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Subramanian S, Kumar M. The Association between the Abundance of Homozygous Deleterious Variants and the Morbidity of Dog Breeds. BIOLOGY 2024; 13:574. [PMID: 39194512 DOI: 10.3390/biology13080574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/26/2024] [Accepted: 07/27/2024] [Indexed: 08/29/2024]
Abstract
It is well known that highly inbred dogs are more prone to diseases than less inbred or outbred dogs. This is because inbreeding increases the load of recessive deleterious variants. Using the genomes of 392 dogs belonging to 83 breeds, we investigated the association between the abundance of homozygous deleterious variants and dog health. We used the number of non-routine veterinary care events for each breed to assess the level of morbidity. Our results revealed a highly significant positive relationship between the number of homozygous deleterious variants located within the runs of homozygosity (RoH) tracts of the breeds and the level of morbidity. The dog breeds with low morbidity had a mean of 87 deleterious SNVs within the RoH, but those with very high morbidity had 187 SNVs. A highly significant correlation was also observed for the loss-of-function (LoF) SNVs within RoH tracts. The dog breeds that required more veterinary care had 2.3 times more homozygous LoF SNVs than those that required less veterinary care (112 vs. 50). The results of this study could be useful for understanding the disease burden on breed dogs and as a guide for dog breeding programs.
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Affiliation(s)
- Sankar Subramanian
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
- School of Science, Technology, and Engineering, University of the Sunshine Coast, Moreton Bay, QLD 4502, Australia
| | - Manoharan Kumar
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD 4502, Australia
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2
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Shastak Y, Pelletier W. Pet Wellness and Vitamin A: A Narrative Overview. Animals (Basel) 2024; 14:1000. [PMID: 38612239 PMCID: PMC11010875 DOI: 10.3390/ani14071000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
The health of companion animals, particularly dogs and cats, is significantly influenced by nutrition, with vitamins playing a crucial role. Vitamin A, in particular, is indispensable, with diverse roles ranging from vision to immune modulation and reproduction. Despite its importance, the metabolism and dietary requirements of vitamin A in companion animals remain complex and not fully understood. This review provides a comprehensive overview of the historical perspective, the digestion, the metabolism, the physiological roles, the deficiency, the excess, and the interactions with other micronutrients of vitamin A in companion animals. Additionally, it highlights future research directions and gaps in our understanding. Insights into the metabolism of vitamin A in companion animals, personalized nutrition strategies based on genetic variability, longitudinal studies tracking the status of vitamin A, and investigations into its immunomodulatory effects are crucial for optimizing pet health and wellness. Furthermore, understanding the stability and bioavailability of vitamin A in pet food formulations is essential for ensuring the provision of adequate micronutrients. Overall, this review underscores the importance of vitamin A in companion animal nutrition and the need for further research to enhance our understanding and to optimize dietary recommendations for pet health and well-being.
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Affiliation(s)
- Yauheni Shastak
- Nutrition & Health Division, BASF SE, 67063 Ludwigshafen am Rhein, Germany
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3
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Leeb T. Special Issue: "Canine Genetics 2". Genes (Basel) 2023; 14:1930. [PMID: 37895280 PMCID: PMC10606197 DOI: 10.3390/genes14101930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Wolves were the first animal species to become domesticated by humans, approximately 30,000-50,000 years ago. Human-directed dog breeding over thousands of generations has generated more than 350 recognized breeds displaying surprisingly different phenotypes with respect to morphology, behavior and disease predispositions. The domestication of wolves and the subsequent breeding of dogs can be viewed as one of humankind's oldest and largest genetic experiments and provides us with unique opportunities for research. Dogs have not only become human's best friend but were also described as geneticists' best friend in a past issue of Science. In recognition of the importance of canine genetics, this Special Issue, entitled "Canine Genetics 2", was compiled. It represents a sequel to the former Special Issue "Canine Genetics", which was published in 2019. During the last 15 years, the canine community has heavily relied on a reference genome derived from the female Boxer Tasha. "Canine Genetics 2" includes an article describing a greatly improved version of this important community resource. This Special Issue further contains several reports related to monogenic or complex inherited diseases in dogs. Finally, important aspects of wild canid research, genetic diversity in different populations and canine morphology were investigated.
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Affiliation(s)
- Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
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4
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Bionda A, Cortellari M, Liotta L, Crepaldi P. The Shepherd and the Hunter: A Genomic Comparison of Italian Dog Breeds. Animals (Basel) 2023; 13:2438. [PMID: 37570247 PMCID: PMC10417656 DOI: 10.3390/ani13152438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Shepherd and hunting dogs have undergone divergent selection for specific tasks, resulting in distinct phenotypic and behavioural differences. Italy is home to numerous recognized and unrecognized breeds of both types, providing an opportunity to compare them genomically. In this study, we analysed SNP data obtained from the CanineHD BeadChip, encompassing 116 hunting dogs (representing 6 breeds) and 158 shepherd dogs (representing 9 breeds). We explored the population structure, genomic background, and phylogenetic relationships among the breeds. To compare the two groups, we employed three complementary methods for selection signature detection: FST, XP-EHH, and ROH. Our results reveal a clear differentiation between shepherd and hunting dogs as well as between gun dogs vs. hounds and guardian vs. herding shepherd dogs. The genomic regions distinguishing these groups harbour several genes associated with domestication and behavioural traits, including gregariousness (WBSRC17) and aggressiveness (CDH12 and HTT). Additionally, genes related to morphology, such as size and coat colour (ASIP and TYRP1) and texture (RSPO2), were identified. This comparative genomic analysis sheds light on the genetic underpinnings of the phenotypic and behavioural variations observed in Italian hunting and shepherd dogs.
