1
|
Pelletier K, Pitchers WR, Mammel A, Northrop-Albrecht E, Márquez EJ, Moscarella RA, Houle D, Dworkin I. Complexities of recapitulating polygenic effects in natural populations: replication of genetic effects on wing shape in artificially selected and wild-caught populations of Drosophila melanogaster. Genetics 2023; 224:iyad050. [PMID: 36961731 PMCID: PMC10324948 DOI: 10.1093/genetics/iyad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/14/2023] [Accepted: 03/18/2023] [Indexed: 03/25/2023] Open
Abstract
Identifying the genetic architecture of complex traits is important to many geneticists, including those interested in human disease, plant and animal breeding, and evolutionary genetics. Advances in sequencing technology and statistical methods for genome-wide association studies have allowed for the identification of more variants with smaller effect sizes, however, many of these identified polymorphisms fail to be replicated in subsequent studies. In addition to sampling variation, this failure to replicate reflects the complexities introduced by factors including environmental variation, genetic background, and differences in allele frequencies among populations. Using Drosophila melanogaster wing shape, we ask if we can replicate allelic effects of polymorphisms first identified in a genome-wide association studies in three genes: dachsous, extra-macrochaete, and neuralized, using artificial selection in the lab, and bulk segregant mapping in natural populations. We demonstrate that multivariate wing shape changes associated with these genes are aligned with major axes of phenotypic and genetic variation in natural populations. Following seven generations of artificial selection along the dachsous shape change vector, we observe genetic differentiation of variants in dachsous and genomic regions containing other genes in the hippo signaling pathway. This suggests a shared direction of effects within a developmental network. We also performed artificial selection with the extra-macrochaete shape change vector, which is not a part of the hippo signaling network, but showed a largely shared direction of effects. The response to selection along the emc vector was similar to that of dachsous, suggesting that the available genetic diversity of a population, summarized by the genetic (co)variance matrix (G), influenced alleles captured by selection. Despite the success with artificial selection, bulk segregant analysis using natural populations did not detect these same variants, likely due to the contribution of environmental variation and low minor allele frequencies, coupled with small effect sizes of the contributing variants.
Collapse
Affiliation(s)
- Katie Pelletier
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - William R Pitchers
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
- BiomeBank, 2 Ann Nelson Dr, Thebarton, Adelaide, SA 5031, Australia
| | - Anna Mammel
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
- Neurocode USA, 3548 Meridian St, Bellingham, WA 98225, USA
| | - Emmalee Northrop-Albrecht
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905USA
| | - Eladio J Márquez
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
- Branch Biosciences, 1 Marina Park Dr., Boston, MA 02210, USA
| | - Rosa A Moscarella
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
- Department of Biology, University of Massachusetts, 221 Morrill Science Center III, 611 North Pleasant Street, Amherst, MA 01003-9297, USA
| | - David Houle
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306-4295, USA
| | - Ian Dworkin
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
2
|
Different diets can affect attractiveness of Drosophila melanogaster males via changes in wing morphology. Anim Behav 2021. [DOI: 10.1016/j.anbehav.2020.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
3
|
Guðbrandsson J, Kapralova KH, Franzdóttir SR, Bergsveinsdóttir ÞM, Hafstað V, Jónsson ZO, Snorrason SS, Pálsson A. Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs. Ecol Evol 2019; 9:10964-10983. [PMID: 31641448 PMCID: PMC6802010 DOI: 10.1002/ece3.5516] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
The availability of diverse ecological niches can promote adaptation of trophic specializations and related traits, as has been repeatedly observed in evolutionary radiations of freshwater fish. The role of genetics, environment, and history in ecologically driven divergence and adaptation, can be studied on adaptive radiations or populations showing ecological polymorphism. Salmonids, especially the Salvelinus genus, are renowned for both phenotypic diversity and polymorphism. Arctic charr (Salvelinus alpinus) invaded Icelandic streams during the glacial retreat (about 10,000 years ago) and exhibits many instances of sympatric polymorphism. Particularly, well studied are the four morphs in Lake Þingvallavatn in Iceland. The small benthic (SB), large benthic (LB), planktivorous (PL), and piscivorous (PI) charr differ in many regards, including size, form, and life history traits. To investigate relatedness and genomic differentiation between morphs, we identified variable sites from RNA-sequencing data from three of those morphs and verified 22 variants in population samples. The data reveal genetic differences between the morphs, with the two benthic morphs being more similar and the PL-charr more genetically different. The markers with high differentiation map to all linkage groups, suggesting ancient and pervasive genetic separation of these three morphs. Furthermore, GO analyses suggest differences in collagen metabolism, odontogenesis, and sensory systems between PL-charr and the benthic morphs. Genotyping in population samples from all four morphs confirms the genetic separation and indicates that the PI-charr are less genetically distinct than the other three morphs. The genetic separation of the other three morphs indicates certain degree of reproductive isolation. The extent of gene flow between the morphs and the nature of reproductive barriers between them remain to be elucidated.
Collapse
Affiliation(s)
- Jóhannes Guðbrandsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Marine and Freshwater Research InstituteReykjavikIceland
| | - Kalina H. Kapralova
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
| | - Sigríður R. Franzdóttir
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
| | | | - Völundur Hafstað
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
| | - Zophonías O. Jónsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
| | | | - Arnar Pálsson
- Institute of Life and Environmental SciencesUniversity of IcelandReykjavikIceland
- Biomedical CenterUniversity of IcelandReykjavikIceland
| |
Collapse
|
4
|
A Multivariate Genome-Wide Association Study of Wing Shape in Drosophila melanogaster. Genetics 2019; 211:1429-1447. [PMID: 30792267 DOI: 10.1534/genetics.118.301342] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/03/2019] [Indexed: 02/02/2023] Open
Abstract
Due to the complexity of genotype-phenotype relationships, simultaneous analyses of genomic associations with multiple traits will be more powerful and informative than a series of univariate analyses. However, in most cases, studies of genotype-phenotype relationships have been analyzed only one trait at a time. Here, we report the results of a fully integrated multivariate genome-wide association analysis of the shape of the Drosophila melanogaster wing in the Drosophila Genetic Reference Panel. Genotypic effects on wing shape were highly correlated between two different laboratories. We found 2396 significant SNPs using a 5% false discovery rate cutoff in the multivariate analyses, but just four significant SNPs in univariate analyses of scores on the first 20 principal component axes. One quarter of these initially significant SNPs retain their effects in regularized models that take into account population structure and linkage disequilibrium. A key advantage of multivariate analysis is that the direction of the estimated phenotypic effect is much more informative than a univariate one. We exploit this fact to show that the effects of knockdowns of genes implicated in the initial screen were on average more similar than expected under a null model. A subset of SNP effects were replicable in an unrelated panel of inbred lines. Association studies that take a phenomic approach, considering many traits simultaneously, are an important complement to the power of genomics.
Collapse
|
5
|
Carreira VP, Mensch J, Hasson E, Fanara JJ. Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster. PLoS One 2016; 11:e0160069. [PMID: 27459710 PMCID: PMC4961385 DOI: 10.1371/journal.pone.0160069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 07/13/2016] [Indexed: 11/21/2022] Open
Abstract
Body size is a complex character associated to several fitness related traits that vary within and between species as a consequence of environmental and genetic factors. Latitudinal and altitudinal clines for different morphological traits have been described in several species of Drosophila and previous work identified genomic regions associated with such variation in D. melanogaster. However, the genetic factors that orchestrate morphological variation have been barely studied. Here, our main objective was to investigate genetic variation for different morphological traits associated to the second chromosome in natural populations of D. melanogaster along latitudinal and altitudinal gradients in Argentina. Our results revealed weak clinal signals and a strong population effect on morphological variation. Moreover, most pairwise comparisons between populations were significant. Our study also showed important within-population genetic variation, which must be associated to the second chromosome, as the lines are otherwise genetically identical. Next, we examined the contribution of different candidate genes to natural variation for these traits. We performed quantitative complementation tests using a battery of lines bearing mutated alleles at candidate genes located in the second chromosome and six second chromosome substitution lines derived from natural populations which exhibited divergent phenotypes. Results of complementation tests revealed that natural variation at all candidate genes studied, invected, Fasciclin 3, toucan, Reticulon-like1, jing and CG14478, affects the studied characters, suggesting that they are Quantitative Trait Genes for morphological traits. Finally, the phenotypic patterns observed suggest that different alleles of each gene might contribute to natural variation for morphological traits. However, non-additive effects cannot be ruled out, as wild-derived strains differ at myriads of second chromosome loci that may interact epistatically with mutant alleles.
