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Bacon EK, Donnelly CG, Bellone RR, Haase B, Finno CJ, Velie BD. Preliminary investigation of potential links between pigmentation variants and opioid analgesic effectiveness in horses during cerebrospinal fluid centesis. BMC Vet Res 2024; 20:311. [PMID: 38997753 PMCID: PMC11245827 DOI: 10.1186/s12917-024-04139-z] [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: 03/25/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND The pleiotropic effects of the melanocortin system show promise in overcoming limitations associated with large variations in opioid analgesic effectiveness observed in equine practice. Of particular interest is variation in the melanocortin-1-receptor (MC1R) gene, which dictates pigment type expression through its epistatic interaction with the agouti signalling protein (ASIP) gene. MC1R has previously been implicated in opioid efficacy in other species; however, this relationship is yet to be explored in horses. In this study, analgesic effectiveness was scored (1-3) based on noted response to dura penetration during the performance of cerebrospinal fluid centisis after sedation and tested for association with known genetic regions responsible for pigmentation variation in horses. RESULTS The chestnut phenotype was statistically significant (P < 0.05) in lowering analgesic effectiveness when compared to the bay base coat colour. The 11bp indel in ASIP known to cause the black base coat colour was not significant (P>0.05); however, six single nucleotide polymorphisms (SNPs) within the genomic region encoding the ASIP gene and one within MC1R were identified as being nominally significant (P<0.05) in association with opioid analgesic effectiveness. This included the location of the known e MC1R variant resulting in the chestnut coat colour. CONCLUSIONS The current study provides promising evidence for important links between pigmentation genes and opioid effectiveness in horses. The application of an easily identifiable phenotype indicating variable sensitivity presents a promising opportunity for accessible precision medicine in the use of analgesics and warrants further investigation.
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Affiliation(s)
- Elouise K Bacon
- Equine Genetics and Genomics Group, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
| | - Callum G Donnelly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithica, NY, 14850, USA
| | - Rebecca R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Bianca Haase
- School of Veterinary Science, University of Sydney, Sydney, NSW, Australia
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Brandon D Velie
- Equine Genetics and Genomics Group, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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Basal Reactivity Evaluated by Infrared Thermography in the "Caballo de Deporte Español" Horse Breed According to Its Coat Color. Animals (Basel) 2022; 12:ani12192515. [PMID: 36230256 PMCID: PMC9559532 DOI: 10.3390/ani12192515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/05/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
Horses have been valued for their diversity of coat color since prehistoric times. In particular, the pleiotropic effect that coat color genes have on behavior determines the way the horse perceives and reacts to its environment. The primary aim of this study was to evaluate the influence of coat color on basal reactivity assessed with infrared thermography as eye temperature at rest (ETR), determine their relation with the results obtained by these horses in Show Jumping competitions and to estimate the genetic parameters for this variable to test its suitability for genetic selection. A General Linear Model (GLM) and Duncan post-hoc analysis indicated differences in ETR due to coat color, sex, age, location, and breed-group factors. A Spearman’s rank correlation of 0.11 (p < 0.05) was found with ranking, indicating that less reactive horses were more likely to achieve better rankings. Heritability values ranged from 0.17 to 0.22 and were computed with a model with genetic groups and a model with residual variance heterogeneity. Breeding values were higher with the last genetic model, thus demonstrating the pleiotropic effect of coat color. These results indicate that ETR has a suitable genetic basis to be used in the breeding program to select for basal reactivity due to coat color.
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Perdomo-González DI, García de Paredes RDLA, Valera M, Bartolomé E, Gómez MD. Morpho-Functional Traits in Pura Raza Menorquina Horses: Genetic Parameters and Relationship with Coat Color Variables. Animals (Basel) 2022; 12:ani12182319. [PMID: 36139184 PMCID: PMC9495247 DOI: 10.3390/ani12182319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 01/11/2023] Open
Abstract
Simple Summary In this study, we estimated genetic parameters of 46 linear morpho-functional traits, and analyzed the relationship between two coat color traits (quality of black coat color [QB] and the quantity of white marks [WM]) and other linear morpho-functional traits within the breeding program of Pura Raza Menorquina horses, whose studbook only permits the use of black-coated animals with a small quantity of white marks as breeding stock. A total of 772 records from 333 animals were analyzed to estimate genetic parameters for 46 linear traits scored by four appraisers using seven classes. Heritability values for morpho-functional traits were low to medium and matched the range in the bibliography. Medium heritability values were obtained for both coat color traits (0.36 for QB and 0.23 for WM). Genetic correlations between coat and morpho-functional traits ranged between 0.015 and 0.816 in absolute value for QB and between 0.014 and 0.638 in absolute value for WM. The highest correlation values were obtained between QB and upper neck line (0.816) and between WM and form of the hoof (0.638). It was observed that the animal group with low and the group with high breeding values for QB and WM had a clear differentiation of the other mor-pho-functional traits. Abstract The studbook of Pura Raza Menorquina horses only permits the use of black-coated animals with a small quantity of white marks as breeding stock. Its breeding program uses linear morpho-functional traits as selection criteria. Our aim was to estimate the genetic parameters of linear morpho-functional traits, and reveal relationship of quality of black coat color (QB) and percentage of white marks (WM) with the other morphological and functional linear traits in this breed. A total of 46 linear traits were scored by four appraisers using seven classes, with a total of 772 records from 333 animals (≥4 years old). Univariate animal models using a Bayesian approach were used, with a pedigree of 757 animals. Sex (two) and appraiser-season (13) were included as fixed effects, age as a linear covariate, and permanent environmental and additive genetic as random effect. The heritabilities of the morpho-functional traits were low to medium (0.09–0.58) and matched the range in the bibliography. Heritabilities for coat color traits were 0.36 for QB and 0.23 for WM. The highest genetic correlations were obtained between QB and upper neck line (0.816) and between WM and form of the hoof (0.638). The negative signs of most of the genetic correlations between WM and the functional traits is also remarkable, contributing to the selection of functional traits against the presence of white marks in this population. A clear genetic differentiation was observed between animals with better breeding values for QB and WM, corroborated by a study on founders. In conclusion, QB and WM could show different genetic backgrounds.
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Affiliation(s)
- Davinia I. Perdomo-González
- Escuela Técnica Superior de Ingeniería Agronómica (ETSIA), Universidad de Sevilla, Carretera de Utrera km1, 41013 Sevilla, Spain
| | | | - Mercedes Valera
- Escuela Técnica Superior de Ingeniería Agronómica (ETSIA), Universidad de Sevilla, Carretera de Utrera km1, 41013 Sevilla, Spain
| | - Ester Bartolomé
- Escuela Técnica Superior de Ingeniería Agronómica (ETSIA), Universidad de Sevilla, Carretera de Utrera km1, 41013 Sevilla, Spain
| | - María Dolores Gómez
- Escuela Técnica Superior de Ingeniería Agronómica (ETSIA), Universidad de Sevilla, Carretera de Utrera km1, 41013 Sevilla, Spain
- Asociación de Criadores y Propietarios de Caballos de Raza Menorquina, Edificio Sa Roqueta, C/ Bijuters, 36, Bajos, 07760 Ciutadella de Menorca, Spain
- Correspondence:
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4
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Gibert JM. [Small scale evolution]. Biol Aujourdhui 2022; 216:41-47. [PMID: 35876520 DOI: 10.1051/jbio/2022008] [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: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Small-scale evolution or microevolution concerns evolution at the intra-specific level or between closely related species. At the intra-specific level, it allows the analysis of the evolutionary forces at work: mutation, genetic drift, migration and selection. Moreover, because of the short evolutionary time, it is easier to identify the genetic basis of observed phenotypic differences. Most studies focus on current populations but more and more analyses are performed on ancient DNA. This provides important information for tracing the history of populations and also allows the reconstruction of phenotypes of individuals that disappeared several thousand years ago. In this short review, I present studies showing how pre-zygotic or post-zygotic barriers involved in species formation are set up using the example of the geographical barrier due to the formation of the Isthmus of Panama and that of the heterochromatin divergence in Drosophilidae. I also describe the different approaches that have been used to identify the genetic basis of well known phenotypic variations: candidate gene approach (about melanism in felines), QTL mapping (variation in the number of lateral bone plates in sticklebacks), association study (pigmentation in the Asian ladybird). Finally, I illustrate the key impact of natural selection with the iconic example of the evolution of the beak of Galapagos finches, and the role of certain developmental genes in its morphological diversification.
