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Nomura T. Ballou's Ancestral Inbreeding Coefficient: Formulation and New Estimate with Higher Reliability. Animals (Basel) 2024; 14:1844. [PMID: 38997956 PMCID: PMC11240364 DOI: 10.3390/ani14131844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Inbreeding is unavoidable in small populations. However, the deleterious effects of inbreeding on fitness-related traits (inbreeding depression) may not be an inevitable phenomenon, since deleterious recessive alleles causing inbreeding depression might be purged from populations through inbreeding and selection. Inbreeding purging has been of great interest in conservation biology and animal breeding, because populations manifesting lower inbreeding depression could be created even with a small number of breeding animals, if inbreeding purging exists. To date, many studies intending to detect inbreeding purging in captive and domesticated animal populations have been carried out using pedigree analysis. Ballou's ancestral inbreeding coefficient (FBAL-ANC) is one of the most widely used measurements to detect inbreeding purging, but the theoretical basis for FBAL-ANC has not been fully established. In most of the published works, estimates from stochastic simulation (gene-dropping simulation) have been used. In this report, the author provides a mathematical basis for FBAL-ANC and proposes a new estimate by hybridizing stochastic and deterministic computation processes. A stochastic simulation suggests that the proposed method could considerably reduce the variance of estimates, compared to ordinary gene-dropping simulation, in which whole gene transmissions in a pedigree are stochastically determined. The favorable property of the proposed method results from the bypass of a part of the stochastic process in the ordinary gene-dropping simulation. Using the proposed method, the reliability of the estimates of FBAL-ANC could be remarkably enhanced. The relationship between FBAL-ANC and other pedigree-based parameters is also discussed.
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Affiliation(s)
- Tetsuro Nomura
- Department of Industrial Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
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Laurent R, Gineau L, Utge J, Lafosse S, Phoeung CL, Hegay T, Olaso R, Boland A, Deleuze JF, Toupance B, Heyer E, Leutenegger AL, Chaix R. Measuring the Efficiency of Purging by non-random Mating in Human Populations. Mol Biol Evol 2024; 41:msae094. [PMID: 38839045 PMCID: PMC11184347 DOI: 10.1093/molbev/msae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024] Open
Abstract
Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs of Asian populations exhibiting different alliance rules and rates of inbreeding, but with similar effective population sizes. The results show that populations with higher rates of inbred matings do not purge deleterious variants more efficiently. Purging therefore has a low efficiency in human populations, and different mating practices lead to a similar mutational load.
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Affiliation(s)
- Romain Laurent
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | - Laure Gineau
- IRD, MERIT, Université Paris Cité, 75006 Paris, France
| | - José Utge
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | - Sophie Lafosse
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | | | - Tatyana Hegay
- Laboratory of Genome-cell technology, Institute of Immunology and Human genomics, Academy of Sciences, Tashkent, Uzbekistan
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Université Paris-Saclay, 91057, Evry, France
| | - Bruno Toupance
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
- Eco-Anthropologie, Université Paris Cité, 75006 Paris, France
| | - Evelyne Heyer
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
| | | | - Raphaëlle Chaix
- Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, 75016 Paris, France
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Nagy I, Nguyen TA. Characterizing and Eliminating the Inbreeding Load. Vet Sci 2023; 11:8. [PMID: 38250914 PMCID: PMC10819885 DOI: 10.3390/vetsci11010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
The authors evaluated the relevant literature related to purging, which is the interaction between selection and inbreeding in which the population may eliminate its inbreeding load at least partially. According to the relevant literature, the inbreeding load and the process of purging were evaluated via pedigree methods based on ancestral inbreeding, the inbreeding-purging model, and expressed opportunity of purging, along with genomic methods. Most ancestral inbreeding-related studies were performed in zoos, where only a small proportion of the studied populations show signs of purging. The inbreeding-purging model was developed with Drosophila, and it was used to evaluate different zoo ungulates and Pannon white rabbits. Purging was detected in both studies. The expressed opportunity of purging was applied in Jersey cattle and Pannon white rabbits. In the Jersey cattle, it had an effect of 12.6% for fitness, while in the Pannon white rabbits, the inbreeding load was between 40% and 80% of its original value. The genomic studies also signalled purging, but they also made it clear that, contrary to the detected purging, the evaluated populations still suffered from inbreeding depression. Therefore, especially for domesticated animals, it can be concluded that deliberate inbreeding with the purpose of generating purging is not advocated.