Collapse
Affiliation(s)
- Valeria Paula Carreira
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
| | - Julián Mensch
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Esteban Hasson
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Juan José Fanara
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
6
|
The sex-limited effects of mutations in the EGFR and TGF-β signaling pathways on shape and size sexual dimorphism and allometry in the Drosophila wing. Dev Genes Evol 2016; 226:159-71. [PMID: 27038022 DOI: 10.1007/s00427-016-0534-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/18/2016] [Indexed: 10/22/2022]
Abstract
Much of the morphological diversity in nature-including among sexes within a species-is a direct consequence of variation in size and shape. However, disentangling variation in sexual dimorphism for both shape (SShD), size (SSD), and their relationship with one another remains complex. Understanding how genetic variation influences both size and shape together, and how this in turn influences SSD and SShD, is challenging. In this study, we utilize Drosophila wing size and shape as a model system to investigate how mutations influence size and shape as modulated by sex. Previous work has demonstrated that mutations in epidermal growth factor receptor (EGFR) and transforming growth factor-β (TGF-β) signaling components can influence both wing size and shape. In this study, we re-analyze this data to specifically address how they impact the relationship between size and shape in a sex-specific manner, in turn altering the pattern of sexual dimorphism. While most mutations influence shape overall, only a subset have a genotypic specific effect that influences SShD. Furthermore, while we observe sex-specific patterns of allometric shape variation, the effects of most mutations on allometry tend to be small. We discuss this within the context of using mutational analysis to understand sexual size and shape dimorphism.
Collapse
|
7
|
Kapralova KH, Jónsson ZO, Palsson A, Franzdóttir SR, le Deuff S, Kristjánsson BK, Snorrason SS. Bones in motion: Ontogeny of craniofacial development in sympatric arctic charr morphs. Dev Dyn 2015; 244:1168-1178. [DOI: 10.1002/dvdy.24302] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/17/2015] [Accepted: 04/30/2015] [Indexed: 12/22/2022] Open
Affiliation(s)
- Kalina H. Kapralova
- Institute of Life and Environmental Sciences; University of Iceland; Reykjavik Iceland
| | - Zophonías O. Jónsson
- Institute of Life and Environmental Sciences; University of Iceland; Reykjavik Iceland
| | - Arnar Palsson
- Institute of Life and Environmental Sciences; University of Iceland; Reykjavik Iceland
| | | | | | | | - Sigurður S. Snorrason
- Institute of Life and Environmental Sciences; University of Iceland; Reykjavik Iceland
| |
Collapse
|
8
|
Gudbrandsson J, Ahi EP, Franzdottir SR, Kapralova KH, Kristjansson BK, Steinhaeuser SS, Maier VH, Johannesson IM, Snorrason SS, Jonsson ZO, Palsson A. The developmental transcriptome of contrasting Arctic charr ( Salvelinus alpinus) morphs. F1000Res 2015; 4:136. [PMID: 27635217 PMCID: PMC5007756 DOI: 10.12688/f1000research.6402.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/05/2016] [Indexed: 12/23/2022] Open
Abstract
Species and populations with parallel evolution of specific traits can help illuminate how predictable adaptations and divergence are at the molecular and developmental level. Following the last glacial period, dwarfism and specialized bottom feeding morphology evolved rapidly in several landlocked Arctic charr
Salvelinus alpinus populations in Iceland. To study the genetic divergence between small benthic morphs and limnetic morphs, we conducted RNA-sequencing charr embryos at four stages in early development. We studied two stocks with contrasting morphologies: the small benthic (SB) charr from Lake Thingvallavatn and Holar aquaculture (AC) charr. The data reveal significant differences in expression of several biological pathways during charr development. There was also an expression difference between SB- and AC-charr in genes involved in energy metabolism and blood coagulation genes. We confirmed differing expression of five genes in whole embryos with qPCR, including
lysozyme and
natterin-like which was previously identified as a fish-toxin of a lectin family that may be a putative immunopeptide. We also verified differential expression of 7 genes in the developing head that associated consistently with benthic v.s.limnetic morphology (studied in 4 morphs). Comparison of single nucleotide polymorphism (SNP) frequencies reveals extensive genetic differentiation between the SB and AC-charr (~1300 with more than 50% frequency difference). Curiously, three derived alleles in the otherwise conserved 12s and 16s mitochondrial ribosomal RNA genes are found in benthic charr. The data implicate multiple genes and molecular pathways in divergence of small benthic charr and/or the response of aquaculture charr to domestication. Functional, genetic and population genetic studies on more freshwater and anadromous populations are needed to confirm the specific loci and mutations relating to specific ecological traits in Arctic charr.
Collapse
Affiliation(s)
- Johannes Gudbrandsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Ehsan P Ahi
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Sigridur R Franzdottir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Kalina H Kapralova
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | | | - S Sophie Steinhaeuser
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Valerie H Maier
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Isak M Johannesson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Sigurdur S Snorrason
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Zophonias O Jonsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| | - Arnar Palsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, 101, Iceland
| |
Collapse
|
9
|
Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer. PLoS One 2014; 9:e91924. [PMID: 24786295 PMCID: PMC4006794 DOI: 10.1371/journal.pone.0091924] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 02/18/2014] [Indexed: 11/23/2022] Open
Abstract
Changes in regulatory DNA contribute to phenotypic differences within and between taxa. Comparative studies show that many transcription factor binding sites (TFBS) are conserved between species whereas functional studies reveal that some mutations segregating within species alter TFBS function. Consistently, in this analysis of 13 regulatory elements in Drosophila melanogaster populations, single base and insertion/deletion polymorphism are rare in characterized regulatory elements. Experimentally defined TFBS are nearly devoid of segregating mutations and, as has been shown before, are quite conserved. For instance 8 of 11 Hunchback binding sites in the stripe 3+7 enhancer of even-skipped are conserved between D. melanogaster and Drosophila virilis. Oddly, we found a 72 bp deletion that removes one of these binding sites (Hb8), segregating within D. melanogaster. Furthermore, a 45 bp deletion polymorphism in the spacer between the stripe 3+7 and stripe 2 enhancers, removes another predicted Hunchback site. These two deletions are separated by ∼250 bp, sit on distinct haplotypes, and segregate at appreciable frequency. The Hb8Δ is at 5 to 35% frequency in the new world, but also shows cosmopolitan distribution. There is depletion of sequence variation on the Hb8Δ-carrying haplotype. Quantitative genetic tests indicate that Hb8Δ affects developmental time, but not viability of offspring. The Eve expression pattern differs between inbred lines, but the stripe 3 and 7 boundaries seem unaffected by Hb8Δ. The data reveal segregating variation in regulatory elements, which may reflect evolutionary turnover of characterized TFBS due to drift or co-evolution.