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Affiliation(s)
- Jean-Michel Gibert
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, UMR 7622, 9 quai St-Bernard 75005 Paris, France
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Derks MFL, Steensma M. Review: Balancing Selection for Deleterious Alleles in Livestock. Front Genet 2021; 12:761728. [PMID: 34925454 PMCID: PMC8678120 DOI: 10.3389/fgene.2021.761728] [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: 08/20/2021] [Accepted: 11/19/2021] [Indexed: 01/04/2023] Open
Abstract
Harmful alleles can be under balancing selection due to an interplay of artificial selection for the variant in heterozygotes and purifying selection against the variant in homozygotes. These pleiotropic variants can remain at moderate to high frequency expressing an advantage for favorable traits in heterozygotes, while harmful in homozygotes. The impact on the population and selection strength depends on the consequence of the variant both in heterozygotes and homozygotes. The deleterious phenotype expressed in homozygotes can range from early lethality to a slightly lower fitness in the population. In this review, we explore a range of causative variants under balancing selection including loss-of-function variation (i.e., frameshift, stop-gained variants) and regulatory variation (affecting gene expression). We report that harmful alleles often affect orthologous genes in different species, often influencing analogous traits. The recent discoveries are mainly driven by the increasing genomic and phenotypic resources in livestock populations. However, the low frequency and sometimes subtle effects in homozygotes prevent accurate mapping of such pleiotropic variants, which requires novel strategies to discover. After discovery, the selection strategy for deleterious variants under balancing selection is under debate, as variants can contribute to the heterosis effect in crossbred animals in various livestock species, compensating for the loss in purebred animals. Nevertheless, gene-assisted selection is a useful tool to decrease the frequency of the harmful allele in the population, if desired. Together, this review marks various deleterious variants under balancing selection and describing the functional consequences at the molecular, phenotypic, and population level, providing a resource for further study.
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Affiliation(s)
- Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands.,Topigs Norsvin Research Center, Beuningen, Netherlands
| | - Marije Steensma
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, Netherlands
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Coss RG, Charles EP. The Saliency of Snake Scales and Leopard Rosettes to Infants: Its Relevance to Graphical Patterns Portrayed in Prehistoric Art. Front Psychol 2021; 12:763436. [PMID: 34880813 PMCID: PMC8645795 DOI: 10.3389/fpsyg.2021.763436] [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: 08/23/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
Geometrically arranged spots and crosshatched incised lines are frequently portrayed in prehistoric cave and mobiliary art. Two experiments examined the saliency of snake scales and leopard rosettes to infants that are perceptually analogous to these patterns. Experiment 1 examined the investigative behavior of 23 infants at three daycare facilities. Four plastic jars (15×14.5cm) with snake scales, leopard rosettes, geometric plaid, and plain patterns printed on yellowish-orange paper inside were placed individually on the floor on separate days during playtime. Fourteen 7–15-month-old infants approached each jar hesitantly and poked it before handling it for five times, the criterion selected for statistical analyses of poking frequency. The jars with snake scales and leopard rosettes yielded reliably higher poking frequencies than the geometric plaid and plain jars. The second experiment examined the gaze and grasping behavior of 15 infants (spanning 5months of age) seated on the laps of their mothers in front of a table. For paired comparisons, the experimenter pushed two of four upright plastic cylinders (13.5×5.5cm) with virtually the same colored patterns simultaneously toward each infant for 6s. Video recordings indicated that infants gazed significantly longer at the cylinders with snake scales and leopard rosettes than the geometric plaid and plain cylinders prior to grasping them. Logistic regression of gaze duration predicting cylinder choice for grasping indicated that seven of 24 paired comparisons were not significant, all of which involved choices of cylinders with snake scales and leopard rosettes that diverted attention before reaching. Evidence that these biological patterns are salient to infants during an early period of brain development might characterize the integration of subcortical and neocortical visual processes known to be involved in snake recognition. In older individuals, memorable encounters with snakes and leopards coupled with the saliency of snake scales and leopard rosettes possibly biased artistic renditions of similar patterns during prehistoric times.
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Affiliation(s)
- Richard G Coss
- Psychology Department, University of California, Davis, Davis, CA, United States
| | - Eric P Charles
- Psychology Department, University of California, Davis, Davis, CA, United States
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7
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Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00192-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractA new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics.MaTrics was developed within a project aimed to find genetic causes of phenotypic traits of mammals using Forward Genomics. This approach requires genomes and comprehensive and recorded information on homologous phenotypes that are coded as discrete categories in a matrix. MaTrics is an evolving online resource providing information on phenotypic traits in numeric code; traits are coded either as absent/present or with several states as multistate. The state record for each species is linked to at least one reference (e.g., literature, photographs, histological sections, CT scans, or museum specimens) and so MaTrics contributes to digitalization of museum collections. Currently, MaTrics covers 147 mammalian species and includes 231 characters related to structure, morphology, physiology, ecology, and ethology and available in a machine actionable NEXUS-format*. Filling MaTrics revealed substantial knowledge gaps, highlighting the need for phenotyping efforts. Studies based on selected data from MaTrics and using Forward Genomics identified associations between genes and certain phenotypes ranging from lifestyles (e.g., aquatic) to dietary specializations (e.g., herbivory, carnivory). These findings motivate the expansion of phenotyping in MaTrics by filling research gaps and by adding taxa and traits. Only databases like MaTrics will provide machine actionable information on phenotypic traits, an important limitation to genomics. MaTrics is available within the data repository Morph·D·Base (www.morphdbase.de).
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Lovász L, Fages A, Amrhein V. Konik, Tarpan, European wild horse: An origin story with conservation implications. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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9
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Zeller U, Göttert T. Humans, megafauna and landscape structure – Rock engravings from Namibia encourage a comparative approach to central Europe and southern Africa. VERTEBRATE ZOOLOGY 2021. [DOI: 10.3897/vz.71.e72811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This paper deals with reflections that arose after observing prehistoric rock engravings at different locations in Namibia. These observations stimulated comparative considerations with focus on southern Africa and central Europe. Similar to the Aurignacian rock art of European origin, the most common motifs in the Namibian rock engravings are large animals. While in Europe, the species that served as a blueprint for the illustration of Aurignacian rock art have mostly disappeared, the megafauna illustrated on the rock engravings in Namibia can still be found in the immediate vicinity of the rock art. Against this background, we discuss and further develop a comparative regional approach. We reconstruct and evaluate the suitability of African savannas and still-existing megafauna communities as an appropriate reference-frame for natural European grassland systems and extinct associated warm-adapted megafauna (Eemian Interglacial megafauna). Special attention is laid on the unique situation in Africa in the light of a global extinction wave of megafauna following increasing human activity in the Late Quaternary. This leads us to discuss the use of domesticated ungulates as surrogate taxa to fulfill ecosystem functions in Europe as part of concepts termed “rewilding” or “naturalistic grazing”. After critically examining these concepts, we conclude that using domesticated forms as representatives of extinct or locally disappeared species in Europe has its justification to some extent. If, however, the naturally occurring megaherbivore community still exists (Africa), these naturally occurring species should be given priority due to their organismic abilities and limitations adapted to the harsh conditions in their specific environment. Finally, we discuss the application of (transboundary) protected areas as effective instruments to mitigate human-wildlife conflicts. A holistic approach, including nature conservation and preservation of cultural achievements (domesticated forms, grazing systems), appears promising for the effective protection of the natural African savanna ecosystems with their unique fauna elements, as illustrated in rock engravings that inspired us to write this paper.
