | - C M Darwent
- Department of Anthropology, University of California, Davis, CA, USA
| | - E J Wictum
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, CA, USA
| | - B N Sacks
- Mammalian Ecology and Conservation Unit, Center for Veterinary Genetics, University of California, Davis, CA, USA.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
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Kropatsch R, Melis C, Stronen AV, Jensen H, Epplen JT. Molecular Genetics of Sex Identification, Breed Ancestry and Polydactyly in the Norwegian Lundehund Breed. J Hered 2015; 106:403-6. [PMID: 25994807 DOI: 10.1093/jhered/esv031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 04/13/2015] [Indexed: 11/14/2022] Open
Abstract
The Norwegian Lundehund breed of dog has undergone a severe loss of genetic diversity as a result of inbreeding and epizootics of canine distemper. As a consequence, the breed is extremely homogeneous and accurate sex identification is not always possible by standard screening of X-chromosomal loci. To improve our genetic understanding of the breed we genotyped 17 individuals using a genome-wide array of 170 000 single nucleotide polymorphisms (SNPs). Standard analyses based on expected homozygosity of X-chromosomal loci failed in assigning individuals to the correct sex, as determined initially by physical examination and confirmed with the Y-chromosomal marker, amelogenin. This demonstrates that identification of sex using standard SNP assays can be erroneous in highly inbred individuals.
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Affiliation(s)
- Regina Kropatsch
- From the Department of Human Genetics, Ruhr University, Universitätsstr. 150, 44801 Bochum, Germany (Kropatsch and Epplen); the Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway (Melis and Jensen); the Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg Øst, Denmark (Stronen); and the Faculty of Health, University Witten/Herdecke, Witten, Germany (Epplen).
| | - Claudia Melis
- From the Department of Human Genetics, Ruhr University, Universitätsstr. 150, 44801 Bochum, Germany (Kropatsch and Epplen); the Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway (Melis and Jensen); the Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg Øst, Denmark (Stronen); and the Faculty of Health, University Witten/Herdecke, Witten, Germany (Epplen)
| | - Astrid V Stronen
- From the Department of Human Genetics, Ruhr University, Universitätsstr. 150, 44801 Bochum, Germany (Kropatsch and Epplen); the Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway (Melis and Jensen); the Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg Øst, Denmark (Stronen); and the Faculty of Health, University Witten/Herdecke, Witten, Germany (Epplen)
| | - Henrik Jensen
- From the Department of Human Genetics, Ruhr University, Universitätsstr. 150, 44801 Bochum, Germany (Kropatsch and Epplen); the Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway (Melis and Jensen); the Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg Øst, Denmark (Stronen); and the Faculty of Health, University Witten/Herdecke, Witten, Germany (Epplen)
| | - Joerg T Epplen
- From the Department of Human Genetics, Ruhr University, Universitätsstr. 150, 44801 Bochum, Germany (Kropatsch and Epplen); the Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway (Melis and Jensen); the Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg Øst, Denmark (Stronen); and the Faculty of Health, University Witten/Herdecke, Witten, Germany (Epplen)
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14
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Omeir R, Thomas R, Teferedegne B, Williams C, Foseh G, Macauley J, Brinster L, Beren J, Peden K, Breen M, Lewis AM. A novel canine kidney cell line model for the evaluation of neoplastic development: karyotype evolution associated with spontaneous immortalization and tumorigenicity. Chromosome Res 2015; 23:663-80. [PMID: 25957863 PMCID: PMC4666904 DOI: 10.1007/s10577-015-9474-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/12/2015] [Accepted: 04/14/2015] [Indexed: 01/01/2023]
Abstract
The molecular mechanisms underlying spontaneous neoplastic transformation in cultured mammalian cells remain poorly understood, confounding recognition of parallels with the biology of naturally occurring cancer. The broad use of tumorigenic canine cell lines as research tools, coupled with the accumulation of cytogenomic data from naturally occurring canine cancers, makes the domestic dog an ideal system in which to investigate these relationships. We developed a canine kidney cell line, CKB1-3T7, which allows prospective examination of the onset of spontaneous immortalization and tumorigenicity. We documented the accumulation of cytogenomic aberrations in CKB1-3T7 over 24 months in continuous culture. The majority of aberrations emerged in parallel with key phenotypic changes in cell morphology, growth kinetics, and tumor incidence and latency. Focal deletion of CDKN2A/B emerged first, preceding the onset and progression of tumorigenic potential, and progressed to a homozygous deletion across the cell population during extended culture. Interestingly, CKB1-3T7 demonstrated a tumorigenic phenotype in vivo prior to exhibiting loss of contact inhibition in vitro. We also performed the first genome-wide characterization of the canine tumorigenic cell line MDCK, which also exhibited CDKN2A/B deletion. MDCK and CKB1-3T7 cells shared several additional aberrations that we have reported previously as being highly recurrent in spontaneous canine cancers, many of which, as with CDKN2A/B deletion, are evolutionarily conserved in their human counterparts. The conservation of these molecular events across multiple species, in vitro and in vivo, despite their contrasting karyotypic architecture, is a powerful indicator of a common mechanism underlying emerging neoplastic activity. Through integrated cytogenomic and phenotypic characterization of serial passages of CKB1-3T7 from initiation to development of a tumorigenic phenotype, we present a robust and readily accessible model (to be made available through the American Type Culture Collection) of spontaneous neoplastic transformation that overcomes many of the limitations of earlier studies.
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Affiliation(s)
- R Omeir
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - R Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, 27607, USA
| | - B Teferedegne
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - C Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - G Foseh
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - J Macauley
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - L Brinster
- Division of Veterinary Resources, National Institutes of Health, Bethesda, MD, 20892, USA
| | - J Beren
- Office of Counter-Terrorism and Emergency Coordination, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - K Peden
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - M Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA. .,Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, NC, 27607, USA. .,Cancer Genetics Program, University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, 27599, USA. .,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27607, USA.
| | - A M Lewis
- Laboratory of DNA Viruses, Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA.