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Affiliation(s)
- István Nagy
- Institute of Animal Sciences, Hungarian University of Agriculture and Life Sciences (MATE), Guba Sándor u. 40, 7400 Kaposvár, Hungary;
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Choi J, Park J. Exploring inbreeding dynamics by considering reproductive bound and polygyny. CHAOS (WOODBURY, N.Y.) 2023; 33:081103. [PMID: 38060769 DOI: 10.1063/5.0160583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/18/2023] [Indexed: 12/18/2023]
Abstract
Inbreeding is a clinically significant measure of a population dependent on human social structures including the population size or the cultural traits. Here, we propose an expanded and elaborate model to analyze the inbreeding within a population where explicit polygyny and inbreeding bounds are taken into account. Unlike the models presented so far, we implemented biologically realistic assumptions that there is the disproportionate probability of males to reproduce (polygyny) and female reproduction is bounded. Using the proposed model equations, we changed the parameters that represent the polygyny degree, the female reproductive bound correlated to the mutation rate, and the total population size. The disappearance of the polygyny that numerous human societies experienced results in the long-lasting effect of the decreasing inbreeding coefficient. Decreased female reproductive bound correlated with a higher mutation rate reveals similar results. After the effect of each factor is analyzed, we modeled the dynamics of the inbreeding coefficient throughout an imaginary human population where polygyny disappears and late marriage becomes prevalent. In this group, the population size gradually and exponentially increases reflecting the traits of prehistoric human society and rising agricultural productivity. To observe how late and less marriage, the feature of the modern developed society, affects the inbreeding dynamics, the female reproductive bound and the population size were assumed to decrease after the population upsurge. The model can explain the decreasing trend of the prehistoric inbreeding coefficient of the actual human population and predict how the trend will be shifted when traits of modern societies continue.
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Affiliation(s)
- Jibeom Choi
- Department of Applied Mathematics, College of Applied Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Junpyo Park
- Department of Applied Mathematics, College of Applied Science, Kyung Hee University, Yongin 17104, Republic of Korea
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The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India. Genes Genomics 2023; 45:813-825. [PMID: 36807878 DOI: 10.1007/s13258-023-01367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders. OBJECTIVE The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes. METHODS For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (FROH) and homozygous loci-based inbreeding estimate (FHOM). RESULTS A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of FROH, FHOM, and pedigree-based inbreeding estimate (FPED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity. CONCLUSIONS This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.
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6
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Dorsey OC, Rosenthal GG. A taste for the familiar: explaining the inbreeding paradox. Trends Ecol Evol 2023; 38:132-142. [PMID: 36241551 DOI: 10.1016/j.tree.2022.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 09/04/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022]
Abstract
The negative consequences of inbreeding have led animal biologists to assume that mate choice is generally biased against relatives. However, inbreeding avoidance is highly variable and by no means the rule across animal taxa. Even when inbreeding is costly, there are numerous examples of animals failing to avoid inbreeding or even preferring to mate with close kin. We argue that selective and mechanistic constraints interact to limit the evolution of inbreeding avoidance, notably when there is a risk of mating with heterospecifics and losing fitness through hybridization. Further, balancing inbreeding avoidance with conspecific mate preference may drive the evolution of multivariate sexual communication. Studying different social and sexual decisions within the same species can illuminate trade-offs among mate-choice mechanisms.
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Affiliation(s)
- Owen C Dorsey
- Program in Ecology and Evolutionary Biology and Department of Biology, Texas A&M University, TX, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca", Calnali, Hidalgo, Mexico.
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca", Calnali, Hidalgo, Mexico; Department of Biology, University of Padua, Padua, Italy
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Analysis of Inbreeding Effects on Survival at Birth of Pannon White Rabbits Using the Inbreeding-Purging Model. DIVERSITY 2023. [DOI: 10.3390/d15010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mating between related animals is an inevitable consequence of a closed population structure especially when it coincides with a small population size. As a result, inbreeding depression may be encountered especially when considering fitness traits. However, under certain circumstances, the joint effects of inbreeding and selection may at least partly purge the detrimental genes from the population. In the course of this study, our objective was to determine the status of purging and to quantify the magnitude of the eliminated genetic load for the survival at birth of Pannon White rabbit kits maintained in a closed nucleus population. The evolution of the survival at birth was evaluated by applying the PurgeR R package based on the inbreeding-purging model. In the period from 1992 to 2017, 22.718 kindling records were analyzed. According to the heuristic approach, the purging coefficient reached the maximum possible value of 0.5 when estimating between 1992 and 1997. Based on the expected fitness over generations and on the expressed opportunity of purging, the beneficial effects of purging could be expected after 10 generations. The proportion of the purged genetic load could be between 20% and 60%. While the results obtained are not entirely conclusive, they do raise the possibility that some of the inbreeding load was caused, at least in part, by genes that could be successfully removed from the population by purging.