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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From the Eurasian Steppes to the Roman Circuses: A Review of Early Development of Horse Breeding and Management. Animals (Basel) 2021; 11:ani11071859. [PMID: 34206575 PMCID: PMC8300240 DOI: 10.3390/ani11071859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 01/14/2023] Open
Abstract
Simple Summary Horses were domesticated later than any other major livestock species. Their role in shaping ancient civilizations cannot be overestimated. As a primary means of transportation, an essential asset in warfare, and later one of the key elements of circus entertainment, horses quickly became luxurious goods. Vast amounts of money were invested in the horse industry resulted resulting in the rapid development of horse breeding and husbandry. This review examines paleogenetic, archeological, and classical studies on managing horses in antiquity. Many ancient approaches and practices in horse management are still relevant today and some of them, now abandoned, are worth re-examination. Abstract The domestication of the horse began about 5500 years ago in the Eurasian steppes. In the following millennia horses spread across the ancient world, and their role in transportation and warfare affected every ancient culture. Ownership of horses became an indicator of wealth and social status. The importance of horses led to a growing interest in their breeding and management. Many phenotypic traits, such as height, behavior, and speed potential, have been proven to be a subject of selection; however, the details of ancient breeding practices remain mostly unknown. From the fourth millennium BP, through the Iron Age, many literature sources thoroughly describe horse training systems, as well as various aspects of husbandry, many of which are still in use today. The striking resemblance of ancient and modern equine practices leaves us wondering how much was accomplished through four thousand years of horse breeding.
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Plasteeva NA, Gasilin VV, Devjashin MM, Kosintsev PA. Holocene Distribution and Extinction of Ungulates in Northern Eurasia. BIOL BULL+ 2021. [DOI: 10.1134/s1062359020080105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Orlando L. The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics. Annu Rev Genet 2020; 54:563-581. [PMID: 32960653 DOI: 10.1146/annurev-genet-021920-011805] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.
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Affiliation(s)
- Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse, Faculté de Médecine Purpan, Université Toulouse III-Paul Sabatier, 31000 Toulouse, France;
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He Z, Dai X, Beaumont M, Yu F. Detecting and Quantifying Natural Selection at Two Linked Loci from Time Series Data of Allele Frequencies with Forward-in-Time Simulations. Genetics 2020; 216:521-541. [PMID: 32826299 PMCID: PMC7536848 DOI: 10.1534/genetics.120.303463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 08/15/2020] [Indexed: 12/16/2022] Open
Abstract
Recent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time. This improvement provides an opportunity for us to study natural selection based on time serial samples of genomes while accounting for genetic recombination effect and local linkage information. Such time series genomic data allow for more accurate estimation of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel Bayesian statistical framework for inferring natural selection at a pair of linked loci by capitalising on the temporal aspect of DNA data with the additional flexibility of modeling the sampled chromosomes that contain unknown alleles. Our approach is built on a hidden Markov model where the underlying process is a two-locus Wright-Fisher diffusion with selection, which enables us to explicitly model genetic recombination and local linkage. The posterior probability distribution for selection coefficients is computed by applying the particle marginal Metropolis-Hastings algorithm, which allows us to efficiently calculate the likelihood. We evaluate the performance of our Bayesian inference procedure through extensive simulations, showing that our approach can deliver accurate estimates of selection coefficients, and the addition of genetic recombination and local linkage brings about significant improvement in the inference of natural selection. We also illustrate the utility of our method on real data with an application to ancient DNA data associated with white spotting patterns in horses.
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Affiliation(s)
- Zhangyi He
- School of Mathematics, University of Bristol, BS8 1UG, United Kingdom
| | - Xiaoyang Dai
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Feng Yu
- School of Mathematics, University of Bristol, BS8 1UG, United Kingdom
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15
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He Z, Dai X, Beaumont M, Yu F. Estimation of Natural Selection and Allele Age from Time Series Allele Frequency Data Using a Novel Likelihood-Based Approach. Genetics 2020; 216:463-480. [PMID: 32769100 PMCID: PMC7536852 DOI: 10.1534/genetics.120.303400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/29/2020] [Indexed: 11/18/2022] Open
Abstract
Temporally spaced genetic data allow for more accurate inference of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel likelihood-based method for jointly estimating selection coefficient and allele age from time series data of allele frequencies. Our approach is based on a hidden Markov model where the underlying process is a Wright-Fisher diffusion conditioned to survive until the time of the most recent sample. This formulation circumvents the assumption required in existing methods that the allele is created by mutation at a certain low frequency. We calculate the likelihood by numerically solving the resulting Kolmogorov backward equation backward in time while reweighting the solution with the emission probabilities of the observation at each sampling time point. This procedure reduces the two-dimensional numerical search for the maximum of the likelihood surface, for both the selection coefficient and the allele age, to a one-dimensional search over the selection coefficient only. We illustrate through extensive simulations that our method can produce accurate estimates of the selection coefficient and the allele age under both constant and nonconstant demographic histories. We apply our approach to reanalyze ancient DNA data associated with horse base coat colors. We find that ignoring demographic histories or grouping raw samples can significantly bias the inference results.
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Affiliation(s)
- Zhangyi He
- Department of Statistics, University of Oxford, OX1 3LB, United Kingdom
| | - Xiaoyang Dai
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Feng Yu
- School of Mathematics, University of Bristol, BS8 1UG, United Kingdom
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Guimaraes S, Arbuckle BS, Peters J, Adcock SE, Buitenhuis H, Chazin H, Manaseryan N, Uerpmann HP, Grange T, Geigl EM. Ancient DNA shows domestic horses were introduced in the southern Caucasus and Anatolia during the Bronze Age. SCIENCE ADVANCES 2020; 6:eabb0030. [PMID: 32938680 PMCID: PMC7494339 DOI: 10.1126/sciadv.abb0030] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/31/2020] [Indexed: 05/12/2023]
Abstract
Despite the important roles that horses have played in human history, particularly in the spread of languages and cultures, and correspondingly intensive research on this topic, the origin of domestic horses remains elusive. Several domestication centers have been hypothesized, but most of these have been invalidated through recent paleogenetic studies. Anatolia is a region with an extended history of horse exploitation that has been considered a candidate for the origins of domestic horses but has never been subject to detailed investigation. Our paleogenetic study of pre- and protohistoric horses in Anatolia and the Caucasus, based on a diachronic sample from the early Neolithic to the Iron Age (~8000 to ~1000 BCE) that encompasses the presumed transition from wild to domestic horses (4000 to 3000 BCE), shows the rapid and large-scale introduction of domestic horses at the end of the third millennium BCE. Thus, our results argue strongly against autochthonous independent domestication of horses in Anatolia.
