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Barbour AG, Duong JV, Long AD. Lyme Disease Agent Reservoirs Peromyscus leucopus and P. maniculatus Have Natively Inactivated Genes for the High-Affinity Immunoglobulin Gamma Fc Receptor I (CD64). Pathogens 2023; 12:1056. [PMID: 37624016 PMCID: PMC10458454 DOI: 10.3390/pathogens12081056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023] Open
Abstract
The abundant and widely distributed deermice Peromyscus leucopus and P. maniculatus are important reservoirs for several different zoonotic agents in North America. For the pathogens they persistently harbor, these species are also examples of the phenomenon of infection tolerance. In the present study a prior observation of absent expression of the high-affinity Fc immunoglobulin gamma receptor I (FcγRI), or CD64, in P. leucopus was confirmed in an experimental infection with Borreliella burgdorferi, a Lyme disease agent. We demonstrate that the null phenotype is attributable to a long-standing inactivation of the Fcgr1 gene in both species by a deletion of the promoter and coding sequence for the signal peptide for FcγRI. The Fcgr1 pseudogene was also documented in the related species P. polionotus. Six other Peromyscus species, including P. californicus, have coding sequences for a full-length FcγRI, including a consensus signal peptide. An inference from reported phenotypes for null Fcgr1 mutations engineered in Mus musculus is that one consequence of pseudogenization of Fcgr1 is comparatively less inflammation during infection than in animals, including humans, with undisrupted, fully active genes.
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Affiliation(s)
- Alan G. Barbour
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA 92697, USA;
- Department of Medicine, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Jonathan V. Duong
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA 92697, USA;
| | - Anthony D. Long
- Department of Ecology & Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA;
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2
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Huynh K, Smith BR, Macdonald SJ, Long AD. Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster. PLoS Genet 2023; 19:e1010439. [PMID: 37146087 PMCID: PMC10191298 DOI: 10.1371/journal.pgen.1010439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/17/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
We use ATAC-seq to examine chromatin accessibility for four different tissues in Drosophila melanogaster: adult female brain, ovaries, and both wing and eye-antennal imaginal discs from males. Each tissue is assayed in eight different inbred strain genetic backgrounds, seven associated with a reference quality genome assembly. We develop a method for the quantile normalization of ATAC-seq fragments and test for differences in coverage among genotypes, tissues, and their interaction at 44099 peaks throughout the euchromatic genome. For the strains with reference quality genome assemblies, we correct ATAC-seq profiles for read mis-mapping due to nearby polymorphic structural variants (SVs). Comparing coverage among genotypes without accounting for SVs results in a highly elevated rate (55%) of identifying false positive differences in chromatin state between genotypes. After SV correction, we identify 1050, 30383, and 4508 regions whose peak heights are polymorphic among genotypes, among tissues, or exhibit genotype-by-tissue interactions, respectively. Finally, we identify 3988 candidate causative variants that explain at least 80% of the variance in chromatin state at nearby ATAC-seq peaks.
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Affiliation(s)
- Khoi Huynh
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
| | - Brittny R. Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Anthony D. Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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3
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Linder RA, Zabanavar B, Majumder A, Hoang HCS, Delgado VG, Tran R, La VT, Leemans SW, Long AD. Adaptation in Outbred Sexual Yeast is Repeatable, Polygenic and Favors Rare Haplotypes. Mol Biol Evol 2022; 39:msac248. [PMID: 36366952 PMCID: PMC9728589 DOI: 10.1093/molbev/msac248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We carried out a 200 generation Evolve and Resequence (E&R) experiment initiated from an outbred diploid recombined 18-way synthetic base population. Replicate populations were evolved at large effective population sizes (>105 individuals), exposed to several different chemical challenges over 12 weeks of evolution, and whole-genome resequenced. Weekly forced outcrossing resulted in an average between adjacent-gene per cell division recombination rate of ∼0.0008. Despite attempts to force weekly sex, roughly half of our populations evolved cheaters and appear to be evolving asexually. Focusing on seven chemical stressors and 55 total evolved populations that remained sexual we observed large fitness gains and highly repeatable patterns of genome-wide haplotype change within chemical challenges, with limited levels of repeatability across chemical treatments. Adaptation appears highly polygenic with almost the entire genome showing significant and consistent patterns of haplotype change with little evidence for long-range linkage disequilibrium in a subset of populations for which we sequenced haploid clones. That is, almost the entire genome is under selection or drafting with selected sites. At any given locus adaptation was almost always dominated by one of the 18 founder's alleles, with that allele varying spatially and between treatments, suggesting that selection acts primarily on rare variants private to a founder or haplotype blocks harboring multiple mutations.
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Affiliation(s)
- Robert A Linder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Behzad Zabanavar
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Arundhati Majumder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Hannah Chiao-Shyan Hoang
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Vanessa Genesaret Delgado
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Ryan Tran
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Vy Thoai La
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
| | - Simon William Leemans
- Department of Biomedical Engineering, School of Engineering, University of California, Irvine
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine
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4
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Macdonald SJ, Long AD. Discovery of malathion resistance QTL in Drosophila melanogaster using a bulked phenotyping approach. G3 (Bethesda) 2022; 12:jkac279. [PMID: 36250804 PMCID: PMC9713458 DOI: 10.1093/g3journal/jkac279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/09/2022] [Indexed: 12/03/2022]
Abstract
Drosophila melanogaster has proved an effective system with which to understand the evolutionary genetics and molecular mechanisms of insecticide resistance. Insecticide use has left signatures of selection in the fly genome, and both functional and quantitative genetic studies in the system have identified genes and variants associated with resistance. Here, we use D. melanogaster and leverage a bulk phenotyping and pooled sequencing "extreme quantitative trait loci" approach to genetically dissect variation in resistance to malathion, an organophosphate insecticide. We resolve 2 quantitative trait loci, one of which implicates allelic variation at the cytochrome P450 gene Cyp6g1, a strong candidate based on previous work. The second shows no overlap with hits from a previous genome-wide association study for malathion resistance, recapitulating other studies showing that different strategies for complex trait dissection in flies can yield apparently different architectures. Notably, we see no genetic signal at the Ace gene. Ace encodes the target of organophosphate insecticide inhibition, and genome-wide association studies have identified strong Ace-linked associations with resistance in flies. The absence of quantitative trait locus implicating Ace here is most likely because our mapping population does not segregate for several of the known functional polymorphisms impacting resistance at Ace, perhaps because our population is derived from flies collected prior to the widespread use of organophosphate insecticides. Our fundamental approach can be an efficient, powerful strategy to dissect genetic variation in resistance traits. Nonetheless, studies seeking to interrogate contemporary insecticide resistance variation may benefit from deriving mapping populations from more recently collected strains.
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Affiliation(s)
- Stuart J Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66046, USA
- Center for Computational Biology, University of Kansas, Lawrence, KS 66047, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, CA 92697, USA
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Long PN, Cook VJ, Majumder A, Barbour AG, Long AD. The utility of a closed breeding colony of Peromyscus leucopus for dissecting complex traits. Genetics 2022; 221:iyac026. [PMID: 35143664 PMCID: PMC9071557 DOI: 10.1093/genetics/iyac026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Deermice of the genus Peromyscus are well suited for addressing several questions of biologist interest, including the genetic bases of longevity, behavior, physiology, adaptation, and their ability to serve as disease vectors. Here, we explore a diversity outbred approach for dissecting complex traits in Peromyscus leucopus, a nontraditional genetic model system. We take advantage of a closed colony of deer-mice founded from 38 individuals and subsequently maintained for ∼40-60 generations. From 405 low-pass short-read sequenced deermice we accurate impute genotypes at 16 million single nucleotide polymorphisms. Conditional on observed genotypes simulations were conducted in which three different sized quantitative trait loci contribute to a complex trait under three different genetic models. Using a stringent significance threshold power was modest, largely a function of the percent variation attributable to the simulated quantitative trait loci, with the underlying genetic model having only a subtle impact. We additionally simulated 2,000 pseudo-individuals, whose genotypes were consistent with those observed in the genotyped cohort and carried out additional power simulations. In experiments employing more than 1,000 mice power is high to detect quantitative trait loci contributing greater than 2.5% to a complex trait, with a localization ability of ∼100 kb. We finally carried out a Genome-Wide Association Study on two demonstration traits, bleeding time and body weight, and uncovered one significant region. Our work suggests that complex traits can be dissected in founders-unknown P. leucopus colony mice and similar colonies in other systems using easily obtained genotypes from low-pass sequencing.