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Aghbolaghi MA, Rezaei HR, Scandura M, Kaboli M. Low gene flow between Iranian Grey Wolves(Canis lupus)and dogs documented using uniparental genetic markers. ZOOLOGY IN THE MIDDLE EAST 2014. [DOI: 10.1080/09397140.2014.914708] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Abstract
Several studies based on a variety of genetic markers have attempted to establish the origins of horse domestication. Thus far a discrepancy between the results of mitochondrial DNA analysis, which show high levels of diversity, and results from the Y-chromosome, with almost no genetic variability, has been identified. Most previous work on the horse Y-chromosome has focused on widespread, popular breeds or local Asian breeds. It is possible that these breeds represent a reduced set of the genetic variation present in the species. Additional genetic variation may be present in local breeds and ancient feral populations, such as the Retuertas horse in Spain. In this study we analyzed the Y-chromosome of the Retuertas horse, a feral horse population on the Iberian Peninsula that is at least several hundred years old, and whose genetic diversity and morphology suggests that it has been reproductively isolated for a long time. Data from the Retuertas horse was compared to another 11 breeds from the region (Portugal, Spain and France) or likely of Iberian origin, and then to data from 15 more breeds from around the globe. We sequenced 31 introns, Zinc finger Y-chromosomal protein (ZFY) and anonymous Y-linked fragments and genotyped 6 microsatellite loci found on the Y-chromosome. We found no sequence variation among all individuals and all breeds studied. However, fifteen differences were discovered between our data set and reference sequences in GenBank. We show that these likely represent errors within the deposited sequences, and suggest that they should not be used as comparative data for future projects.
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Sacks BN, Brown SK, Stephens D, Pedersen NC, Wu JT, Berry O. Y Chromosome Analysis of Dingoes and Southeast Asian Village Dogs Suggests a Neolithic Continental Expansion from Southeast Asia Followed by Multiple Austronesian Dispersals. Mol Biol Evol 2013; 30:1103-18. [DOI: 10.1093/molbev/mst027] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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18
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Pedersen N, Liu H, Theilen G, Sacks B. The effects of dog breed development on genetic diversity and the relative influences of performance and conformation breeding. J Anim Breed Genet 2012; 130:236-48. [PMID: 23679949 DOI: 10.1111/jbg.12017] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/02/2012] [Indexed: 12/22/2022]
Abstract
Genetic diversity was compared among eight dog breeds selected primarily for conformation (Standard Poodle, Italian Greyhound and show English Setter), conformation and performance (Brittany), predominantly performance (German Shorthaired and Wirehaired Pointers) or solely performance (field English Setter and Red Setter). Modern village dogs, which better reflect ancestral genetic diversity, were used as the standard. Four to seven maternal and one to two Y haplotypes were found per breed, with one usually dominant. Diversity of maternal haplotypes was greatest in village dogs, intermediate in performance breeds and lowest in conformation breeds. Maternal haplotype sharing occurred across all breeds, while Y haplotypes were more breed specific. Almost all paternal haplotypes were identified among village dogs, with the exception of the dominant Y haplotype in Brittanys, which has not been identified heretofore. The highest heterozygosity based on 24 autosomal microsatellites was found in village dogs and the lowest in conformation (show) breeds. Principal coordinate analysis indicated that conformation-type breeds were distinct from breeds heavily used for performance, the latter clustering more closely with village dogs. The Brittany, a well-established dual show and field breed, was also genetically intermediate between the conformation and performance breeds. The number of DLA-DRB1 alleles varied from 3 to 10 per breed with extensive sharing. SNPs across the wider DLA region were more frequently homozygous in all pure breeds than in village dogs. Compared with their village dog relatives, all modern breed dogs exhibit reduced genetic diversity. Genetic diversity was even more reduced among breeds under selection for show/conformation.
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Affiliation(s)
- N Pedersen
- Koret Foundation Center for Veterinary Genetics of the Center for Companion Animal Health, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
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19
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Hindrikson M, Männil P, Ozolins J, Krzywinski A, Saarma U. Bucking the trend in wolf-dog hybridization: first evidence from europe of hybridization between female dogs and male wolves. PLoS One 2012; 7:e46465. [PMID: 23056315 PMCID: PMC3463576 DOI: 10.1371/journal.pone.0046465] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 09/03/2012] [Indexed: 11/21/2022] Open
Abstract
Studies on hybridization have proved critical for understanding key evolutionary processes such as speciation and adaptation. However, from the perspective of conservation, hybridization poses a concern, as it can threaten the integrity and fitness of many wild species, including canids. As a result of habitat fragmentation and extensive hunting pressure, gray wolf (Canis lupus) populations have declined dramatically in Europe and elsewhere during recent centuries. Small and fragmented populations have persisted, but often only in the presence of large numbers of dogs, which increase the potential for hybridization and introgression to deleteriously affect wolf populations. Here, we demonstrate hybridization between wolf and dog populations in Estonia and Latvia, and the role of both genders in the hybridization process, using combined analysis of maternal, paternal and biparental genetic markers. Eight animals exhibiting unusual external characteristics for wolves - six from Estonia and two from Latvia - proved to be wolf-dog hybrids. However, one of the hybridization events was extraordinary. Previous field observations and genetic studies have indicated that mating between wolves and dogs is sexually asymmetrical, occurring predominantly between female wolves and male dogs. While this was also the case among the Estonian hybrids, our data revealed the existence of dog mitochondrial genomes in the Latvian hybrids and, together with Y chromosome and autosomal microsatellite data, thus provided the first evidence from Europe of mating between male wolves and female dogs. We discuss patterns of sexual asymmetry in wolf-dog hybridization.
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Affiliation(s)
- Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Peep Männil
- Estonian Environment Information Centre, Tartu, Estonia
| | - Janis Ozolins
- State Forest Research Institute “Silava”, Salaspils, Latvia
| | | | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- * E-mail:
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20
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An Account of the Taxonomy of North American Wolves From Morphological and Genetic Analyses. ACTA ACUST UNITED AC 2012. [DOI: 10.3996/nafa.77.0001] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
The available scientific literature was reviewed to assess the taxonomic standing of North American wolves, including subspecies of the gray wolf, Canis lupus. The recent scientific proposal that the eastern wolf, C. l. lycaon, is not a subspecies of gray wolf, but a full species, Canis lycaon, is well-supported by both morphological and genetic data. This species' range extends westward to Minnesota, and it hybridizes with gray wolves where the two species are in contact in eastern Canada and the Upper Peninsula of Michigan, Wisconsin, and Minnesota. Genetic data support a close relationship between eastern wolf and red wolf Canis rufus, but do not support the proposal that they are the same species; it is more likely that they evolved independently from different lineages of a common ancestor with coyotes. The genetic distinctiveness of the Mexican wolf Canis lupus baileyi supports its recognition as a subspecies. The available genetic and morphometric data do not provide clear support for the recognition of the Arctic wolf Canis lupus arctos, but the available genetic data are almost entirely limited to one group of genetic markers (microsatellite DNA) and are not definitive on this question. Recognition of the northern timber wolf Canis lupus occidentalis and the plains wolf Canis lupus nubilus as subspecies is supported by morphological data and extensive studies of microsatellite DNA variation where both subspecies are in contact in Canada. The wolves of coastal areas in southeastern Alaska and British Columbia should be assigned to C. lupus nubilus. There is scientific support for the taxa recognized here, but delineation of exact geographic boundaries presents challenges. Rather than sharp boundaries between taxa, boundaries should generally be thought of as intergrade zones of variable width.