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Affiliation(s)
- Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
| | - Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, University of Messina, Viale Palatucci 13, 98168 Messina, Italy;
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali—Produzione, Territorio, Agroenergia, University of Milano, Via Celoria 2, 20133 Milano, Italy; (A.B.); (P.C.)
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5
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Son KH, Aldonza MBD, Nam AR, Lee KH, Lee JW, Shin KJ, Kang K, Cho JY. Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies. SCIENCE ADVANCES 2023; 9:eade3399. [PMID: 37406108 DOI: 10.1126/sciadv.ade3399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 06/02/2023] [Indexed: 07/07/2023]
Abstract
Dogs have become a valuable model in exploring multifaceted diseases and biology relevant to human health. Despite large-scale dog genome projects producing high-quality draft references, a comprehensive annotation of functional elements is still lacking. We addressed this through integrative next-generation sequencing of transcriptomes paired with five histone marks and DNA methylome profiling across 11 tissue types, deciphering the dog's epigenetic code by defining distinct chromatin states, super-enhancer, and methylome landscapes, and thus showed that these regions are associated with a wide range of biological functions and cell/tissue identity. In addition, we confirmed that the phenotype-associated variants are enriched in tissue-specific regulatory regions and, therefore, the tissue of origin of the variants can be traced. Ultimately, we delineated conserved and dynamic epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog that can be used for comparative biology and medical research.
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Affiliation(s)
- Keun Hong Son
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Mark Borris D Aldonza
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - A-Reum Nam
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Kang-Hoon Lee
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Jeong-Woon Lee
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Kyung-Ju Shin
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, Korea
| | - Je-Yoel Cho
- Department of Biochemistry, College of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine and Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul, Korea
- BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
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6
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Benítez-Burraco A, Pörtl D, Jung C. Did Dog Domestication Contribute to Language Evolution? Front Psychol 2021; 12:695116. [PMID: 34589022 PMCID: PMC8473740 DOI: 10.3389/fpsyg.2021.695116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022] Open
Abstract
Different factors seemingly account for the emergence of present-day languages in our species. Human self-domestication has been recently invoked as one important force favoring language complexity mostly via a cultural mechanism. Because our self-domestication ultimately resulted from selection for less aggressive behavior and increased prosocial behavior, any evolutionary or cultural change impacting on aggression levels is expected to have fostered this process. Here, we hypothesize about a parallel domestication of humans and dogs, and more specifically, about a positive effect of our interaction with dogs on human self-domestication, and ultimately, on aspects of language evolution, through the mechanisms involved in the control of aggression. We review evidence of diverse sort (ethological mostly, but also archeological, genetic, and physiological) supporting such an effect and propose some ways of testing our hypothesis.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain
| | - Daniela Pörtl
- Psychiatric Department, Saale-Unstrut Klinikum, Teaching Hospital Leipzig and Jena Universities, Naumburg, Germany
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Berger C, Heinrich J, Berger B, Hecht W, Parson W. Towards Forensic DNA Phenotyping for Predicting Visible Traits in Dogs. Genes (Basel) 2021; 12:genes12060908. [PMID: 34208207 PMCID: PMC8230911 DOI: 10.3390/genes12060908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
The popularity of dogs as human companions explains why these pets regularly come into focus in forensic cases such as bite attacks or accidents. Canine evidence, e.g., dog hairs, can also act as a link between the victim and suspect in a crime case due to the close contact between dogs and their owners. In line with human DNA identification, dog individualization from crime scene evidence is mainly based on the analysis of short tandem repeat (STR) markers. However, when the DNA profile does not match a reference, additional information regarding the appearance of the dog may provide substantial intelligence value. Key features of the dog's appearance, such as the body size and coat colour are well-recognizable and easy to describe even to non-dog experts, including most investigating officers and eyewitnesses. Therefore, it is reasonable to complement eyewitnesses' testimonies with externally visible traits predicted from associated canine DNA samples. Here, the feasibility and suitability of canine DNA phenotyping is explored from scratch in the form of a proof of concept study. To predict the overall appearance of an unknown dog from its DNA as accurately as possible, the following six traits were chosen: (1) coat colour, (2) coat pattern, (3) coat structure, (4) body size, (5) ear shape, and (6) tail length. A total of 21 genetic markers known for high predicting values for these traits were selected from previously published datasets, comprising 15 SNPs and six INDELS. Three of them belonged to SINE insertions. The experiments were designed in three phases. In the first two stages, the performance of the markers was tested on DNA samples from dogs with well-documented physical characteristics from different breeds. The final blind test, including dogs with initially withheld appearance information, showed that the majority of the selected markers allowed to develop composite sketches, providing a realistic impression of the tested dogs. We regard this study as the first attempt to evaluate the possibilities and limitations of forensic canine DNA phenotyping.