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Poczai P, Santiago-Blay JA, Sekerák J, Bariska I, Szabó AT. Mimush Sheep and the Spectre of Inbreeding: Historical Background for Festetics's Organic and Genetic Laws Four Decades Before Mendel's Experiments in Peas. JOURNAL OF THE HISTORY OF BIOLOGY 2022; 55:495-536. [PMID: 35670984 PMCID: PMC9668798 DOI: 10.1007/s10739-022-09678-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
The upheavals of late eighteenth century Europe encouraged people to demand greater liberties, including the freedom to explore the natural world, individually or as part of investigative associations. The Moravian Agricultural and Natural Science Society, organized by Christian Carl André, was one such group of keen practitioners of theoretical and applied scientific disciplines. Headquartered in the "Moravian Manchester" Brünn (nowadays Brno), the centre of the textile industry, society members debated the improvement of sheep wool to fulfil the needs of the Habsburg armies fighting in the Napoleonic Wars. Wool, as the raw material of soldiers' clothing, could influence the war's outcome. During the early nineteenth century, wool united politics, economics, and science in Brno, where breeders and natural scientists investigated the possibilities of increasing wool production. They regularly discussed how "climate" or "seed" characteristics influenced wool quality and quantity. Breeders and academics put their knowledge into immediate practice to create sheep with better wool traits through consanguineous matching of animals and artificial selection. This apparent disregard for the incest taboo, however, was viewed as violating natural laws and cultural norms. The debate intensified between 1817 and 1820, when a Hungarian veteran soldier, sheep breeder, and self-taught natural scientist, Imre (Emmerich) Festetics, displayed his inbred Mimush sheep, which yielded wool extremely well suited for the fabrication of light but strong garments. Members of the Society questioned whether such "bastard sheep" would be prone to climatic degeneration, should be regarded as freaks of nature, or could be explained by natural laws. The exploration of inbreeding in sheep began to be distilled into hereditary principles that culminated in 1819 with Festetics's "laws of organic functions" and "genetic laws of nature," four decades before Gregor Johann Mendel's seminal work on heredity in peas.
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Affiliation(s)
- Péter Poczai
- Finnish Museum of Natural History, University of Helsinki, PO Box 7, 00014, Helsinki, Finland.
- Institute of Advanced Studies Kőszeg (iASK), PO Box 4, Kőszeg, 9731, Hungary.
- Museomics Research Group, Department of Biosciences, Viikki Plant Science Centre (ViPS), University of Helsinki, PO Box 65, 00014, Helsinki, Finland.
| | - Jorge A Santiago-Blay
- Department of Paleobiology, National Museum of Natural History, Washington, DC, 20560, USA
- The Pennsylvania State University, 1031 Edgecomb Avenue, York, PA, 17403, USA
| | - Jiří Sekerák
- Department of the History of Biological Science, The Moravian Museum, Zelny trh 6, 659 37, Brno, Czech Republic
| | - István Bariska
- Vas County Archives Kőszeg, Hungarian National Archives, Kőszeg, Jurisics tér 2, 9730, Hungary
| | - Attila T Szabó
- BioDatLab, Balatonfüred, Bartók Béla u. 13, 8230, Hungary
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9
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Poczai P, Santiago-Blay JA. Chip Off the Old Block: Generation, Development, and Ancestral Concepts of Heredity. Front Genet 2022; 13:814436. [PMID: 35356423 PMCID: PMC8959437 DOI: 10.3389/fgene.2022.814436] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
Heredity is such a fundamental concept that it is hard to imagine a world where the connection between parents and offspring is not understood. Three hundred years ago thinking of the phenomenon of heredity bore on a cluster of distinct philosophical questions inherited from antiquity concerning the nature and origin of substances or beings that lacked biological meaning. We are reminded of this philosophical heritage by the fact that in the 18th century the study of reproduction, embryology and development was referred to as “the science of generation”. It is now clear that reproduction, the biological process by which parents produce offspring, is a fundamental feature of all life on Earth. Heredity, the transmission of traits from parents to offspring via sexual or asexual reproduction, allows differences between individuals to accumulate and evolve through natural selection. Genetics is the study of heredity, and in particular, variation of fundamental units responsible for heredity. Ideas underlying this theory evolved in considerably different and unrelated ways across a number of knowledge domains, including philosophy, medicine, natural history, and breeding. The fusion of these different domains into a single comprehensive theory in 19th century biology was a historically and culturally interdependent process, thus examining genetic prehistory should unravel these entanglements. The major goal of our review is tracing the various threads of thought that gradually converged into our contemporary understanding of heredity.