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Frynta D, Baudyšová J, Hradcová P, Faltusová K, Kratochvíl L. Allometry of sexual size dimorphism in domestic dog. PLoS One 2012; 7:e46125. [PMID: 23049956 PMCID: PMC3458007 DOI: 10.1371/journal.pone.0046125] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 08/28/2012] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The tendency for male-larger sexual size dimorphism (SSD) to scale with body size - a pattern termed Rensch's rule - has been empirically supported in many animal lineages. Nevertheless, its theoretical elucidation is a subject of debate. Here, we exploited the extreme morphological variability of domestic dog (Canis familiaris) to gain insights into evolutionary causes of this rule. METHODOLOGY/PRINCIPAL FINDINGS We studied SSD and its allometry among 74 breeds ranging in height from less than 19 cm in Chihuahua to about 84 cm in Irish wolfhound. In total, the dataset included 6,221 individuals. We demonstrate that most dog breeds are male-larger, and SSD in large breeds is comparable to SSD of their wolf ancestor. Among breeds, SSD becomes smaller with decreasing body size. The smallest breeds are nearly monomorphic. CONCLUSIONS/SIGNIFICANCE SSD among dog breeds follows the pattern consistent with Rensch's rule. The variability of body size and corresponding changes in SSD among breeds of a domestic animal shaped by artificial selection can help to better understand processes leading to emergence of Rensch's rule.
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Affiliation(s)
- Daniel Frynta
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jana Baudyšová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Petra Hradcová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Kateřina Faltusová
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
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22
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Pedersen NC, Liu H, McLaughlin B, Sacks BN. Genetic characterization of healthy and sebaceous adenitis affected Standard Poodles from the United States and the United Kingdom. ACTA ACUST UNITED AC 2012; 80:46-57. [PMID: 22512808 DOI: 10.1111/j.1399-0039.2012.01876.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The degree of heterogeneity associated with geographic origin and sebaceous adenitis (SA) status in Standard Poodles from the United States (US) and the United Kingdom (UK) was assessed. Healthy and SA-affected Standard Poodles from the US and the UK shared a major mitochondrial DNA (mtDNA) haplotype and a single Y chromosome haplotype. However, minor mtDNA haplotypes and frequencies were somewhat different between US and UK dogs and were significantly less associated with SA than major haplotypes across both populations. The US and UK populations exhibited recent divergence from a common gene pool, based on allele frequencies of 24 highly polymorphic short tandem repeats and principle coordinates and cluster analyses of genotype frequencies. However, there was no differentiation between SA affected and unaffected dogs. Over 90% of US and UK Poodles shared a common dog leukocyte antigen (DLA) class II haplotype, but showed some differentiation in minor haplotype frequency. No difference was observed in haplotype heterozygosity between SA affected and unaffected dogs from the same country and no disease association for SA was found within the DLA region by a high density single nucleotide polymorphism (SNP) scan. Zygosity mapping in the DLA region of Poodles indicated much lower site-specific diversity than in an outbred population of street dogs from Bali, Indonesia, reflecting the degree that breed associated historical bottlenecks have reduced diversity in a polymorphic region of the genome. This study shows possible pitfalls in more extensive genome-wide association studies, such as case and control numbers, population stratification, the involvement of multiple genes, and/or the possibility that SA susceptibility is fixed or nearly fixed within the breed, which can reduce power to detect genetic associations.
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Affiliation(s)
- N C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA.
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23
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Brown SK, Pedersen NC, Jafarishorijeh S, Bannasch DL, Ahrens KD, Wu JT, Okon M, Sacks BN. Phylogenetic distinctiveness of Middle Eastern and Southeast Asian village dog Y chromosomes illuminates dog origins. PLoS One 2011; 6:e28496. [PMID: 22194840 PMCID: PMC3237445 DOI: 10.1371/journal.pone.0028496] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 11/09/2011] [Indexed: 12/04/2022] Open
Abstract
Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.
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Affiliation(s)
- Sarah K. Brown
- Canid Diversity and Conservation Laboratory, Center for Veterinary Genetics, University of California Davis, Davis, California, United States of America
- Veterinary Genetics Laboratory, University of California at Davis, Davis, California, United States of America
| | - Niels C. Pedersen
- Veterinary Genetics Laboratory, University of California at Davis, Davis, California, United States of America
- Center for Companion Animal Health, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Sardar Jafarishorijeh
- Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Danika L. Bannasch
- Veterinary Genetics Laboratory, University of California at Davis, Davis, California, United States of America
- Department of Population, Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Kristen D. Ahrens
- Canid Diversity and Conservation Laboratory, Center for Veterinary Genetics, University of California Davis, Davis, California, United States of America
- Biological Sciences Department, California State University Sacramento, Sacramento, California, United States of America
| | - Jui-Te Wu
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan, Republic of China
| | - Michaella Okon
- Ruah Midbar Kennel for Desert Bred Salukis, Herzliya, Israel
| | - Benjamin N. Sacks
- Canid Diversity and Conservation Laboratory, Center for Veterinary Genetics, University of California Davis, Davis, California, United States of America
- Veterinary Genetics Laboratory, University of California at Davis, Davis, California, United States of America
- Department of Population, Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- Biological Sciences Department, California State University Sacramento, Sacramento, California, United States of America
- * E-mail:
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Pedersen NC, Liu H, Greenfield DL, Echols LG. Multiple autoimmune diseases syndrome in Italian Greyhounds: preliminary studies of genome-wide diversity and possible associations within the dog leukocyte antigen (DLA) complex. Vet Immunol Immunopathol 2011; 145:264-76. [PMID: 22178273 DOI: 10.1016/j.vetimm.2011.11.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Revised: 10/24/2011] [Accepted: 11/17/2011] [Indexed: 12/14/2022]
Abstract
A disorder manifested by multiple autoimmune disorders, and resembling autoimmune polyendocrine syndrome type 2 (APS-2) in humans, may exist in Italian Greyhounds. The incidence of this disorder is increasing and its potential impact on the health of the breed is becoming of great concern. The aims of the present study were to document the existence of this syndrome, conduct a preliminary assessment of genetic diversity across the breed and within affected and unaffected dogs, determine whether the disorder associates with the dog leukocyte antigen (DLA) complex, and demonstrate similarities to APS-2 of humans. To these ends, information on disease, pedigrees, and blood or buccal swab samples were collected from affected and healthy Italian Greyhounds and extracted DNA analyzed. Analysis of Y chromosome markers and mitochondrial DNA sequences showed that Italian Greyhounds evolved from a single patriline and two major and four minor matrilines. A panel of 24 highly polymorphic simple tandem repeat (STR) markers across 20 autosomes demonstrated that affected and unaffected dogs were not distinguishable from the population as a whole by heterozygosity, F-statistics, and principal component analysis (PCA). However, analysis of allele frequencies at each STR loci identified regions of increased or decreased disease risk on four chromosomes. A similar genetic analysis using 109 single nucleotide polymorphisms (SNPs) across the DLA region showed differences between affected and unaffected dogs. PCA and zygosity mapping of DLA SNPs from unrelated dogs demonstrated two distinct subpopulations among the affected individuals. One population was very homozygous and the other closely resembled unaffected dogs in its heterozygosity, suggesting the evolution of a disease prone bloodline as a result of non-random selection. Exon 2 sequencing of the DLA class II genes demonstrated 5-8 alleles at each locus and 14 three loci haplotypes. Two specific haplotypes containing DRB1*00203 or DRB1*02901 were associated with increased disease risk in about one-third of affected dogs. However, high density SNP association mapping across the DLA region and CFA12 did not corroborate the association.