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Affiliation(s)
- Phillip N Long
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697-2525, USA
| | - Vanessa J Cook
- Departments of Microbiology & Molecular Genetics and Medicine, School of Medical Sciences, University of California Irvine, Irvine, CA 92687-2525, USA
| | - Arundhati Majumder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697-2525, USA
| | - Alan G Barbour
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697-2525, USA
- Departments of Microbiology & Molecular Genetics and Medicine, School of Medical Sciences, University of California Irvine, Irvine, CA 92687-2525, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697-2525, USA
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6
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Macdonald SJ, Cloud-Richardson KM, Sims-West DJ, Long AD. Powerful, efficient QTL mapping in Drosophila melanogaster using bulked phenotyping and pooled sequencing. Genetics 2022; 220:iyab238. [PMID: 35100395 PMCID: PMC8893256 DOI: 10.1093/genetics/iyab238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/19/2021] [Indexed: 01/22/2024] Open
Abstract
Despite the value of recombinant inbred lines for the dissection of complex traits, large panels can be difficult to maintain, distribute, and phenotype. An attractive alternative to recombinant inbred lines for many traits leverages selecting phenotypically extreme individuals from a segregating population, and subjecting pools of selected and control individuals to sequencing. Under a bulked or extreme segregant analysis paradigm, genomic regions contributing to trait variation are revealed as frequency differences between pools. Here, we describe such an extreme quantitative trait locus, or extreme quantitative trait loci, mapping strategy that builds on an existing multiparental population, the Drosophila Synthetic Population Resource, and involves phenotyping and genotyping a population derived by mixing hundreds of Drosophila Synthetic Population Resource recombinant inbred lines. Simulations demonstrate that challenging, yet experimentally tractable extreme quantitative trait loci designs (≥4 replicates, ≥5,000 individuals/replicate, and selecting the 5-10% most extreme animals) yield at least the same power as traditional recombinant inbred line-based quantitative trait loci mapping and can localize variants with sub-centimorgan resolution. We empirically demonstrate the effectiveness of the approach using a 4-fold replicated extreme quantitative trait loci experiment that identifies 7 quantitative trait loci for caffeine resistance. Two mapped extreme quantitative trait loci factors replicate loci previously identified in recombinant inbred lines, 6/7 are associated with excellent candidate genes, and RNAi knock-downs support the involvement of 4 genes in the genetic control of trait variation. For many traits of interest to drosophilists, a bulked phenotyping/genotyping extreme quantitative trait loci design has considerable advantages.
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Affiliation(s)
- Stuart J Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
- Center for Computational Biology, University of Kansas, Lawrence, KS 66047, USA
| | | | - Dylan J Sims-West
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, CA 92697, USA
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7
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Shahrestani P, King E, Ramezan R, Phillips M, Riddle M, Thornburg M, Greenspan Z, Estrella Y, Garcia K, Chowdhury P, Malarat G, Zhu M, Rottshaefer SM, Wraight S, Griggs M, Vandenberg J, Long AD, Clark AG, Lazzaro BP. The molecular architecture of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping. G3 (Bethesda) 2021; 11:6371870. [PMID: 34534291 PMCID: PMC8664422 DOI: 10.1093/g3journal/jkab324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/17/2021] [Indexed: 12/02/2022]
Abstract
Little is known about the genetic architecture of antifungal immunity in natural populations. Using two population genetic approaches, quantitative trait locus (QTL) mapping and evolve and resequence (E&R), we explored D. melanogaster immune defense against infection with the fungus Beauveria bassiana. The immune defense was highly variable both in the recombinant inbred lines from the Drosophila Synthetic Population Resource used for our QTL mapping and in the synthetic outbred populations used in our E&R study. Survivorship of infection improved dramatically over just 10 generations in the E&R study, and continued to increase for an additional nine generations, revealing a trade-off with uninfected longevity. Populations selected for increased defense against B. bassiana evolved cross resistance to a second, distinct B. bassiana strain but not to bacterial pathogens. The QTL mapping study revealed that sexual dimorphism in defense depends on host genotype, and the E&R study indicated that sexual dimorphism also depends on the specific pathogen to which the host is exposed. Both the QTL mapping and E&R experiments generated lists of potentially causal candidate genes, although these lists were nonoverlapping.
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Affiliation(s)
- Parvin Shahrestani
- Department of Biological Science, California State University Fullerton, Fullerton CA, 92831, USA
| | - Elizabeth King
- Division of Biological Sciences, University of Missouri, Columbia MO, 65211, USA
| | - Reza Ramezan
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo ON, N2L 3G1, Canada
| | - Mark Phillips
- Department of Integrative Biology, Oregon State University, Corvallis OR, 97331, USA
| | - Melissa Riddle
- Department of Biological Science, California State University Fullerton, Fullerton CA, 92831, USA
| | - Marisa Thornburg
- Department of Biological Science, California State University Fullerton, Fullerton CA, 92831, USA
| | - Zachary Greenspan
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA, 92692, USA
| | | | - Kelly Garcia
- Department of Entomology, Cornell University, Ithaca NY, 14853, USA
| | - Pratik Chowdhury
- Department of Entomology, Cornell University, Ithaca NY, 14853, USA
| | - Glen Malarat
- Department of Entomology, Cornell University, Ithaca NY, 14853, USA
| | - Ming Zhu
- Department of Entomology, Cornell University, Ithaca NY, 14853, USA
| | | | - Stephen Wraight
- USDA ARS Emerging Pets and Pathogens Research Unit, Robert W. Holley Center for Agriculture & Health, Ithaca NY, 14853, USA
| | - Michael Griggs
- USDA ARS Emerging Pets and Pathogens Research Unit, Robert W. Holley Center for Agriculture & Health, Ithaca NY, 14853, USA
| | - John Vandenberg
- USDA ARS Emerging Pets and Pathogens Research Unit, Robert W. Holley Center for Agriculture & Health, Ithaca NY, 14853, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA, 92692, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY, 14853, USA
| | - Brian P Lazzaro
- Department of Entomology, Cornell University, Ithaca NY, 14853, USA
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Solares EA, Tao Y, Long AD, Gaut BS. HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding. BMC Bioinformatics 2021; 22:9. [PMID: 33407090 PMCID: PMC7788845 DOI: 10.1186/s12859-020-03939-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding. RESULTS Here we illustrate a new method, which we call HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost function can be defined by the user but by default considers the number of missing, duplicated and single BUSCO genes within the assembly. HapSolo performs hill climbing to minimize cost over thousands of candidate assemblies. We illustrate the performance of HapSolo on genome data from three species: the Chardonnay grape (Vitis vinifera), with a genome of 490 Mb, a mosquito (Anopheles funestus; 200 Mb) and the Thorny Skate (Amblyraja radiata; 2650 Mb). CONCLUSIONS HapSolo rapidly identified candidate assemblies that yield improvements in assembly metrics, including decreased genome size and improved N50 scores. Contig N50 scores improved by 35%, 9% and 9% for Chardonnay, mosquito and the thorny skate, respectively, relative to unreduced primary assemblies. The benefits of HapSolo were amplified by down-stream analyses, which we illustrated by scaffolding with Hi-C data. We found, for example, that prior to the application of HapSolo, only 52% of the Chardonnay genome was captured in the largest 19 scaffolds, corresponding to the number of chromosomes. After the application of HapSolo, this value increased to ~ 84%. The improvements for the mosquito's largest three scaffolds, representing the number of chromosomes, were from 61 to 86%, and the improvement was even more pronounced for thorny skate. We compared the scaffolding results to assemblies that were based on PurgeDups for identifying secondary contigs, with generally superior results for HapSolo.
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Affiliation(s)
- Edwin A Solares
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, 92697-2525, USA
| | - Yuan Tao
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, 92697-2525, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, 92697-2525, USA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, 92697-2525, USA.
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Phillips MA, Kutch IC, Long AD, Burke MK. Increased time sampling in an evolve-and-resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change. Mol Ecol 2020; 29:4898-4912. [PMID: 33135198 DOI: 10.1111/mec.15687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/28/2022]
Abstract
"Evolve and resequence" (E&R) studies combine experimental evolution and whole-genome sequencing to interrogate the genetics underlying adaptation. Due to ease of handling, E&R work with asexual organisms such as bacteria can employ optimized experimental design, with large experiments and many generations of selection. By contrast, E&R experiments with sexually reproducing organisms are more difficult to implement, and design parameters vary dramatically among studies. Thus, efforts have been made to assess how these differences, such as number of independent replicates, or size of experimental populations, impact inference. We add to this work by investigating the role of time sampling-the number of discrete time points sequence data are collected from evolving populations. Using data from an E&R experiment with outcrossing Saccharomyces cerevisiae in which populations were sequenced 17 times over ~540 generations, we address the following questions: (a) Do more time points improve the ability to identify candidate regions underlying selection? And (b) does high-resolution sampling provide unique insight into evolutionary processes driving adaptation? We find that while time sampling does not improve the ability to identify candidate regions, high-resolution sampling does provide valuable opportunities to characterize evolutionary dynamics. Increased time sampling reveals three distinct trajectories for adaptive alleles: one consistent with classic population genetic theory (i.e., models assuming constant selection coefficients), and two where trajectories suggest more context-dependent responses (i.e., models involving dynamic selection coefficients). We conclude that while time sampling has limited impact on candidate region identification, sampling eight or more time points has clear benefits for studying complex evolutionary dynamics.
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Affiliation(s)
- Mark A Phillips
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Ian C Kutch
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Molly K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
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Abstract
Vernal pools are unique in their isolation and the strong selection acting on their resident species. Vernal pool clam shrimp (Eulimnadia texana) are a promising model due to ease of culturing, short generation time, small genomes, and obligate desiccated diapaused eggs. Clam shrimp are also androdioecious (sexes include males and hermaphrodites), and here we use population-scaled recombination rates to support the hypothesis that the heterogametic sex is recombination free in these shrimp. We collected short-read sequence data from pooled samples from different vernal pools to gain insights into local adaptation. We identify genomic regions in which some populations have allele frequencies that differ significantly from the metapopulation. BayPass (Gautier M. 2015. Genome-wide scan for adaptive divergence and association with population-specific covariates. Genetics 201(4):1555-1579.) detected 19 such genomic regions showing an excess of population subdivision. These regions on average are 550 bp in size and had 2.5 genes within 5 kb of them. Genes located near these regions are involved in Malpighian tubule function and osmoregulation, an essential function in vernal pools. It is likely that salinity profiles vary between pools and over time, and variants at these genes are adapted to local salinity conditions.
