DOCSLIB.ORG

Widespread Genetic Incompatibility in C. Elegans Maintained By

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Widespread Genetic Incompatibility in C. Elegans Maintained By RESEARCH ARTICLE Lethality caused by a paternal effect by zygotic interaction. The segregation of em- bryonic lethality opposite the visible marker Widespread Genetic Incompatibility implied that the arrested embryos represented those homozygous for the Hawaii allele of a locus linked in C. Elegans Maintained by to the marker, on the left arm of chromosome I. Because embryonic lethality within the Hawaii Balancing Selection strain itself is very low (less than 1%), we reasoned that F2 lethality reflected an incompatibility Hannah S. Seidel,*† Matthew V. Rockman,*† Leonid Kruglyak* between the Hawaii allele of this locus and an element in the Bristol genome. We also reasoned Natural selection is expected to eliminate genetic incompatibilities from interbreeding populations. that it did not reflect two synthetically lethal alleles We have discovered a globally distributed incompatibility in the primarily selfing species segregatingintheF2 population because such an Caenorhabditis elegans that has been maintained despite its negative consequences for fitness. interaction would affect less than one-quarter of F2 Embryos homozygous for a naturally occurring deletion of the zygotically acting gene zeel-1 embryos (up to 3/16, depending on linkage and arrest if their sperm parent carries an incompatible allele of a second, paternal-effect locus, peel-1. dominance). One-quarter lethality is expected, The two interacting loci are tightly linked, with incompatible alleles occurring in linkage however, if the incompatibility involves an inter- disequilibrium in two common haplotypes. These haplotypes exhibit elevated sequence action between the genotype of the zygote and a divergence, and population genetic analyses of this region indicate that natural selection is maternal or paternal effect. preserving both haplotypes in the population. Our data suggest that long-term maintenance To test this possibility, Hawaii × Bristol F1 of a balanced polymorphism has permitted the incompatibility to persist despite gene flow males and hermaphrodites were separately back- across the rest of the genome. crossed to Hawaii individuals, and lethality was scored among the resulting embryos. We ob- aenorhabditis elegans is a globally dis- study natural genetic variation in C. elegans, served 50% lethality when F1 males were mated tributed species of free-living bacteria- and we genotyped the RILs at 1450 single- to Hawaii hermaphrodites but less than 2% C eating nematode. Although rare males nucleotide polymorphism (SNP) markers (8). lethality in the reciprocal cross (Fig. 1). Thus, on February 9, 2008 contribute at a low rate to outcrossing, C. elegans We noted that a region on the left arm of lethality depends on both paternal and zygotic occurs primarily as inbred self-fertilizing her- chromsome I exhibited a dramatic deficit of genotype, but is independent of maternal cyto- maphrodites (1–4). A wild isolate from Hawaii, Hawaii alleles among the RILs. Of 239 RILs, plasm. (Both Hawaii and F1 hermaphrodites CB4856, has been identified among well-studied only 5 carried the Hawaii allele at the most produced dead embryos, 50% and 25%, respec- isolates as the most divergent at the sequence skewed marker, and simulations of the intercross tively, when mated to F1 males.) In sum, lethal- level from the standard laboratory strain, N2, pedigree indicated that this allele frequency skew ity appears to result from a paternal effect by derived from an isolate from Bristol, England could not have arisen by drift, suggesting that zygotic interaction, whereby embryos homozy- (5–7). As a result of this sequence divergence, selection had acted during construction of the gous for the Hawaii allele of a zygotically act- — the Hawaiian strain is widely used to map RILs (fig. S1). We then crossed Hawaii to a ing locus fail to hatch when the sperm parent www.sciencemag.org mutations induced in the Bristol background. Bristol strain carrying