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Affiliation(s)
- Niels C Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California, One Shields Avenue, Davis, CA 95616, USA.
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Ding ZL, Oskarsson M, Ardalan A, Angleby H, Dahlgren LG, Tepeli C, Kirkness E, Savolainen P, Zhang YP. Origins of domestic dog in southern East Asia is supported by analysis of Y-chromosome DNA. Heredity (Edinb) 2011; 108:507-14. [PMID: 22108628 PMCID: PMC3330686 DOI: 10.1038/hdy.2011.114] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Global mitochondrial DNA (mtDNA) data indicates that the dog originates from domestication of wolf in Asia South of Yangtze River (ASY), with minor genetic contributions from dog–wolf hybridisation elsewhere. Archaeological data and autosomal single nucleotide polymorphism data have instead suggested that dogs originate from Europe and/or South West Asia but, because these datasets lack data from ASY, evidence pointing to ASY may have been overlooked. Analyses of additional markers for global datasets, including ASY, are therefore necessary to test if mtDNA phylogeography reflects the actual dog history and not merely stochastic events or selection. Here, we analyse 14 437 bp of Y-chromosome DNA sequence in 151 dogs sampled worldwide. We found 28 haplotypes distributed in five haplogroups. Two haplogroups were universally shared and included three haplotypes carried by 46% of all dogs, but two other haplogroups were primarily restricted to East Asia. Highest genetic diversity and virtually complete phylogenetic coverage was found within ASY. The 151 dogs were estimated to originate from 13–24 wolf founders, but there was no indication of post-domestication dog–wolf hybridisations. Thus, Y-chromosome and mtDNA data give strikingly similar pictures of dog phylogeography, most importantly that roughly 50% of the gene pools are shared universally but only ASY has nearly the full range of genetic diversity, such that the gene pools in all other regions may derive from ASY. This corroborates that ASY was the principal, and possibly sole region of wolf domestication, that a large number of wolves were domesticated, and that subsequent dog–wolf hybridisation contributed modestly to the dog gene pool.
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Affiliation(s)
- Z-L Ding
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
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GODINHO RAQUEL, LLANEZA LUIS, BLANCO JUANC, LOPES SUSANA, ÁLVARES FRANCISCO, GARCÍA EMILIOJ, PALACIOS VICENTE, CORTÉS YOLANDA, TALEGÓN JAVIER, FERRAND NUNO. Genetic evidence for multiple events of hybridization between wolves and domestic dogs in the Iberian Peninsula. Mol Ecol 2011; 20:5154-66. [DOI: 10.1111/j.1365-294x.2011.05345.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
This review assesses evidence from DNA analysis to determine whether there is sufficient genetic diversity within breeds to ensure that populations are sustainable in the absence of cross breeding and to determine whether genetic diversity is declining. On average, dog breeds currently retain approximately 87% of the available domestic canine genetic diversity. Requirements that breeding stock must be 'clear' for all genetic disorders may firstly place undue genetic pressure on animals tested as being 'clear' of known genetic disorders, secondly may contribute to loss of diversity and thirdly may result in the dissemination of new recessive disorders for which no genetic tests are available. Global exchange of genetic material may hasten the loss of alleles and this practice should be discussed in relation to the current effective population size of a breed and its expected future popularity. Genomic data do not always support the results from pedigree analysis and possible reasons for this are discussed.
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Affiliation(s)
- Claire M Wade
- Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia.
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Pedersen N, Liu H, Millon L, Greer K. Dog leukocyte antigen class II-associated genetic risk testing for immune disorders of dogs: simplified approaches using Pug dog necrotizing meningoencephalitis as a model. J Vet Diagn Invest 2011; 23:68-76. [PMID: 21217030 DOI: 10.1177/104063871102300110] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A significantly increased risk for a number of autoimmune and infectious diseases in purebred and mixed-breed dogs has been associated with certain alleles or allele combinations of the dog leukocyte antigen (DLA) class II complex containing the DRB1, DQA1, and DQB1 genes. The exact level of risk depends on the specific disease, the alleles in question, and whether alleles exist in a homozygous or heterozygous state. The gold standard for identifying high-risk alleles and their zygosity has involved direct sequencing of the exon 2 regions of each of the 3 genes. However, sequencing and identification of specific alleles at each of the 3 loci are relatively expensive and sequencing techniques are not ideal for additional parentage or identity determination. However, it is often possible to get the same information from sequencing only 1 gene given the small number of possible alleles at each locus in purebred dogs, extensive homozygosity, and tendency for disease-causing alleles at each of the 3 loci to be strongly linked to each other into haplotypes. Therefore, genetic testing in purebred dogs with immune diseases can be often simplified by sequencing alleles at 1 rather than 3 loci. Further simplification of genetic tests for canine immune diseases can be achieved by the use of alternative genetic markers in the DLA class II region that are also strongly linked with the disease genotype. These markers consist of either simple tandem repeats or single nucleotide polymorphisms that are also in strong linkage with specific DLA class II genotypes and/or haplotypes. The current study uses necrotizing meningoencephalitis of Pug dogs as a paradigm to assess simple alternative genetic tests for disease risk. It was possible to attain identical necrotizing meningoencephalitis risk assessments to 3-locus DLA class II sequencing by sequencing only the DQB1 gene, using 3 DLA class II-linked simple tandem repeat markers, or with a small single nucleotide polymorphism array designed to identify breed-specific DQB1 alleles.