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Affiliation(s)
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California Irvine
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11
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Barbour AG, Shao H, Cook VJ, Baldwin-Brown J, Tsao JI, Long AD. Genomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses. Sci Rep 2019; 9:17618. [PMID: 31772306 PMCID: PMC6879569 DOI: 10.1038/s41598-019-54389-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 11/12/2019] [Indexed: 12/20/2022] Open
Abstract
The cricetine rodents Peromyscus leucopus and P. maniculatus are key reservoirs for several zoonotic diseases in North America. We determined the complete circular mitochondrial genome sequences of representatives of 3 different stock colonies of P. leucopus, one stock colony of P. maniculatus and two wild populations of P. leucopus. The genomes were syntenic with that of the murids Mus musculus and Rattus norvegicus. Phylogenetic analysis confirmed that these two Peromyscus species are sister taxa in a clade with P. polionotus and also uncovered a distinction between P. leucopus populations in the eastern and the central United States. In one P. leucopus lineage four extended regions of mitochondrial pseudogenes were identified in the nuclear genome. RNA-seq analysis revealed transcription of the entire genome and differences from controls in the expression profiles of mitochondrial genes in the blood, but not in liver or brain, of animals infected with the zoonotic pathogen Borrelia hermsii. PCR and sequencing of the D-loop of the mitochondrion identified 32 different haplotypes among 118 wild P. leucopus at a Connecticut field site. These findings help to further establish P. leucopus as a model organism for studies of emerging infectious diseases, ecology, and in other disciplines.
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Affiliation(s)
- Alan G Barbour
- Departments of Microbiology & Molecular Genetics and Medicine, School of Medicine, University of California Irvine, Irvine, CA, 92697, USA.
| | - Hanjuan Shao
- Departments of Microbiology & Molecular Genetics and Medicine, School of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Vanessa J Cook
- Departments of Microbiology & Molecular Genetics and Medicine, School of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - James Baldwin-Brown
- Department of Ecology & Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Jean I Tsao
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Anthony D Long
- Department of Ecology & Evolutionary Biology, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697, USA
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Apitanyasai K, Huang SW, Ng TH, He ST, Huang YH, Chiu SP, Tseng KC, Lin SS, Chang WC, Baldwin-Brown JG, Long AD, Lo CF, Yu HT, Wang HC. The gene structure and hypervariability of the complete Penaeus monodon Dscam gene. Sci Rep 2019; 9:16595. [PMID: 31719551 PMCID: PMC6851185 DOI: 10.1038/s41598-019-52656-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/17/2019] [Indexed: 12/19/2022] Open
Abstract
Using two advanced sequencing approaches, Illumina and PacBio, we derive the entire Dscam gene from an M2 assembly of the complete Penaeus monodon genome. The P. monodon Dscam (PmDscam) gene is ~266 kbp, with a total of 44 exons, 5 of which are subject to alternative splicing. PmDscam has a conserved architectural structure consisting of an extracellular region with hypervariable Ig domains, a transmembrane domain, and a cytoplasmic tail. We show that, contrary to a previous report, there are in fact 26, 81 and 26 alternative exons in N-terminal Ig2, N-terminal Ig3 and the entirety of Ig7, respectively. We also identified two alternatively spliced exons in the cytoplasmic tail, with transmembrane domains in exon variants 32.1 and 32.2, and stop codons in exon variants 44.1 and 44.2. This means that alternative splicing is involved in the selection of the stop codon. There are also 7 non-constitutive cytoplasmic tail exons that can either be included or skipped. Alternative splicing and the non-constitutive exons together produce more than 21 million isoform combinations from one PmDscam locus in the P. monodon gene. A public-facing database that allows BLAST searches of all 175 exons in the PmDscam gene has been established at http://pmdscam.dbbs.ncku.edu.tw/.
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Affiliation(s)
- Kantamas Apitanyasai
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Shiao-Wei Huang
- Department of Life Sciences, National Taiwan University, Taipei, Taiwan
| | - Tze Hann Ng
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Shu-Ting He
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Hsun Huang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Shen-Po Chiu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Kuan-Chien Tseng
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Wen-Chi Chang
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - James G Baldwin-Brown
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
| | - Chu-Fang Lo
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Hon-Tsen Yu
- Department of Life Sciences, National Taiwan University, Taipei, Taiwan
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan. .,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan.
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13
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Long AD, Baldwin-Brown J, Tao Y, Cook VJ, Balderrama-Gutierrez G, Corbett-Detig R, Mortazavi A, Barbour AG. The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections. Sci Adv 2019; 5:eaaw6441. [PMID: 31355335 PMCID: PMC6656541 DOI: 10.1126/sciadv.aaw6441] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
The rodent Peromyscus leucopus is the natural reservoir of several tick-borne infections, including Lyme disease. To expand the knowledge base for this key species in life cycles of several pathogens, we assembled and scaffolded the P. leucopus genome. The resulting assembly was 2.45 Gb in total length, with 24 chromosome-length scaffolds harboring 97% of predicted genes. RNA sequencing following infection of P. leucopus with Borreliella burgdorferi, a Lyme disease agent, shows that, unlike blood, the skin is actively responding to the infection after several weeks. P. leucopus has a high level of segregating nucleotide variation, suggesting that natural resistance alleles to Crispr gene targeting constructs are likely segregating in wild populations. The reference genome will allow for experiments aimed at elucidating the mechanisms by which this widely distributed rodent serves as natural reservoir for several infectious diseases of public health importance, potentially enabling intervention strategies.
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Affiliation(s)
- Anthony D. Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - James Baldwin-Brown
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Yuan Tao
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Vanessa J. Cook
- Departments of Microbiology and Molecular Genetics and Medicine, University of California, Irvine, Irvine, CA, USA
| | | | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Alan G. Barbour
- Departments of Microbiology and Molecular Genetics and Medicine, University of California, Irvine, Irvine, CA, USA
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14
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Baldwin-Brown JG, Weeks SC, Long AD. A New Standard for Crustacean Genomes: The Highly Contiguous, Annotated Genome Assembly of the Clam Shrimp Eulimnadia texana Reveals HOX Gene Order and Identifies the Sex Chromosome. Genome Biol Evol 2018; 10:143-156. [PMID: 29294012 PMCID: PMC5765565 DOI: 10.1093/gbe/evx280] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2017] [Indexed: 02/06/2023] Open
Abstract
Vernal pool clam shrimp (Eulimnadia texana) are a promising model system due to their ease of lab culture, short generation time, modest sized genome, a somewhat rare stable androdioecious sex determination system, and a requirement to reproduce via desiccated diapaused eggs. We generated a highly contiguous genome assembly using 46× of PacBio long read data and 216× of Illumina short reads, and annotated using Illumina RNAseq obtained from adult males or hermaphrodites. Of the 120 Mb genome 85% is contained in the largest eight contigs, the smallest of which is 4.6 Mb. The assembly contains 98% of transcripts predicted via RNAseq. This assembly is qualitatively different from scaffolded Illumina assemblies: It is produced from long reads that contain sequence data along their entire length, and is thus gap free. The contiguity of the assembly allows us to order the HOX genes within the genome, identifying two loci that contain HOX gene orthologs, and which approximately maintain the order observed in other arthropods. We identified a partial duplication of the Antennapedia complex adjacent to the few genes homologous to the Bithorax locus. Because the sex chromosome of an androdioecious species is of special interest, we used existing allozyme and microsatellite markers to identify the E. texana sex chromosome, and find that it comprises nearly half of the genome of this species. Linkage patterns indicate that recombination is extremely rare and perhaps absent in hermaphrodites, and as a result the location of the sex determining locus will be difficult to refine using recombination mapping.
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Affiliation(s)
| | | | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California Irvine
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15
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Mahdipour-Shirayeh A, Darooneh AH, Long AD, Komarova NL, Kohandel M. Genotype by random environmental interactions gives an advantage to non-favored minor alleles. Sci Rep 2017; 7:5193. [PMID: 28701726 PMCID: PMC5507875 DOI: 10.1038/s41598-017-05375-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 05/30/2017] [Indexed: 12/11/2022] Open
Abstract
Fixation probability, the probability that the frequency of a newly arising mutation in a population will eventually reach unity, is a fundamental quantity in evolutionary genetics. Here we use a number of models (several versions of the Moran model and the haploid Wright-Fisher model) to examine fixation probabilities for a constant size population where the fitness is a random function of both allelic state and spatial position, despite neither allele being favored on average. The concept of fitness varying with respect to both genotype and environment is important in models of cancer initiation and progression, bacterial dynamics, and drug resistance. Under our model spatial heterogeneity redefines the notion of neutrality for a newly arising mutation, as such mutations fix at a higher rate than that predicted under neutrality. The increased fixation probability appears to be due to rare alleles having an advantage. The magnitude of this effect can be large, and is an increasing function of the spatial variance and skew in fitness. The effect is largest when the fitness values of the mutants and wild types are anti-correlated across environments. We discuss results for both a spatial ring geometry of cells (such as that of a colonic crypt), a 2D lattice and a mass-action (complete graph) arrangement.
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Affiliation(s)
- A Mahdipour-Shirayeh
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - A H Darooneh
- Department of Physics, University of Zanjan, P.O. Box 45196-313, Zanjan, Iran
| | - A D Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - N L Komarova
- Department of Mathematics, University of California, Irvine, CA, 92697, USA.
| | - M Kohandel
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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16
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Phillips MA, Long AD, Greenspan ZS, Greer LF, Burke MK, Villeponteau B, Matsagas KC, Rizza CL, Mueller LD, Rose MR. Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster. Sci Rep 2016; 6:39281. [PMID: 28004838 PMCID: PMC5177908 DOI: 10.1038/srep39281] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/21/2016] [Indexed: 01/07/2023] Open
Abstract
Experimental evolutionary genomics now allows biologists to test fundamental theories concerning the genetic basis of adaptation. We have conducted one of the longest laboratory evolution experiments with any sexually-reproducing metazoan, Drosophila melanogaster. We used next-generation resequencing data from this experiment to examine genome-wide patterns of genetic variation over an evolutionary time-scale that approaches 1,000 generations. We also compared measures of variation within and differentiation between our populations to simulations based on a variety of evolutionary scenarios. Our analysis yielded no clear evidence of hard selective sweeps, whereby natural selection acts to increase the frequency of a newly-arising mutation in a population until it becomes fixed. We do find evidence for selection acting on standing genetic variation, as independent replicate populations exhibit similar population-genetic dynamics, without obvious fixation of candidate alleles under selection. A hidden-Markov model test for selection also found widespread evidence for selection. We found more genetic variation genome-wide, and less differentiation between replicate populations genome-wide, than arose in any of our simulated evolutionary scenarios.