Collapse
|
10
|
Abstract
Drosophila melanogaster has been widely used as a model of human Mendelian disease, but its value in modeling complex disease has received little attention. Fly models of complex disease would enable high-resolution mapping of disease-modifying loci and the identification of novel targets for therapeutic intervention. Here, we describe a fly model of permanent neonatal diabetes mellitus and explore the complexity of this model. The approach involves the transgenic expression of a misfolded mutant of human preproinsulin, hINSC96Y, which is a cause of permanent neonatal diabetes. When expressed in fly imaginal discs, hINSC96Y causes a reduction of adult structures, including the eye, wing, and notum. Eye imaginal discs exhibit defects in both the structure and the arrangement of ommatidia. In the wing, expression of hINSC96Y leads to ectopic expression of veins and mechano-sensory organs, indicating disruption of wild-type signaling processes regulating cell fates. These readily measurable “disease” phenotypes are sensitive to temperature, gene dose, and sex. Mutant (but not wild-type) proinsulin expression in the eye imaginal disc induces IRE1-mediated XBP1 alternative splicing, a signal for endoplasmic reticulum stress response activation, and produces global change in gene expression. Mutant hINS transgene tester strains, when crossed to stocks from the Drosophila Genetic Reference Panel, produce F1 adults with a continuous range of disease phenotypes and large broad-sense heritability. Surprisingly, the severity of mutant hINS-induced disease in the eye is not correlated with that in the notum in these crosses, nor with eye reduction phenotypes caused by the expression of two dominant eye mutants acting in two different eye development pathways, Drop (Dr) or Lobe (L), when crossed into the same genetic backgrounds. The tissue specificity of genetic variability for mutant hINS-induced disease has, therefore, its own distinct signature. The genetic dominance of disease-specific phenotypic variability in our model of misfolded human proinsulin makes this approach amenable to genome-wide association study in a simple F1 screen of natural variation.
Collapse
|
11
|
Kapralova KH, Gudbrandsson J, Reynisdottir S, Santos CB, Baltanás VC, Maier VH, Snorrason SS, Palsson A. Differentiation at the MHCIIα and Cath2 loci in sympatric Salvelinus alpinus resource morphs in Lake Thingvallavatn. PLoS One 2013; 8:e69402. [PMID: 23894470 PMCID: PMC3722248 DOI: 10.1371/journal.pone.0069402] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 06/09/2013] [Indexed: 11/19/2022] Open
Abstract
Northern freshwater fish may be suitable for the genetic dissection of ecological traits because they invaded new habitats after the last ice age (∼10.000 years ago). Arctic charr (Salvelinus alpinus) colonizing streams and lakes in Iceland gave rise to multiple populations of small benthic morphotypes, often in sympatry with a pelagic morphotype. Earlier studies have revealed significant, but subtle, genetic differentiation between the three most common morphs in Lake Thingvallavatn. We conducted a population genetic screen on four immunological candidate genes Cathelicidin 2 (Cath2), Hepcidin (Hamp), Liver expressed antimicrobial peptide 2a (Leap-2a), and Major Histocompatibility Complex IIα (MHCIIα) and a mitochondrial marker (D-loop) among the three most common Lake Thingvallavatn charr morphs. Significant differences in allele frequencies were found between morphs at the Cath2 and MHCIIα loci. No such signal was detected in the D-loop nor in the other two immunological genes. In Cath2 the small benthic morph deviated from the other two (FST = 0.13), one of the substitutions detected constituting an amino acid replacement polymorphism in the antimicrobial peptide. A more striking difference was found in the MHCIIα. Two haplotypes were very common in the lake, and their frequency differed greatly between the morphotypes (from 22% to 93.5%, FST = 0.67). We then expanded our study by surveying the variation in Cath2 and MHCIIα in 9 Arctic charr populations from around Iceland. The populations varied greatly in terms of allele frequencies at Cath2, but the variation did not correlate with morphotype. At the MHCIIα locus, the variation was nearly identical to the variation in the two benthic morphs of Lake Thingvallavatn. The results are consistent with a scenario where parts of the immune systems have diverged substantially among Arctic charr populations in Iceland, after colonizing the island ∼10.000 years ago.
Collapse
Affiliation(s)
- Kalina H. Kapralova
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Johannes Gudbrandsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Sigrun Reynisdottir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Cristina B. Santos
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Vanessa C. Baltanás
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Valerie H. Maier
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Sigurdur S. Snorrason
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Arnar Palsson
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| |
Collapse
|
12
|
Cridland JM, Macdonald SJ, Long AD, Thornton KR. Abundance and distribution of transposable elements in two Drosophila QTL mapping resources. Mol Biol Evol 2013; 30:2311-27. [PMID: 23883524 PMCID: PMC3773372 DOI: 10.1093/molbev/mst129] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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.
Collapse
Affiliation(s)
- Julie M Cridland
- Department of Ecology, Evolution and Physiology, University of California, Irvine
| | | | | | | |
Collapse
|
13
|
Abstract
Theoretical explanations of empirically observed standing genetic variation, mutation, and selection suggest that many alleles must jointly affect fitness and metric traits. However, there are few direct demonstrations of the nature and extent of these pleiotropic associations. We implemented a mutation accumulation (MA) divergence experimental design in Drosophila serrata to segregate genetic variants for fitness and metric traits. By exploiting naturally occurring MA line extinctions as a measure of line-level total fitness, manipulating sexual selection, and measuring productivity we were able to demonstrate genetic covariance between fitness and standard metric traits, wing size, and shape. Larger size was associated with lower total fitness and male sexual fitness, but higher productivity. Multivariate wing shape traits, capturing major axes of wing shape variation among MA lines, evolved only in the absence of sexual selection, and to the greatest extent in lines that went extinct, indicating that mutations contributing wing shape variation also typically had deleterious effects on both total fitness and male sexual fitness. This pleiotropic covariance of metric traits with fitness will drive their evolution, and generate the appearance of selection on the metric traits even in the absence of a direct contribution to fitness.
Collapse
Affiliation(s)
- Katrina McGuigan
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | | |
Collapse
|
14
|
A test for selection employing quantitative trait locus and mutation accumulation data. Genetics 2012; 190:1533-45. [PMID: 22298701 DOI: 10.1534/genetics.111.137075] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evolutionary biologists attribute much of the phenotypic diversity observed in nature to the action of natural selection. However, for many phenotypic traits, especially quantitative phenotypic traits, it has been challenging to test for the historical action of selection. An important challenge for biologists studying quantitative traits, therefore, is to distinguish between traits that have evolved under the influence of strong selection and those that have evolved neutrally. Most existing tests for selection employ molecular data, but selection also leaves a mark on the genetic architecture underlying a trait. In particular, the distribution of quantitative trait locus (QTL) effect sizes and the distribution of mutational effects together provide information regarding the history of selection. Despite the increasing availability of QTL and mutation accumulation data, such data have not yet been effectively exploited for this purpose. We present a model of the evolution of QTL and employ it to formulate a test for historical selection. To provide a baseline for neutral evolution of the trait, we estimate the distribution of mutational effects from mutation accumulation experiments. We then apply a maximum-likelihood-based method of inference to estimate the range of selection strengths under which such a distribution of mutations could generate the observed QTL. Our test thus represents the first integration of population genetic theory and QTL data to measure the historical influence of selection.
Collapse
|
15
|
Rockman MV. The QTN program and the alleles that matter for evolution: all that's gold does not glitter. Evolution 2011; 66:1-17. [PMID: 22220860 DOI: 10.1111/j.1558-5646.2011.01486.x] [Citation(s) in RCA: 464] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The search for the alleles that matter, the quantitative trait nucleotides (QTNs) that underlie heritable variation within populations and divergence among them, is a popular pursuit. But what is the question to which QTNs are the answer? Although their pursuit is often invoked as a means of addressing the molecular basis of phenotypic evolution or of estimating the roles of evolutionary forces, the QTNs that are accessible to experimentalists, QTNs of relatively large effect, may be uninformative about these issues if large-effect variants are unrepresentative of the alleles that matter. Although 20th century evolutionary biology generally viewed large-effect variants as atypical, the field has recently undergone a quiet realignment toward a view of readily discoverable large-effect alleles as the primary molecular substrates for evolution. I argue that neither theory nor data justify this realignment. Models and experimental findings covering broad swaths of evolutionary phenomena suggest that evolution often acts via large numbers of small-effect polygenes, individually undetectable. Moreover, these small-effect variants are different in kind, at the molecular level, from the large-effect alleles accessible to experimentalists. Although discoverable QTNs address some fundamental evolutionary questions, they are essentially misleading about many others.