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Affiliation(s)
- Niels Pedersen
- Center for Companion Animal Health, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
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Gerding WM, Schreiber S, Dekomien G, Epplen JT. Tracing the origin of 'blue Weimaraner' dogs by molecular genetics. J Anim Breed Genet 2011; 128:153-60. [PMID: 21385230 DOI: 10.1111/j.1439-0388.2010.00888.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Weimaraner dogs are defined by light brown coat colour termed grey including several shadings ranging from silver and deer to mouse grey. In contrast, the so-called blue Weimaraners (BW) with lightened black-pigmented coat have been proposed to represent spontaneous revertants in the Weimaraner breed. In order to investigate the genetic determinants of the characteristic grey coat colour versus those of BW, known variation in coat colour genes including TYRP1 and MLPH were analysed in a number of grey and blue dogs. Variations at the B locus cause grey coat colour in Weimaraners via two non-functional TYRP1 copies (bb) including the b(s), b(d) and b(c) alleles. In all BW, at least one functional TYRP1 allele (Bb or BB genotype) was identified. Defined microsatellite alleles in TYRP1 intron 4 are linked to this functional B allele in BW. These alleles were also detected in various other dog breeds, but not in grey Weimaraners. The combination of a dominant trait for blue versus grey together with a specific TYRP1 haplotype in BW suggests that blue coat colour is not the result of spontaneous (back-) mutation in grey Weimaraners. This inference is even emphasized by the presence of a unique Y-chomosomal haplotype in a male offspring of the supposed ancestor of the BW population which - according to pedigree information - carries a copy of the original Y chromosome. Thus, molecular genetic analyses of coat colours combined with Y-chromosomal haplotypes allow tracing the origin of atypical dogs in respective canine populations.
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Affiliation(s)
- W M Gerding
- Human Genetics, Ruhr-University, Bochum, Germany.
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Nakayama K, Kakinoki R, Ikeguchi R, Yamakawa T, Ohta S, Fujita S, Noguchi T, Duncan SF, Hyon SH, Nakamura T. Storage and allogeneic transplantation of peripheral nerve using a green tea polyphenol solution in a canine model. J Brachial Plex Peripher Nerve Inj 2010; 5:17. [PMID: 21110896 PMCID: PMC3003657 DOI: 10.1186/1749-7221-5-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 11/28/2010] [Indexed: 12/13/2022] Open
Abstract
Background In our previous study, allogeneic-transplanted peripheral nerve segments preserved for one month in a polyphenol solution at 4°C could regenerate nerves in rodents demonstrated the same extent of nerve regeneration as isogeneic fresh nerve grafts. The present study investigated whether the same results could be obtained in a canine model. Methods A sciatic nerve was harvested from a male beagle dog, divided into fascicules of < 1.5 mm diameter, and stored in a polyphenol solution (1 mg/ml) for one month at 4°C. The nerve fascicles were transplanted into 10 female beagle dogs to bridge 3-cm right ulnar nerve gaps. In the left ulnar nerve in each dog, a 3-cm nerve segment was harvested, turned in the opposite direction, and sutured in situ. Starting one day before transplantation, the immunosuppressant FK506 was administered subcutaneously at doses of 0.1 mg/kg daily in four dogs (PA0.1 group), 0.05 mg/kg daily in four dogs (PA0.05 group), or 0.05 mg/kg every other day in two dogs (PA0.025 group). Twelve weeks after surgery, electrophysiological and morphological studies were performed to assess the regeneration of the right and left ulnar nerves. The data for the right ulnar nerve were expressed as percentages relative to the left ulnar nerve. Polymerase chain reaction (PCR) was used to identify the sex-determining region of the Y-chromosome (Sry) and β-actin to investigate whether cells of donor origin remained in the allogeneic nerve segments. FK506 concentration was measured in blood samples taken before the animals were killed. Results The total myelinated axon numbers and amplitudes of the muscle action potentials correlated significantly with the blood FK506 concentration. Few axons were observed in the allogeneic-transplanted nerve segments in the PA0.025 group. PCR showed clear Sry-specific bands in specimens from the PA0.1 and PA0.05 groups but not from the PA0.025 group. Conclusions Successful nerve regeneration was observed in the polyphenol-treated nerve allografts when transplanted in association with a therapeutic dose of FK506. The data indicate that polyphenols can protect nerve tissue from ischemic damage for one month; however, the effects of immune suppression seem insufficient to permit allogeneic transplantation of peripheral nerves in a canine model.
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Affiliation(s)
- Ken Nakayama
- Department of Orthopedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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Kropatsch R, Streitberger K, Schulte-Middelmann T, Dekomien G, Epplen J. On ancestors of dog breeds with focus on Weimaraner hunting dogs. J Anim Breed Genet 2010; 128:64-72. [DOI: 10.1111/j.1439-0388.2010.00874.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Greer KA, Wong AK, Liu H, Famula TR, Pedersen NC, Ruhe A, Wallace M, Neff MW. Necrotizing meningoencephalitis of Pug dogs associates with dog leukocyte antigen class II and resembles acute variant forms of multiple sclerosis. ACTA ACUST UNITED AC 2010; 76:110-8. [PMID: 20403140 DOI: 10.1111/j.1399-0039.2010.01484.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Necrotizing meningoencephalitis (NME) is a disorder of Pug Dogs that appears to have an immune etiology and high heritability based on population studies. The present study was undertaken to identify a genetic basis for the disease. A genome-wide association scan with single tandem repeat (STR) markers showed a single strong association near the dog leukocyte antigen (DLA) complex on CFA12. Fine resolution mapping with 27 STR markers on CFA12 further narrowed association to the region containing DLA-DRB1, -DQA1 and, -DQB1 genes. Sequencing confirmed that affected dogs were more likely to be homozygous for specific alleles at each locus and that these alleles were linked, forming a single high risk haplotype. The strong DLA class II association of NME in Pug Dogs resembles that of human multiple sclerosis (MS). Like MS, NME appears to have an autoimmune basis, involves genetic and nongenetic factors, has a relatively low incidence, is more frequent in females than males, and is associated with a vascularly orientated nonsuppurative inflammation. However, NME of Pug Dogs is more aggressive in disease course than classical human MS, appears to be relatively earlier in onset, and involves necrosis rather than demyelination as the central pathobiologic feature. Thus, Pug Dog encephalitis (PDE) shares clinical features with the less common acute variant forms of MS. Accordingly, NME of Pug Dogs may represent a naturally occurring canine model of certain idiopathic inflammatory disorders of the human central nervous system.
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Affiliation(s)
- K A Greer
- School of Natural Sciences and Mathematics, Indiana University East, Richmond, IN 47374, USA.