a visible marker located male or hermaphrodite—is a Hawaii × Bristol Genetic incompatibility between Bristol 10 cM from the most skewed RIL marker, and heterozygote. An interaction between a paternal and Hawaii. We generated recombinant inbred we examined F2 progeny produced by self- effect and a zygotically acting gene is surprising lines (RILs) from the 10th generation of an ad- fertilizing F1 hermaphrodites. Surprisingly, ap- because sperm-supplied factors are expected to vanced intercross between Bristol and Hawaii to proximately 25% of F2 progeny arrested as act during fertilization and first cleavage (9), embryos, and embryonic lethality segregated whereas early embryogenesis is primarily con- Lewis-Sigler Institute for Integrative Genomics and Depart- opposite the visible marker (Table 1). F2 lethality trolled by maternally contributed factors, and ment of Ecology and Evolutionary Biology, Princeton was not an effect of the marker: Self-fertilizing F zygotic transcription is not known to occur be- Downloaded from University, Princeton, NJ 08544, USA. 1 hermaphrodites derived from reciprocal crosses fore the four-cell stage (10). *To whom correspondence should be addressed. E-mail: [email protected] (H.S.S.); mrockman@princeton. between Hawaii and wild-type Bristol produced Tight linkage of the zygotically acting and edu (M.V.R.); [email protected] (L.K.) 25% dead embryos, as did F1 hermaphrodites paternal-effect loci. To understand the genetic †These authors contributed equally to this work. mated to F1 males (Fig. 1). basis of the incompatibility, we used the RILs F F F F Hawaii Hawaii F Table 1. F2 lethality segregates opposite visible 1 1 1 1 1 marker bli-3, located 10 cM from the most skewed RIL marker. Genotypes of F2 progeny from selfing x x x Bristol/bli-3 and Hawaii/bli-3 hermaphrodites were scored. Embryonic lethality from selfing Hawaii/bli-3 hermaphrodites was slightly greater than 25% because the visible marker introduces a small percentage of lethality. Bristol/bli-3 Hawaii/bli-3 F2 genotype 24.0%(880) 26.5%(1764) 50.4%(4432) 1.7%(4160) hermaphrodite hermaphrodite bli-3/bli-3 21.7% (128) 21.8% (128) Fig. 1. Paternal effect by zygotic lethality. The percent of embryonic lethality (total) was scored from the crosses shown. Orange and blue indicate Bristol and Hawaii haplotypes, respectively. Pie charts show the bli-3/+ 49.9% (295) 42.0% (246) proportions of embryos that hatched (white) and failed to hatch (black). F individuals were derived from +/+ 24.5% (145) 5.1% (30) 1 reciprocal Bristol × Hawaii crosses. Embryonic lethality from selfing Bristol and Hawaii hermaphrodites, Arrested embryos 3.9% (23) 31.1% (182) reciprocal Bristol × Hawaii, and reciprocal Bristol × F1 crosses was less than 0.8% (n > 240 embryos for each). www.sciencemag.org SCIENCE VOL 319 1 FEBRUARY 2008 589 RESEARCH ARTICLE to map both the zygotically acting locus, zeel-1 (zygotic epistatic embryonic lethal–1), and the paternal-effect locus, peel-1 (paternal effect epistatic embryonic lethal–1). We crossed RILs to Bristol and Hawaii and scored lethality subclone. Arrows among embryos laid by self-fertilizing F1 her- 2,376k maphrodites and Hawaii hermaphrodites mated to F1 males. The pattern of lethality among F2 and backcross embryos was consistent with each RIL carrying either the Bristol alleles of Y39G10AR.5 both zeel-1 and peel-1 or the Hawaii alleles of both. We identified only one genomic interval in which all lines of the former class carried the Bristol haplotype and all lines of the latter class carried the Hawaii haplotype. Thus, both zeel-1 2,366k and peel-1 map to this interval, a 62-kb region on chromosome I (position 2,317,234 to 2,379,249) (Fig. 2A). We confirmed tight linkage between the two loci; they do not segregate independently among backcross progeny (table S1). Incomplete penetrance of the incompatibility. The penetrance of the incompatibility (i.e., the extent of lethality among zeel-1Hawaii homozy- ). We used default parameters and Bristol as the reference sequence. The gotes sired by peel-1 heterozygotes) was com- 34 2,356k plete when oocytes were fertilized by male ) mVista alignment of Hawaii and Bristol sequence across a portion of the sperm but incomplete when they were fertilized B by hermaphrodite sperm. We collected embryos on February 9, 2008 interval ( from self-fertilizing F1 hermaphrodites and from F1 hermaphrodites mated to F1 males and geno- peel-1 / typed surviving progeny at the zeel-1 locus. Among self-progeny, approximately 10% of zeel-1Hawaii in red. A black asterisk indicates the frame shift introduced into the zeel-1 indicate markersdisequilibrium. used ( to genotype wild isolates. All markers are in complete linkage black box surrounds the intervalbp) of deletions elevated (green) divergence and betweenbelow insertions Bristol the (gray) and alignment. in Hawaii. Hawaii Large relative (>50 to the Bristol sequence are shown 8M 10M 11M 12M 13M 14M 15M homozygotes survived to hatching, although most had retarded development and abnormal subclone morphologies (8). In contrast, none survived 2,346k * when fertilized by F1 males. Penetrance of the incompatibility also appeared complete among www.sciencemag.org . Gray bars ), fosmid B embryos from F1 males backcrossed to Hawaii Hawaii Bristol Y39G10AR.5 (zeel-1) hermaphrodites, as these broods lacked the peel-1 deformed larvae characteristic of surviving zeel- peel-1 peel-1 fosmid B 1 homozygotes. and Hawaii The morphological defects of surviving Bristol Hawaii WRM0614dC06 zeel-1Hawaii homozygotes were highly variable zeel-1 zeel-1 zeel-1 and often similar to the terminal phenotype ob- 2,336k Downloaded from ) Colored bars represent Bristol served in arrested embryos, which usually showed subclone A tissue differentiation but no elongation past the ugt-31 twofold stage. Nevertheless, some zeel-1Hawaii subclone homozygotes matured to adulthood and produced progeny. These progeny were entirely wild type, implying that the paternal effect is not caused by Y39G10AR.16 heritable defects such as DNA damage or subclone aneuploidy in zeel-1Hawaii sperm. srbc-64 Globally distributed incompatibility. To determine the distribution of alleles causing the Bristol-Hawaii incompatibility in the global C.
Load more

Recommended publications
  • Purebred Dog Breeds Into the Twenty-First Century: Achieving Genetic Health for Our Dogs
    Purebred Dog Breeds into the Twenty-First Century: Achieving Genetic Health for Our Dogs BY JEFFREY BRAGG WHAT IS A CANINE BREED? What is a breed? To put the question more precisely, what are the necessary conditions that enable us to say with conviction, "this group of animals constitutes a distinct breed?" In the cynological world, three separate approaches combine to constitute canine breeds. Dogs are distinguished first by ancestry , all of the individuals descending from a particular founder group (and only from that group) being designated as a breed. Next they are distinguished by purpose or utility, some breeds existing for the purpose of hunting particular kinds of game,others for the performance of particular tasks in cooperation with their human masters, while yet others owe their existence simply to humankind's desire for animal companionship. Finally dogs are distinguished by typology , breed standards (whether written or unwritten) being used to describe and to recognize dogs of specific size, physical build, general appearance, shape of head, style of ears and tail, etc., which are said to be of the same breed owing to their similarity in the foregoing respects. The preceding statements are both obvious and known to all breeders and fanciers of the canine species. Nevertheless a correct and full understanding of these simple truisms is vital to the proper functioning of the entire canine fancy and to the health and well being of the animals which are the object of that fancy. It is my purpose in this brief to elucidate the interrelationship of the above three approaches, to demonstrate how distortions and misunderstandings of that interrelationship now threaten the health of all of our dogs and the very existence of the various canine breeds, and to propose reforms which will restore both balanced breed identity and genetic health to CKC breeds.