Collapse
Affiliation(s)
- Matthew V Rockman
- Department of Biology and Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.
| |
Collapse
|
16
|
Carreira VP, Soto IM, Mensch J, Fanara JJ. Genetic basis of wing morphogenesis in Drosophila: sexual dimorphism and non-allometric effects of shape variation. BMC DEVELOPMENTAL BIOLOGY 2011; 11:32. [PMID: 21635778 PMCID: PMC3129315 DOI: 10.1186/1471-213x-11-32] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 06/02/2011] [Indexed: 12/17/2022]
Abstract
BACKGROUND The Drosophila wing represents a particularly appropriate model to investigate the developmental control of phenotypic variation. Previous studies which aimed to identify candidate genes for wing morphology demonstrated that the genetic basis of wing shape variation in D. melanogaster is composed of numerous genetic factors causing small, additive effects. In this study, we analyzed wing shape in males and females from 191 lines of D. melanogaster, homozygous for a single P-element insertion, using geometric morphometrics techniques. The analysis allowed us to identify known and novel candidate genes that may contribute to the expression of wing shape in each sex separately and to compare them to candidate genes affecting wing size which have been identified previously using the same lines. RESULTS Our results indicate that more than 63% of induced mutations affected wing shape in one or both sexes, although only 33% showed significant differences in both males and females. The joint analysis of wing size and shape revealed that only 19% of the P-element insertions caused coincident effects on both components of wing form in one or both sexes. Further morphometrical analyses revealed that the intersection between veins showed the smallest displacements in the proximal region of the wing. Finally, we observed that mutations causing general deformations were more common than expected in both sexes whereas the opposite occurred with those generating local changes. For most of the 94 candidate genes identified, this seems to be the first record relating them with wing shape variation. CONCLUSIONS Our results support the idea that the genetic architecture of wing shape is complex with many different genes contributing to the trait in a sexually dimorphic manner. This polygenic basis, which is relatively independent from that of wing size, is composed of genes generally involved in development and/or metabolic functions, especially related to the regulation of different cellular processes such as motility, adhesion, communication and signal transduction. This study suggests that understanding the genetic basis of wing shape requires merging the regulation of vein patterning by signalling pathways with processes that occur during wing development at the cellular level.
Collapse
Affiliation(s)
- Valeria P Carreira
- Departamento de Ecología, Genética y Evolución. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Ciudad Universitaria, Pabellón II (C1428 EHA) Buenos Aires. Argentina
| | - Ignacio M Soto
- Departamento de Ecología, Genética y Evolución. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Ciudad Universitaria, Pabellón II (C1428 EHA) Buenos Aires. Argentina
| | - Julián Mensch
- Departamento de Ecología, Genética y Evolución. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Ciudad Universitaria, Pabellón II (C1428 EHA) Buenos Aires. Argentina
| | - Juan J Fanara
- Departamento de Ecología, Genética y Evolución. Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Ciudad Universitaria, Pabellón II (C1428 EHA) Buenos Aires. Argentina
| |
Collapse
|
17
|
The effects of weak genetic perturbations on the transcriptome of the wing imaginal disc and its association with wing shape in Drosophila melanogaster. Genetics 2011; 187:1171-84. [PMID: 21288875 DOI: 10.1534/genetics.110.125922] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
A major objective of genomics is to elucidate the mapping between genotypic and phenotypic space as a step toward understanding how small changes in gene function can lead to elaborate phenotypic changes. One approach that has been utilized is to examine overall patterns of covariation between phenotypic variables of interest, such as morphology, physiology, and behavior, and underlying aspects of gene activity, in particular transcript abundance on a genome-wide scale. Numerous studies have demonstrated that such patterns of covariation occur, although these are often between samples with large numbers of unknown genetic differences (different strains or even species) or perturbations of large effect (sexual dimorphism or strong loss-of-function mutations) that may represent physiological changes outside of the normal experiences of the organism. We used weak mutational perturbations in genes affecting wing development in Drosophila melanogaster that influence wing shape relative to a co-isogenic wild type. We profiled transcription of 1150 genes expressed during wing development in 27 heterozygous mutants, as well as their co-isogenic wild type and one additional wild-type strain. Despite finding clear evidence of expression differences between mutants and wild type, transcriptional profiles did not covary strongly with shape, suggesting that information from transcriptional profiling may not generally be predictive of final phenotype. We discuss these results in the light of possible attractor states of gene expression and how this would affect interpretation of covariation between transcriptional profiles and other phenotypes.
Collapse
|
18
|
TROTTA VINCENZO, CAVICCHI SANDRO, GUERRA DANIELA, ANDERSEN DITTEH, BABBITT GREGORYA, KRISTENSEN TORSTENN, PEDERSEN KAMILLAS, LOESCHCKE VOLKER, PERTOLDI CINO. Allometric and non-allometric consequences of inbreeding on Drosophila melanogaster wings. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2010.01588.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
19
|
Mackay TFC. Mutations and quantitative genetic variation: lessons from Drosophila. Philos Trans R Soc Lond B Biol Sci 2010; 365:1229-39. [PMID: 20308098 DOI: 10.1098/rstb.2009.0315] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A central issue in evolutionary quantitative genetics is to understand how genetic variation for quantitative traits is maintained in natural populations. Estimates of genetic variation and of genetic correlations and pleiotropy among multiple traits, inbreeding depression, mutation rates for fitness and quantitative traits and of the strength and nature of selection are all required to evaluate theoretical models of the maintenance of genetic variation. Studies in Drosophila melanogaster have shown that a substantial fraction of segregating variation for fitness-related traits in Drosophila is due to rare deleterious alleles maintained by mutation-selection balance, with a smaller but significant fraction attributable to intermediate frequency alleles maintained by alleles with antagonistic pleiotropic effects, and late-age-specific effects. However, the nature of segregating variation for traits under stabilizing selection is less clear and requires more detailed knowledge of the loci, mutation rates, allelic effects and frequencies of molecular polymorphisms affecting variation in suites of pleiotropically connected traits. Recent studies in D. melanogaster have revealed unexpectedly complex genetic architectures of many quantitative traits, with large numbers of pleiotropic genes and alleles with sex-, environment- and genetic background-specific effects. Future genome wide association analyses of many quantitative traits on a common panel of fully sequenced Drosophila strains will provide much needed empirical data on the molecular genetic basis of quantitative traits.
Collapse
Affiliation(s)
- Trudy F C Mackay
- Department of Genetics, W. M. Keck Center for Behavioral Biology, North Carolina State University, , Campus Box 7614, Raleigh, NC 27697, USA.
| |
Collapse
|
20
|
Brock MT, Maloof JN, Weinig C. Genes underlying quantitative variation in ecologically important traits: PIF4 (phytochrome interacting factor 4) is associated with variation in internode length, flowering time, and fruit set in Arabidopsis thaliana. Mol Ecol 2010; 19:1187-99. [PMID: 20456226 DOI: 10.1111/j.1365-294x.2010.04538.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Association studies utilize the action of recombination over numerous generations to identify loci that underlie quantitative traits. We use a candidate-gene association approach, segregation analyses and analyses of local linkage disequilibrium (LD) to evaluate the potentially causal effects of molecular variation at PIF4 (PHYTOCROME INTERACTING FACTOR 4) on ecologically important traits in Arabidopsis thaliana. A preliminary analysis of sequence diversity in 14 natural genotypes revealed one intermediate-frequency replacement polymorphism at PIF4. A sample of 161 natural accessions was genotyped at PIF4 and screened for average length of early internodes, inflorescence length, days to flowering and flowering interval (days between bolting and flowering) under high- and low-density environments to test for genotype-phenotype associations. PIF4 was associated with early internode lengths, while the PIF4x treatment interaction was associated with flowering interval in the panel of 161 accessions. Further, in a set of recombinant inbred lines that segregate for the PIF4 polymorphism, nucleotide substitutions at PIF4 co-segregated with early internode lengths, days to flowering and fruit set, suggesting that cryptic population structure in the association-mapping panel and attendant LD with a physically distant locus do not account for the observed association. Finally, in a panel of pseudochromosomes from 20 re-sequenced genotypes, LD appeared to decay rapidly in the immediate vicinity of PIF4, suggesting that flanking loci contribute little to the observed association. In sum, the results suggest that PIF4 causally affects early internode lengths on the primary inflorescence, potentially via effects on reproductive timing and that these traits in turn affect fitness.