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Affiliation(s)
- Mark A Phillips
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA
| | - Anthony D Long
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA.,Genescient Inc., Fountain Valley, CA 92708, USA
| | - Zachary S Greenspan
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA
| | - Lee F Greer
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA.,Genescient Inc., Fountain Valley, CA 92708, USA
| | - Molly K Burke
- Oregon State University, Department of Integrative Biology, Corvallis, OR 97331, USA
| | | | | | | | - Laurence D Mueller
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA.,Genescient Inc., Fountain Valley, CA 92708, USA
| | - Michael R Rose
- University of California, Irvine, Department of Ecology and Evolutionary Biology, Irvine, CA, 92617, USA
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17
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Chakraborty M, Baldwin-Brown JG, Long AD, Emerson JJ. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Res 2016; 44:e147. [PMID: 27458204 PMCID: PMC5100563 DOI: 10.1093/nar/gkw654] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 07/09/2016] [Indexed: 01/19/2023] Open
Abstract
Genome assemblies that are accurate, complete and contiguous are essential for identifying important structural and functional elements of genomes and for identifying genetic variation. Nevertheless, most recent genome assemblies remain incomplete and fragmented. While long molecule sequencing promises to deliver more complete genome assemblies with fewer gaps, concerns about error rates, low yields, stringent DNA requirements and uncertainty about best practices may discourage many investigators from adopting this technology. Here, in conjunction with the platinum standard Drosophila melanogaster reference genome, we analyze recently published long molecule sequencing data to identify what governs completeness and contiguity of genome assemblies. We also present a hybrid meta-assembly approach that achieves remarkable assembly contiguity for both Drosophila and human assemblies with only modest long molecule sequencing coverage. Our results motivate a set of preliminary best practices for obtaining accurate and contiguous assemblies, a ‘missing manual’ that guides key decisions in building high quality de novo genome assemblies, from DNA isolation to polishing the assembly.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
| | - James G Baldwin-Brown
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA.,Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA .,Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
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18
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Najarro MA, Hackett JL, Smith BR, Highfill CA, King EG, Long AD, Macdonald SJ. Identifying Loci Contributing to Natural Variation in Xenobiotic Resistance in Drosophila. PLoS Genet 2015; 11:e1005663. [PMID: 26619284 PMCID: PMC4664282 DOI: 10.1371/journal.pgen.1005663] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/21/2015] [Indexed: 12/12/2022] Open
Abstract
Natural populations exhibit a great deal of interindividual genetic variation in the response to toxins, exemplified by the variable clinical efficacy of pharmaceutical drugs in humans, and the evolution of pesticide resistant insects. Such variation can result from several phenomena, including variable metabolic detoxification of the xenobiotic, and differential sensitivity of the molecular target of the toxin. Our goal is to genetically dissect variation in the response to xenobiotics, and characterize naturally-segregating polymorphisms that modulate toxicity. Here, we use the Drosophila Synthetic Population Resource (DSPR), a multiparent advanced intercross panel of recombinant inbred lines, to identify QTL (Quantitative Trait Loci) underlying xenobiotic resistance, and employ caffeine as a model toxic compound. Phenotyping over 1,700 genotypes led to the identification of ten QTL, each explaining 4.5-14.4% of the broad-sense heritability for caffeine resistance. Four QTL harbor members of the cytochrome P450 family of detoxification enzymes, which represent strong a priori candidate genes. The case is especially strong for Cyp12d1, with multiple lines of evidence indicating the gene causally impacts caffeine resistance. Cyp12d1 is implicated by QTL mapped in both panels of DSPR RILs, is significantly upregulated in the presence of caffeine, and RNAi knockdown robustly decreases caffeine tolerance. Furthermore, copy number variation at Cyp12d1 is strongly associated with phenotype in the DSPR, with a trend in the same direction observed in the DGRP (Drosophila Genetic Reference Panel). No additional plausible causative polymorphisms were observed in a full genomewide association study in the DGRP, or in analyses restricted to QTL regions mapped in the DSPR. Just as in human populations, replicating modest-effect, naturally-segregating causative variants in an association study framework in flies will likely require very large sample sizes.
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Affiliation(s)
- Michael A. Najarro
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Jennifer L. Hackett
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Brittny R. Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Chad A. Highfill
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Elizabeth G. King
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Anthony D. Long
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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19
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Long AD, Macdonald SJ, King EG. Dissecting complex traits using the Drosophila Synthetic Population Resource. Trends Genet 2014; 30:488-95. [PMID: 25175100 DOI: 10.1016/j.tig.2014.07.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/28/2014] [Accepted: 07/28/2014] [Indexed: 11/25/2022]
Abstract
For most complex traits we have a poor understanding of the positions, phenotypic effects, and population frequencies of the underlying genetic variants contributing to their variation. Recently, several groups have developed multi-parent advanced intercross mapping panels in different model organisms in an attempt to improve our ability to characterize causative genetic variants. These panels are powerful and are particularly well suited to the dissection of phenotypic variation generated by rare alleles and loci segregating multiple functional alleles. We describe studies using one such panel, the Drosophila Synthetic Population Resource (DSPR), and the implications for our understanding of the genetic basis of complex traits. In particular, we note that many loci of large effect appear to be multiallelic. If multiallelism is a general rule, analytical approaches designed to identify multiallelic variants should be a priority for both genome-wide association studies (GWASs) and multi-parental panels.
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Affiliation(s)
- Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.
| | - Stuart J Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Elizabeth G King
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
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20
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Burke MK, Liti G, Long AD. Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae. Mol Biol Evol 2014; 31:3228-39. [PMID: 25172959 DOI: 10.1093/molbev/msu256] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In "evolve-and-resequence" (E&R) experiments, whole-genome sequence data from laboratory-evolved populations can potentially uncover mechanisms of adaptive change. E&R experiments with initially isogenic, asexually reproducing microbes have repeatedly shown that beneficial de novo mutations drive adaptation, and these mutations are not shared among independently evolving replicate populations. Recent E&R experiments with higher eukaryotes that maintain genetic variation via sexual reproduction implicate largely different mechanisms; adaptation may act primarily on pre-existing genetic variation and occur in parallel among independent populations. But this is currently a debated topic, and generalizing these conclusions is problematic because E&R experiments with sexual species are difficult to implement and important elements of experimental design suffer for practical reasons. We circumvent potentially confounding limitations with a yeast model capable of shuffling genotypes via sexual recombination. Our starting population consisted of a highly intercrossed diploid Saccharomyces cerevisiae initiated from four wild haplotypes. We imposed a laboratory domestication treatment on 12 independent replicate populations for 18 weeks, where each week included 2 days as diploids in liquid culture and a forced recombination/mating event. We then sequenced pooled population samples at weeks 0, 6, 12, and 18. We show that adaptation is highly parallel among replicate populations, and can be localized to a modest number of genomic regions. We also demonstrate that despite hundreds of generations of evolution and large effective population sizes, de novo beneficial mutations do not play a large role in this adaptation. Further, we have high power to detect the signal of change in these populations but show how this power is dramatically reduced when fewer timepoints are sampled, or fewer replicate populations are analyzed. As ours is the most highly replicated and sampled E&R study in a sexual species to date, this evokes important considerations for past and future experiments.
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Affiliation(s)
- Molly K Burke
- Department of Ecology and Evolutionary Biology, University of California, Irvine
| | - Gianni Liti
- Institute of Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284-INSERM U1081, Faculté de Médecine, Université de Nice Sophia Antipolis, Nice, France
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine
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21
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Abstract
Human genome-wide association studies (GWAS) of longevity attempt to identify alleles at different frequencies in the extremely old, relative to a younger control sample. Here, we apply a GWAS approach to “synthetic” populations of Drosophila melanogaster derived from a small number of inbred founders. We used next-generation DNA sequencing to estimate allele and haplotype frequencies in the oldest surviving individuals of an age cohort and compared these frequencies with those of randomly sampled individuals from the same cohort. We used this case–control strategy in four independent cohorts and identified eight significantly differentiated regions of the genome potentially harboring genes with relevance for longevity. By modeling the effects of local haplotypes, we have more power to detect regions enriched for longevity genes than marker-based GWAS. Most significant regions occur near chromosome ends or centromeres where recombination is infrequent, consistent with these regions harboring unconditionally deleterious alleles impacting longevity. Genes in regions of normal recombination are enriched for those relevant to immune function and a gene family involved in oxidative stress response. Genetic differentiation between our experimental cohorts is comparable to that between human populations, suggesting in turn that our results may help explain heterogeneous signals in human association studies of extreme longevity when panels have diverse ancestry.