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Affiliation(s)
- Silvia Guimaraes
- Institut Jacques Monod, CNRS, University of Paris, Paris, France
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joris Peters
- ArchaeoBioCenter and Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication and the History of Veterinary Medicine, Ludwig Maximilian University Munich, Kaulbachstraße 37/111, 80539 Munich, Germany
- State Collection of Anthropology and Palaeoanatomy Munich, Bavarian Natural History Collections, Karolinenplatz 2a, 80333 Munich, Germany
| | - Sarah E Adcock
- Department of Anthropology, University of Chicago, 1126 East 59th Street, Chicago, IL 60637, USA
| | - Hijlke Buitenhuis
- Groningen Institute of Archaeology, University of Groningen, 9712 ER Groningen, Netherlands
| | - Hannah Chazin
- Department of Anthropology, Columbia University, 1200 Amsterdam Avenue, New York, NY 10031, USA
| | - Ninna Manaseryan
- Scientific Center of Zoology and Hydroecology, Institute of Zoology, National Academy of Sciences of the Republic of Armenia, 7 Paruyr Sevak Str., Yerevan 0014, Armenia
| | - Hans-Peter Uerpmann
- Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung für Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Universität Tübingen, Rümelinstraße 23, 72070 Tübingen, Germany
| | - Thierry Grange
- Institut Jacques Monod, CNRS, University of Paris, Paris, France
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, University of Paris, Paris, France.
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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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Rockwell H, Mack M, Famula T, Sandmeyer L, Bauer B, Dwyer A, Lassaline M, Beeson S, Archer S, McCue M, Bellone RR. Genetic investigation of equine recurrent uveitis in Appaloosa horses. Anim Genet 2019; 51:111-116. [PMID: 31793009 DOI: 10.1111/age.12883] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2019] [Indexed: 01/05/2023]
Abstract
Equine recurrent uveitis (ERU) is characterized by intraocular inflammation that often leads to blindness in horses. Appaloosas are more likely than any other breed to develop insidious ERU, distinguished by low-grade chronic intraocular inflammation, suggesting a genetic predisposition. Appaloosas are known for their white coat spotting patterns caused by the leopard complex spotting allele (LP) and the modifier PATN1. A marker linked to LP on ECA1 and markers near MHC on ECA20 were previously associated with increased ERU risk. This study aims to further investigate these loci and identify additional genetic risk factors. A GWAS was performed using the Illumina Equine SNP70 BeadChip in 91 horses. Additive mixed model approaches were used to correct for relatedness. Although they do not reach a strict Bonferroni genome-wide significance threshold, two SNPs on ECA1 and one SNP each on ECA12 and ECA29 were among the highest ranking SNPs and thus warranted further analysis (P = 1.20 × 10-5 , P = 5.91 × 10-6 , P = 4.91 × 10-5 , P = 6.46 × 10-5 ). In a second cohort (n = 98), only an association with the LP allele on ECA1 was replicated (P = 5.33 × 10-5 ). Modeling disease risk with LP, age and additional depigmentation factors (PATN1 genotype and extent of roaning) supports an additive role for LP and suggests an additive role for PATN1. Genotyping for LP and PATN1 may help predict ERU risk (AUC = 0.83). The functional role of LP and PATN1 in ERU development requires further investigation. Testing samples across breeds with leopard complex spotting patterns and a denser set of markers is warranted to further refine the genetic components of ERU.
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Affiliation(s)
- H Rockwell
- Veterinary Genetics Laboratory, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, 95616, CA, USA
| | - M Mack
- Veterinary Genetics Laboratory, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, 95616, CA, USA
| | - T Famula
- Appaloosa Project, Davis, 95616, CA, USA
| | - L Sandmeyer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - B Bauer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - A Dwyer
- Genesee Valley Equine Clinic, LLC, Scottsville, NY, 14546, USA
| | - M Lassaline
- Department of Radiological and Surgical Sciences, School of Veterinary Medicine, University of California - Davis, Davis, CA, 95616, USA
| | - S Beeson
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St Paul, MN, 55108, USA
| | - S Archer
- Appaloosa Project, Sayward, V0P 1R0, BC, Canada
| | - M McCue
- Veterinary Population Medicine Department, College of Veterinary Medicine, University of Minnesota, St Paul, MN, 55108, USA
| | - R R Bellone
- Veterinary Genetics Laboratory, Department of Population Health and Reproduction, School of Veterinary Medicine, University of California - Davis, Davis, 95616, CA, USA
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19
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Drawbacks and consequences of selective strategies in the design of semen banks: Case study of the Pura Raza Español horse breed. Livest Sci 2019. [DOI: 10.1016/j.livsci.2019.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Grilz-Seger G, Druml T, Neuditschko M, Mesarič M, Cotman M, Brem G. Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size. Anim Genet 2019; 50:334-346. [PMID: 31199540 PMCID: PMC6617995 DOI: 10.1111/age.12797] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2019] [Indexed: 12/24/2022]
Abstract
Overlapping runs of homozygosity (ROH islands) shared by the majority of a population are hypothesized to be the result of selection around a target locus. In this study we investigated the impact of selection for coat color within the Noriker horse on autozygosity and ROH patterns. We analyzed overlapping homozygous regions (ROH islands) for gene content in fragments shared by more than 50% of horses. Long‐term assortative mating of chestnut horses and the small effective population size of leopard spotted and tobiano horses resulted in higher mean genome‐wide ROH coverage (SROH) within the range of 237.4–284.2 Mb, whereas for bay, black and roan horses, where rotation mating is commonly applied, lower autozygosity (SROH from 176.4–180.0 Mb) was determined. We identified seven common ROH islands considering all Noriker horses from our dataset. Specific islands were documented for chestnut, leopard spotted, roan and bay horses. The ROH islands contained, among others, genes associated with body size (ZFAT, LASP1 and LCORL/NCAPG), coat color (MC1R in chestnut and the factor PATN1 in leopard spotted horses) and morphogenesis (HOXB cluster in all color strains except leopard spotted horses). This study demonstrates that within a closed population sharing the same founders and ancestors, selection on a single phenotypic trait, in this case coat color, can result in genetic fragmentation affecting levels of autozygosity and distribution of ROH islands and enclosed gene content.
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Affiliation(s)
- G Grilz-Seger
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, Vienna, A-1210, Austria
| | - T Druml
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, Vienna, A-1210, Austria
| | - M Neuditschko
- Swiss National Stud Farm, Agroscope, Les Longs Prés, Avenches, CH-1580, Switzerland
| | - M Mesarič
- Clinic for Reproduction and Large Animals, University of Ljubljana, Veterinary Faculty, Cesta v Mestni log 47, Ljubljana, 1000, Slovenia
| | - M Cotman
- Institute for Preclinical Sciences, University of Ljubljana, Veterinary Faculty, Gerbičeva 60, Ljubljana, 1000, Slovenia
| | - G Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Sciences Vienna, Veterinärplatz 1, Vienna, A-1210, Austria
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21
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Sánchez-Guerrero MJ, Negro-Rama S, Demyda-Peyras S, Solé-Berga M, Azor-Ortiz PJ, Valera-Córdoba M. Morphological and genetic diversity of Pura Raza Español horse with regard to the coat colour. Anim Sci J 2018; 90:14-22. [PMID: 30467923 DOI: 10.1111/asj.13102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 07/04/2018] [Accepted: 07/13/2018] [Indexed: 11/27/2022]
Abstract
Gene mutations influencing melanocytes also impact on physiological and behavioural functions. In this study, we investigated their association with four different coat colours in the Pura Raza Español (PRE) horse using morphological traits and molecular datasets. Four different subpopulations were identified according to individual coat colour: grey, bay, chestnut and black. Coat colour significantly associated with morphological measurements. Observed and expected heterozygosity values were low in grey compared with the other three subpopulations, suggesting the presence of unique ancestral alleles probably arisen by genetic drift and selection mechanism effects. Nei's distance demonstrated a clear division among subpopulations, the grey being the most divergent group. Gene flow estimates were similar, showing the lowest values in grey. Divergence times among subpopulations assessed with the average square distance suggested that grey was the original PRE population which diverged from bay, chestnut and black. Our results also demonstrated a clear morphological differentiation according to coat colour. The close genetic structure of bay and chestnut PRE subpopulations and the clear differences in most morphological traits of grey and chestnut PRE mares would suggest the pleiotropic effect of genomic regions determining coat colour in horses. However, further analysis including genomic information would be necessary to elucidate the mechanisms involved.