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Affiliation(s)
- Cordula Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Correspondence: ; Tel.: +43-512-9003-70640
| | - Josephin Heinrich
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Burkhard Berger
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
| | - Werner Hecht
- Institute of Veterinary Pathology, Justus-Liebig-University Giessen, 35390 Giessen, Germany;
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (J.H.); (B.B.); (W.P.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
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8
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Greco A, Costanza D, Senatore A, Bruzzese D, Micieli F, Chiavaccini L, Di Giancamillo M, Della Valle G, Vesce G, Brunetti A, Meomartino L. A computed tomography-based method for the assessment of canine retrobulbar cone volume for ophthalmic anaesthesia. Vet Anaesth Analg 2021; 48:759-766. [PMID: 34391668 DOI: 10.1016/j.vaa.2021.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 01/01/2021] [Accepted: 03/12/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To develop a comprehensive formula for calculating the volume of local anaesthetic solution used for retrobulbar anaesthesia in dogs with different skull morphologies. STUDY DESIGN Retrospective cohort imaging study. ANIMALS Skull computed tomography (CT) images of 188 dogs of different breeds collected between January 2009 and December 2017. METHODS Anatomical integrity of the orbit and adjacent structures, presenting complaint, clinical signs and CT findings were verified to exclude ocular abnormalities. The volume of the retrobulbar cone of 376 eyes was calculated using CT scans of the dogs' skulls. Additional data recorded included morphology of the skull, body weight, sex and size of the dogs, all of which were matched for possible association to the retrobulbar cone volume through univariable and multivariable linear regression models. Results of linear regression models were expressed as estimated beta coefficients with the corresponding 95% confidence intervals (95% CIs). RESULTS Using univariate analysis, the retrobulbar cone volume was positively associated with weight and male sex. In addition, brachycephalic and dolichocephalic dogs showed a larger retrobulbar cone volume than mesocephalic dogs, while sex was no longer significantly associated with the retrobulbar cone volume. In multivariate analysis, when considering all variables in the model, weight emerged as the strongest predictor (beta coefficient: 0.062 mL kg-1, 95% CI: 0.056-0.067 mL kg-1, p < 0.001). CONCLUSIONS and clinical relevance In the veterinary literature, there is no agreement on the precise volume of local anaesthetic solution that should be used to achieve intraconal retrobulbar anaesthesia in dogs. Here we suggest a formula to calculate the retrobulbar cone volume and, accordingly, the injection volume of local anaesthetic solution for effective retrobulbar anaesthesia.
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Affiliation(s)
- Adelaide Greco
- Centro Interdipartimentale di Radiologia Veterinaria, Università di Napoli 'Federico II', Naples, Italy; Dipartimento di Medicina Veterinaria e Produzioni animali, Università di Napoli 'Federico II', Naples, Italy.
| | - Dario Costanza
- Centro Interdipartimentale di Radiologia Veterinaria, Università di Napoli 'Federico II', Naples, Italy
| | - Andrea Senatore
- Centro Intedipartimentale di Ricerca sui Biomateriali, Università degli Studi di Napoli 'Federico II', Naples, Italy
| | - Dario Bruzzese
- Dipartimento di Sanità Pubblica, Università di Napoli 'Federico II', Naples, Italy
| | - Fabiana Micieli
- Dipartimento di Medicina Veterinaria e Produzioni animali, Università di Napoli 'Federico II', Naples, Italy
| | - Ludovica Chiavaccini
- Department of Molecular and Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Mauro Di Giancamillo
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milan, Italy
| | - Giovanni Della Valle
- Dipartimento di Medicina Veterinaria e Produzioni animali, Università di Napoli 'Federico II', Naples, Italy
| | - Giancarlo Vesce
- Dipartimento di Medicina Veterinaria e Produzioni animali, Università di Napoli 'Federico II', Naples, Italy
| | - Arturo Brunetti
- Dipartimento di Scienze Biomediche Avanzate, Università di Napoli 'Federico II', Naples, Italy
| | - Leonardo Meomartino
- Centro Interdipartimentale di Radiologia Veterinaria, Università di Napoli 'Federico II', Naples, Italy; Dipartimento di Medicina Veterinaria e Produzioni animali, Università di Napoli 'Federico II', Naples, Italy
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9
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Abstract
The domestic dog, as a highly successful domestication model, is well known as a favored human companion. Exploring its domestication history should provide great insight into our understanding of the prehistoric development of human culture and productivity. Furthermore, investigation on the mechanisms underpinning the morphological and behavioral traits associated with canid domestication syndrome is of significance not only for scientific study but also for human medical research. Current development of a multidisciplinary canine genome database, which includes enormous omics data, has substantially improved our understanding of the genetic makeup of dogs. Here, we reviewed recent advances associated with the original history and genetic basis underlying environmental adaptations and phenotypic diversities in domestic dogs, which should provide perspectives on improving the communicative relationship between dogs and humans.
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Affiliation(s)
- Zhe Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Saber Khederzadeh
- State Key Laboratory of Genetic Resources and Evolution, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Yan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China. E-mail:
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10
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Abstract
The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.