Collapse
Affiliation(s)
- Marcus T Brock
- Department of Botany, University of Wyoming, 1000 E. University Avenue, Laramie, WY 82071, USA.
| | | | | |
Collapse
|
21
|
Tarka M, Akesson M, Beraldi D, Hernández-Sánchez J, Hasselquist D, Bensch S, Hansson B. A strong quantitative trait locus for wing length on chromosome 2 in a wild population of great reed warblers. Proc Biol Sci 2010; 277:2361-9. [PMID: 20335216 DOI: 10.1098/rspb.2010.0033] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Wing length is a key character for essential behaviours related to bird flight such as migration and foraging. In the present study, we initiate the search for the genes underlying wing length in birds by studying a long-distance migrant, the great reed warbler (Acrocephalus arundinaceus). In this species wing length is an evolutionary interesting trait with pronounced latitudinal gradient and sex-specific selection regimes in local populations. We performed a quantitative trait locus (QTL) scan for wing length in great reed warblers using phenotypic, genotypic, pedigree and linkage map data from our long-term study population in Sweden. We applied the linkage analysis mapping method implemented in GridQTL (a new web-based software) and detected a genome-wide significant QTL for wing length on chromosome 2, to our knowledge, the first detected QTL in wild birds. The QTL extended over 25 cM and accounted for a substantial part (37%) of the phenotypic variance of the trait. A genome scan for tarsus length (a body-size-related trait) did not show any signal, implying that the wing-length QTL on chromosome 2 was not associated with body size. Our results provide a first important step into understanding the genetic architecture of avian wing length, and give opportunities to study the evolutionary dynamics of wing length at the locus level.
Collapse
Affiliation(s)
- Maja Tarka
- Section for Animal Ecology, Department of Biology, Lund University, 223 62 Lund, Sweden
| | | | | | | | | | | | | |
Collapse
|
22
|
Klingenberg CP. Morphometric integration and modularity in configurations of landmarks: tools for evaluating a priori hypotheses. Evol Dev 2009; 11:405-21. [PMID: 19601974 PMCID: PMC2776930 DOI: 10.1111/j.1525-142x.2009.00347.x] [Citation(s) in RCA: 345] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Identifying the modular components of a configuration of landmarks is an important task of morphometric analyses in evolutionary developmental biology. Modules are integrated internally by many interactions among their component parts, but are linked to one another only by few or weak interactions. Accordingly, traits within modules are tightly correlated with each other, but relatively independent of traits in other modules. Hypotheses concerning the boundaries of modules in a landmark configuration can therefore be tested by comparing the strength of covariation among alternative partitions of the configuration into subsets of landmarks. If a subdivision coincides with the true boundaries between modules, the correlations among subsets should be minimal. This article introduces Escoufier's RV coefficient and the multi-set RV coefficient as measures of the correlation between two or more subsets of landmarks. These measures can be compared between alternative partitions of the configuration into subsets. Because developmental interactions are tissue bound, it is sensible to require that modules should be spatially contiguous. I propose a criterion for spatial contiguity for sets of landmarks using an adjacency graph. The new methods are demonstrated with data on shape of the wing in Drosophila melanogaster and the mandible of the house mouse.
Collapse
Affiliation(s)
- Christian Peter Klingenberg
- Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
| |
Collapse
|
23
|
Abstract
A major challenge in current biology is to understand the genetic basis of variation for quantitative traits. We review the principles of quantitative trait locus mapping and summarize insights about the genetic architecture of quantitative traits that have been obtained over the past decades. We are currently in the midst of a genomic revolution, which enables us to incorporate genetic variation in transcript abundance and other intermediate molecular phenotypes into a quantitative trait locus mapping framework. This systems genetics approach enables us to understand the biology inside the 'black box' that lies between genotype and phenotype in terms of causal networks of interacting genes.
Collapse
|
24
|
Gidaszewski NA, Baylac M, Klingenberg CP. Evolution of sexual dimorphism of wing shape in the Drosophila melanogaster subgroup. BMC Evol Biol 2009; 9:110. [PMID: 19457235 PMCID: PMC2691407 DOI: 10.1186/1471-2148-9-110] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 05/20/2009] [Indexed: 11/10/2022] Open
Abstract
Background Sexual dimorphism of body size has been the subject of numerous studies, but few have examined sexual shape dimorphism (SShD) and its evolution. Allometry, the shape change associated with size variation, has been suggested to be a main component of SShD. Yet little is known about the relative importance of the allometric and non-allometric components for the evolution of SShD. Results We investigated sexual dimorphism in wing shape in the nine species of the Drosophila melanogaster subgroup. We used geometric morphometrics to characterise wing shape and found significant SShD in all nine species. The amount of shape difference and the diversity of the shape changes evolved across the group. However, mapping the divergence of SShD onto the phylogeny of the Drosophila melanogaster subgroup indicated that there is little phylogenetic signal. Finally, allometry accounted for a substantial part of SShD, but did not explain the bulk of evolutionary divergence in SShD because allometry itself was found to be evolutionarily plastic. Conclusion SShD in the Drosophila wing can evolve rapidly and therefore shows only weak phylogenetic structure. The variable contribution of allometric and non-allometric components to the evolutionary divergence of SShD and the evolutionary plasticity of allometry suggest that SShD and allometry are influenced by a complex interaction of processes.
Collapse
Affiliation(s)
- Nelly A Gidaszewski
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, UK.
| | | | | |
Collapse
|
25
|
Abstract
We compare and contrast the genetic architecture of quantitative phenotypes in two genetically well-characterized model organisms, the laboratory mouse, Mus musculus, and the fruit fly, Drosophila melanogaster, with that found in our own species from recent successes in genome-wide association studies. We show that the current model of large numbers of loci, each of small effect, is true for all species examined, and that discrepancies can be largely explained by differences in the experimental designs used. We argue that the distribution of effect size of common variants is the same for all phenotypes regardless of species, and we discuss the importance of epistasis, pleiotropy, and gene by environment interactions. Despite substantial advances in mapping quantitative trait loci, the identification of the quantitative trait genes and ultimately the sequence variants has proved more difficult, so that our information on the molecular basis of quantitative variation remains limited. Nevertheless, available data indicate that many variants lie outside genes, presumably in regulatory regions of the genome, where they act by altering gene expression. As yet there are very few instances where homologous quantitative trait loci, or quantitative trait genes, have been identified in multiple species, but the availability of high-resolution mapping data will soon make it possible to test the degree of overlap between species.
Collapse
|
26
|
|
27
|
Abstract
Evolutionary quantitative genetics has recently advanced in two distinct streams. Many biologists address evolutionary questions by estimating phenotypic selection and genetic (co)variances (G matrices). Simultaneously, an increasing number of studies have applied quantitative trait locus (QTL) mapping methods to dissect variation. Both conceptual and practical difficulties have isolated these two foci of quantitative genetics. A conceptual integration follows from the recognition that QTL allele frequencies are the essential variables relating the G-matrix to marker-based mapping experiments. Breeding designs initiated from randomly selected parental genotypes can be used to estimate QTL-specific genetic (co)variances. These statistics appropriately distill allelic variation and provide an explicit population context for QTL mapping estimates. Within this framework, one can parse the G-matrix into a set of mutually exclusive genomic components and ask whether these parts are similar or dissimilar in their respective features, for example the magnitude of phenotypic effects and the extent and nature of pleiotropy. As these features are critical determinants of sustained response to selection, the integration of QTL mapping methods into G-matrix estimation can provide a concrete, genetically based experimental program to investigate the evolutionary potential of natural populations.