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Affiliation(s)
| | - Sara Negro-Rama
- Departamento de Ciencias Agroforestales, ETSIA, Universidad de Sevilla, Sevilla, España
| | - Sebastián Demyda-Peyras
- Facultad de Ciencias Veterinarias, IGEVET-Instituto de Genética Veterinaria "Ing. Fernando N. Dulout" (UNLP-CONICET LA PLATA), Universidad Nacional de La Plata, La Plata, Argentina
| | - Marina Solé-Berga
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Pedro J Azor-Ortiz
- Departamento de Ciencias Agroforestales, ETSIA, Universidad de Sevilla, Sevilla, España
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22
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Population study of the Pura Raza Español Horse regarding its coat colour. ANNALS OF ANIMAL SCIENCE 2018. [DOI: 10.2478/aoas-2018-0016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
Coat colour has always been a valuable trait for horse breeders. However, preferences for this feature have changed over the years. In this research, the Pura Raza Español horse (PRE) population was divided into four subpopulations (Grey, Bay, Black and Others), according to the most frequent coat colours and those of their ancestors. The purpose was to analyse genetic variability, reproductive parameters and distances among subpopulations during three key periods in the history of the breed: before 1960, from 1960 to 2000 and after 2000. The subpopulations composed of animals with ancestors with the same coat colour showed higher values of recent inbreeding (ranging from 7.13% to 10.44%) and a greater Nei’s minimum distance between them, as a result of more inbred matings than those carried out in families with members with different coat colours. Non-pure subpopulations also showed more similar recent inbreeding values (between 6.63% and 6.74%). Strikingly, the productive life of Pure bay, Pure black and other subpopulations with minority coat colours was considerably longer (10.79, 10.08 and 9.11 years, respectively) compared to the values of grey PRE horses (6.01 and 7.98 years), which is the subpopulation with the highest census. These results, together with shorter generation intervals of black stallion-offspring (5.51 years via father-son and 6.39 years via father-daughter) and the fact that this coat colour was not present in the breed until two decades ago, highlight the recent trend towards the breeding of black animals.
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23
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May-Davis S, Brown W, Vermeulen Z. The Disappearing Lamellae: Implications of New Findings in the Family Equidae Suggest the Loss of Nuchal Ligament Lamellae on C6 and C7 Occurred After Domestication. J Equine Vet Sci 2018; 68:108-114. [PMID: 31256881 DOI: 10.1016/j.jevs.2018.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/14/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
Abstract
Conflicting data predominantly describes the equine nuchal ligament lamellae (NLL) attachments as C2-C6 or C2-C7; however, preliminary evidence suggests C2-C5. This study aimed to identify morphological variations in the attachments of the NLL in four species of the family equidae and determine if the variations were species or breed linked. Cadaveric examination evaluated 98 equids; Equusasinus (n = 2), Equus ferus caballus (n = 93), Equus przewalskii (n = 2), and Equus quagga boehmi (n = 1). Twenty breeds of E. f. caballus were included according to breed type-modern horse (n = 81), ancient type (n = 10), primitive (n = 4). Of the 98 equids, observations were divided into three categories according to the NLL attachments: C2-C5, C2-C6, and C2-C7; in category C2-C7, E. f. caballus (n = 3/93), modern horse 0 of 81, ancient 1 of 8, primitive 2 of 4; in category C2-C6, modern horse 2 of 81; in category C2-C5, modern horse 79 of 81, ancient type 7 of 8, primitive 2 of 4. Equus asinus, E. przewalskii, and E. q. boehmi all expressed category C2-C7. In total, 88 of 98 expressed category C2-C5; 2 of 98 category C2-C6; and 8 of 98 category C2-C7. These findings suggest that category C2-C5 provides sufficient evidence to suggest a normal occurrence. The high incidence of an absent NLL on C6 and C7 may be considered a contributing factor in caudal cervical osteoarthritis. Furthermore, category C2-C7 still exists in an ancient and primitive breed closely related to the tarpan, implying the NLL may have been attached from C2 to C7 in prehistoric horse before domestication. This hypothesis is supported by the findings of E. asinus, E. przewalskii, and E. q. boehmi, displaying attachments from C2 to C7.
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Affiliation(s)
- Sharon May-Davis
- The University of New England, Canine and Equine Research Group, Armidale, New South Wales, Australia.
| | - Wendy Brown
- The University of New England, Canine and Equine Research Group, Armidale, New South Wales, Australia
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24
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The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics 2017; 204:423-434. [PMID: 27729493 DOI: 10.1534/genetics.116.194860] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/17/2016] [Indexed: 12/21/2022] Open
Abstract
The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses.
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25
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Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. Ancient genomic changes associated with domestication of the horse. Science 2017; 356:442-445. [DOI: 10.1126/science.aam5298] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Ancient genomics of horse domesticationThe domestication of the horse was a seminal event in human cultural evolution. Libradoet al.obtained genome sequences from 14 horses from the Bronze and Iron Ages, about 2000 to 4000 years ago, soon after domestication. They identified variants determining coat color and genes selected during the domestication process. They could also see evidence of admixture with archaic horses and the demography of the domestication process, which included the accumulation of deleterious variants. The horse appears to have undergone a different type of domestication process than animals that were domesticated simply for food.Science, this issue p.442
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Affiliation(s)
- Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Charleen Gaunitz
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Mélanie Pruvost
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris Diderot, 75205 Paris cedex 13, France
| | - Anders Albrechtsen
- Bioinformatics Center, Department of Biology, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Antoine Fages
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Naveed Khan
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | | | - Aitor Serres-Armero
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Lukas F. K. Kuderna
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Inna S. Povolotskaya
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- National High-Throughput DNA Sequencing Center, Copenhagen, Denmark
| | - Sébastien Lepetz
- Centre National de la Recherche Scientifique, Muséum national d’histoire naturelle, Sorbonne Universités, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 55 rue Buffon, 75005 Paris, France
| | | | - Catherine Thèves
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Saleh Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed H. Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khaled Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, 1580 Avenches, Switzerland
| | - Zainolla Samashev
- Branch of Institute of Archaeology Margulan, Republic Avenue 24-405, 010000 Astana, Republic of Kazakhstan
| | - Henri-Paul Francfort
- CNRS, UMR 7041 Archéologie et Sciences de l’Antiquité, Archéologie de l'Asie Centrale, Maison René Ginouvès, 21 allée de l’Université, 92023 Nanterre, France
| | - Norbert Benecke
- German Archaeological Institute, Department of Natural Sciences, Berlin, 14195 Berlin, Germany
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin 10315, Germany
| | - Christine Keyser
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - Bertrand Ludes
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut Médico-Légal, Université Paris Descartes, Paris, France
| | - Eric Crubézy
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
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26
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Wutke S, Benecke N, Sandoval-Castellanos E, Döhle HJ, Friederich S, Gonzalez J, Hallsson JH, Hofreiter M, Lõugas L, Magnell O, Morales-Muniz A, Orlando L, Pálsdóttir AH, Reissmann M, Ruttkay M, Trinks A, Ludwig A. Spotted phenotypes in horses lost attractiveness in the Middle Ages. Sci Rep 2016; 6:38548. [PMID: 27924839 PMCID: PMC5141471 DOI: 10.1038/srep38548] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 11/09/2016] [Indexed: 01/08/2023] Open
Abstract
Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in ~3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.