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11
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Rosenfeld CS, Hekman JP, Johnson JL, Lyu Z, Ortega MT, Joshi T, Mao J, Vladimirova AV, Gulevich RG, Kharlamova AV, Acland GM, Hecht EE, Wang X, Clark AG, Trut LN, Behura SK, Kukekova AV. Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions. GENES BRAIN AND BEHAVIOR 2019; 19:e12614. [PMID: 31605445 DOI: 10.1111/gbb.12614] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/15/2022]
Abstract
The underlying neurological events accompanying dog domestication remain elusive. To reconstruct the domestication process in an experimental setting, silver foxes (Vulpes vulpes) have been deliberately bred for tame vs aggressive behaviors for more than 50 generations at the Institute for Cytology and Genetics in Novosibirsk, Russia. The hypothalamus is an essential part of the hypothalamic-pituitary-adrenal axis and regulates the fight-or-flight response, and thus, we hypothesized that selective breeding for tameness/aggressiveness has shaped the hypothalamic transcriptomic profile. RNA-seq analysis identified 70 differentially expressed genes (DEGs). Seven of these genes, DKKL1, FBLN7, NPL, PRIMPOL, PTGRN, SHCBP1L and SKIV2L, showed the same direction expression differences in the hypothalamus, basal forebrain and prefrontal cortex. The genes differentially expressed across the three tissues are involved in cell division, differentiation, adhesion and carbohydrate processing, suggesting an association of these processes with selective breeding. Additionally, 159 transcripts from the hypothalamus demonstrated differences in the abundance of alternative spliced forms between the tame and aggressive foxes. Weighted gene coexpression network analyses also suggested that gene modules in hypothalamus were significantly associated with tame vs aggressive behavior. Pathways associated with these modules include signal transduction, interleukin signaling, cytokine-cytokine receptor interaction and peptide ligand-binding receptors (eg, G-protein coupled receptor [GPCR] ligand binding). Current studies show the selection for tameness vs aggressiveness in foxes is associated with unique hypothalamic gene profiles partly shared with other brain regions and highlight DEGs involved in biological processes such as development, differentiation and immunological responses. The role of these processes in fox and dog domestication remains to be determined.
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Affiliation(s)
- Cheryl S Rosenfeld
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri.,Biomedical Sciences, University of Missouri, Columbia, Missouri.,Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, Missouri.,MU Informatics Institute, University of Missouri, Columbia, Missouri
| | - Jessica P Hekman
- Department of Animal Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana, Illinois.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jennifer L Johnson
- Department of Animal Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana, Illinois
| | - Zhen Lyu
- Department of Computer Science, University of Missouri, Columbia, Missouri
| | - Madison T Ortega
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri.,Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Trupti Joshi
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri.,MU Informatics Institute, University of Missouri, Columbia, Missouri.,Department of Computer Science, University of Missouri, Columbia, Missouri.,Department of Health Management and Informatics, University of Missouri, Columbia, Missouri
| | - Jiude Mao
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri.,Biomedical Sciences, University of Missouri, Columbia, Missouri
| | - Anastasiya V Vladimirova
- The Laboratory of Evolutionary Genetics, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Rimma G Gulevich
- The Laboratory of Evolutionary Genetics, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya V Kharlamova
- The Laboratory of Evolutionary Genetics, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Gregory M Acland
- Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, New York
| | - Erin E Hecht
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Xu Wang
- Department of Pathobiology, Auburn University, College of Veterinary Medicine, Auburn, Alabama
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
| | - Lyudmila N Trut
- The Laboratory of Evolutionary Genetics, Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Susanta K Behura
- MU Informatics Institute, University of Missouri, Columbia, Missouri.,Division of Animal Sciences, University of Missouri, Columbia, Missouri
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer, and Environmental Sciences, University of Illinois, Urbana, Illinois
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12
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Clark H, Elsherif MM, Leavens DA. Ontogeny vs. phylogeny in primate/canid comparisons: A meta-analysis of the object choice task. Neurosci Biobehav Rev 2019; 105:178-189. [PMID: 31170434 DOI: 10.1016/j.neubiorev.2019.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/25/2019] [Accepted: 06/02/2019] [Indexed: 10/26/2022]
Abstract
The Object Choice Task (OCT) is a widely used paradigm with which researchers measure the ability of a subject to comprehend deictic (directional) cues, such as pointing gestures and eye gaze. There is a widespread belief that nonhuman primates evince only a weak capacity to use deictic cues; in contrast, domestic dogs (Canis lupus familiaris) tend to demonstrate high success rates. This pattern of canid superiority has been taken to support the Domestication Hypothesis, which posits enhancing effects of artificial selection on the sociocognitive abilities of dogs and humans. Here we review nearly two decades of published findings, using variants of the OCT. We find systematic confounds with species classification in task-relevant preparation of the subjects, in the imposition of a barrier between reward and subject, and in the specific deictic cues used to indicate the location of hidden objects. Thus, the widespread belief that dogs outperform primates on OCTs is undermined by the systematic procedural differences in the assessments of these skills, differences that are confounded with taxonomic classification.
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Affiliation(s)
- Hannah Clark
- School of Psychology, University of Sussex, Falmer, East Sussex, BN1 9QH, United Kingdom
| | - Mahmoud M Elsherif
- School of Psychology, University of Sussex, Falmer, East Sussex, BN1 9QH, United Kingdom; School of Psychology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - David A Leavens
- School of Psychology, University of Sussex, Falmer, East Sussex, BN1 9QH, United Kingdom.
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13
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Andreis ME, Polito U, Veronesi MC, Faustini M, Di Giancamillo M, Modina SC. Novel contributions in canine craniometry: Anatomic and radiographic measurements in newborn puppies. PLoS One 2018; 13:e0196959. [PMID: 29738556 PMCID: PMC5940217 DOI: 10.1371/journal.pone.0196959] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 04/23/2018] [Indexed: 12/14/2022] Open
Abstract
The largest differences in intraspecific head shape among the Carnivora order are to be found in dogs. Based on their skull morphotypes, dog breeds are currently classified as dolichocephalic, mesaticephalic and brachycephalic. Due to the fact that some breeds have not been yet defined, this classification is incomplete; moreover, multi-breed studies on the skull morphology of puppies have never been performed. The aim of this work was to verify (i) whether differences in the skull conformation of purebred puppies are already present within the first week of age; (ii) whether radiographic and anatomic measures could be considered interchangeable, and (iii) to possibly classify puppies from non-categorized breeds thanks to their radiographic cranial measurements using neural nets. One hundred and thirty-seven dead puppies aged 0–7 days were examined considering their anatomic and radiographic measures. All linear measures and anatomic indices significantly differed among brachycephalic and non-brachycephalic puppies. Radiographic indices, with the exception of CI, identified the three skull morphotypes (p<0.05, for all comparisons). Radiographic and anatomic measures proved to be non-interchangeable in newborn puppies. Finally, nineteen puppies belonging to 5 non-categorized breeds could be classified thanks to neural nets in the three skull morphotypes with different probability (P between 0,66 and 0,95).