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35
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Abstract
The increased battery of molecular markers, derived from comparative genomics, is aiding our understanding of the genetics of domestication. The recent BMC Biology article pertaining to the evolution of small size in dogs is an example of how such methods can be used to study the origin and diversification of the domestic dog. We are still challenged, however, to appreciate the genetic mechanisms responsible for the phenotypic diversity seen in 'our best friend'.
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Affiliation(s)
- Rodney L Honeycutt
- Department of Biology, National Science Division, Pepperdine University, 24255 Pacific Coast Highway, Malibu, California 90263-4321, USA.
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36
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Séguin B, Zwerdling T, McCallan JL, DeCock HEV, Dewe LL, Naydan DK, Young AE, Bannasch DL, Foreman O, Kent MS. Development of a new canine osteosarcoma cell line. Vet Comp Oncol 2009; 4:232-40. [PMID: 19754807 DOI: 10.1111/j.1476-5829.2006.00112.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Establishing a canine osteosarcoma (OSA) cell line can be useful to develop in vivo and in vitro models of OSA. The goal of this study was to develop, characterize and authenticate a new canine OSA cell line and a clone. A cell line and a clone were developed with standard cell culture techniques from a naturally occurring OSA in a dog. The clonal cell line induced a tumour after injection in RAG 1-deficient mouse. Histology was consistent with OSA. The original tumour from the dog and the tumour induced in the mouse were both reactive with vimentin and osteonectin (ON). The parent cell line and clonal cell line were reactive with ON, osteocalcin and alkaline phosphatase. Loss of heterozygosity was found in the same three microsatellite markers in the parent and clonal cell lines, and the tumour tissue grown in the mouse.
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Affiliation(s)
- B Séguin
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, CA, USA.
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37
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Pribánová M, Horák P, Schröffelová D, Urban T, Bechynová R, Musilová L. Analysis of genetic variability in the Czech Dachshund population using microsatellite markers. J Anim Breed Genet 2009; 126:311-8. [PMID: 19630882 DOI: 10.1111/j.1439-0388.2008.00772.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The primary goal of this study was to analyse genetic variation within and among six Dachshund varieties in the Czech Republic using 10 microsatellites from StockMarks Paternity Polymerase Chain Reaction (PCR) Typing kit. A total of 632 Dachshunds were sampled - 99 Standard Smooth-haired, 72 Standard Long-haired, 272 Standard Wire-haired, 42 Miniature Smooth-haired, 73 Miniature Long-haired and 74 Miniature Wire-haired. Average observed heterozygosity and polymorphic information content ranged in particular Dachshund varieties between 0.58-0.70 and 0.57-0.64, respectively. Subsequent analysis of the population structure (F-statistics; Nei's genetic identity) showed that Standard Dachshunds shared allele frequencies most closely with their miniature equivalents, and smooth coat type is closer to Wire-haired coat type than to the Long-haired one. Analysis of molecular variance revealed that 11.81% of the total variance occurred among varieties. The value of combined exclusion probability (0.9955) validated usefulness of this panel of microsatellites for parentage verification in all analysed populations. We carried out 234 parentage verifications with 1.28% cases where parentage did not match.
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Affiliation(s)
- M Pribánová
- Laboratory of Immunogenetics, Czech Moravian Breeders Corporation, Hradistko, Czech Republic
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38
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Kanthaswamy S, Tom BK, Mattila AM, Johnston E, Dayton M, Kinaga J, Joy-Alise Erickson B, Halverson J, Fantin D, DeNise S, Kou A, Malladi V, Satkoski J, Budowle B, Glenn Smith D, Koskinen MT. Canine Population Data Generated from a Multiplex STR Kit for Use in Forensic Casework. J Forensic Sci 2009; 54:829-40. [DOI: 10.1111/j.1556-4029.2009.01080.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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KOBLMÜLLER STEPHAN, NORD MARIA, WAYNE ROBERTK, LEONARD JENNIFERA. Origin and status of the Great Lakes wolf. Mol Ecol 2009; 18:2313-26. [DOI: 10.1111/j.1365-294x.2009.04176.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Li Q, Liu Z, Li Y, Zhao X, Dong L, Pan Z, Sun Y, Li N, Xu Y, Xie Z. Origin and phylogenetic analysis of Tibetan Mastiff based on the mitochondrial DNA sequence. J Genet Genomics 2009; 35:335-40. [PMID: 18571121 DOI: 10.1016/s1673-8527(08)60049-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 02/20/2008] [Accepted: 03/28/2008] [Indexed: 10/21/2022]
Abstract
At present, the Tibetan Mastiff is the oldest and most ferocious dog in the world. However, the origin of the Tibetan Mastiff and its phylogenetic relationship with other large breed dogs such as Saint Bernard are unclear. In this study, the primers were designed according to the mitochondrial genome sequence of the domestic dog, and the 2,525 bp mitochondrial sequence, containing the whole sequence of Cytochrome b, tRNA-Thr, tRNA-Pro, and control region of the Tibetan Mastiff, was obtained. Using grey wolves and coyotes as outgroups, the Tibetan Mastiff and 12 breeds of domestic dogs were analyzed in phylogenesis. Tibetan Mastiff, domestic dog breeds, and grey wolves were clustered into a group and coyotes were clustered in a group separately. This indicated that the Tibetan Mastiff and the other domestic dogs originated from the grey wolf, and the Tibetan Mastiff belonged to Carnivora, Canidae, Canis, Canis lupus, Canis lupus familiaris on the animal taxonomy. In domestic dogs, the middle and small breed dogs were clustered at first; German Sheepdog, Swedish Elkhound, and Black Russian Terrier were clustered into one group, and the Tibetan Mastiff, Old English Sheepdog, Leonberger, and Saint Bernard were clustered in another group. This confirmed the viewpoint that many of the famous large breed dogs worldwide such as Saint Bernard possibly had the blood lineage of the Tibetan Mastiff, based on the molecular data. According to the substitution rate, we concluded that the approximate divergence time between Tibetan Mastiff and grey wolf was 58,000 years before the present (YBP), and the approximate divergence time between other domestic dogs and grey wolf was 42,000 YBP, demonstrating that the time of origin of the Tibetan Mastiff was earlier than that of the other domestic dogs.