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Affiliation(s)
- Péter Poczai
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Institute of Advanced Science Kőszeg (iASK), Kőszeg, Hungary
| | - Jorge A Santiago-Blay
- Department of Paleobiology, National Museum of Natural History, Washington, DC, United States.,The Pennsylvania State University, York, PA, United States
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Parental relatedness through time revealed by runs of homozygosity in ancient DNA. Nat Commun 2021; 12:5425. [PMID: 34521843 PMCID: PMC8440622 DOI: 10.1038/s41467-021-25289-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 07/21/2021] [Indexed: 02/08/2023] Open
Abstract
Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide.
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Ceballos FC, Gürün K, Altınışık NE, Gemici HC, Karamurat C, Koptekin D, Vural KB, Mapelli I, Sağlıcan E, Sürer E, Erdal YS, Götherström A, Özer F, Atakuman Ç, Somel M. Human inbreeding has decreased in time through the Holocene. Curr Biol 2021; 31:3925-3934.e8. [PMID: 34216555 DOI: 10.1016/j.cub.2021.06.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/19/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022]
Abstract
The history of human inbreeding is controversial.1 In particular, how the development of sedentary and/or agricultural societies may have influenced overall inbreeding levels, relative to those of hunter-gatherer communities, is unclear.2-5 Here, we present an approach for reliable estimation of runs of homozygosity (ROHs) in genomes with ≥3× mean sequence coverage across >1 million SNPs and apply this to 411 ancient Eurasian genomes from the last 15,000 years.5-34 We show that the frequency of inbreeding, as measured by ROHs, has decreased over time. The strongest effect is associated with the Neolithic transition, but the trend has since continued, indicating a population size effect on inbreeding prevalence. We further show that most inbreeding in our historical sample can be attributed to small population size instead of consanguinity. Cases of high consanguinity were rare and only observed among members of farming societies in our sample. Despite the lack of evidence for common consanguinity in our ancient sample, consanguineous traditions are today prevalent in various modern-day Eurasian societies,1,35-37 suggesting that such practices may have become widespread within the last few millennia.
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Affiliation(s)
- Francisco C Ceballos
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - N Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Ankara, Turkey
| | - Hasan Can Gemici
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Cansu Karamurat
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Dilek Koptekin
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Igor Mapelli
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Yılmaz Selim Erdal
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Ankara, Turkey
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
| | - Füsun Özer
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Ankara, Turkey
| | - Çiğdem Atakuman
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey.
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The genetic structure of the Turkish population reveals high levels of variation and admixture. Proc Natl Acad Sci U S A 2021; 118:2026076118. [PMID: 34426522 DOI: 10.1073/pnas.2026076118] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The construction of population-based variomes has contributed substantially to our understanding of the genetic basis of human inherited disease. Here, we investigated the genetic structure of Turkey from 3,362 unrelated subjects whose whole exomes (n = 2,589) or whole genomes (n = 773) were sequenced to generate a Turkish (TR) Variome that should serve to facilitate disease gene discovery in Turkey. Consistent with the history of present-day Turkey as a crossroads between Europe and Asia, we found extensive admixture between Balkan, Caucasus, Middle Eastern, and European populations with a closer genetic relationship of the TR population to Europeans than hitherto appreciated. We determined that 50% of TR individuals had high inbreeding coefficients (≥0.0156) with runs of homozygosity longer than 4 Mb being found exclusively in the TR population when compared to 1000 Genomes Project populations. We also found that 28% of exome and 49% of genome variants in the very rare range (allele frequency < 0.005) are unique to the modern TR population. We annotated these variants based on their functional consequences to establish a TR Variome containing alleles of potential medical relevance, a repository of homozygous loss-of-function variants and a TR reference panel for genotype imputation using high-quality haplotypes, to facilitate genome-wide association studies. In addition to providing information on the genetic structure of the modern TR population, these data provide an invaluable resource for future studies to identify variants that are associated with specific phenotypes as well as establishing the phenotypic consequences of mutations in specific genes.