    [Show full text]
  • Review of the Current State of Genetic Testing - a Living Resource
    Review of the Current State of Genetic Testing - A Living Resource Prepared by Liza Gershony, DVM, PhD and Anita Oberbauer, PhD of the University of California, Davis Editorial input by Leigh Anne Clark, PhD of Clemson University July, 2020 Contents Introduction .................................................................................................................................................. 1 I. The Basics ......................................................................................................................................... 2 II. Modes of Inheritance ....................................................................................................................... 7 a. Mendelian Inheritance and Punnett Squares ................................................................................. 7 b. Non-Mendelian Inheritance ........................................................................................................... 10 III. Genetic Selection and Populations ................................................................................................ 13 IV. Dog Breeds as Populations ............................................................................................................. 15 V. Canine Genetic Tests ...................................................................................................................... 16 a. Direct and Indirect Tests ................................................................................................................ 17 b. Single
    [Show full text]
  • Balancing Selection at the Prion Protein Gene Consistent with Prehistoric Kurulike Epidemics Simon Mead,1 Michael P
    Balancing Selection at the Prion Protein Gene Consistent with Prehistoric Kurulike Epidemics Simon Mead,1 Michael P. H. Stumpf,2 Jerome Whitfield,1,3 Jonathan A. Beck,1 Mark Poulter,1 Tracy Campbell,1 James Uphill,1 David Goldstein,2 Michael Alpers,1,3,4 Elizabeth M. C. Fisher,1 John Collinge1* 1Medical Research Council, Prion Unit, and Department of Neurodegenerative Disease, Institute of Neurology, University College, Queen Square, London WC1N 3BG, UK. 2Department of Biology (Galton Laboratory), University College London, Gower Street, London WC1E 6BT, UK. 3Institute of Medical Research, Goroka, EHP, Papua New Guinea. 4Curtin University of Technology, Perth, WA, Australia. *To whom correspondence should be addressed. E-mail: [email protected] Kuru is an acquired prion disease largely restricted to the cannibalism imposed by the Australian authorities in the mid- Fore linguistic group of the Papua New Guinea Highlands 1950s led to a decline in kuru incidence, and although rare which was transmitted during endocannibalistic feasts. cases still occur these are all in older individuals and reflect Heterozygosity for a common polymorphism in the the long incubation periods possible in human prion human prion protein gene (PRNP) confers relative diseasekuru has not been recorded in any individual born after the late 1950s (4). resistance to prion diseases. Elderly survivors of the kuru A coding polymorphism at codon 129 of PRNP is a strong epidemic, who had multiple exposures at mortuary feasts, susceptibility factor for human prion diseases. Methionine are, in marked contrast to younger unexposed Fore, homozygotes comprise 37% of the UK population whereas predominantly PRNP 129 heterozygotes.
    [Show full text]
  • Strong Balancing Selection at HLA Loci: Evidence from Segregation In
    Proc. Natl. Acad. Sci. USA Vol. 94, pp. 12452–12456, November 1997 Evolution Strong balancing selection at HLA loci: Evidence from segregation in South Amerindian families (heterozygote advantageymaternal–fetal interactionymajor histocompatibility complexypolymorphismyreciprocal matings) FRANCIS L. BLACK† AND PHILIP W. HEDRICK‡§ †Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520; and ‡Department of Biology, Arizona State University, Tempe, AZ 85287-1501 Edited by Margaret G. Kidwell, University of Arizona, Tucson, AZ, and approved September 3, 1997 (received for review July 23, 1997) ABSTRACT The genotypic proportions for major histo- The reduced proportion of HLA-A and HLA-B homozygotes compatibility complex loci, HLA-A and HLA-B, of progeny in observed in population samples of South Amerindians (8) needs families in 23 South Amerindian tribes in which segregation an s value of 0.425 to explain the deficiency (12). These results for homozygotes and heterozygotes could occur are examined. may not necessarily be in conflict if by chance the observations in Overall, there is a large deficiency of homozygotes compared refs. 8 and 9 are high values that would average away with lower with Mendelian expectations (for HLA-A, 114 observed and values in the past. In fact, there has probably been strong selection 155.50 expected and for HLA-B 110 observed and 144.75 in recent generations, if not the present one (3, 13). expected), consistent with strong balancing selection favoring Here, we present data showing a large excess of heterozy- heterozygotes. There is no evidence that these deficiencies gotes (a large deficiency of homozygotes) compared with were associated with particular alleles or with the age of the Mendelian expectations in 510 offspring from parents with individuals sampled.