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Affiliation(s)
- Qifa Li
- Laboratory of Animal Reproductive Genetics and Molecular Evolution, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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41
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Meadows JRS, Kijas JW. Re-sequencing regions of the ovine Y chromosome in domestic and wild sheep reveals novel paternal haplotypes. Anim Genet 2009; 40:119-23. [DOI: 10.1111/j.1365-2052.2008.01799.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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42
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Ginja C, Telo da Gama L, Penedo MCT. Y chromosome haplotype analysis in Portuguese cattle breeds using SNPs and STRs. ACTA ACUST UNITED AC 2008; 100:148-57. [PMID: 18832111 DOI: 10.1093/jhered/esn080] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
DNA samples from 307 males of 13 Portuguese native cattle breeds, 57 males of the 3 major exotic breeds in Portugal (Charolais, Friesian, and Limousin), and 5 Brahman (Bos indicus) were tested for 5 single nucleotide polymorphisms, 1 "indel," and 7 microsatellites specific to the Y chromosome. The 13 Y-haplotypes defined included 3 previously described patrilines (Y1, Y2, and Y3) and 10 new haplotypes within Bos taurus. Native cattle contained most of the diversity with 7 haplotypes (H2Y1, H3Y1, H5Y1, H7Y2, H8Y2, H10Y2, and H12Y2) found only in these breeds. H6Y2 and H11Y2 occurred in high frequency across breeds including the exotics. Introgression of Friesian cattle into Ramo Grande was inferred through their sharing of haplotype H4Y1. Among the native breeds, Mertolenga had the highest haplotype diversity (0.68 +/- 0.07), Brava de Lide was the least differentiated. The analyses of molecular variance showed significant (P < 0.0001) differences between breeds with more than 64% of the total genetic variation found among breeds within groups and 33-35% within breeds. The detection of INRA189-104 allele in 8 native breeds suggested influence of African cattle in breeds of the Iberian Peninsula. The presence in Portuguese breeds of Y1 patrilines, also found in aurochs, could represent more ancient local haplotypes.
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Affiliation(s)
- Catarina Ginja
- Instituto Superior de Agronomia, Tapada da Ajuda, Lisboa, Portugal.
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43
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Sacks BN, Bannasch DL, Chomel BB, Ernest HB. Coyotes demonstrate how habitat specialization by individuals of a generalist species can diversify populations in a heterogeneous ecoregion. Mol Biol Evol 2008; 25:1384-94. [PMID: 18391065 DOI: 10.1093/molbev/msn082] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The tendency for individuals to disperse into habitat similar to their natal habitat has been observed in a wide range of species, although its population genetic consequences have received little study. Such behavior could lead to discrete habitat-specific population subdivisions even in the absence of physical dispersal barriers or habitat gaps. Previous studies of coyotes have supported this hypothesis in a small region of California, but its evolutionary significance ultimately depends on the extent and magnitude of habitat-specific subdivision. Here, we investigated these questions using autosomal, Y chromosome, and mitochondrial markers and >2,000 coyotes from a broad region, including 2 adjacent ecoregions with contrasting levels of habitat heterogeneity--the California Floristic Province (CFP) (heterogeneous landscape) and the Desert-Prairie ecoregion (DPE) (homogeneous landscape). Consistent with predictions, we found a close correspondence between population genetic structure and habitat subdivisions throughout the CFP and virtual panmixia over the larger DPE. Conversely, although genetic diversity was similar in these 2 ecoregions overall, it was lower within sites of the CFP, as would be the expected consequence of greater genetic drift within subregions. The magnitude of habitat-specific genetic subdivisions (i.e., genetic distance) in the CFP varied considerably, indicating complexity (e.g., asymmetric gene flow or extinction/recolonization), but, in general, was higher than that due to geographic distance or recent human-related barriers. Because habitat-specific structure can enhance a species' adaptive potential and resilience to changing environments, these findings suggest the CFP may constitute an evolutionarily important portion of the range for coyotes and sympatric species exhibiting habitat-specific population structure.
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Affiliation(s)
- Benjamin N Sacks
- Veterinary Genetics Laboratory, University of California, Davis, CA, USA.
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44
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Lessons learned from the dog genome. Trends Genet 2007; 23:557-67. [DOI: 10.1016/j.tig.2007.08.013] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 08/23/2007] [Accepted: 08/23/2007] [Indexed: 12/11/2022]
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45
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Galis F, Van der Sluijs I, Van Dooren TJM, Metz JAJ, Nussbaumer M. Do large dogs die young? JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2007; 308:119-26. [PMID: 16788896 DOI: 10.1002/jez.b.21116] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In most animal taxa, longevity increases with body size across species, as predicted by the oxidative stress theory of aging. In contrast, in within-species comparisons of mammals and especially domestic dogs (e.g. Patronek et al., '97; Michell, '99; Egenvall et al., 2000; Speakman et al., 2003), longevity decreases with body size. We explore two datasets for dogs and find support for a negative relationship between size and longevity if we consider variation across breeds. Within breeds, however, the relationship is not negative and is slightly, but significantly, positive in the larger of the two datasets. The negative across-breed relationship is probably the consequence of short life spans in large breeds. Artificial selection for extremely high growth rates in large breeds appears to have led to developmental diseases that seriously diminish longevity.
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Affiliation(s)
- Frietson Galis
- Institute of Biology, Leiden University, 2300 RA Leiden, The Netherlands.
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46
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Runstadler JA, Angles JM, Pedersen NC. Dog leucocyte antigen class II diversity and relationships among indigenous dogs of the island nations of Indonesia (Bali), Australia and New Guinea. ACTA ACUST UNITED AC 2006; 68:418-26. [PMID: 17092255 DOI: 10.1111/j.1399-0039.2006.00696.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The genetic polymorphism at the dog leucocyte antigen (DLA) class II loci DQA1, DQB1 and DRB1 was studied in a large genetically diverse population of feral and wild-type dogs from the large island nations of Indonesia (Bali), Australia and New Guinea (Bali street dog, dingo and New Guinea singing dog, respectively). Sequence-based typing (SBT) of the hypervariable region of DLA-DRB1, -DQA1 and -DQB1 alleles was used to determine genetic diversity. No new DQA1 alleles were recognized among the three dog populations, but five novel DLA-DRB1 and 2 novel DLA-DQB1 allele sequences were detected. Additional unknown alleles were postulated to exist in Bali street dogs, as indicated by the large percentage of individuals (15%-33%) that had indeterminate DRB1, DQA1 and DQB1 alleles by SBT. All three groups of dogs possessed alleles that were relatively uncommon in conventional purebreds. The New Guinea singing dog and dingo shared alleles that were not present in the Bali street dogs. These findings suggested that the dingo was more closely related to indigenous dogs from New Guinea. Feral dog populations, in particular large ones such as that of Bali, show genetic diversity that existed prior to phenotypic selection for breeds originating from their respective regions. This diversity needs to be identified and maintained in the face of progressive Westernization. These populations deserve further study as potential model populations for the evolution of major histocompatibility complex alleles, for the study of canine genetic diversity, for the development of dog breeds and for studies on the comigration of ancestral human and dog populations.