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Curik I, Kövér G, Farkas J, Szendrő Z, Romvári R, Sölkner J, Nagy I. Inbreeding depression for kit survival at birth in a rabbit population under long-term selection. Genet Sel Evol 2020; 52:39. [PMID: 32640975 PMCID: PMC7346452 DOI: 10.1186/s12711-020-00557-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 06/26/2020] [Indexed: 01/01/2023] Open
Abstract
Background Accumulation of detrimental mutations in small populations leads to inbreeding depression of fitness traits and a higher frequency of genetic defects, thus increasing risk of extinction. Our objective was to quantify the magnitude of inbreeding depression for survival at birth, in a closed rabbit population under long-term selection. Methods We used an information theory-based approach and multi-model inference to estimate inbreeding depression and its purging with respect to the trait ‘kit survival at birth’ over a 25-year period in a closed population of Pannon White rabbits, by analysing 22,718 kindling records. Generalised linear mixed models based on the logit link function were applied, which take polygenic random effects into account. Results Our results indicated that inbreeding depression occurred during the period 1992–1997, based on significant estimates of the z-standardised classical inbreeding coefficient z.FL (CI95% − 0.12 to − 0.03) and of the new inbreeding coefficient of the litter z.FNEWL (CI95% − 0.13 to − 0.04) as well as a 59.2% reduction in contributing founders. Inbreeding depression disappeared during the periods 1997–2007 and 2007–2017. For the period 1992–1997, the best model resulted in a significantly negative standardised estimate of the new inbreeding coefficient of the litter and a significantly positive standardised estimate of Kalinowski’s ancestral inbreeding coefficient of the litter (CI95% 0.01 to 0.17), which indicated purging of detrimental load. Kindling season and parity had effects on survival at birth that differed across the three periods of 1992–1997, 1997–2007 and 2007–2017. Conclusions Our results support the existence of inbreeding depression and its purging with respect to kit survival at birth in this Pannon White rabbit population. However, we were unable to exclude possible confounding from the effects of parity and potentially other environmental factors during the study period, thus our results need to be extended and confirmed in other populations.
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Affiliation(s)
- Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia.
| | - György Kövér
- Institute of Methodology, Faculty of Economic Science, Kaposvár University, Kaposvár, Hungary
| | - János Farkas
- Institute of Methodology, Faculty of Economic Science, Kaposvár University, Kaposvár, Hungary
| | - Zsolt Szendrő
- Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, Kaposvár University, Kaposvár, Hungary
| | - Róbert Romvári
- Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, Kaposvár University, Kaposvár, Hungary
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - Istvan Nagy
- Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, Kaposvár University, Kaposvár, Hungary.
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Vilas R, Ceballos FC, Al-Soufi L, González-García R, Moreno C, Moreno M, Villanueva L, Ruiz L, Mateos J, González D, Ruiz J, Cinza A, Monje F, Álvarez G. Is the "Habsburg jaw" related to inbreeding? Ann Hum Biol 2019; 46:553-561. [PMID: 31786955 DOI: 10.1080/03014460.2019.1687752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Background: The "Habsburg jaw" has long been associated with inbreeding due to the high prevalence of consanguineous marriages in the Habsburg dynasty. However, it is thought that mandibular prognathism (MP) is under the influence of a dominant major gene.Aim: To investigate the relationship between the "Habsburg jaw" and the pedigree-based inbreeding coefficient (F) as a relative measure of genome homozygosity.Subjects and methods: The degree of MP and maxillary deficiency (MD) of 15 members of the Habsburg dynasty was quantified through the clinical analysis of 18 dysmorphic features diagnosed from 66 portraits.Results: A statistically significant correlation (r = 0.711, p = 0.003) between MP and MD was observed among individuals. Only MP showed a statistically significant positive regression on F as evidenced from univariate analysis (b = 6.36 ± 3.34, p = 0.040) and multivariate analysis (PCA) performed from single dysmorphic features (b = 14.10 ± 6.62, p = 0.027, for the first PC).Conclusion: Both MP and MD are generally involved in the "Habsburg jaw." The results showed a greater sensitivity to inbreeding for the lower third of the face and suggest a positive association between the "Habsburg jaw" and homozygosity and therefore a basically recessive inheritance pattern.
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Affiliation(s)
- Román Vilas
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco C Ceballos
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Laila Al-Soufi
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Raúl González-García
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Carlos Moreno
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Manuel Moreno
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Laura Villanueva
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Luis Ruiz
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Jesús Mateos
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - David González
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Jennifer Ruiz
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Aitor Cinza
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Florencio Monje
- Department of Oral and Maxillofacial Surgery, University Hospital Infanta Cristina, Badajoz, Spain
| | - Gonzalo Álvarez
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela, Spain
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15
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Álvarez G, Vilas R, Ceballos FC, Carvalhal H, Peters TJ. Inbreeding in the last ruling dynasty of Portugal: The house of Braganza. Am J Hum Biol 2019; 31:e23210. [PMID: 30585365 DOI: 10.1002/ajhb.23210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/19/2018] [Accepted: 12/06/2018] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVES To determine whether: (1) there are high levels of inbreeding in a European royal dynasty that continues until the 20th century, and (2) whether inbreeding is negatively associated with pre-reproductive survival and longevity. METHODS Genealogical information of all Braganza monarchs (1640-1910) was used to compute the individual's inbreeding coefficient (F) and the coefficient of kinship (θ) of the marriage which were examined in relation to two life-history traits. RESULTS Mean F of the monarchs was 0.0530, close to that corresponding to the progeny of first cousins (F = 0.0625). A statistically significant effect of maternal inbreeding on offspring longevity (P = 0.037) and a significant effect of individual's F on survival from birth to 10 years (P = 0.023) were detected. CONCLUSIONS Another European royal dynasty besides the Habsburgs had high levels of inbreeding, especially high during a period after the early modern age. The lineage showed evidence of inbreeding depression. Results support the hypothesis that an increase in maternal homozygosity affects the lifespan of the progeny.