    [Show full text]
  • Balancing Selection at a Premature Stop Mutation in the Myostatin Gene Underlies A
    bioRxiv preprint doi: https://doi.org/10.1101/442012; this version posted October 12, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Balancing selection at a premature stop mutation in the myostatin gene underlies a 2 recessive leg weakness syndrome in pigs 3 Oswald Matika1, Diego Robledo1, Ricardo Pong-Wong1, Stephen C. Bishop1@, Valentina 4 Riggio1, Heather Finlayson1, Natalie R. Lowe1, Annabelle E. Hoste2, Grant A. Walling2, 5 Alan L. Archibald1, John A. Woolliams1‡, and Ross D. Houston1‡ 6 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, 7 Midlothian, EH25 9RG, UK 8 2JSR Genetics, Southburn, Driffield, East Yorkshire, YO25 9ED, UK. 9 @Deceased 10 ‡ These authors contributed equally to this work 11 ABSTRACT 12 Balancing selection provides a plausible explanation for the maintenance of deleterious 13 alleles at moderate frequency in livestock, including lethal recessives exhibiting 14 heterozygous advantage in carriers. In the current study, a leg weakness syndrome 15 causing mortality of piglets in a commercial line showed monogenic recessive 16 inheritance, and a region on chromosome 15 associated with the syndrome was identified 17 by homozygosity mapping. Whole genome resequencing of cases and controls identified 18 a mutation coding for a premature stop codon within exon 3 of the porcine Myostatin 19 (MSTN) gene, similar to those causing a double-muscling phenotype observed in several 20 mammalian species.
    [Show full text]
  • Hitch-Hiking to a Locus Under Balancing Selection: High Sequence Diversity and Low Population Subdivision at the S-Locus Genomic Region in Arabidopsis Halleri
    Genet. Res., Camb. (2008), 90, pp. 37–46. f 2008 Cambridge University Press 37 doi:10.1017/S0016672307008932 Printed in the United Kingdom Hitch-hiking to a locus under balancing selection: high sequence diversity and low population subdivision at the S-locus genomic region in Arabidopsis halleri MARIA VALERIA RUGGIERO, BERTRAND JACQUEMIN, VINCENT CASTRIC AND XAVIER VEKEMANS* Universite´ des Sciences et Technologies de Lille 1, Laboratoire de ge´ne´tique et e´volution des populations ve´ge´tales, CNRS UMR 8016, 59655 Villeneuve d’Ascq, France (Received 8 September 2007 and in revised form 15 October 2007) Summary Hitch-hiking to a site under balancing selection is expected to produce a local increase in nucleotide polymorphism and a decrease in population differentiation compared with the background genomic level, but empirical evidence supporting these predictions is scarce. We surveyed molecular diversity at four genes flanking the region controlling self-incompatibility (the S-locus) in samples from six populations of the herbaceous plant Arabidopsis halleri, and compared their polymorphism with sequences from five control genes unlinked to the S-locus. As a preliminary verification, the S-locus flanking genes were shown to co-segregate with SRK, the gene involved in the self-incompatibility reaction at the pistil level. In agreement with theory, our results demonstrated a significant peak of nucleotide diversity around the S-locus as well as a significant decrease in population genetic structure in the S-locus region compared with both control genes and a set of seven unlinked microsatellite markers. This is consistent with the theoretical expectation that balancing selection is increasing the effective migration rate in subdivided populations.
    [Show full text]
  • Genomic Insights Into Positive Selection
    Review TRENDS in Genetics Vol.22 No.8 August 2006 Genomic insights into positive selection Shameek Biswas and Joshua M. Akey Department of Genome Sciences, University of Washington, 1705 NE Pacific, Seattle, WA 98195, USA The traditional way of identifying targets of adaptive more utilitarian benefits, each target of positive selection evolution has been to study a few loci that one has a story to tell about the historical forces and events hypothesizes a priori to have been under selection. that have shaped the history of a population. This approach is complicated because of the confound- Several genome-wide analyses for positive selection ing effects that population demographic history and have been performed in a variety of species. In this review, selection have on patterns of DNA sequence variation. In we summarize some of the recent studies, primarily principle, multilocus analyses can facilitate robust focusing on humans, critically evaluate what genome- inferences of selection at individual loci. The deluge of wide scans for selection are and are not likely to find and large-scale catalogs of genetic variation has stimulated suggest future avenues of research. A brief overview of many genome-wide scans for positive selection in statistical methods used to detect deviations from several species. Here, we review some of the salient neutrality is summarized in Box 1. For more detailed observations of these studies, identify important chal- discussions, see Refs [6,7]. lenges ahead, consider the limitations of genome-wide scans for selection and discuss the potential significance Thinking genomically of a comprehensive understanding of genomic patterns Positive selection perturbs patterns of genetic variation of selection for disease-related research.