Collapse
Affiliation(s)
- John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA.
| |
Collapse
|
28
|
Hsieh WP, Passador-Gurgel G, Stone EA, Gibson G. Mixture modeling of transcript abundance classes in natural populations. Genome Biol 2008; 8:R98. [PMID: 17547747 PMCID: PMC2394757 DOI: 10.1186/gb-2007-8-6-r98] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 04/16/2007] [Accepted: 06/04/2007] [Indexed: 01/05/2023] Open
Abstract
Expression profiling of Drosophila melanogaster adult female heads for 108 nearly isogenic lines from two different populations, and of CEPH lymphoblastoid lines, shows that differential expression of transcripts among individuals is due to a complex interplay of cis- and trans-acting factors. Background Populations diverge in genotype and phenotype under the influence of such evolutionary processes as genetic drift, mutation accumulation, and natural selection. Because genotype maps onto phenotype by way of transcription, it is of interest to evaluate how these evolutionary factors influence the structure of variation at the level of transcription. Here, we explore the distributions of cis-acting and trans-acting factors and their relative contributions to expression of transcripts that exhibit two or more classes of abundance among individuals within populations. Results Expression profiling using cDNA microarrays was conducted in Drosophila melanogaster adult female heads for 58 nearly isogenic lines from a North Carolina population and 50 from a California population. Using a mixture modeling approach, transcripts were identified that exhibit more than one mode of transcript abundance across the samples. Power studies indicate that sample sizes of 50 individuals will generally be sufficient to detect divergent transcript abundance classes. The distribution of transcript abundance classes is skewed toward low frequency minor classes, which is reminiscent of the typical skew in genotype frequencies. Similar results are observed in reported data on gene expression in human lymphoblast cell lines, in which analysis of association with linked polymorphisms implies that cis-acting single nucleotide polymorphisms make only a modest contribution to bimodal distributions of transcript abundance. Conclusion Population surveys of gene expression may complement genetical genomics as a general approach to quantifying sources of transcriptional variation. Differential expression of transcripts among individuals is due to a complex interplay of cis-acting and trans-acting factors.
Collapse
Affiliation(s)
- Wen-Ping Hsieh
- Department of Genetics, Gardner Hall, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
- Department of Statistics, 825 General Building III, National Tsing Hua University, Kuang-Fu Road, Hsinchu, 30013, Taiwan
| | - Gisele Passador-Gurgel
- Department of Genetics, Gardner Hall, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| | - Eric A Stone
- Department of Statistics, and Bioinformatics Research Center, 1500 Partners II Building, 840 Main Campus Drive, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Greg Gibson
- Department of Genetics, Gardner Hall, North Carolina State University, Raleigh, North Carolina 27695-7614, USA
| |
Collapse
|
29
|
Fiumera AC, Dumont BL, Clark AG. Associations between sperm competition and natural variation in male reproductive genes on the third chromosome of Drosophila melanogaster. Genetics 2007; 176:1245-60. [PMID: 17435238 PMCID: PMC1894588 DOI: 10.1534/genetics.106.064915] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 04/07/2007] [Indexed: 01/10/2023] Open
Abstract
We applied association analysis to elucidate the genetic basis for variation in phenotypes affecting postcopulatory sexual selection in a natural population of Drosophila melanogaster. We scored 96 third chromosome substitution lines for nine phenotypes affecting sperm competitive ability and genotyped them at 72 polymorphisms in 13 male reproductive genes. Significant heterogeneity among lines (P < 0.01) was detected for all phenotypes except male-induced refractoriness (P = 0.053). We identified 24 associations (8 single-marker associations, 12 three-marker haplotype associations, and 4 cases of epistasis revealed by single-marker interactions). Fewer than 9 of these associations are likely to be false positives. Several associations were consistent with previous findings [Acp70A with the male's influence on the female's refractoriness to remating (refractory), Esterase-6 with a male's remating probability (remating) and a measure of female offspring production (fecundity)], but many are novel associations with uncharacterized seminal fluid proteins. Four genes showed evidence for pleiotropic effects [CG6168 with a measure of sperm competition (P2') and refractory, CG14560 with a defensive measure of sperm competition (P1') and a measure of female fecundity, Acp62F with P2' and a measure of female fecundity, and Esterase-6 with remating and a measure of female fecundity]. Our findings provide evidence that pleiotropy and epistasis are important factors in the genetic architecture of male reproductive success and show that haplotype analyses can identify associations missed in the single-marker approach.
Collapse
Affiliation(s)
- Anthony C Fiumera
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.
| | | | | |
Collapse
|
30
|
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] [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.
Collapse
Affiliation(s)
- Stuart J Macdonald
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA.
| | | |
Collapse
|
31
|
Stinchcombe JR, Hoekstra HE. Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity (Edinb) 2007; 100:158-70. [PMID: 17314923 DOI: 10.1038/sj.hdy.6800937] [Citation(s) in RCA: 380] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A central challenge in evolutionary biology is to identify genes underlying ecologically important traits and describe the fitness consequences of naturally occurring variation at these loci. To address this goal, several novel approaches have been developed, including 'population genomics,' where a large number of molecular markers are scored in individuals from different environments with the goal of identifying markers showing unusual patterns of variation, potentially due to selection at linked sites. Such approaches are appealing because of (1) the increasing ease of generating large numbers of genetic markers, (2) the ability to scan the genome without measuring phenotypes and (3) the simplicity of sampling individuals without knowledge of their breeding history. Although such approaches are inherently applicable to non-model systems, to date these studies have been limited in their ability to uncover functionally relevant genes. By contrast, quantitative genetics has a rich history, and more recently, quantitative trait locus (QTL) mapping has had some success in identifying genes underlying ecologically relevant variation even in novel systems. QTL mapping, however, requires (1) genetic markers that specifically differentiate parental forms, (2) a focus on a particular measurable phenotype and (3) controlled breeding and maintenance of large numbers of progeny. Here we present current advances and suggest future directions that take advantage of population genomics and quantitative genetic approaches - in both model and non-model systems. Specifically, we discuss advantages and limitations of each method and argue that a combination of the two provides a powerful approach to uncovering the molecular mechanisms responsible for adaptation.
Collapse
Affiliation(s)
- J R Stinchcombe
- Department of Ecology and Evolutionary Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
| | | |
Collapse
|
32
|
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] [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.
Collapse
Affiliation(s)
- Jonathan D Gruber
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA.
| | | | | | | |
Collapse
|
33
|
Passador-Gurgel G, Hsieh WP, Hunt P, Deighton N, Gibson G. Quantitative trait transcripts for nicotine resistance in Drosophila melanogaster. Nat Genet 2007; 39:264-8. [PMID: 17237783 DOI: 10.1038/ng1944] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 11/17/2006] [Indexed: 11/09/2022]
Abstract
Although most genetic association studies are performed with the intention of detecting nucleotide polymorphisms that are correlated with a complex trait, transcript abundance should also be expected to associate with diseases or phenotypes. We performed a scan for such quantitative trait transcripts in adult female heads of the fruit fly (Drosophila melanogaster) that might explain variation for nicotine resistance. The strongest association was seen for abundance of ornithine aminotransferase transcripts, implicating detoxification and neurotransmitter biosynthesis as mediators of the quantitative response to the drug. Subsequently, genetic analysis and metabolite profiling confirmed a complex role for ornithine and GABA levels in modification of survival time upon chronic nicotine exposure. Differences between populations from North Carolina and California suggest that the resistance mechanism may be an evolved response to environmental exposure.
Collapse
Affiliation(s)
- Gisele Passador-Gurgel
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | | | | | | |
Collapse
|
34
|
Weinig C, Brock MT, Dechaine JA, Welch SM. Resolving the genetic basis of invasiveness and predicting invasions. Genetica 2006; 129:205-16. [PMID: 16955329 DOI: 10.1007/s10709-006-9015-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Accepted: 06/18/2006] [Indexed: 11/28/2022]
Abstract
Considerable effort has been invested in determining traits underlying invasiveness. Yet, identifying a set of traits that commonly confers invasiveness in a range of species has proven elusive, and almost nothing is known about genetic loci affecting invasive success. Incorporating genetic model organisms into ecologically relevant studies is one promising avenue to begin dissecting the genetic underpinnings of invasiveness. Molecular biologists are rapidly characterizing genes mediating developmental responses to diverse environmental cues, i.e., genes for plasticity, as well as to environmental factors likely to impose strong selection on invading species, e.g., resistance to herbivores and competitors, coordination of life-history events with seasonal changes, and physiological tolerance of heat, drought, or cold. Here, we give an overview of molecular genetic tools increasingly used to characterize the genetic basis of adaptation and that may be used to begin identifying genetic mechanisms of invasiveness. Given the divergent traits that affect invasiveness, "invasiveness genes" common to many clades are unlikely, but the combination of developmental genetic advances with further evolutionary studies and modeling may provide a framework for identifying genes that account for invasiveness in related species.