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Affiliation(s)
- J A Runstadler
- Center for Veterinary Genetics, School of Veterinary Medicine, University of California, Davis, CA, USA.
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47
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Natanaelsson C, Oskarsson MCR, Angleby H, Lundeberg J, Kirkness E, Savolainen P. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery. BMC Genet 2006; 7:45. [PMID: 17026745 PMCID: PMC1630699 DOI: 10.1186/1471-2156-7-45] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 10/06/2006] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. RESULTS The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. CONCLUSION We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and giving a first description of the dog Y-chromosome phylogeny.
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Affiliation(s)
- Christian Natanaelsson
- School of Biotechnology, KTH, Royal Institute of Technology, AlbaNova University Center, 10691 Stockholm, Sweden
| | - Mattias CR Oskarsson
- School of Biotechnology, KTH, Royal Institute of Technology, AlbaNova University Center, 10691 Stockholm, Sweden
| | - Helen Angleby
- School of Biotechnology, KTH, Royal Institute of Technology, AlbaNova University Center, 10691 Stockholm, Sweden
| | - Joakim Lundeberg
- School of Biotechnology, KTH, Royal Institute of Technology, AlbaNova University Center, 10691 Stockholm, Sweden
| | - Ewen Kirkness
- The Institute for Genomic Research (TIGR), Rockville, MD 20850, USA
| | - Peter Savolainen
- School of Biotechnology, KTH, Royal Institute of Technology, AlbaNova University Center, 10691 Stockholm, Sweden
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48
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Meadows JRS, Hanotte O, Drögemüller C, Calvo J, Godfrey R, Coltman D, Maddox JF, Marzanov N, Kantanen J, Kijas JW. Globally dispersed Y chromosomal haplotypes in wild and domestic sheep. Anim Genet 2006; 37:444-53. [PMID: 16978172 DOI: 10.1111/j.1365-2052.2006.01496.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To date, investigations of genetic diversity and the origins of domestication in sheep have utilised autosomal microsatellites and variation in the mitochondrial genome. We present the first analysis of both domestic and wild sheep using genetic markers residing on the ovine Y chromosome. Analysis of a single nucleotide polymorphism (oY1) in the SRY promoter region revealed that allele A-oY1 was present in all wild bighorn sheep (Ovis canadensis), two subspecies of thinhorn sheep (Ovis dalli), European Mouflon (Ovis musimon) and the Barbary (Ammontragis lervia). A-oY1 also had the highest frequency (71.4%) within 458 domestic sheep drawn from 65 breeds sampled from Africa, Asia, Australia, the Caribbean, Europe, the Middle East and Central Asia. Sequence analysis of a second locus, microsatellite SRYM18, revealed a compound repeat array displaying fixed differences, which identified bighorn and thinhorn sheep as distinct from the European Mouflon and domestic animals. Combined genotypic data identified 11 male-specific haplotypes that represented at least two separate lineages. Investigation of the geographical distribution of each haplotype revealed that one (H6) was both very common and widespread in the global sample of domestic breeds. The remaining haplotypes each displayed more restricted and informative distributions. For example, H5 was likely founded following the domestication of European breeds and was used to trace the recent transportation of animals to both the Caribbean and Australia. A high rate of Y chromosomal dispersal appears to have taken place during the development of domestic sheep as only 12.9% of the total observed variation was partitioned between major geographical regions.
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Affiliation(s)
- J R S Meadows
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia 4067, Australia
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49
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Handley LJL, Berset-Brändli L, Perrin N. Disentangling reasons for low Y chromosome variation in the greater white-toothed shrew (Crocidura russula). Genetics 2006; 173:935-42. [PMID: 16582448 PMCID: PMC1526517 DOI: 10.1534/genetics.105.050203] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Y chromosome variation is determined by several confounding factors including mutation rate, effective population size, demography, and selection. Disentangling these factors is essential to better understand the evolutionary properties of the Y chromosome. We analyzed genetic variation on the Y chromosome, X chromosome, and mtDNA of the greater white-toothed shrew, a species with low variance in male reproductive success and limited sex-biased dispersal, which enables us to control to some extent for life-history effects. We also compared ancestral (Moroccan) to derived (European) populations to investigate the role of demographic history in determining Y variation. Recent colonization of Europe by a small number of founders (combined with low mutation rates) is largely responsible for low diversity observed on the European Y and X chromosomes compared to mtDNA. After accounting for mutation rate, copy number, and demography, the Y chromosome still displays a deficit in variation relative to the X in both populations. This is possibly influenced by directional selection, but the slightly higher variance in male reproductive success is also likely to play a role, even though the difference is small compared to that in highly polygynous species. This study illustrates that demography and life-history effects should be scrutinized before inferring strong selective pressure as a reason for low diversity on the Y chromosome.
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Affiliation(s)
- Lori J Lawson Handley
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland.
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50
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Thomas R, Scott A, Langford CF, Fosmire SP, Jubala CM, Lorentzen TD, Hitte C, Karlsson EK, Kirkness E, Ostrander EA, Galibert F, Lindblad-Toh K, Modiano JF, Breen M. Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors. Genome Res 2006; 15:1831-7. [PMID: 16339382 PMCID: PMC1356122 DOI: 10.1101/gr.3825705] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recognition of the domestic dog as a model for the comparative study of human genetic traits has led to major advances in canine genomics. The pathophysiological similarities shared between many human and dog diseases extend to a range of cancers. Human tumors frequently display recurrent chromosome aberrations, many of which are hallmarks of particular tumor subtypes. Using a range of molecular cytogenetic techniques we have generated evidence indicating that this is also true of canine tumors. Detailed knowledge of these genomic abnormalities has the potential to aid diagnosis, prognosis, and the selection of appropriate therapy in both species. We recently improved the efficiency and resolution of canine cancer cytogenetics studies by developing a small-scale genomic microarray comprising a panel of canine BAC clones representing subgenomic regions of particular interest. We have now extended these studies to generate a comprehensive canine comparative genomic hybridization (CGH) array that comprises 1158 canine BAC clones ordered throughout the genome with an average interval of 2 Mb. Most of the clones (84.3%) have been assigned to a precise cytogenetic location by fluorescence in situ hybridization (FISH), and 98.5% are also directly anchored within the current canine genome assembly, permitting direct translation from cytogenetic aberration to DNA sequence. We are now using this resource routinely for high-throughput array CGH and single-locus probe analysis of a range of canine cancers. Here we provide examples of the varied applications of this resource to tumor cytogenetics, in combination with other molecular cytogenetic techniques.
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Affiliation(s)
- Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina 27606, USA
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