    [Show full text]
  • Balancing Selection on Allorecognition Genes in the Colonial Ascidian Botryllus Schlosseri
    Developmental and Comparative Immunology 69 (2017) 60e74 Contents lists available at ScienceDirect Developmental and Comparative Immunology journal homepage: www.elsevier.com/locate/dci Balancing selection on allorecognition genes in the colonial ascidian Botryllus schlosseri * Marie L. Nydam a, , Emily E. Stephenson a, b, Claire E. Waldman a, Anthony W. De Tomaso c a Division of Science and Mathematics, Centre College, 600 W. Walnut Street, Danville, KY 40422, United States b Centre for Infectious Disease Research, P.O. Box 34681, Lusaka, 10101, Zambia c Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, United States article info abstract Article history: Allorecognition is the capability of an organism to recognize its own or related tissues. The colonial Received 24 November 2016 ascidian Botryllus schlosseri, which comprises five genetically distinct and divergent species (Clades A-E), Received in revised form contains two adjacent genes that control allorecognition: fuhcsec and fuhctm. These genes have been 22 December 2016 characterized extensively in Clade A and are highly polymorphic. Using alleles from 10 populations Accepted 22 December 2016 across the range of Clade A, we investigated the type and strength of selection maintaining this variation. Available online 24 December 2016 Both fuhc genes exhibit higher within-population variation and lower population differentiation mea- sures (FST) than neutral loci. The fuhc genes contain a substantial number of codons with >95% posterior Keywords: > sec tm Botryllus schlosseri probability of dN/dS 1. fuhc and fuhc also have polymorphisms shared between Clade A and Clade E Allorecognition that were present prior to speciation (trans-species polymorphisms).
    [Show full text]
  • Hybridization with Mountain Hares Increases the Functional Allelic Repertoire in Brown Hares Jaakko L
    www.nature.com/scientificreports OPEN Hybridization with mountain hares increases the functional allelic repertoire in brown hares Jaakko L. O. Pohjoismäki 1*, Craig Michell 1, Riikka Levänen1 & Steve Smith 2 Brown hares (Lepus europaeus Pallas) are able to hybridize with mountain hares (L. timidus Linnaeus) and produce fertile ofspring, which results in cross-species gene fow. However, not much is known about the functional signifcance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic diversity in the Finnish brown hare to be small, likely due to founder efect and range expansion, while gene fow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1), might have adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study ofers a rare example where an expanding species can increase its allelic variability through hybridization with a congeneric native species, ofering a route to shortcut evolutionary adaptation to the local environmental conditions. Understanding of the ecological and evolutionary processes underlying species’ dispersal and range limits is a fundamental theme in evolutionary biology 1. Te leading edge of the species range expansion is typically popu- lated by few individuals, which are also living at the boundary of their specifc habitat preferences. Te genetic landscape of these boundary populations is infuenced by founder efect as well as low population densities resulting in increased genetic drif and further loss of genetic diversity 2.