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Affiliation(s)
- Gonzalo Álvarez
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Román Vilas
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco C Ceballos
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Timothy J Peters
- Ironbridge Institute, University of Birmingham, Birmingham, United Kingdom
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16
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Ríos L, Kivell TL, Lalueza-Fox C, Estalrrich A, García-Tabernero A, Huguet R, Quintino Y, de la Rasilla M, Rosas A. Skeletal Anomalies in The Neandertal Family of El Sidrón (Spain) Support A Role of Inbreeding in Neandertal Extinction. Sci Rep 2019; 9:1697. [PMID: 30737446 PMCID: PMC6368597 DOI: 10.1038/s41598-019-38571-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 12/31/2018] [Indexed: 12/12/2022] Open
Abstract
Neandertals disappeared from the fossil record around 40,000 bp, after a demographic history of small and isolated groups with high but variable levels of inbreeding, and episodes of interbreeding with other Paleolithic hominins. It is reasonable to expect that high levels of endogamy could be expressed in the skeleton of at least some Neandertal groups. Genetic studies indicate that the 13 individuals from the site of El Sidrón, Spain, dated around 49,000 bp, constituted a closely related kin group, making these Neandertals an appropriate case study for the observation of skeletal signs of inbreeding. We present the complete study of the 1674 identified skeletal specimens from El Sidrón. Altogether, 17 congenital anomalies were observed (narrowing of the internal nasal fossa, retained deciduous canine, clefts of the first cervical vertebra, unilateral hypoplasia of the second cervical vertebra, clefting of the twelfth thoracic vertebra, diminutive thoracic or lumbar rib, os centrale carpi and bipartite scaphoid, tripartite patella, left foot anomaly and cuboid-navicular coalition), with at least four individuals presenting congenital conditions (clefts of the first cervical vertebra). At 49,000 years ago, the Neandertals from El Sidrón, with genetic and skeletal evidence of inbreeding, could be representative of the beginning of the demographic collapse of this hominin phenotype.
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Affiliation(s)
- L Ríos
- Department of Physical Anthropology, Aranzadi Zientzia Elkartea, Zorroagagaina 11, 20014, Donostia, Gipuzkoa, Basque Country, Spain.
| | - T L Kivell
- Skeletal Biology Research Centre, School of Anthropology and Conservation, University of Kent, Marlowe Building, Canterbury, CT2 7NR, UK.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - C Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
| | - A Estalrrich
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria IIIPC (Universidad de Cantabria, Santander, Gobierno de Cantabria), Avda. de los Castros 52, 39005, Santander, Cantabria, Spain
| | - A García-Tabernero
- Paleoanthropology Group, Department of Paleobiology. Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain
| | - R Huguet
- IPHES, Institut Catala de Paleoecologia Humana i Evolució Social, Campus Sescelades URV (Edifici W3), 43007, Tarragona, Spain.,Area de Prehistoria, Universitat Rovira i Virgili, Avda. Catalunya 35, 43002, Tarragona, Spain.,Unidad asociada al CSIC, Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, Calle José Gutierrez Abascal 2, 28006, Madrid, Spain
| | - Y Quintino
- Laboratorio de Evolución Humana, Dpto. de Ciencias Históricas y Geografía, Universidad de Burgos, Edificio I+D+i, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain
| | - M de la Rasilla
- Área de Prehistoria Departamento de Historia, Universidad de Oviedo, Calle Teniente Alfonso Martínez s/n, 33011, Oviedo, Spain
| | - A Rosas
- Paleoanthropology Group, Department of Paleobiology. Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain.