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Affiliation(s)
- Saskia Wutke
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, 10315 Berlin, Germany
| | - Norbert Benecke
- German Archaeological Institute, Department of Natural Sciences, Berlin, 14195 Berlin, Germany
| | | | - Hans-Jürgen Döhle
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie Sachsen-Anhalt - Landesmuseum für Vorgeschichte, 06114 Halle (Saale), Germany
| | - Javier Gonzalez
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Jón Hallsteinn Hallsson
- The Agricultural University of Iceland, Faculty of Land and Animal Resources, IS-112 Reykjavik, Iceland
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Lembi Lõugas
- Archaeological Research Collection, Tallinn University, Rüütli 10, 10130 Tallinn, Estonia
| | - Ola Magnell
- National Historical Museums, Contract Archaeology, 226 60 Lund, Sweden
| | | | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Albína Hulda Pálsdóttir
- The Agricultural University of Iceland, Faculty of Land and Animal Resources, IS-112 Reykjavik, Iceland
| | - Monika Reissmann
- Humboldt University Berlin, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute, 10115 Berlin, Germany
| | - Matej Ruttkay
- Slovak Academy of Sciences, Institute of Archaeology, 949 21 Nitra, Slovak Republic
| | - Alexandra Trinks
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, 14476 Potsdam, Germany
| | - Arne Ludwig
- Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, 10315 Berlin, Germany
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MacHugh DE, Larson G, Orlando L. Taming the Past: Ancient DNA and the Study of Animal Domestication. Annu Rev Anim Biosci 2016; 5:329-351. [PMID: 27813680 DOI: 10.1146/annurev-animal-022516-022747] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. In this review, we show how our understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods. These techniques have been particularly informative in revealing high-resolution patterns of artificial and natural selection and evidence for significant admixture between early domestic animal populations and their wild congeners.
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Affiliation(s)
- David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland; .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; .,Université de Toulouse, University Paul Sabatier, Laboratoire AMIS, CNRS UMR 5288, 31000 Toulouse, France
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Abstract
The Neanderthals' northern distribution, hunting techniques, and orbit breadths suggest that they were more active in dim light than modern humans. We surveyed visual opsin genes from four Neanderthals and two other archaic hominids to see if they provided additional support for this hypothesis. This analysis was motivated by the observation that alleles responsible for anomalous trichromacy in humans are more common in northern latitudes, by data suggesting that these variants might enhance vision in mesopic conditions, and by the observation that dim light active species often have fewer opsin genes than diurnal relatives. We also looked for evidence of convergent amino acid substitutions in Neanderthal opsins and orthologs from crepuscular or nocturnal species. The Altai Neanderthal, the Denisovan, and the Ust'-Ishim early modern human had opsin genes that encoded proteins identical to orthologs in the human reference genome. Opsins from the Vindija Cave Neanderthals (three females) had many nonsynonymous substitutions, including several predicted to influence colour vision (e.g., stop codons). However, the functional implications of these observations were difficult to assess, given that "control" loci, where no substitutions were expected, differed from humans to the same extent. This left unresolved the test for colour vision deficiencies in Vindija Cave Neanderthals.
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Affiliation(s)
- John S Taylor
- Department of Biology, University of Victoria, Station CSC, P.O. Box 3020, Victoria, BC V8W 3N5, Canada.,Department of Biology, University of Victoria, Station CSC, P.O. Box 3020, Victoria, BC V8W 3N5, Canada
| | - Thomas E Reimchen
- Department of Biology, University of Victoria, Station CSC, P.O. Box 3020, Victoria, BC V8W 3N5, Canada.,Department of Biology, University of Victoria, Station CSC, P.O. Box 3020, Victoria, BC V8W 3N5, Canada
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30
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Scott ML, John EE, Bellone RR, Ching JCH, Loewen ME, Sandmeyer LS, Grahn BH, Forsyth GW. Redundant contribution of a Transient Receptor Potential cation channel Member 1 exon 11 single nucleotide polymorphism to equine congenital stationary night blindness. BMC Vet Res 2016; 12:121. [PMID: 27329127 PMCID: PMC4915136 DOI: 10.1186/s12917-016-0745-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 06/14/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Congenital stationary night-blindness (CSNB) is a recessive autosomal defect in low-light vision in Appaloosa and other horse breeds. This condition has been mapped by linkage analysis to a gene coding for the Transient Receptor Potential cation channel Member 1 (TRPM1). TRPM1 is normally expressed in the ON-bipolar cells of the inner nuclear layer of the retina. Down-regulation of TRPM1 expression in CSNB results from a transposon-like insertion in intron 1 of the TRPM1 gene. Stop transcription signals in this transposon significantly reduce TRPM1 primary transcript levels in CSNB horses. This study describes additional contributions by a second mutation of the TRPM1 gene, the ECA1 108,249,293 C > T SNP, to down-regulation of transcription of the TRPM1 gene in night-blind horses. This TRPM1 SNP introduces a consensus binding site for neuro-oncological ventral antigen 1 (Nova-1) protein in the primary transcript. Nova-1 binding disrupts normal splicing signals, producing unstable, non-functional mRNA transcripts. RESULTS Retinal bipolar cells express both TRPM1 and Nova-1 proteins. In vitro addition of Nova-1 protein retards electrophoretic migration of TRPM1 RNA containing the ECA1 108,249,293 C > T SNP. Up-regulating Nova-1 expression in primary cultures of choroidal melanocytes carrying the intron 11 SNP caused an average log 2-fold reduction of ~6 (64-fold) of TRPM1 mRNA expression. CONCLUSIONS These finding suggest that the equine TRPM1 SNP can act independently to reduce survival of TRPM1 mRNA escaping the intron 1 transcriptional stop signals in CSNB horses. Coexistence and co-inheritance of two independent TRPM1 mutations across 1000 equine generations suggests a selective advantage for the apparently deleterious CSNB trait.
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Affiliation(s)
- Michelle L Scott
- Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Emily E John
- Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | | | - John C H Ching
- Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Matthew E Loewen
- Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Lynne S Sandmeyer
- Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Bruce H Grahn
- Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - George W Forsyth
- Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada.
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Németh A, Bárány A, Csorba G, Magyari E, Pazonyi P, Pálfy J. Holocene mammal extinctions in the Carpathian Basin: a review. Mamm Rev 2016. [DOI: 10.1111/mam.12075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Attila Németh
- MTA‐MTM‐ELTE Research Group for Paleontology Ludovika tér 2. Budapest H‐1083 Hungary
| | - Annamária Bárány
- Hungarian National Museum Múzeum körút 14‐16. Budapest H‐1088 Hungary
| | - Gábor Csorba
- Hungarian Natural History Museum Baross u. 13. Budapest H‐1088 Hungary
| | - Enikö Magyari
- MTA‐MTM‐ELTE Research Group for Paleontology Pázmány P. sétány 1/CBudapestH‐1117Hungary
| | - Piroska Pazonyi
- MTA‐MTM‐ELTE Research Group for Paleontology Ludovika tér 2. Budapest H‐1083 Hungary
| | - József Pálfy
- MTA‐MTM‐ELTE Research Group for Paleontology and Eötvös Loránd University Department of Physical and Applied Geology Pázmány P. sétány 1/C Budapest H-1117 Hungary
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Distribution of coat-color-associated alleles in the domestic horse population and Przewalski's horse. J Appl Genet 2016; 57:519-525. [PMID: 27194311 DOI: 10.1007/s13353-016-0352-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 04/03/2016] [Accepted: 05/04/2016] [Indexed: 10/21/2022]
Abstract
Considering the hidden mode of inheritance of some coat-color-associated alleles, we investigated the presence/absence of coat-color-associated alleles in 1093 domestic horses of 55 breeds and 20 specimens of Przewalski's horse. For coat-color genotyping, allele specific PCR, pyrosequencing and Li-Cor analyses were conducted on 12 coat-color-associated alleles of five genes. Our data provide deep insight into the distribution of coat-color-associated alleles within breeds. We found that the alleles for the basic colorations (bay, black, and chestnut) are widely distributed and occur in nearly all breeds. Alleles leading to dilutions or patterns are rare in domestic breeds and were not found in Przewalski's horse. Higher frequencies of these alleles are only found in breeds that are selected for their expressed phenotypes (e.g., Kinsky horse, Lewitzer, Tinker). Nevertheless, our study produced strong evidence that molecular testing of the coat color is necessary for well-defined phenotyping to avoid unexpected colorations of offspring that can result in legal action.