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Affiliation(s)
- Molly K Burke
- Department of Ecology and Evolutionary Biology, University of California, Irvine
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22
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King EG, Sanderson BJ, McNeil CL, Long AD, Macdonald SJ. Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity. PLoS Genet 2014; 10:e1004322. [PMID: 24810915 PMCID: PMC4014434 DOI: 10.1371/journal.pgen.1004322] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 03/10/2014] [Indexed: 12/01/2022] Open
Abstract
Modern genetic mapping is plagued by the “missing heritability” problem, which refers to the discordance between the estimated heritabilities of quantitative traits and the variance accounted for by mapped causative variants. One major potential explanation for the missing heritability is allelic heterogeneity, in which there are multiple causative variants at each causative gene with only a fraction having been identified. The majority of genome-wide association studies (GWAS) implicitly assume that a single SNP can explain all the variance for a causative locus. However, if allelic heterogeneity is prevalent, a substantial amount of genetic variance will remain unexplained. In this paper, we take a haplotype-based mapping approach and quantify the number of alleles segregating at each locus using a large set of 7922 eQTL contributing to regulatory variation in the Drosophila melanogaster female head. Not only does this study provide a comprehensive eQTL map for a major community genetic resource, the Drosophila Synthetic Population Resource, but it also provides a direct test of the allelic heterogeneity hypothesis. We find that 95% of cis-eQTLs and 78% of trans-eQTLs are due to multiple alleles, demonstrating that allelic heterogeneity is widespread in Drosophila eQTL. Allelic heterogeneity likely contributes significantly to the missing heritability problem common in GWAS studies. For traits with complex genetic inheritance it has generally proven very difficult to identify the majority of the specific causative variants involved. A range of hypotheses have been put forward to explain this so-called “missing heritability”. One idea—allelic heterogeneity, where genes each harbor multiple different causative variants—has received little attention, because it is difficult to detect with most genetic mapping designs. Here we make use of a panel of Drosophila melanogaster lines derived from multiple founders, allowing us to directly test for the presence of multiple alleles at a large set of genetic loci influencing gene expression. We find that the vast majority of loci harbor more than two functional alleles, demonstrating extensive allelic heterogeneity at the level of gene expression and suggesting that such heterogeneity is an important factor determining the genetic basis of complex trait variation in general.
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Affiliation(s)
- Elizabeth G. King
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
- * E-mail:
| | - Brian J. Sanderson
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Casey L. McNeil
- Department of Biology, Newman University, Wichita, Kansas, United States of America
| | - Anthony D. Long
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
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23
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Baldwin-Brown JG, Long AD, Thornton KR. The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms. Mol Biol Evol 2014; 31:1040-55. [PMID: 24441104 PMCID: PMC3969567 DOI: 10.1093/molbev/msu048] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
A novel approach for dissecting complex traits is to experimentally evolve laboratory populations under a controlled environment shift, resequence the resulting populations, and identify single nucleotide polymorphisms (SNPs) and/or genomic regions highly diverged in allele frequency. To better understand the power and localization ability of such an evolve and resequence (E&R) approach, we carried out forward-in-time population genetics simulations of 1 Mb genomic regions under a large combination of experimental conditions, then attempted to detect significantly diverged SNPs. Our analysis indicates that the ability to detect differentiation between populations is primarily affected by selection coefficient, population size, number of replicate populations, and number of founding haplotypes. We estimate that E&R studies can detect and localize causative sites with 80% success or greater when the number of founder haplotypes is over 500, experimental populations are replicated at least 25-fold, population size is at least 1,000 diploid individuals, and the selection coefficient on the locus of interest is at least 0.1. More achievable experimental designs (less replicated, fewer founder haplotypes, smaller effective population size, and smaller selection coefficients) can have power of greater than 50% to identify a handful of SNPs of which one is likely causative. Similarly, in cases where s ≥ 0.2, less demanding experimental designs can yield high power.
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24
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Abstract
Here we present computational machinery to efficiently and accurately identify transposable element (TE) insertions in 146 next-generation sequenced inbred strains of Drosophila melanogaster. The panel of lines we use in our study is composed of strains from a pair of genetic mapping resources: the Drosophila Genetic Reference Panel (DGRP) and the Drosophila Synthetic Population Resource (DSPR). We identified 23,087 TE insertions in these lines, of which 83.3% are found in only one line. There are marked differences in the distribution of elements over the genome, with TEs found at higher densities on the X chromosome, and in regions of low recombination. We also identified many more TEs per base pair of intronic sequence and fewer TEs per base pair of exonic sequence than expected if TEs are located at random locations in the euchromatic genome. There was substantial variation in TE load across genes. For example, the paralogs derailed and derailed-2 show a significant difference in the number of TE insertions, potentially reflecting differences in the selection acting on these loci. When considering TE families, we find a very weak effect of gene family size on TE insertions per gene, indicating that as gene family size increases the number of TE insertions in a given gene within that family also increases. TEs are known to be associated with certain phenotypes, and our data will allow investigators using the DGRP and DSPR to assess the functional role of TE insertions in complex trait variation more generally. Notably, because most TEs are very rare and often private to a single line, causative TEs resulting in phenotypic differences among individuals may typically fail to replicate across mapping panels since individual elements are unlikely to segregate in both panels. Our data suggest that “burden tests” that test for the effect of TEs as a class may be more fruitful.
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Affiliation(s)
- Julie M Cridland
- Department of Ecology, Evolution and Physiology, University of California, Irvine
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25
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Thornton KR, Foran AJ, Long AD. Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect. PLoS Genet 2013; 9:e1003258. [PMID: 23437004 PMCID: PMC3578756 DOI: 10.1371/journal.pgen.1003258] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/02/2012] [Indexed: 01/08/2023] Open
Abstract
Current genome-wide association studies (GWAS) have high power to detect intermediate frequency SNPs making modest contributions to complex disease, but they are underpowered to detect rare alleles of large effect (RALE). This has led to speculation that the bulk of variation for most complex diseases is due to RALE. One concern with existing models of RALE is that they do not make explicit assumptions about the evolution of a phenotype and its molecular basis. Rather, much of the existing literature relies on arbitrary mapping of phenotypes onto genotypes obtained either from standard population-genetic simulation tools or from non-genetic models. We introduce a novel simulation of a 100-kilobase gene region, based on the standard definition of a gene, in which mutations are unconditionally deleterious, are continuously arising, have partially recessive and non-complementing effects on phenotype (analogous to what is widely observed for most Mendelian disorders), and are interspersed with neutral markers that can be genotyped. Genes evolving according to this model exhibit a characteristic GWAS signature consisting of an excess of marginally significant markers. Existing tests for an excess burden of rare alleles in cases have low power while a simple new statistic has high power to identify disease genes evolving under our model. The structure of linkage disequilibrium between causative mutations and significantly associated markers under our model differs fundamentally from that seen when rare causative markers are assumed to be neutral. Rather than tagging single haplotypes bearing a large number of rare causative alleles, we find that significant SNPs in a GWAS tend to tag single causative mutations of small effect relative to other mutations in the same gene. Our results emphasize the importance of evaluating the power to detect associations under models that are genetically and evolutionarily motivated. Current GWA studies typically only explain a small fraction of heritable variation in complex traits, resulting in speculation that a large fraction of variation in such traits may be due to rare alleles of large effect (RALE). The most parsimonious evolutionary mechanism that results in an inverse relationship between the frequency and effect size of causative alleles is an equilibrium between newly arising deleterious mutations and selection eliminating those mutations, resulting in an inverse relation between effect size and average frequency. This assumption is not built into many current models of RALE and, as a result, power calculations may be misleading. We use forward population genetic simulations to explore the ability of GWAS to detect genes in which unconditionally deleterious, partially recessive mutations arise each generation. Our model is based on the standard definition of a gene as a region within which loss-of-function mutations fail to complement, consistent with the multi-allelic basis for Mendelian disorders. Our model predicts that it may not be uncommon for single genes evolving under our model to contribute upwards of 5% to variation in a complex trait, and that such genes could be routinely detected via modified GWAS approaches.
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Affiliation(s)
- Kevin R. Thornton
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
- * E-mail: (KRT); (ADL)
| | - Andrew J. Foran
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Anthony D. Long
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
- * E-mail: (KRT); (ADL)
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26
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Abstract
Combining experimental evolution with whole-genome resequencing is a promising new strategy for investigating the dynamics of evolutionary change. Published studies that have resequenced laboratory-selected populations of sexual organisms have typically focused on populations sampled at the end of an evolution experiment. These studies have attempted to associate particular alleles with phenotypic change and attempted to distinguish between different theoretical models of adaptation. However, neither the population used to initiate the experiment nor multiple time points sampled during the evolutionary trajectory are generally available for examination. In this issue of Molecular Ecology, Orozco-terWengel et al. (2012) take a significant step forward by estimating genome-wide allele frequencies at the start, 15 generations into and at the end of a 37-generation Drosophila experimental evolution study. The authors identify regions of the genome that have responded to laboratory selection and describe the temporal dynamics of allele frequency change. They identify two common trajectories for putatively adaptive alleles: alleles either gradually increase in frequency throughout the entire 37 generations or alleles plateau at a new frequency by generation 15. The identification of complex trajectories of alleles under selection contributes to a growing body of literature suggesting that simple models of adaptation, whereby beneficial alleles arise and increase in frequency unimpeded until they become fixed, may not adequately describe short-term response to selection.
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Affiliation(s)
- Molly K Burke
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA
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27
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Riehle MM, Bennett AF, Long AD. Differential Patterns of Gene Expression and Gene Complement in Laboratory-Evolved Lines of E. coli. Integr Comp Biol 2012; 45:532-8. [PMID: 21676798 DOI: 10.1093/icb/45.3.532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Laboratory selection experiments play a prominent role in understanding organismal adaptation. Although bacteria are not yet commonly used for such experiments, they are well suited for analyses of both the organismic and the genetic basis of adaptation. Bacteria can be maintained in large populations while occupying limited laboratory space, have short generation times, are well characterized physiologically, biochemically, and genetically, and are readily frozen and revived from the freezer. In addition, the genomes of many species are completely sequenced and knowledge of gene function is unparalleled. Here we review general aspects of selection experiments, the history of using selection experiments in combination with thermal biology and genomics, and highlight findings from six lines of Escherichia coli adapted to high temperature (41.5°C), including changes in organismal fitness, physiological performance, gene complement and gene expression. Our results are an example of the powerful insights that can be discovered by combining the tools and analyses of many biological disciplines including genomics, evolutionary biology, genetics, and evolutionary physiology.