Collapse
Affiliation(s)
- Cynthia Weinig
- Department of Plant Biology, University of Minnesota, 250 Biological Sciences Center, 1445 Gortner Avenue, St Paul, MN 55108, USA.
| | | | | | | |
Collapse
|
35
|
Cresko WA, McGuigan KL, Phillips PC, Postlethwait JH. Studies of threespine stickleback developmental evolution: progress and promise. Genetica 2006; 129:105-26. [PMID: 16897450 DOI: 10.1007/s10709-006-0036-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2004] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
A promising route for understanding the origin and diversification of organismal form is through studies at the intersection of evolution and development (evo-devo). While much has been learned over the last two decades concerning macroevolutionary patterns of developmental change, a fundamental gap in the evo-devo synthesis is the integration of mathematical population and quantitative genetics with studies of how genetic variation in natural populations affects developmental processes. This micro-evo-devo synthesis requires model organisms with which to ask empirical questions. Threespine stickleback fish (Gasterosteus aculeatus), long a model for studying behavior, ecology and evolution, is emerging as a prominent model micro-evo-devo system. Research on stickleback over the last decade has begun to address the genetic basis of morphological variation and sex determination, and much of this work has important implications for understanding the genetics of speciation. In this paper we review recent threespine stickleback micro-evo-devo results, and outline the resources that have been developed to make this synthesis possible. The prospects for stickleback research to speed the micro-(and macro-) evo-devo syntheses are great, and this workhorse model system is well situated to continue contributing to our understanding of the generation of diversity in organismal form for many more decades.
Collapse
Affiliation(s)
- William A Cresko
- Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403-5289, USA.
| | | | | | | |
Collapse
|
36
|
Dworkin I, Gibson G. Epidermal growth factor receptor and transforming growth factor-beta signaling contributes to variation for wing shape in Drosophila melanogaster. Genetics 2006; 173:1417-31. [PMID: 16648592 PMCID: PMC1526698 DOI: 10.1534/genetics.105.053868] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wing development in Drosophila is a common model system for the dissection of genetic networks and their roles during development. In particular, the RTK and TGF-beta regulatory networks appear to be involved with numerous aspects of wing development, including patterning, cell determination, growth, proliferation, and survival in the developing imaginal wing disc. However, little is known as to how subtle changes in the function of these genes may contribute to quantitative variation for wing shape, per se. In this study 50 insertional mutations, representing 43 loci in the RTK, Hedgehog, TGF-beta pathways, and their genetically interacting factors were used to study the role of these networks on wing shape. To concurrently examine how genetic background modulates the effects of the mutation, each insertion was introgressed into two wild-type genetic backgrounds. Using geometric morphometric methods, it is shown that the majority of these mutations have profound effects on shape but not size of the wing when measured as heterozygotes. To examine the relationships between how each mutation affects wing shape hierarchical clustering was used. Unlike previous observations of environmental canalization, these mutations did not generally increase within-line variation relative to their wild-type counterparts. These results provide an entry point into the genetics of wing shape and are discussed within the framework of the dissection of complex phenotypes.
Collapse
Affiliation(s)
- Ian Dworkin
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA.
| | | |
Collapse
|
37
|
Leips J, Gilligan P, Mackay TFC. Quantitative trait loci with age-specific effects on fecundity in Drosophila melanogaster. Genetics 2005; 172:1595-605. [PMID: 16272414 PMCID: PMC1456283 DOI: 10.1534/genetics.105.048520] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Life-history theory and evolutionary theories of aging assume the existence of alleles with age-specific effects on fitness. While various studies have documented age-related changes in the genetic contribution to variation in fitness components, we know very little about the underlying genetic architecture of such changes. We used a set of recombinant inbred lines to map and characterize the effects of quantitative trait loci (QTL) affecting fecundity of Drosophila melanogaster females at 1 and 4 weeks of age. We identified one QTL on the second chromosome and one or two QTL affecting fecundity on the third chromosome, but these QTL affected fecundity only at 1 week of age. There was more genetic variation for fecundity at 4 weeks of age than at 1 week of age and there was no genetic correlation between early and late-age fecundity. These results suggest that different loci contribute to the variation in fecundity as the organism ages. Our data provide support for the mutation accumulation theory of aging as applied to reproductive senescence. Comparing the results from this study with our previous work on life-span QTL, we also find evidence that antagonistic pleiotropy may contribute to the genetic basis of senescence in these lines as well.
Collapse
Affiliation(s)
- Jeff Leips
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21250, USA.
| | | | | |
Collapse
|
38
|
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] [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.
Collapse
Affiliation(s)
- Stuart J Macdonald
- Department of Ecology and Evolutionary Biology, University of California-Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA.
| | | | | |
Collapse
|
39
|
Palsson A, Dodgson J, Dworkin I, Gibson G. Tests for the replication of an association between Egfr and natural variation in Drosophila melanogaster wing morphology. BMC Genet 2005; 6:44. [PMID: 16102176 PMCID: PMC1208880 DOI: 10.1186/1471-2156-6-44] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2005] [Accepted: 08/15/2005] [Indexed: 11/25/2022] Open
Abstract
Background Quantitative differences between individuals stem from a combination of genetic and environmental factors, with the heritable variation being shaped by evolutionary forces. Drosophila wing shape has emerged as an attractive system for genetic dissection of multi-dimensional traits. We utilize several experimental genetic methods to validation of the contribution of several polymorphisms in the Epidermal growth factor receptor (Egfr) gene to wing shape and size, that were previously mapped in populations of Drosophila melanogaster from North Carolina (NC) and California (CA). This re-evaluation utilized different genetic testcrosses to generate heterozygous individuals with a variety of genetic backgrounds as well as sampling of new alleles from Kenyan stocks. Results Only one variant, in the Egfr promoter, had replicable effects in all new experiments. However, expanded genotyping of the initial sample of inbred lines rendered the association non-significant in the CA population, while it persisted in the NC sample, suggesting population specific modification of the quantitative trait nucleotide QTN effect. Conclusion Dissection of quantitative trait variation to the nucleotide level can identify sites with replicable effects as small as one percent of the segregating genetic variation. However, the testcross approach to validate QTNs is both labor intensive and time-consuming, and is probably less useful than resampling of large independent sets of outbred individuals.
Collapse
Affiliation(s)
- Arnar Palsson
- Department of Genetics' North Carolina State University, Raleigh, NC 27695, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - James Dodgson
- Department of Genetics' North Carolina State University, Raleigh, NC 27695, USA
- The Department of Biochemistry, University of Sussex, Brighton, BN1 9QG, UK
| | - Ian Dworkin
- Department of Genetics' North Carolina State University, Raleigh, NC 27695, USA
| | - Greg Gibson
- Department of Genetics' North Carolina State University, Raleigh, NC 27695, USA
| |
Collapse
|
40
|
Abstract
A considerable body of theory pertaining to the evolution of canalization has emerged recently, yet there have been few empirical investigations of their predictions. To address this, patterns of canalization and trait correlation were investigated under the individual and joint effects of the introgression of a loss-of-function allele of the Distal-less gene and high-temperature stress on a panel of iso-female lines. Variation was examined for number of sex comb teeth and the length of the basi-tarsus on the pro-thoracic leg of male Drosophila melanogaster. I demonstrate that whereas there is evidence for trait canalization, there is no evidence to support the hypothesis of the evolution of genetic canalization as a response to microenvironmental canalization. Furthermore, I demonstrate that although there are genetic correlations between these traits, there is no association between their measures of canalization. I discuss the prospects of the evolutionary lability of the Distal-less gene within the context of changes in genetic variation and covariation.