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Finn JL, Haase B, Willet CE, van Rooy D, Chew T, Wade CM, Hamilton NA, Velie BD. The relationship between coat colour phenotype and equine behaviour: A pilot study. Appl Anim Behav Sci 2016. [DOI: 10.1016/j.applanim.2015.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses. Nat Genet 2015; 48:152-8. [PMID: 26691985 DOI: 10.1038/ng.3475] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 11/25/2015] [Indexed: 01/15/2023]
Abstract
Dun is a wild-type coat color in horses characterized by pigment dilution with a striking pattern of dark areas termed primitive markings. Here we show that pigment dilution in Dun horses is due to radially asymmetric deposition of pigment in the growing hair caused by localized expression of the T-box 3 (TBX3) transcription factor in hair follicles, which in turn determines the distribution of hair follicle melanocytes. Most domestic horses are non-dun, a more intensely pigmented phenotype caused by regulatory mutations impairing TBX3 expression in the hair follicle, resulting in a more circumferential distribution of melanocytes and pigment granules in individual hairs. We identified two different alleles (non-dun1 and non-dun2) causing non-dun color. non-dun2 is a recently derived allele, whereas the Dun and non-dun1 alleles are found in ancient horse DNA, demonstrating that this polymorphism predates horse domestication. These findings uncover a new developmental role for T-box genes and new aspects of hair follicle biology and pigmentation.
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Ludwig A, Reissmann M, Benecke N, Bellone R, Sandoval-Castellanos E, Cieslak M, Fortes GG, Morales-Muñiz A, Hofreiter M, Pruvost M. Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130386. [PMID: 25487337 DOI: 10.1098/rstb.2013.0386] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times.
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Affiliation(s)
- Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Monika Reissmann
- Department for Crop and Animal Sciences, Humboldt University Berlin, Berlin, Germany
| | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, Berlin, Germany
| | - Rebecca Bellone
- Department of Population Health and Reproduction and the Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA
| | | | - Michael Cieslak
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Gloria G Fortes
- Department of Biology, University of York, Heslington, York, UK Instituto Universitario de Xeología (IUX), A Coruña, Spain
| | | | - Michael Hofreiter
- Department of Biology, University of York, Heslington, York, UK Adaptive and Evolutionary Genomics, Institute for Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Strasse 24-24, 14476 Potsdam, Germany
| | - Melanie Pruvost
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany Department of Natural Sciences, German Archaeological Institute, Berlin, Germany Institut Jacques Monod, UMR 7592 CNRS, Université Paris Diderot, Paris, France
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36
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Major transitions in human evolution revisited: a tribute to ancient DNA. J Hum Evol 2014; 79:4-20. [PMID: 25532800 DOI: 10.1016/j.jhevol.2014.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 06/06/2014] [Accepted: 06/19/2014] [Indexed: 11/23/2022]
Abstract
The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists.
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Hedrick PW. Heterozygote Advantage: The Effect of Artificial Selection in Livestock and Pets. J Hered 2014; 106:141-54. [DOI: 10.1093/jhered/esu070] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Bellone RR, Holl H, Setaluri V, Devi S, Maddodi N, Archer S, Sandmeyer L, Ludwig A, Foerster D, Pruvost M, Reissmann M, Bortfeldt R, Adelson DL, Lim SL, Nelson J, Haase B, Engensteiner M, Leeb T, Forsyth G, Mienaltowski MJ, Mahadevan P, Hofreiter M, Paijmans JLA, Gonzalez-Fortes G, Grahn B, Brooks SA. Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse. PLoS One 2013; 8:e78280. [PMID: 24167615 PMCID: PMC3805535 DOI: 10.1371/journal.pone.0078280] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/10/2013] [Indexed: 12/21/2022] Open
Abstract
Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ2=1022.00, p<<0.0005), and CSNB, testing 43 horses (χ2=43, p<<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.
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Affiliation(s)
- Rebecca R. Bellone
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
- * E-mail:
| | - Heather Holl
- Department of Animal Science, Cornell University, Ithaca, New York, United States of America
| | - Vijayasaradhi Setaluri
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Sulochana Devi
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Nityanand Maddodi
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | | | - Lynne Sandmeyer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Daniel Foerster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Melanie Pruvost
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Epigenomic and Palaeogenomic Group, Institut Jacques Monod, Paris, France
| | - Monika Reissmann
- Department of Breeding Biology and Molecular Genetics, Humboldt University Berlin, Berlin, Germany
| | - Ralf Bortfeldt
- Department of Breeding Biology and Molecular Genetics, Humboldt University Berlin, Berlin, Germany
| | - David L. Adelson
- School of Molecular and Biomedical Science, the University of Adelaide, South Australia, Australia
| | - Sim Lin Lim
- School of Molecular and Biomedical Science, the University of Adelaide, South Australia, Australia
| | - Janelle Nelson
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
| | - Bianca Haase
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | | | - Tosso Leeb
- Institute of Genetics, University of Bern, Bern, Switzerland
| | - George Forsyth
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Michael J. Mienaltowski
- Department of Molecular Pharmacology & Physiology, College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Padmanabhan Mahadevan
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
| | | | | | | | - Bruce Grahn
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Samantha A. Brooks
- Department of Animal Science, Cornell University, Ithaca, New York, United States of America
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Kreutz M, Hochstein N, Kaiser J, Narz F, Peist R. Pyrosequencing: powerful and quantitative sequencing technology. ACTA ACUST UNITED AC 2013; 104:7.15.1-7.15.23. [PMID: 24510299 DOI: 10.1002/0471142727.mb0715s104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Pyrosequencing is a sequencing-by-synthesis method for DNA analysis that has emerged as a platform not only for de novo sequencing applications, but also for quantitative analysis of genomic methylation, single-nucleotide polymorphisms, and allele quantification. In this unit, we describe a complete workflow from sample to result that is suitable for each of these applications. As cytosine conversion is a key element of successful methylation analysis using pyrosequencing, a support protocol for bisulfite treatment is also included.
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Fortes GG, Speller CF, Hofreiter M, King TE. Phenotypes from ancient DNA: approaches, insights and prospects. Bioessays 2013; 35:690-5. [PMID: 23703035 DOI: 10.1002/bies.201300036] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The great majority of phenotypic characteristics are complex traits, complicating the identification of the genes underlying their expression. However, both methodological and theoretical progress in genome-wide association studies have resulted in a much better understanding of the underlying genetics of many phenotypic traits, including externally visible characteristics (EVCs) such as eye and hair color. Consequently, it has become possible to predict EVCs from human samples lacking phenotypic information. Predicting EVCs from genetic evidence is clearly appealing for forensic applications involving the personal identification of human remains. Now, a recent paper has reported the genetic determination of eye and hair color in samples up to 800 years old. The ability to predict EVCs from ancient human remains opens up promising perspectives for ancient DNA research, as this could allow studies to directly address archaeological and evolutionary questions related to the temporal and geographical origins of the genetic variants underlying phenotypes.