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Affiliation(s)
- Maria Elena Andreis
- Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, Milano, Italy
| | - Umberto Polito
- Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, Milano, Italy
| | | | - Massimo Faustini
- Department of Veterinary Medicine, Università degli Studi di Milano, Milano, Italy
| | - Mauro Di Giancamillo
- Department of Veterinary Medicine, Università degli Studi di Milano, Milano, Italy
- * E-mail:
| | - Silvia C. Modina
- Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, Milano, Italy
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Parker HG, Harris A, Dreger DL, Davis BW, Ostrander EA. The bald and the beautiful: hairlessness in domestic dog breeds. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0488. [PMID: 27994129 PMCID: PMC5182420 DOI: 10.1098/rstb.2015.0488] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 11/12/2022] Open
Abstract
An extraordinary amount of genomic variation is contained within the chromosomes of domestic dogs, manifesting as dramatic differences in morphology, behaviour and disease susceptibility. Morphology, in particular, has been a topic of enormous interest as biologists struggle to understand the small window of dog domestication from wolves, and the division of dogs into pure breeding, closed populations termed breeds. Many traits related to morphology, including body size, leg length and skull shape, have been under selection as part of the standard descriptions for the nearly 400 breeds recognized worldwide. Just as important, however, are the minor traits that have undergone selection by fanciers and breeders to define dogs of a particular appearance, such as tail length, ear position, back arch and variation in fur (pelage) growth patterns. In this paper, we both review and present new data for traits associated with pelage including fur length, curl, growth, shedding and even the presence or absence of fur. Finally, we report the discovery of a new gene associated with the absence of coat in the American Hairless Terrier breed.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander Harris
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dayna L Dreger
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brian W Davis
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Ostrander EA, Wayne RK, Freedman AH, Davis BW. Demographic history, selection and functional diversity of the canine genome. Nat Rev Genet 2017; 18:705-720. [DOI: 10.1038/nrg.2017.67] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Jain S, Aresu L, Comazzi S, Shi J, Worrall E, Clayton J, Humphries W, Hemmington S, Davis P, Murray E, Limeneh AA, Ball K, Ruckova E, Muller P, Vojtesek B, Fahraeus R, Argyle D, Hupp TR. The Development of a Recombinant scFv Monoclonal Antibody Targeting Canine CD20 for Use in Comparative Medicine. PLoS One 2016; 11:e0148366. [PMID: 26894679 PMCID: PMC4760772 DOI: 10.1371/journal.pone.0148366] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 01/19/2016] [Indexed: 01/08/2023] Open
Abstract
Monoclonal antibodies are leading agents for therapeutic treatment of human diseases, but are limited in use by the paucity of clinically relevant models for validation. Sporadic canine tumours mimic the features of some human equivalents. Developing canine immunotherapeutics can be an approach for modeling human disease responses. Rituximab is a pioneering agent used to treat human hematological malignancies. Biologic mimics that target canine CD20 are just being developed by the biotechnology industry. Towards a comparative canine-human model system, we have developed a novel anti-CD20 monoclonal antibody (NCD1.2) that binds both human and canine CD20. NCD1.2 has a sub-nanomolar Kd as defined by an octet red binding assay. Using FACS, NCD1.2 binds to clinically derived canine cells including B-cells in peripheral blood and in different histotypes of B-cell lymphoma. Immunohistochemical staining of canine tissues indicates that the NCD1.2 binds to membrane localized cells in Diffuse Large B-cell lymphoma, Marginal Zone Lymphoma, and other canine B-cell lymphomas. We cloned the heavy and light chains of NCD1.2 from hybridomas to determine whether active scaffolds can be acquired as future biologics tools. The VH and VL genes from the hybridomas were cloned using degenerate primers and packaged as single chains (scFv) into a phage-display library. Surprisingly, we identified two scFv (scFv-3 and scFv-7) isolated from the hybridoma with bioactivity towards CD20. The two scFv had identical VH genes but different VL genes and identical CDR3s, indicating that at least two light chain mRNAs are encoded by NCD1.2 hybridoma cells. Both scFv-3 and scFv-7 were cloned into mammalian vectors for secretion in CHO cells and the antibodies were bioactive towards recombinant CD20 protein or peptide. The scFv-3 and scFv-7 were cloned into an ADEPT-CPG2 bioconjugate vector where bioactivity was retained when expressed in bacterial systems. These data identify a recombinant anti-CD20 scFv that might form a useful tool for evaluation in bioconjugate-directed anti-CD20 immunotherapies in comparative medicine.