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Affiliation(s)
- Michelle M Riehle
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697-2525
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28
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Abstract
The examination of spatial variation can act as a substitute for temporal variation in population studies. Of particular use in the effort to understand the selective forces that govern spatial variation are the sibling species Drosophila melanogaster and D. simulans. Recent work at the level of both molecules and morphology has uncovered a great deal of spatial variation within and between these two species. Here we summarize these data, with reference to what they tell us about the history and nature of selection operating in these species.
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Affiliation(s)
- R S Singh
- Rama Singh and Anthony Long are at the Dept of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1
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29
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Martin A, Papa R, Nadeau NJ, Hill RI, Counterman BA, Halder G, Jiggins CD, Kronforst MR, Long AD, McMillan WO, Reed RD. Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand. Proc Natl Acad Sci U S A 2012; 109:12632-7. [PMID: 22802635 PMCID: PMC3411988 DOI: 10.1073/pnas.1204800109] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Although animals display a rich variety of shapes and patterns, the genetic changes that explain how complex forms arise are still unclear. Here we take advantage of the extensive diversity of Heliconius butterflies to identify a gene that causes adaptive variation of black wing patterns within and between species. Linkage mapping in two species groups, gene-expression analysis in seven species, and pharmacological treatments all indicate that cis-regulatory evolution of the WntA ligand underpins discrete changes in color pattern features across the Heliconius genus. These results illustrate how the direct modulation of morphogen sources can generate a wide array of unique morphologies, thus providing a link between natural genetic variation, pattern formation, and adaptation.
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Affiliation(s)
- Arnaud Martin
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.
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30
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King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S, Broman KW, Long AD, Macdonald SJ. Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Res 2012; 22:1558-66. [PMID: 22496517 PMCID: PMC3409269 DOI: 10.1101/gr.134031.111] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Genetic dissection of complex, polygenic trait variation is a key goal of medical and evolutionary genetics. Attempts to identify genetic variants underlying complex traits have been plagued by low mapping resolution in traditional linkage studies, and an inability to identify variants that cumulatively explain the bulk of standing genetic variation in genome-wide association studies (GWAS). Thus, much of the heritability remains unexplained for most complex traits. Here we describe a novel, freely available resource for the Drosophila community consisting of two sets of recombinant inbred lines (RILs), each derived from an advanced generation cross between a different set of eight highly inbred, completely resequenced founders. The Drosophila Synthetic Population Resource (DSPR) has been designed to combine the high mapping resolution offered by multiple generations of recombination, with the high statistical power afforded by a linkage-based design. Here, we detail the properties of the mapping panel of >1600 genotyped RILs, and provide an empirical demonstration of the utility of the approach by genetically dissecting alcohol dehydrogenase (ADH) enzyme activity. We confirm that a large fraction of the variation in this classic quantitative trait is due to allelic variation at the Adh locus, and additionally identify several previously unknown modest-effect trans-acting QTL (quantitative trait loci). Using a unique property of multiparental linkage mapping designs, for each QTL we highlight a relatively small set of candidate causative variants for follow-up work. The DSPR represents an important step toward the ultimate goal of a complete understanding of the genetics of complex traits in the Drosophila model system.
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Affiliation(s)
- Elizabeth G King
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
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31
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Abstract
To estimate the number and diversity of beneficial mutations, we experimentally evolved 115 populations of Escherichia coli to 42.2°C for 2000 generations and sequenced one genome from each population. We identified 1331 total mutations, affecting more than 600 different sites. Few mutations were shared among replicates, but a strong pattern of convergence emerged at the level of genes, operons, and functional complexes. Our experiment uncovered a set of primary functional targets of high temperature, but we estimate that many other beneficial mutations could contribute to similar adaptive outcomes. We inferred the pervasive presence of epistasis among beneficial mutations, which shaped adaptive trajectories into at least two distinct pathways involving mutations either in the RNA polymerase complex or the termination factor rho.
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Affiliation(s)
- Olivier Tenaillon
- Department of Ecology and Evolutionary Biology, University of California-Irvine, CA 92697, USA.
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32
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Conceição IC, Long AD, Gruber JD, Beldade P. Genomic sequence around butterfly wing development genes: annotation and comparative analysis. PLoS One 2011; 6:e23778. [PMID: 21909358 PMCID: PMC3166123 DOI: 10.1371/journal.pone.0023778] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 07/27/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Analysis of genomic sequence allows characterization of genome content and organization, and access beyond gene-coding regions for identification of functional elements. BAC libraries, where relatively large genomic regions are made readily available, are especially useful for species without a fully sequenced genome and can increase genomic coverage of phylogenetic and biological diversity. For example, no butterfly genome is yet available despite the unique genetic and biological properties of this group, such as diversified wing color patterns. The evolution and development of these patterns is being studied in a few target species, including Bicyclus anynana, where a whole-genome BAC library allows targeted access to large genomic regions. METHODOLOGY/PRINCIPAL FINDINGS We characterize ∼1.3 Mb of genomic sequence around 11 selected genes expressed in B. anynana developing wings. Extensive manual curation of in silico predictions, also making use of a large dataset of expressed genes for this species, identified repetitive elements and protein coding sequence, and highlighted an expansion of Alcohol dehydrogenase genes. Comparative analysis with orthologous regions of the lepidopteran reference genome allowed assessment of conservation of fine-scale synteny (with detection of new inversions and translocations) and of DNA sequence (with detection of high levels of conservation of non-coding regions around some, but not all, developmental genes). CONCLUSIONS The general properties and organization of the available B. anynana genomic sequence are similar to the lepidopteran reference, despite the more than 140 MY divergence. Our results lay the groundwork for further studies of new interesting findings in relation to both coding and non-coding sequence: 1) the Alcohol dehydrogenase expansion with higher similarity between the five tandemly-repeated B. anynana paralogs than with the corresponding B. mori orthologs, and 2) the high conservation of non-coding sequence around the genes wingless and Ecdysone receptor, both involved in multiple developmental processes including wing pattern formation.
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MESH Headings
- Alcohol Dehydrogenase/genetics
- Animals
- Base Composition/genetics
- Base Sequence
- Bombyx/genetics
- Butterflies/genetics
- Butterflies/growth & development
- Chromosomes, Artificial, Bacterial/genetics
- Computational Biology
- Conserved Sequence/genetics
- DNA Transposable Elements/genetics
- DNA, Intergenic/genetics
- Databases, Genetic
- Expressed Sequence Tags
- Gene Order/genetics
- Genes, Developmental/genetics
- Genes, Insect/genetics
- MicroRNAs/genetics
- Molecular Sequence Annotation
- Molecular Sequence Data
- Open Reading Frames/genetics
- Phylogeny
- Repetitive Sequences, Nucleic Acid/genetics
- Reproducibility of Results
- Sequence Homology, Nucleic Acid
- Synteny/genetics
- Wings, Animal/growth & development
- Wings, Animal/metabolism
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Affiliation(s)
| | - Anthony D. Long
- University of California Irvine, Irvine, California, United States of America
| | - Jonathan D. Gruber
- University of California Irvine, Irvine, California, United States of America
| | - Patrícia Beldade
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Institute of Biology, Leiden University, Leiden, The Netherlands
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33
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Burke MK, Dunham JP, Shahrestani P, Thornton KR, Rose MR, Long AD. Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 2010; 467:587-90. [PMID: 20844486 DOI: 10.1038/nature09352] [Citation(s) in RCA: 297] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 07/15/2010] [Indexed: 11/09/2022]
Abstract
Experimental evolution systems allow the genomic study of adaptation, and so far this has been done primarily in asexual systems with small genomes, such as bacteria and yeast. Here we present whole-genome resequencing data from Drosophila melanogaster populations that have experienced over 600 generations of laboratory selection for accelerated development. Flies in these selected populations develop from egg to adult ∼20% faster than flies of ancestral control populations, and have evolved a number of other correlated phenotypes. On the basis of 688,520 intermediate-frequency, high-quality single nucleotide polymorphisms, we identify several dozen genomic regions that show strong allele frequency differentiation between a pooled sample of five replicate populations selected for accelerated development and pooled controls. On the basis of resequencing data from a single replicate population with accelerated development, as well as single nucleotide polymorphism data from individual flies from each replicate population, we infer little allele frequency differentiation between replicate populations within a selection treatment. Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with 'classic' sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include 'incomplete' sweep models, in which mutations have not had enough time to fix, and 'soft' sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.
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Affiliation(s)
- Molly K Burke
- Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, California 92697-2525, USA.
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34
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Beldade P, Van't Hof AE, Jerónimo MA, Long AD. Microsatellite markers associated with genes expressed in developing wings of Bicyclus anynana butterflies. Mol Ecol Resour 2009; 9:1487-92. [PMID: 21564941 DOI: 10.1111/j.1755-0998.2009.02691.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Deriving useful microsatellite markers in lepidopterans has been challenging when relying on scans of genomic DNA libraries, presumably due to repetitiveness in their genomes. We assayed 96 of 320 microsatellites identified in silico from a collection of Bicyclus anynana ESTs, in 11 independent individuals from a laboratory population. From the 68 successful assays, we identified 40 polymorphic markers including 22 with BLAST-based annotation. Nine of 12 selected polymorphic markers tested in a panel of 24 wild-caught individuals converted to successful assays and were all polymorphic. We discuss how microsatellite discovery in ESTs is an efficient strategy with important attendant advantages.