    [Show full text]
  • Detecting Ancient Balancing Selection: Methods and Application to Human Katherine Siewert University of Pennsylvania, [email protected]
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2019 Detecting Ancient Balancing Selection: Methods And Application To Human Katherine Siewert University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Evolution Commons, and the Genetics Commons Recommended Citation Siewert, Katherine, "Detecting Ancient Balancing Selection: Methods And Application To Human" (2019). Publicly Accessible Penn Dissertations. 3313. https://repository.upenn.edu/edissertations/3313 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/3313 For more information, please contact [email protected]. Detecting Ancient Balancing Selection: Methods And Application To Human Abstract Balancing selection can maintain genetic variation in a population over long evolutionary time periods. Identifying genomic loci under this type of selection not only elucidates selective pressures and adaptations but can also help interpret common genetic variation contributing to disease. Summary statistics which capture signatures in the site frequency spectrum are frequently used to scan the genome to detect loci showing evidence of balancing selection. However, these approaches have limited power because they rely on imprecise signatures such as a general excess of heterozygosity or number of genetic variants. A second class of statistics, based on likelihoods, have higher power but are often computationally prohibitive. In addition, a majority of methods in both classes require a high-quality sequenced outgroup, which is unavailable for many species of interest. Therefore, there is a need for a well-powered and widely-applicable statistical approach to detect balancing selection. Theory suggests that long-term balancing selection will result in a genealogy with very long internal branches.
    [Show full text]
  • Divergent Allele Advantage Provides a Quantitative Model for Maintaining Alleles with a Wide Range of Intrinsic Merits
    HIGHLIGHTED ARTICLE | INVESTIGATION Divergent Allele Advantage Provides a Quantitative Model for Maintaining Alleles with a Wide Range of Intrinsic Merits Thorsten Stefan,*,†,1,2 Louise Matthews,* Joaquin M. Prada,*,3 Colette Mair,*,4 Richard Reeve,* and Michael J. Stear*,5 *Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, G12 8QQ, United Kingdom and †Institute of Applied Mathematics and Statistics, University of Hohenheim, 70593 Stuttgart, Germany ORCID IDs: 0000-0002-0599-6412 (T.S.); 0000-0001-5054-1348 (M.J.S.) ABSTRACT The Major Histocompatibility Complex (MHC) is the most genetically diverse region of the genome in most vertebrates. Some form of balancing selection is necessary to account for the extreme diversity, but the precise mechanism of balancing selection is unknown. Due to the way MHC molecules determine immune recognition, overdominance (also referred to as heterozygote advantage) has been suggested as the main driving force behind this unrivalled diversity. However, both theoretical results and simulation models have shown that overdominance in its classical form cannot maintain large numbers of alleles unless all alleles confer unrealistically similar levels of fitness. There is increasing evidence that heterozygotes containing genetically divergent alleles allow for broader antigen presentation to immune cells, providing a selective mechanism for MHC polymorphism. By framing competing models of overdominance within a general framework, we show that a model based on Divergent Allele Advantage (DAA) provides a superior mechanism for maintaining alleles with a wide range of intrinsic merits, as intrinsically less-fit MHC alleles that are more divergent can survive under DAA.
    [Show full text]
  • Lessons Learned from the Dog Genome
    Review TRENDS in Genetics Vol.23 No.11 Lessons learned from the dog genome Robert K. Wayne1 and Elaine A. Ostrander2 1 Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 91302, USA 2 Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA Extensive genetic resources and a high-quality genome sequencing of the dog genome and related genomic sequence position the dog as an important model resources, powerful new approaches for uncovering the species for understanding genome evolution, popu- genetic basis of phenotypic variation and disease are emer- lation genetics and genes underlying complex phenoty- ging. ‘Selective sweep’ approaches are particularly prom- pic traits. Newly developed genomic resources have ising in the search for the genomic signal of positive expanded our understanding of canine evolutionary selection [5–7]. Furthermore, canine genomic resources history and dog origins. Domestication involved genetic have a wide variety of applications including systematics, contributions from multiple populations of gray wolves population genetics, endangered species conservation as probably through backcrossing. More recently, the well as gene mapping of specific phenotypic traits [4,8]. advent of controlled breeding practices has segregated genetic variability into distinct dog breeds that possess The evolutionary history of dog-like carnivores specific phenotypic traits. Consequently, genome-wide The dog family is a phenotypically diverse group including association and selective sweep scans now allow the 35 closely related extant species [9,10]. This recent radi- discovery of genes underlying breed-specific character- ation has resulted in an evolutionary branching pattern istics. The dog is finally emerging as a novel resource for that is often difficult to resolve because many branches are studying the genetic basis of complex traits, including closely spaced in time.
    [Show full text]