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Affiliation(s)
- Saurabh Jain
- University of Edinburgh, Institute of Genetic and Molecular Medicine and School of Veterinary Medicine, Edinburgh, EH4 2XR, United Kingdom
| | - Luca Aresu
- Dipartimento di Biomedicina Comparata e Alimentazione (BCA) Department of Comparative Biomedicine and Food Science, Università di Padova 35020 Legnaro (PD), Italy
| | - Stefano Comazzi
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
| | - Jianguo Shi
- University of Edinburgh, Institute of Genetic and Molecular Medicine and School of Veterinary Medicine, Edinburgh, EH4 2XR, United Kingdom
| | - Erin Worrall
- University of Edinburgh, Institute of Genetic and Molecular Medicine and School of Veterinary Medicine, Edinburgh, EH4 2XR, United Kingdom
| | - John Clayton
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedford, MK44 2YP, United Kingdom
| | - William Humphries
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedford, MK44 2YP, United Kingdom
| | - Sandra Hemmington
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedford, MK44 2YP, United Kingdom
| | - Paul Davis
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedford, MK44 2YP, United Kingdom
| | - Euan Murray
- University of Edinburgh, Institute of Genetic and Molecular Medicine and School of Veterinary Medicine, Edinburgh, EH4 2XR, United Kingdom
- INSERM Unité 940, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St Louis, 27 rue Juliette Dodu, Paris, France
| | - Asmare A. Limeneh
- Bahit Dar University College of Medicine and Health Sciences Department of Medical Biochemistry and Molecular Biology, Bahir Dar, Ethiopia
| | - Kathryn Ball
- University of Edinburgh, Institute of Genetic and Molecular Medicine and School of Veterinary Medicine, Edinburgh, EH4 2XR, United Kingdom
| | - Eva Ruckova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Petr Muller
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Borek Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Robin Fahraeus
- INSERM Unité 940, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St Louis, 27 rue Juliette Dodu, Paris, France
| | - David Argyle
- University of Edinburgh, Institute of Genetic and Molecular Medicine and School of Veterinary Medicine, Edinburgh, EH4 2XR, United Kingdom
| | - Ted R. Hupp
- University of Edinburgh, Institute of Genetic and Molecular Medicine and School of Veterinary Medicine, Edinburgh, EH4 2XR, United Kingdom
- * E-mail:
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Diaz RE, Trainor PA. Hand/foot splitting and the 're-evolution' of mesopodial skeletal elements during the evolution and radiation of chameleons. BMC Evol Biol 2015; 15:184. [PMID: 26382964 PMCID: PMC4574539 DOI: 10.1186/s12862-015-0464-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/21/2015] [Indexed: 01/07/2023] Open
Abstract
Background One of the most distinctive traits found within Chamaeleonidae is their split/cleft autopodia and the simplified and divergent morphology of the mesopodial skeleton. These anatomical characteristics have facilitated the adaptive radiation of chameleons to arboreal niches. To better understand the homology of chameleon carpal and tarsal elements, the process of syndactyly, cleft formation, and how modification of the mesopodial skeleton has played a role in the evolution and diversification of chameleons, we have studied the Veiled Chameleon (Chamaeleo calyptratus). We analysed limb patterning and morphogenesis through in situ hybridization, in vitro whole embryo culture and pharmacological perturbation, scoring for apoptosis, clefting, and skeletogenesis. Furthermore, we framed our data within a phylogenetic context by performing comparative skeletal analyses in 8 of the 12 currently recognized genera of extant chameleons. Results Our study uncovered a previously underappreciated degree of mesopodial skeletal diversity in chameleons. Phylogenetically derived chameleons exhibit a ‘typical’ outgroup complement of mesopodial elements (with the exception of centralia), with twice the number of currently recognized carpal and tarsal elements considered for this clade. In contrast to avians and rodents, mesenchymal clefting in chameleons commences in spite of the maintenance of a robust apical ectodermal ridge (AER). Furthermore, Bmp signaling appears to be important for cleft initiation but not for maintenance of apoptosis. Interdigital cell death therefore may be an ancestral characteristic of the autopodium, however syndactyly is an evolutionary novelty. In addition, we find that the pisiform segments from the ulnare and that chameleons lack an astragalus-calcaneum complex typical of amniotes and have evolved an ankle architecture convergent with amphibians in phylogenetically higher chameleons. Conclusion Our data underscores the importance of comparative and phylogenetic approaches when studying development. Body size may have played a role in the characteristic mesopodial skeletal architecture of chameleons by constraining deployment of the skeletogenic program in the smaller and earliest diverged and basal taxa. Our study challenges the ‘re-evolution’ of osteological features by showing that ‘re-evolving’ a ‘lost’ feature de novo (contrary to Dollo’s Law) may instead be due to so called ‘missing structures’ being present but underdeveloped and/or fused to other adjacent elements (cryptic features) whose independence may be re-established under changes in adaptive selective pressure. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0464-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raul E Diaz
- Department of Biology, La Sierra University, Riverside, CA, 92515, USA. .,Natural History Museum of Los Angeles County, Los Angeles, CA, 90007, USA.
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA. .,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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18
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Abstract
Although most modern dog breeds are less than 200 years old, the symbiosis between man and dog is ancient. Since prehistoric times, repeated selection events have transformed the wolf into man's guardians, laborers, athletes, and companions. The rapid transformation from pack predator to loyal companion is a feat that is arguably unique among domesticated animals. How this transformation came to pass remained a biological mystery until recently: Within the past decade, the deployment of genomic approaches to study population structure, detect signatures of selection, and identify genetic variants that underlie canine phenotypes is ushering into focus novel biological mechanisms that make dogs remarkable. Ironically, the very practices responsible for breed formation also spurned morbidity; today, many diseases are correlated with breed identity. In this review, we discuss man's best friend in the context of a genetic model to understand paradigms of heritable phenotypes, both desirable and disadvantageous.