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Affiliation(s)
- Patrícia Beldade
- Institute of Biology Leiden University, PO Box 9516, 2300 RA, Leiden, The Netherlands Instituto Gulbenkian de Ciência, Apartado 14, P-2781-901 Oeiras, Portugal School of Biological Sciences, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, UK Department of Ecology and Evolutionary Biology, University of California at Irvine, 5210 McGaugh Hall, Irvine, 92697-2525 CA, USA
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35
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Beldade P, Saenko SV, Pul N, Long AD. A gene-based linkage map for Bicyclus anynana butterflies allows for a comprehensive analysis of synteny with the lepidopteran reference genome. PLoS Genet 2009; 5:e1000366. [PMID: 19197358 PMCID: PMC2629579 DOI: 10.1371/journal.pgen.1000366] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 01/05/2009] [Indexed: 11/28/2022] Open
Abstract
Lepidopterans (butterflies and moths) are a rich and diverse order of insects, which, despite their economic impact and unusual biological properties, are relatively underrepresented in terms of genomic resources. The genome of the silkworm Bombyx mori has been fully sequenced, but comparative lepidopteran genomics has been hampered by the scarcity of information for other species. This is especially striking for butterflies, even though they have diverse and derived phenotypes (such as color vision and wing color patterns) and are considered prime models for the evolutionary and developmental analysis of ecologically relevant, complex traits. We focus on Bicyclus anynana butterflies, a laboratory system for studying the diversification of novelties and serially repeated traits. With a panel of 12 small families and a biphasic mapping approach, we first assigned 508 expressed genes to segregation groups and then ordered 297 of them within individual linkage groups. We also coarsely mapped seven color pattern loci. This is the richest gene-based map available for any butterfly species and allowed for a broad-coverage analysis of synteny with the lepidopteran reference genome. Based on 462 pairs of mapped orthologous markers in Bi. anynana and Bo. mori, we observed strong conservation of gene assignment to chromosomes, but also evidence for numerous large- and small-scale chromosomal rearrangements. With gene collections growing for a variety of target organisms, the ability to place those genes in their proper genomic context is paramount. Methods to map expressed genes and to compare maps with relevant model systems are crucial to extend genomic-level analysis outside classical model species. Maps with gene-based markers are useful for comparative genomics and to resolve mapped genomic regions to a tractable number of candidate genes, especially if there is synteny with related model species. This is discussed in relation to the identification of the loci contributing to color pattern evolution in butterflies.
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Affiliation(s)
- Patrícia Beldade
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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36
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Teotónio H, Chelo IM, Bradić M, Rose MR, Long AD. Experimental evolution reveals natural selection on standing genetic variation. Nat Genet 2009; 41:251-7. [DOI: 10.1038/ng.289] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Accepted: 10/27/2008] [Indexed: 10/21/2022]
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37
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Macdonald SJ, Long AD. Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 2007; 176:1261-81. [PMID: 17435224 PMCID: PMC1894589 DOI: 10.1534/genetics.106.069641] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We develop and implement a strategy to map QTL in two synthetic populations of Drosophila melanogaster each initiated with eight inbred founder strains. These recombinant populations allow simultaneous estimates of QTL location, effect, and frequency. Five X-linked QTL influencing bristle number were resolved to intervals of approximately 1.3 cM. We confirm previous observations of bristle number QTL distal to 4A at the tip of the chromosome and identify two novel QTL in 7F-8C, an interval that does not include any classic bristle number candidate genes. If QTL at the tip of the X are biallelic they appear to be intermediate in frequency, although there is evidence that these QTL may reside in multiallelic haplotypes. Conversely, the two QTL mapping to the middle of the X chromosome are likely rare: in each case the minor allele is observed in only 1 of the 16 founders. Assuming additivity and biallelism we estimate that identified QTL contribute 1.0 and 8.7%, respectively, to total phenotypic variation in male abdominal and sternopleural bristle number in nature. Models that seek to explain the maintenance of genetic variation make different predictions about the population frequency of QTL alleles. Thus, mapping QTL in eight-way recombinant populations can distinguish between these models.
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Affiliation(s)
- Stuart J Macdonald
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA.
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38
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Gruber JD, Genissel A, Macdonald SJ, Long AD. How repeatable are associations between polymorphisms in achaete-scute and bristle number variation in Drosophila? Genetics 2007; 175:1987-97. [PMID: 17277365 PMCID: PMC1855119 DOI: 10.1534/genetics.106.067108] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Currently, the relevance of common genetic variants--particularly those significantly associated with phenotypic variation in laboratory studies--to standing phenotypic variation in the wild is poorly understood. To address this, we quantified the relationship between achaete-scute complex (ASC) polymorphisms and Drosophila bristle number phenotypes in several new population samples. MC22 is a biallelic, nonrepetitive-length polymorphism 97 bp downstream of the scute transcript. It has been previously shown to be associated with sternopleural bristle number variation in both sexes in a set of isogenic lines. We replicated this association in a large cohort of wild-caught Drosophila melanogaster. We also detected a significant association at MC22 in an outbred population maintained under laboratory conditions for approximately 25 years, but the phenotypic effects in this sample were opposite from the direction estimated in the initial study. Finally, no significant associations were detected in a second large wild-caught cohort or in a set of 134 nearly isogenic lines. Our ability to repeat the initial association in wild samples suggests that it was not spurious. Nevertheless, inconsistent results from the other three panels suggest that the relationship between polymorphic genetic markers and loci contributing to continuous variation is not a simple one.
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Affiliation(s)
- Jonathan D Gruber
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA.
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39
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Abstract
Recent research indicates that aging is affected by many genes and thus many biochemical pathways. This has led to a failure to find pharmaceuticals that significantly ameliorate the human aging process. Progress in evolutionary and genetic research, however, suggests the possibility of combining experimental evolution, genomic analysis, and mass screening of pharmaceuticals and botanicals to produce effective therapeutics for human aging. The starting point for this strategy is model systems that have outbred populations with substantially increased lifespan. These are easily produced by tuning the force of natural selection in the laboratory. Such biological material is then a good candidate for genomic analysis, leading to the identification of numerous biochemical pathways involved in increased lifespan, in the model system. These biochemical pathways would then be available for pharmaceutical development, first in fruit flies, then in rodents, and eventually in a clinical human population. We include a discussion of the pharmacological methods appropriate to this strategy of drug discovery.
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Affiliation(s)
- Mahtab Jafari
- Program in Pharmaceutical Sciences, College of Health Sciences, University of California, Irvine, California 92697, USA.
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40
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Long AD, Ponte G, Anderson RWG. THE CASR PEDESTRIAN CRASH ANALYSIS: AT-SCENE INVESTIGATION, COMPUTER SIMULATION AND SUB-SYSTEM RECONSTRUCTION. J Biomech 2007. [DOI: 10.1016/s0021-9290(07)70212-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Long AD, Beldade P, Macdonald SJ. Estimation of population heterozygosity and library construction-induced mutation rate from expressed sequence tag collections. Genetics 2006; 176:711-4. [PMID: 17179075 PMCID: PMC1893025 DOI: 10.1534/genetics.106.063610] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unigene alignments obtained from cDNA libraries made using multiple individuals are not currently used to estimate population heterozygosity, as they are known to harbor mutations created during library construction. We describe an estimator of population heterozygosity that utilizes only SNPs unlikely to be library construction artifacts.
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Affiliation(s)
- A D Long
- Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA.
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42
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Beldade P, Rudd S, Gruber JD, Long AD. A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model. BMC Genomics 2006; 7:130. [PMID: 16737530 PMCID: PMC1534037 DOI: 10.1186/1471-2164-7-130] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Accepted: 05/31/2006] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Butterfly wing color patterns are a key model for integrating evolutionary developmental biology and the study of adaptive morphological evolution. Yet, despite the biological, economical and educational value of butterflies they are still relatively under-represented in terms of available genomic resources. Here, we describe an Expression Sequence Tag (EST) project for Bicyclus anynana that has identified the largest available collection to date of expressed genes for any butterfly. RESULTS By targeting cDNAs from developing wings at the stages when pattern is specified, we biased gene discovery towards genes potentially involved in pattern formation. Assembly of 9,903 ESTs from a subtracted library allowed us to identify 4,251 genes of which 2,461 were annotated based on BLAST analyses against relevant gene collections. Gene prediction software identified 2,202 peptides, of which 215 longer than 100 amino acids had no homology to any known proteins and, thus, potentially represent novel or highly diverged butterfly genes. We combined gene and Single Nucleotide Polymorphism (SNP) identification by constructing cDNA libraries from pools of outbred individuals, and by sequencing clones from the 3' end to maximize alignment depth. Alignments of multi-member contigs allowed us to identify over 14,000 putative SNPs, with 316 genes having at least one high confidence double-hit SNP. We furthermore identified 320 microsatellites in transcribed genes that can potentially be used as genetic markers. CONCLUSION Our project was designed to combine gene and sequence polymorphism discovery and has generated the largest gene collection available for any butterfly and many potential markers in expressed genes. These resources will be invaluable for exploring the potential of B. anynana in particular, and butterflies in general, as models in ecological, evolutionary, and developmental genetics.