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17
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Lemes RB, Nunes K, Carnavalli JEP, Kimura L, Mingroni-Netto RC, Meyer D, Otto PA. Inbreeding estimates in human populations: Applying new approaches to an admixed Brazilian isolate. PLoS One 2018; 13:e0196360. [PMID: 29689090 PMCID: PMC5916862 DOI: 10.1371/journal.pone.0196360] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/11/2018] [Indexed: 02/06/2023] Open
Abstract
The analysis of genomic data (~400,000 autosomal SNPs) enabled the reliable estimation of inbreeding levels in a sample of 541 individuals sampled from a highly admixed Brazilian population isolate (an African-derived quilombo in the State of São Paulo). To achieve this, different methods were applied to the joint information of two sets of markers (one complete and another excluding loci in patent linkage disequilibrium). This strategy allowed the detection and exclusion of markers that biased the estimation of the average population inbreeding coefficient (Wright's fixation index FIS), which value was eventually estimated as around 1% using any of the methods we applied. Quilombo demographic inferences were made by analyzing the structure of runs of homozygosity (ROH), which were adapted to cope with a highly admixed population with a complex foundation history. Our results suggest that the amount of ROH <2Mb of admixed populations should be somehow proportional to the genetic contribution from each parental population.
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Affiliation(s)
- Renan B. Lemes
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Juliana E. P. Carnavalli
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Lilian Kimura
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Regina C. Mingroni-Netto
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Paulo A. Otto
- Department of Genetics and Evolutionary Biology, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- * E-mail:
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18
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López-Cortegano E, Bersabé D, Wang J, García-Dorado A. Detection of genetic purging and predictive value of purging parameters estimated in pedigreed populations. Heredity (Edinb) 2018; 121:38-51. [PMID: 29434337 DOI: 10.1038/s41437-017-0045-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 11/09/2022] Open
Abstract
The consequences of inbreeding for fitness are important in evolutionary and conservation biology, but can critically depend on genetic purging. However, estimating purging has proven elusive. Using PURGd software, we assess the performance of the Inbreeding-Purging (IP) model and of ancestral inbreeding (Fa) models to detect purging in simulated pedigreed populations, and to estimate parameters that allow reliably predicting the evolution of fitness under inbreeding. The power to detect purging in a single small population of size N is low for both models during the first few generations of inbreeding (t ≈ N/2), but increases for longer periods of slower inbreeding and is, on average, larger for the IP model. The ancestral inbreeding approach overestimates the rate of inbreeding depression during long inbreeding periods, and produces joint estimates of the effects of inbreeding and purging that lead to unreliable predictions for the evolution of fitness. The IP estimates of the rate of inbreeding depression become downwardly biased when obtained from long inbreeding processes. However, the effect of this bias is canceled out by a coupled downward bias in the estimate of the purging coefficient so that, unless the population is very small, the joint estimate of these two IP parameters yields good predictions of the evolution of mean fitness in populations of different sizes during periods of different lengths. Therefore, our results support the use of the IP model to detect inbreeding depression and purging, and to estimate reliable parameters for predictive purposes.
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Affiliation(s)
- Eugenio López-Cortegano
- Departamento de Genética. Facultad de Biología, Universidad Complutense, 28040, Madrid, Spain
| | - Diego Bersabé
- Departamento de Genética. Facultad de Biología, Universidad Complutense, 28040, Madrid, Spain
| | - Jinliang Wang
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
| | - Aurora García-Dorado
- Departamento de Genética. Facultad de Biología, Universidad Complutense, 28040, Madrid, Spain.
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19
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Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF. Runs of homozygosity: windows into population history and trait architecture. Nat Rev Genet 2018; 19:220-234. [PMID: 29335644 DOI: 10.1038/nrg.2017.109] [Citation(s) in RCA: 395] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Long runs of homozygosity (ROH) arise when identical haplotypes are inherited from each parent and thus a long tract of genotypes is homozygous. Cousin marriage or inbreeding gives rise to such autozygosity; however, genome-wide data reveal that ROH are universally common in human genomes even among outbred individuals. The number and length of ROH reflect individual demographic history, while the homozygosity burden can be used to investigate the genetic architecture of complex disease. We discuss how to identify ROH in genome-wide microarray and sequence data, their distribution in human populations and their application to the understanding of inbreeding depression and disease risk.
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Affiliation(s)
- Francisco C Ceballos
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa.,Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - David W Clark
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Braamfontein 2000, Johannesburg, South Africa
| | - James F Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
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20
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Casellas J. On individual-specific prediction of hidden inbreeding depression load. J Anim Breed Genet 2017; 135:37-44. [PMID: 29230876 DOI: 10.1111/jbg.12308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 11/17/2017] [Indexed: 11/29/2022]
Abstract
Inbreeding depression is caused by increased homozygosity in the genome and merges two genetic mechanisms, a higher impact from recessive mutations and the waste of overdominance contributions. It is of major concern for the conservation of endangered populations of plants and animals, as major abnormalities are more frequent in inbred families than in outcrosses. Nevertheless, we lack appropriate analytical methods to estimate the hidden inbreeding depression load (IDL) in the genome of each individual. Here, a new mixed linear model approach has been developed to account for the inbreeding depression-related background of each individual in the pedigree. Within this context, inbred descendants contributed relevant information to predict the IDL contained in the genome of a given ancestor; moreover, known relationships spread these predictions to the remaining individuals in the pedigree, even if not contributing inbred offspring. Results obtained from the analysis of weaning weight in the MARET rabbit population demonstrated that the genetic background of inbreeding depression distributed heterogeneously across individuals and inherited generation by generation. Moreover, this approach was clearly preferred in terms of model fit and complexity when compared with classical approaches to inbreeding depression. This methodology must be viewed as a new tool for a better understanding of inbreeding in domestic and wild populations.