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Affiliation(s)
- Jeffrey J Schoenebeck
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland 20892;
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19
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Stindl R. The telomeric sync model of speciation: species-wide telomere erosion triggers cycles of transposon-mediated genomic rearrangements, which underlie the saltatory appearance of nonadaptive characters. Naturwissenschaften 2014; 101:163-86. [PMID: 24493020 PMCID: PMC3935097 DOI: 10.1007/s00114-014-1152-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 01/13/2014] [Accepted: 01/16/2014] [Indexed: 12/16/2022]
Abstract
Charles Darwin knew that the fossil record is not overwhelmingly supportive of genetic and phenotypic gradualism; therefore, he developed the core of his theory on the basis of breeding experiments. Here, I present evidence for the existence of a cell biological mechanism that strongly points to the almost forgotten European concept of saltatory evolution of nonadaptive characters, which is in perfect agreement with the gaps in the fossil record. The standard model of chromosomal evolution has always been handicapped by a paradox, namely, how speciation can occur by spontaneous chromosomal rearrangements that are known to decrease the fertility of heterozygotes in a population. However, the hallmark of almost all closely related species is a differing chromosome complement and therefore chromosomal rearrangements seem to be crucial for speciation. Telomeres, the caps of eukaryotic chromosomes, erode in somatic tissues during life, but have been thought to remain stable in the germline of a species. Recently, a large human study spanning three healthy generations clearly found a cumulative telomere effect, which is indicative of transgenerational telomere erosion in the human species. The telomeric sync model of speciation presented here is based on telomere erosion between generations, which leads to identical fusions of chromosomes and triggers a transposon-mediated genomic repatterning in the germline of many individuals of a species. The phenotypic outcome of the telomere-triggered transposon activity is the saltatory appearance of nonadaptive characters simultaneously in many individuals. Transgenerational telomere erosion is therefore the material basis of aging at the species level.
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Affiliation(s)
- Reinhard Stindl
- apo-med-center, Alpharm GesmbH, Plättenstrasse 7-9, 2380, Perchtoldsdorf, Austria,
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20
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Rimbault M, Beale HC, Schoenebeck JJ, Hoopes BC, Allen JJ, Kilroy-Glynn P, Wayne RK, Sutter NB, Ostrander EA. Derived variants at six genes explain nearly half of size reduction in dog breeds. Genome Res 2013; 23:1985-95. [PMID: 24026177 PMCID: PMC3847769 DOI: 10.1101/gr.157339.113] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Selective breeding of dogs by humans has generated extraordinary diversity in body size. A number of multibreed analyses have been undertaken to identify the genetic basis of this diversity. We analyzed four loci discovered in a previous genome-wide association study that used 60,968 SNPs to identify size-associated genomic intervals, which were too large to assign causative roles to genes. First, we performed fine-mapping to define critical intervals that included the candidate genes GHR, HMGA2, SMAD2, and STC2, identifying five highly associated markers at the four loci. We hypothesize that three of the variants are likely to be causative. We then genotyped each marker, together with previously reported size-associated variants in the IGF1 and IGF1R genes, on a panel of 500 domestic dogs from 93 breeds, and identified the ancestral allele by genotyping the same markers on 30 wild canids. We observed that the derived alleles at all markers correlated with reduced body size, and smaller dogs are more likely to carry derived alleles at multiple markers. However, breeds are not generally fixed at all markers; multiple combinations of genotypes are found within most breeds. Finally, we show that 46%–52.5% of the variance in body size of dog breeds can be explained by seven markers in proximity to exceptional candidate genes. Among breeds with standard weights <41 kg (90 lb), the genotypes accounted for 64.3% of variance in weight. This work advances our understanding of mammalian growth by describing genetic contributions to canine size determination in non-giant dog breeds.
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Affiliation(s)
- Maud Rimbault
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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21
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Abstract
A dog's craniofacial diversity is the result of continual human intervention in natural selection, a process that began tens of thousands of years ago. To date, we know little of the genetic underpinnings and developmental mechanisms that make dog skulls so morphologically plastic. In this Perspectives, we discuss the origins of dog skull shapes in terms of history and biology and highlight recent advances in understanding the genetics of canine skull shapes. Of particular interest are those molecular genetic changes that are associated with the development of distinct breeds.