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Affiliation(s)
- Patrícia Beldade
- Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, USA
- Institute of Biology of the University of Leiden, Leiden, The Netherlands
| | - Stephen Rudd
- Bioinformatics Laboratory, Turku Centre for Biotechnology, Turku, Finland
| | - Jonathan D Gruber
- Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, USA
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Macdonald SJ, Long AD. Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura. Genome Biol 2006; 7:R67. [PMID: 16872532 PMCID: PMC1779558 DOI: 10.1186/gb-2006-7-7-r67] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Revised: 04/30/2006] [Accepted: 07/27/2006] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A primary objective of comparative genomics is to identify genomic elements of functional significance that contribute to phenotypic diversity. Complex changes in genome structure (insertions, duplications, rearrangements, translocations) may be widespread, and have important effects on organismal diversity. Any survey of genomic variation is incomplete without an assessment of structural changes. RESULTS We re-examine the genome sequences of the diverged species Drosophila melanogaster and D. pseudoobscura to identify fine-scale structural features that distinguish the genomes. We detect 95 large insertion/deletion events that occur within the introns of orthologous gene pairs, the majority of which represent insertion of transposable elements. We also identify 143 microinversions below 5 kb in size. These microinversions reside within introns or just upstream or downstream of genes, and invert conserved DNA sequence. The sequence conservation within microinversions suggests they may be enriched for functional genetic elements, and their position with respect to known genes implicates them in the regulation of gene expression. Although we found a distinct pattern of GC content across microinversions, this was indistinguishable from the pattern observed across blocks of conserved non-coding sequence. CONCLUSION Drosophila has long been known as a genus harboring a variety of large inversions that disrupt chromosome colinearity. Here we demonstrate that microinversions, many of which are below 1 kb in length, located in/near genes may also be an important source of genetic variation in Drosophila. Further examination of other Drosophila genome sequences will likely identify an array of novel microinversion events.
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Affiliation(s)
- Stuart J Macdonald
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697-2525, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697-2525, USA
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Macdonald SJ, Pastinen T, Genissel A, Cornforth TW, Long AD. A low-cost open-source SNP genotyping platform for association mapping applications. Genome Biol 2005; 6:R105. [PMID: 16356268 PMCID: PMC1414086 DOI: 10.1186/gb-2005-6-12-r105] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Revised: 07/20/2005] [Accepted: 10/21/2005] [Indexed: 02/27/2023] Open
Abstract
Association mapping aimed at identifying DNA polymorphisms that contribute to variation in complex traits entails genotyping a large number of single-nucleotide polymorphisms (SNPs) in a very large panel of individuals. Few technologies, however, provide inexpensive high-throughput genotyping. Here, we present an efficient approach developed specifically for genotyping large fixed panels of diploid individuals. The cost-effective, open-source nature of our methodology may make it particularly attractive to those working in nonmodel systems.
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Affiliation(s)
- Stuart J Macdonald
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697-2525, USA
| | - Tomi Pastinen
- McGill University and Genome Québec Innovation Centre, 740 Docteur Penfield Avenue, Montreal, Québec H3A 1A4, Canada
| | - Anne Genissel
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697-2525, USA
- Section of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA
| | - Theodore W Cornforth
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697-2525, USA
- Institute of Neuroscience, 1254 University of Oregon, Eugene, Oregon 97403-1254, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA 92697-2525, USA
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Drapeau MD, Cyran SA, Viering MM, Geyer PK, Long AD. A cis-regulatory sequence within the yellow locus of Drosophila melanogaster required for normal male mating success. Genetics 2005; 172:1009-30. [PMID: 16272418 PMCID: PMC1456202 DOI: 10.1534/genetics.105.045666] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Drosophila melanogaster males perform a courtship ritual consisting of a series of dependent fixed-action patterns. The yellow (y) gene is required for normal male courtship behavior and subsequent mating success. To better characterize the requirement for y in the manifestation of innate male sexual behavior, we measured the male mating success (MMS) of 12 hypomorphic y mutants and matched-outbred-background controls using a y+ rescue element on a freely segregating minichromosome. We found that 4 hypomorphs significantly reduced MMS to varying degrees. Reduced MMS was largely independent of adult pigmentation patterns. These mutations defined a 300-bp regulatory region upstream of the transcription start, the mating-success regulatory sequence (MRS), whose function is required for normal MMS. Visualization of gene action via GFP and a Yellow antibody suggests that the MRS directs y transcription in a small number of cells in the third instar CNS, the developmental stage previously implicated in the role of y with regard to male courtship behavior. The presence of Yellow protein in these cells positively correlates with MMS in a subset of mutants. The MRS contains a regulatory sequence controlling larval pigmentation and a 35-bp sequence that is highly conserved within the genus Drosophila and is predicted to bind known transcription factors.
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Affiliation(s)
- Mark David Drapeau
- Department of Ecology and Evolutionary Biology, University of California, Irvine 92697, USA.
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Macdonald SJ, Pastinen T, Long AD. The effect of polymorphisms in the enhancer of split gene complex on bristle number variation in a large wild-caught cohort of Drosophila melanogaster. Genetics 2005; 171:1741-56. [PMID: 16143618 PMCID: PMC1456100 DOI: 10.1534/genetics.105.045344] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Enhancer of split complex [E(spl)-C] in Drosophila encompasses a variety of functional elements controlling bristle patterning and on the basis of prior work is a strong candidate for harboring alleles having subtle effects on bristle number variation. Here we extend earlier studies identifying associations between complex phenotypes and polymorphisms segregating among inbred laboratory lines of Drosophila and test the influence of E(spl)-C on bristle number variation in a natural cohort. We describe results from an association mapping study using 203 polymorphisms spread throughout the E(spl)-C genotyped in 2000 wild-caught Drosophila melanogaster. Despite power to detect associations accounting for as little as 2% of segregating variation for bristle number, and saturating the region with single-nucleotide polymorphisms (SNPs), we identified no single SNP marker showing a significant (additive over loci) effect after correcting for multiple tests. Using a newly developed test we conservatively identify six regions of the E(spl)-C in which the insertion of transposable elements as a class contributes to variation in bristle number, apparently in a sex- or trait-limited fashion. Finally, we carry out all possible 20,503 two-way tests for epistasis and identify a slight excess of marginally significant interactions, although none survive multiple-testing correction. It may not be straightforward to extend the results of laboratory-based association studies to natural populations.
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Affiliation(s)
- Stuart J Macdonald
- Department of Ecology and Evolutionary Biology, University of California-Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA.
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Abstract
Understanding the generation of phenotypic variation is an important challenge for modern evolutionary biology, and butterfly wing patterns are an exciting system that can shed some light on this issue. Here, we report on recent advances in the genetics of Bicyclus anynana butterflies. This system provides the potential for a fully integrated study of the evolutionary and developmental processes underlying diversity in morphology.
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Affiliation(s)
- Patrícia Beldade
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA.
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48
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Abstract
The genetic factors contributing to complex trait variation may reside in regulatory, rather than protein-coding portions of the genome. Within noncoding regions, SNPs in regulatory elements are more likely to contribute to phenotypic variation than those in nonregulatory regions. Thus, it is important to be able to identify and annotate noncoding regulatory elements. DNA conservation among diverged species successfully identifies noncoding regulatory regions. However, because rapidly evolving regulatory regions will not generally be conserved across species, these will not detected by using purely conservation-based methods. Here we describe additional approaches that can be used to identify putative regulatory elements via signatures of nonneutral evolution. An examination of the pattern of polymorphism both within and between populations of Drosophila melanogaster, as well as divergence with its sibling species Drosophila simulans, across 24.2 kb of noncoding DNA identifies several nonneutrally evolving regions not identified by conservation. Because different methods tag different regions, it appears that the methods are complementary. Patterns of variation at different elements are consistent with the action of selective sweeps, balancing selection, or population differentiation. Together with regions conserved between D. melanogaster and Drosophila pseudoobscura, we tag 5.3 kb of noncoding DNA as potentially regulatory. Ninety-seven of the 408 common noncoding SNPs surveyed are within putatively regulatory regions. If these methods collectively identify the majority of functional noncoding polymorphisms, genotyping only these SNPs in an association mapping framework would reduce genotyping effort for noncoding regions 4-fold.
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Affiliation(s)
- Stuart J Macdonald
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 92697-2525, USA.
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Riehle MM, Bennett AF, Long AD. Changes in Gene Expression Following High‐Temperature Adaptation in Experimentally Evolved Populations ofE. coli. Physiol Biochem Zool 2005; 78:299-315. [PMID: 15887077 DOI: 10.1086/430035] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2004] [Indexed: 11/03/2022]
Abstract
Transcription profiling (quantitative analysis of RNA abundance) can provide a genome-wide picture of gene expression changes that accompany organismal adaptation to a new environment. Here, we used DNA microarrays to characterize genome-wide changes in transcript abundance in three replicate lines of the bacterium E. coli grown for 2,000 generations at a stressful high temperature (41.5 degrees C). Across these lines, 12% of genes significantly changed expression during high-temperature adaptation; the majority of these changes (55%) were less than twofold increments or decrements. Thirty-nine genes, four times the number expected by chance alone, exhibited moderately or highly replicated expression changes across lines. Expression changes within a priori defined functional categories showed an even greater level of replication than did individual genes. Expression changes in the phenotypically defined stress genes and adaptation functional categories were important in evolutionary adaptation to high temperature.
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Affiliation(s)
- Michelle M Riehle
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA.
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Abstract
To extend results from laboratory genetic mapping experiments to natural populations it is necessary to estimate the phenotypic effects attributable to laboratory-identified genetic factors in nature. We retested a polymorphism found to be strongly associated with an increase of 0.35 sternopleural bristles in laboratory strains in two large samples of wild-caught Drosophila melanogaster. Despite >90% power to detect effects as low as 0.27 bristles (<1% of the total variation in bristle number) we did not replicate the association in nature. Potential explanations for this result are explored.
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Affiliation(s)
- Stuart J Macdonald
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-2525, USA.
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