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Reissmann M, Ludwig A. Pleiotropic effects of coat colour-associated mutations in humans, mice and other mammals. Semin Cell Dev Biol 2013; 24:576-86. [PMID: 23583561 DOI: 10.1016/j.semcdb.2013.03.014] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 03/27/2013] [Accepted: 03/28/2013] [Indexed: 12/20/2022]
Abstract
The characterisation of the pleiotropic effects of coat colour-associated mutations in mammals illustrates that sensory organs and nerves are particularly affected by disorders because of the shared origin of melanocytes and neurocytes in the neural crest; e.g. the eye-colour is a valuable indicator of disorders in pigment production and eye dysfunctions. Disorders related to coat colour-associated alleles also occur in the skin (melanoma), reproductive tract and immune system. Additionally, the coat colour phenotype of an individual influences its general behaviour and fitness. Mutations in the same genes often produce similar coat colours and pleiotropic effects in different species (e.g., KIT [reproductive disorders, lethality], EDNRB [megacolon] and LYST [CHS]). Whereas similar disorders and similar-looking coat colour phenotypes sometimes have a different genetic background (e.g., deafness [EDN3/EDNRB, MITF, PAX and SNAI2] and visual diseases [OCA2, RAB38, SLC24A5, SLC45A2, TRPM1 and TYR]). The human predilection for fancy phenotypes that ignore disorders and genetic defects is a major driving force for the increase of pleiotropic effects in domestic species and laboratory subjects since domestication has commenced approximately 18,000 years ago.
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Key Words
- AS
- ASIP
- ATRN
- Agouti signalling protein
- Albino
- Angelman syndrome
- Attractin (mahogany)
- BLOC
- Biogenesis of lysosomal organelles complex
- CCSD
- CHS
- CSD
- CSNB
- Canine congenital sensorineural deafness
- Chediak-Higashi syndrome
- Coat colour gene
- Congenital sensorineural deafness
- Congenital stationary night blindness
- Disorder
- EDN3
- EDNRB
- Endothelin 3
- Endothelin receptor type B
- Epistasis
- Fitness
- GS
- Griscelli syndrome (type 1 or 2)
- HPS
- HSCR
- Hermansky-Pudlak syndrome with different types
- Hirschsprung disease
- IPE
- Iris pigment epithelium
- KIT
- KIT ligand (steel factor)
- KITLG
- LFS
- LYST
- Lavender foal syndrome
- Lethal
- Leucism
- Lysosomal trafficking regulator
- MC1R
- MCOA
- MCOLN3
- MGRN1
- MITF
- MYO5A
- Mahogunin ring finger 1 (E3 ubiquitin protein ligase)
- Melanocortin 1 receptor
- Melanoma
- Microphthalmia-associated transcription factor
- Mucolipin 3 (TRPML3)
- Multiple congenital ocular anomalies
- Myosin VA (heavy chain 12, myoxin)
- OA
- OCA
- OCA2
- OLWS
- OSTM1
- Ocular albinism
- Oculocutaneous albinism II (pink-eye dilution homolog)
- Oculocutaneous albinism type 1–4
- Osteopetrosis associated transmembrane protein 1 (Grey lethal osteopetrosis)
- Overo lethal white syndrome
- PAX3
- PMEL
- PWS
- Paired box 3
- Pleiotropy
- Prader-Willi syndrome
- Premelanosome protein (Pmel17, SILV)
- RAB27A
- RAB27A member RAS oncogene family
- RAB38
- RAB38 member RAS oncogene family
- RPE
- Reproduction
- Retinal pigmented epithelium
- SLC24A5
- SLC2A9
- SLC45A2
- SNAI2
- STX17
- Snail homolog 2 (Drosophila), (SLUG), SOX10, SRY (sex determining region Y)-box 10
- Solute carrier family 2 (facilitated glucose transporter), member 9
- Solute carrier family 24, member 5
- Solute carrier family 45, member 2, MATP
- Syntaxin 17
- TRPM1
- TYR
- Tameness
- Transient receptor potential cation channel, subfamily M, member 1 (melastatin-1)
- Tyrosinase, TYRP1, Tyrosinase-related protein 1
- V-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog, tyrosine kinase receptor (c-kit)
- WS
- Waardenburg syndrome (type 1, type 2 combined with Tietz syndrome type 3 Klein-Waardenburg syndrome, type 4 Waardenburg-Shah syndrome)
- alpha-melanocyte-stimulating hormone
- αMSH
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Affiliation(s)
- Monika Reissmann
- Humboldt University Berlin, Department for Crop and Animal Sciences, Berlin, Germany.
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Linderholm A, Larson G. The role of humans in facilitating and sustaining coat colour variation in domestic animals. Semin Cell Dev Biol 2013; 24:587-93. [PMID: 23567209 DOI: 10.1016/j.semcdb.2013.03.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 03/28/2013] [Indexed: 11/27/2022]
Abstract
Though the process of domestication results in a wide variety of novel phenotypic and behavioural traits, coat colour variation is one of the few characteristics that distinguishes all domestic animals from their wild progenitors. A number of recent reviews have discussed and synthesised the hundreds of genes known to underlie specific coat colour patterns in a wide range of domestic animals. This review expands upon those studies by asking how what is known about the causative mutations associated with variable coat colours, can be used to address three specific questions related to the appearance of non wild-type coat colours in domestic animals. Firstly, is it possible that coat colour variation resulted as a by-product of an initial selection for tameness during the early phases of domestication? Secondly, how soon after the process began did domestic animals display coat colour variation? Lastly, what evidence is there that intentional human selection, rather than drift, is primarily responsible for the wide range of modern coat colours? By considering the presence and absence of coat colour genes within the context of the different pathways animals travelled from wild to captive populations, we conclude that coat colour variability was probably not a pleiotropic effect of the selection for tameness, that coat colours most likely appeared very soon after the domestication process began, and that humans have been actively selecting for colour novelty and thus allowing for the proliferation of new mutations in coat colour genes.
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Affiliation(s)
- Anna Linderholm
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham, United Kingdom
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Kavar T, Čeh E, Dovč P. A simplified PCR-based method for detection of gray coat color allele in horse. Mol Cell Probes 2012; 26:256-8. [DOI: 10.1016/j.mcp.2012.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 02/16/2012] [Accepted: 02/28/2012] [Indexed: 11/25/2022]
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Hedrick PW. What is the evidence for heterozygote advantage selection? Trends Ecol Evol 2012; 27:698-704. [PMID: 22975220 DOI: 10.1016/j.tree.2012.08.012] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/09/2012] [Accepted: 08/10/2012] [Indexed: 10/27/2022]
Abstract
Recent genomic data have found that many genes show the signal of selection. How many of these genes are undergoing heterozygote advantage selection is only beginning to be known. Initial genomic surveys have suggested that only a small proportion of loci have polymorphisms maintained by heterozygote advantage and this is consistent with the few examples generated from other approaches within given species. Unless further studies provide large numbers of loci with heterozygote advantage, it appears that loci with heterozygote advantage must be considered only a small minority of all loci in a species. This is not to say that some heterozygote advantage loci do not have important adaptive functions, but that their role in overall evolutionary change might be more of an unusual phenomenon than a major player in adaptation.
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Paleolithic cave rock art, animal coloration, and specific animal habitats. Proc Natl Acad Sci U S A 2012; 109:E1212; author reply E1213. [PMID: 22508997 DOI: 10.1073/pnas.1200729109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Kayser M. Editors' pick: of horses and genes'. INVESTIGATIVE GENETICS 2012; 3:4. [PMID: 22340794 PMCID: PMC3311080 DOI: 10.1186/2041-2223-3-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 02/17/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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