Collapse
Affiliation(s)
- Ian Dworkin
- Department of Zoology, University of Toronto, Toronto, ON, Canada M5S 3G5.
| |
Collapse
|
41
|
Abstract
Patterning of the insect eggshell is an excellent system for exploring the molecular basis of phenotypic variation. In Drosophila melanogaster, two dorsal-anterior respiratory appendages are produced in response to signaling through the Epidermal growth factor receptor (Egfr). Previous work implicates Egfr pathway function in both intraspecific variation for dorsal appendage spacing (DAS) on the eggshell, as well as interspecific differences in dorsal appendage number and location. To test the hypothesis that genetic variation in Egfr contributes to variation in eggshell patterning, we have made use of naturally occurring intraspecific variation for DAS as a model quantitative trait. We found that there is substantial segregating genetic variation for DAS in D. melanogaster, and have tested for associations with 289 common polymorphisms in the Egfr locus. A marginal association was seen with two polymorphic sites in Egfr; however, we failed to replicate these findings in a second population, or in a modified quantitative complementation test designed to specifically test the effects of the putative polymorphisms. Therefore, we conclude that the polymorphisms we have identified in Egfr do not contribute to variation in DAS, and further work is required to understand the genetic architecture of this trait.
Collapse
Affiliation(s)
- Lisa M Goering
- Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA.
| | | |
Collapse
|
42
|
Dworkin I, Palsson A, Gibson G. Replication of an Egfr-wing shape association in a wild-caught cohort of Drosophila melanogaster. Genetics 2005; 169:2115-25. [PMID: 15687273 PMCID: PMC1449590 DOI: 10.1534/genetics.104.035766] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2004] [Accepted: 01/10/2005] [Indexed: 11/18/2022] Open
Abstract
Linkage disequilibrium mapping has been used extensively in medical and evolutionary genetics to map causal polymorphisms within genes associated with disease status or phenotypic variation for a trait. However, the initial findings of most nonhuman studies have not been replicated in subsequent studies, due in part to false positives, as well as additional factors that can render true positives unreplicable. These factors may be more severe when the initial study is performed using an experimental population of organisms reared under controlled lab conditions. We demonstrate that despite considerable phenotypic differences for wing shape between a lab-reared experimental population and a wild-caught cohort of Drosophila melanogaster, an association between a putative regulatory polymorphism in Egfr and wing shape can be replicated. These results are discussed both within the framework of future association-mapping studies and within the context of the evolutionary dynamics of alleles in populations.
Collapse
Affiliation(s)
- Ian Dworkin
- Department of Genetics, North Carolina State University, Raleigh, 27695-7614, USA.
| | | | | |
Collapse
|
43
|
Mezey JG, Houle D, Nuzhdin SV. Naturally segregating quantitative trait loci affecting wing shape of Drosophila melanogaster. Genetics 2005; 169:2101-13. [PMID: 15520257 PMCID: PMC1449619 DOI: 10.1534/genetics.104.036988] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Accepted: 01/07/2005] [Indexed: 11/18/2022] Open
Abstract
Variation in vein position and wing shape of Drosophila melanogaster depends on many genes. In the following, we report the results of a QTL analysis of wing shape in D. melanogaster. We identified QTL responsible for natural variation for wing shape and analyzed their interactions with developmental genetic signaling pathways important for vein positioning. The QTL analysis indicated that the total number of QTL segregating in this population is likely to be very large. The locations of putative QTL identified in this study were compared to those identified in previous studies and, while there is more correspondence across studies than expected by chance on the third chromosome, the studies appear to have identified different QTL. Using a complementation design, we tested for interactions among these QTL with the Hedgehog and Decapentaplegic signaling pathways, which are important for the development and position of vein pairs L3-L4 and L2-L5. Three QTL showed strong interactions with these two pathways, supporting the hypothesis that these QTL are involved in these pathways. Naturally segregating variation can therefore act through known signaling pathways to produce variation in vein position.
Collapse
Affiliation(s)
- Jason G Mezey
- Center for Population Biology and Section of Evolution and Ecology, University of California, Davis, 95616, USA.
| | | | | |
Collapse
|
44
|
Palsson A, Rouse A, Riley-Berger R, Dworkin I, Gibson G. Nucleotide variation in the Egfr locus of Drosophila melanogaster. Genetics 2005; 167:1199-212. [PMID: 15280235 PMCID: PMC1470963 DOI: 10.1534/genetics.104.026252] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Epidermal growth factor receptor is an essential gene with diverse pleiotropic roles in development throughout the animal kingdom. Analysis of sequence diversity in 10.9 kb covering the complete coding region and 6.4 kb of potential regulatory regions in a sample of 250 alleles from three populations of Drosophila melanogaster suggests that the intensity of different population genetic forces varies along the locus. A total of 238 independent common SNPs and 20 indel polymorphisms were detected, with just six common replacements affecting >1475 amino acids, four of which are in the short alternate first exon. Sequence diversity is lowest in a 2-kb portion of intron 2, which is also highly conserved in comparison with D. simulans and D. pseudoobscura. Linkage disequilibrium decays to background levels within 500 bp of most sites, so haplotypes are generally restricted to up to 5 polymorphisms. The two North American samples from North Carolina and California have diverged in allele frequency at a handful of individual SNPs, but a Kenyan sample is both more divergent and more polymorphic. The effect of sample size on inference of the roles of population structure, uneven recombination, and weak selection in patterning nucleotide variation in the locus is discussed.
Collapse
Affiliation(s)
- Arnar Palsson
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27513-7614, USA
| | | | | | | | | |
Collapse
|
45
|
Nikoh N, Duty A, Gibson G. Effects of population structure and sex on association between serotonin receptors and Drosophila heart rate. Genetics 2004; 168:1963-74. [PMID: 15611167 PMCID: PMC1448745 DOI: 10.1534/genetics.104.028712] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2004] [Accepted: 07/19/2004] [Indexed: 11/18/2022] Open
Abstract
As a first step toward population and quantitative genetic analysis of neurotransmitter receptors in Drosophila melanogaster, we describe the parameters of nucleotide variation in three serotonin receptors and their association with pupal heart rate. Thirteen kilobases of DNA including the complete coding regions of 5-HT1A, 5-HT1B, and 5-HT2 were sequenced in 216 highly inbred lines extracted from two North American populations in California and North Carolina. Nucleotide and amino acid polymorphism is in the normal range for Drosophila genes and proteins, and linkage disequilibrium decays rapidly such that haplotype blocks are typically only a few SNPs long. However, intron 1 of 5-HT1A consists of two haplotypes that are at significantly different frequencies in the two populations. Neither this region of the gene nor any of the common amino acid polymorphisms in the three loci associate with either heart rate or heart rate variability. A cluster of SNPs in intron 2 of 5-HT1A, including a triallelic site, do show a highly significant interaction between genotype, sex, and population. While it is likely that a combination of weak, complex selection pressures and population structure has helped shape variation in the serotonin receptors of Drosophila, much larger sampling strategies than are currently adopted in evolutionary genetics will be required to disentangle these effects.
Collapse
Affiliation(s)
- Naruo Nikoh
- University of the Air, Chiba City 261-8586, Japan
| | | | | |
Collapse
|
46
|
Abstract
Cryptic genetic variation is the dark matter of biology: it is variation that is not normally seen, but that might be an essential source of physiological and evolutionary potential. It is uncovered by environmental or genetic perturbations, and is thought to modify the penetrance of common diseases, the response of livestock and crops to artificial selection and the capacity of populations to respond to the emergence of a potentially advantageous macro-mutation. We argue in this review that cryptic genetic variation is pervasive but under-appreciated, we highlight recent progress in determining the nature and identity of genes that underlie cryptic genetic effects and we outline future research directions.
Collapse
Affiliation(s)
- Greg Gibson
- Department of Genetics, Gardner Hall, North Carolina State University, Raleigh, North Carolina 27695-7614, USA.
| | | |
Collapse
|