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Affiliation(s)
- J Casellas
- Grup de Recerca en Millora Genètica Molecular Veterinària, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
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21
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Predictive Model and Software for Inbreeding-Purging Analysis of Pedigreed Populations. G3-GENES GENOMES GENETICS 2016; 6:3593-3601. [PMID: 27605515 PMCID: PMC5100858 DOI: 10.1534/g3.116.032425] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The inbreeding depression of fitness traits can be a major threat to the survival of populations experiencing inbreeding. However, its accurate prediction requires taking into account the genetic purging induced by inbreeding, which can be achieved using a “purged inbreeding coefficient”. We have developed a method to compute purged inbreeding at the individual level in pedigreed populations with overlapping generations. Furthermore, we derive the inbreeding depression slope for individual logarithmic fitness, which is larger than that for the logarithm of the population fitness average. In addition, we provide a new software, PURGd, based on these theoretical results that allows analyzing pedigree data to detect purging, and to estimate the purging coefficient, which is the parameter necessary to predict the joint consequences of inbreeding and purging. The software also calculates the purged inbreeding coefficient for each individual, as well as standard and ancestral inbreeding. Analysis of simulation data show that this software produces reasonably accurate estimates for the inbreeding depression rate and for the purging coefficient that are useful for predictive purposes.
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22
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Kirkpatrick BE, Rashkin MD. Ancestry Testing and the Practice of Genetic Counseling. J Genet Couns 2016; 26:6-20. [DOI: 10.1007/s10897-016-0014-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 08/30/2016] [Indexed: 12/20/2022]
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23
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Farrell LL, Schoenebeck JJ, Wiener P, Clements DN, Summers KM. The challenges of pedigree dog health: approaches to combating inherited disease. Canine Genet Epidemiol 2015; 2:3. [PMID: 26401331 PMCID: PMC4579364 DOI: 10.1186/s40575-015-0014-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/13/2015] [Indexed: 01/29/2023] Open
Abstract
The issue of inherited disorders and poor health in pedigree dogs has been widely discussed in recent years. With the advent of genome-wide sequencing technologies and the increasing development of new diagnostic DNA disease tests, the full extent and prevalence of inherited disorders in pedigree dogs is now being realized. In this review we discuss the challenges facing pedigree dog breeds: the common pitfalls and problems associated with combating single gene mediated disorders, phenotypic selection on complex disorders, and ways of managing genetic diversity. Breeding strategies incorporating screening schemes have been shown to be successful in significantly reducing the prevalence of an inherited disorder and improving the overall health in certain breeds. However, with 215 breeds officially recognized by the Kennel Club in the United Kingdom and 396 inherited disorders currently identified, many breeds have reached the point at which successfully breeding away from susceptible individuals at a population-wide scale will require new genomic selection strategies in combination with currently available breeding schemes. Whilst DNA-based tests identifying disease causing mutation(s) remain the most informative and effective approach for single gene disorder disease management, they must be used along with current screening schemes, genomic selection, and pedigree information in breeding programs in the effort to maintain genetic diversity while also significantly reducing the number of inherited disorders in pedigree dogs.
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Affiliation(s)
- Lindsay L Farrell
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Jeffrey J Schoenebeck
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Pamela Wiener
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Dylan N Clements
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
| | - Kim M Summers
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EHG25 9RG UK
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24
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Álvarez G, Ceballos FC, Berra TM. Darwin was right: inbreeding depression on male fertility in the Darwin family. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12433] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Gonzalo Álvarez
- Department of Genetics; Faculty of Biology; University of Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Francisco C. Ceballos
- Department of Genetics; Faculty of Biology; University of Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Tim M. Berra
- Department of Evolution; Ecology and Organismal Biology; The Ohio State University; 1760 University Dr.; Mansfield OH 44906 USA
- Research Institute for the Environment and Livelihoods; Charles Darwin University; Darwin NT Australia
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25
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Callaway E. Inbred royals show traces of natural selection. Nature 2013. [DOI: 10.1038/nature.2013.12837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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