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22
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Hall NJ, Wynne CDL. The canid genome: behavioral geneticists' best friend? GENES BRAIN AND BEHAVIOR 2012; 11:889-902. [DOI: 10.1111/j.1601-183x.2012.00851.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 06/12/2012] [Accepted: 09/04/2012] [Indexed: 12/27/2022]
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23
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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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French AT, Ogden R, Eland C, Hemani G, Pong-Wong R, Corcoran B, Summers KM. Genome-wide analysis of mitral valve disease in Cavalier King Charles Spaniels. Vet J 2012; 193:283-6. [DOI: 10.1016/j.tvjl.2011.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 07/20/2011] [Accepted: 09/19/2011] [Indexed: 12/13/2022]
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Megens HJ, Groenen MAM. Domesticated species form a treasure-trove for molecular characterization of Mendelian traits by exploiting the specific genetic structure of these species in across-breed genome wide association studies. Heredity (Edinb) 2012; 109:1-3. [PMID: 22395158 DOI: 10.1038/hdy.2011.128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Evolutionary genomics of dog domestication. Mamm Genome 2012; 23:3-18. [DOI: 10.1007/s00335-011-9386-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 11/29/2011] [Indexed: 01/07/2023]
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27
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Hahn NM, Bonney PL, Dhawan D, Jones DR, Balch C, Guo Z, Hartman-Frey C, Fang F, Parker HG, Kwon EM, Ostrander EA, Nephew KP, Knapp DW. Subcutaneous 5-azacitidine treatment of naturally occurring canine urothelial carcinoma: a novel epigenetic approach to human urothelial carcinoma drug development. J Urol 2012; 187:302-9. [PMID: 22099988 PMCID: PMC3508763 DOI: 10.1016/j.juro.2011.09.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Indexed: 12/23/2022]
Abstract
PURPOSE We determined the efficacy, biological activity, pharmacokinetics and safety of the hypomethylating agent 5-azacitidine (Celgene Corp., Summit, New Jersey) in dogs with naturally occurring invasive urothelial carcinoma. MATERIALS AND METHODS We performed a preclinical phase I trial in dogs with naturally occurring invasive urothelial carcinoma to examine once daily subcutaneous administration of 5-azacitidine in 28-day cycles at doses of 0.10 to 0.30 mg/kg per day according to 2 dose schedules, including days 1 to 5 (28-day cohort) or days 1 to 5 and 15 to 19 (14-day cohort). Clinical efficacy was assessed by serial cystosonography, radiography and cystoscopy. Urinary 5-azacitidine pharmacokinetic analysis was also done. Pretreatment and posttreatment peripheral blood mononuclear cell and invasive urothelial carcinoma DNA, respectively, was analyzed for global and gene specific [CDKN2A (p14ARF)] methylation changes. RESULTS Enrolled in the study were 19 dogs with naturally occurring invasive urothelial carcinoma. In the 28-day cohort the maximum tolerated dose was 0.20 mg/kg per day with higher doses resulting in grade 3 or 4 neutropenia in 4 of 6 dogs. In the 14-day cohort the maximum tolerated dose was 0.10 mg/kg per day with grade 3 or 4 neutropenia seen in 2 of 3 dogs treated at higher doses. No grade 3 or 4 nonhematological toxicity was observed during either dosing schedule. Of 18 dogs evaluable for tumor response partial remission, stable disease and progressive disease were observed in 4 (22.2%), 9 (50.0%) and 4 (22.2%), respectively. Consistent 5-azacitidine levels (205 to 857 ng/ml) were detected in urine. Pretreatment and posttreatment methylation analysis revealed no significant correlation with clinical response. CONCLUSIONS Subcutaneous 5-azacitidine showed promising clinical activity in a canine invasive urothelial carcinoma model, thus meriting further development in humans with urothelial carcinoma.
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Affiliation(s)
- Noah M Hahn
- Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana 46202, USA.
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Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genet 2011; 7:e1002316. [PMID: 22022279 PMCID: PMC3192833 DOI: 10.1371/journal.pgen.1002316] [Citation(s) in RCA: 273] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 07/30/2011] [Indexed: 12/30/2022] Open
Abstract
The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease. There are hundreds of dog breeds that exhibit massive differences in appearance and behavior sculpted by tightly controlled selective breeding. This large-scale natural experiment has provided an ideal resource that geneticists can use to search for genetic variants that control these differences. With this goal, we developed a high-density array that surveys variable sites at more than 170,000 positions in the dog genome and used it to analyze genetic variation in 46 breeds. We identify 44 chromosomal regions that are extremely variable between breeds and are likely to control many of the traits that vary between them, including curly tails and sociality. Many other regions also bear the signature of strong artificial selection. We characterize one such region, known to associate with body size and ear type, in detail using “next-generation” sequencing technology to identify candidate mutations that may control these traits. Our results suggest that artificial selection has targeted genes involved in development and metabolism and that it may have increased the incidence of disease in dog breeds. Knowledge of these regions will be of great importance for uncovering the genetic basis of variation between dog breeds and for finding mutations that cause disease.
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Bizzarri M, Giuliani A, Cucina A, D'Anselmi F, Soto AM, Sonnenschein C. Fractal analysis in a systems biology approach to cancer. Semin Cancer Biol 2011; 21:175-82. [PMID: 21514387 PMCID: PMC3148285 DOI: 10.1016/j.semcancer.2011.04.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 04/07/2011] [Indexed: 12/22/2022]
Abstract
Cancer is a highly complex disease due to the disruption of tissue architecture. Thus, tissues, and not individual cells, are the proper level of observation for the study of carcinogenesis. This paradigm shift from a reductionist approach to a systems biology approach is long overdue. Indeed, cell phenotypes are emergent modes arising through collective non-linear interactions among different cellular and microenvironmental components, generally described by "phase space diagrams", where stable states (attractors) are embedded into a landscape model. Within this framework, cell states and cell transitions are generally conceived as mainly specified by gene-regulatory networks. However, the system's dynamics is not reducible to the integrated functioning of the genome-proteome network alone; the epithelia-stroma interacting system must be taken into consideration in order to give a more comprehensive picture. Given that cell shape represents the spatial geometric configuration acquired as a result of the integrated set of cellular and environmental cues, we posit that fractal-shape parameters represent "omics" descriptors of the epithelium-stroma system. Within this framework, function appears to follow form, and not the other way around.
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Abstract
The domestic dog genome - shaped by domestication, adaptation to human-dominated environments and artificial selection - encodes tremendous phenotypic diversity. Recent developments have improved our understanding of the genetics underlying this diversity, unleashing the dog as an important model organism for complex-trait analysis.
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Affiliation(s)
- Adam R Boyko
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305-5120, USA.
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