1
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Chhichholiya Y, Suryan AK, Suman P, Munshi A, Singh S. SNPs in miRNAs and Target Sequences: Role in Cancer and Diabetes. Front Genet 2021; 12:793523. [PMID: 34925466 PMCID: PMC8673831 DOI: 10.3389/fgene.2021.793523] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/28/2021] [Indexed: 12/27/2022] Open
Abstract
miRNAs are fascinating molecular players for gene regulation as individual miRNA can control multiple targets and a single target can be regulated by multiple miRNAs. Loss of miRNA regulated gene expression is often reported to be implicated in various human diseases like diabetes and cancer. Recently, geneticists across the world started reporting single nucleotide polymorphism (SNPs) in seed sequences of miRNAs. Similarly, SNPs are also reported in various target sequences of these miRNAs. Both the scenarios lead to dysregulated gene expression which may result in the progression of diseases. In the present paper, we explore SNPs in various miRNAs and their target sequences reported in various human cancers as well as diabetes. Similarly, we also present evidence of these mutations in various other human diseases.
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Affiliation(s)
- Yogita Chhichholiya
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | - Aman Kumar Suryan
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | - Prabhat Suman
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
| | - Sandeep Singh
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
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2
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Lagunas-Rangel FA. G protein-coupled receptors that influence lifespan of human and animal models. Biogerontology 2021; 23:1-19. [PMID: 34860303 PMCID: PMC8888397 DOI: 10.1007/s10522-021-09945-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/22/2021] [Indexed: 12/16/2022]
Abstract
Humanity has always sought to live longer and for this, multiple strategies have been tried with varying results. In this sense, G protein-coupled receptors (GPCRs) may be a good option to try to prolong our life while maintaining good health since they have a substantial participation in a wide variety of processes of human pathophysiology and are one of the main therapeutic targets. In this way, we present the analysis of a series of GPCRs whose activity has been shown to affect the lifespan of animal and human models, and in which we put a special interest in describing the molecular mechanisms involved. Our compilation of data revealed that the mechanisms most involved in the role of GPCRs in lifespan are those that mimic dietary restriction, those related to insulin signaling and the AMPK and TOR pathways, and those that alter oxidative homeostasis and severe and/or chronic inflammation. We also discuss the possibility of using agonist or antagonist drugs, depending on the beneficial or harmful effects of each GPCR, in order to prolong people's lifespan and healthspan.
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3
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Rodrigues MF, Vibranovski MD, Cogni R. Clinal and seasonal changes are correlated in Drosophila melanogaster natural populations. Evolution 2021; 75:2042-2054. [PMID: 34184262 DOI: 10.1111/evo.14300] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022]
Abstract
Spatial and seasonal variations in the environment are ubiquitous. Environmental heterogeneity can affect natural populations and lead to covariation between environment and allele frequencies. Drosophila melanogaster is known to harbor polymorphisms that change both with latitude and seasons. Identifying the role of selection in driving these changes is not trivial, because nonadaptive processes can cause similar patterns. Given the environment changes in similar ways across seasons and along the latitudinal gradient, one promising approach may be to look for parallelism between clinal and seasonal changes. Here, we test whether there is a genome-wide correlation between clinal and seasonal changes, and whether the pattern is consistent with selection. Allele frequency estimates were obtained from pooled samples from seven different locations along the east coast of the United States, and across seasons within Pennsylvania. We show that there is a genome-wide correlation between clinal and seasonal variations, which cannot be explained by linked selection alone. This pattern is stronger in genomic regions with higher functional content, consistent with natural selection. We derive a way to biologically interpret these correlations and show that around 3.7% of the common, autosomal variants could be under parallel seasonal and spatial selection. Our results highlight the contribution of natural selection in driving fluctuations in allele frequencies in natural fly populations and point to a shared genomic basis to climate adaptation that happens over space and time in D. melanogaster.
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Affiliation(s)
- Murillo F Rodrigues
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil.,Current Address: Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, 97403
| | - Maria D Vibranovski
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
| | - Rodrigo Cogni
- Department of Ecology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
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4
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Betancourt NJ, Rajpurohit S, Durmaz E, Fabian DK, Kapun M, Flatt T, Schmidt P. Allelic polymorphism at foxo contributes to local adaptation in Drosophila melanogaster. Mol Ecol 2021; 30:2817-2830. [PMID: 33914989 PMCID: PMC8693798 DOI: 10.1111/mec.15939] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 04/13/2021] [Indexed: 01/09/2023]
Abstract
The insulin/insulin-like growth factor signalling pathway has been hypothesized as a major determinant of life-history profiles that vary adaptively in natural populations. In Drosophila melanogaster, multiple components of this pathway vary predictably with latitude; this includes foxo, a conserved gene that regulates insulin signalling and has pleiotropic effects on a variety of fitness-associated traits. We hypothesized that allelic variation at foxo contributes to genetic variance for size-related traits that vary adaptively with latitude. We first examined patterns of variation among natural populations along a latitudinal transect in the eastern United States and show that thorax length, wing area, wing loading, and starvation tolerance exhibit significant latitudinal clines for both males and females but that development time does not vary predictably with latitude. We then generated recombinant outbred populations and show that naturally occurring allelic variation at foxo, which exhibits stronger clinality than expected, is associated with the same traits that vary with latitude in the natural populations. Our results suggest that allelic variation at foxo contributes to adaptive patterns of life-history variation in natural populations of this genetic model.
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Affiliation(s)
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Division of Biological and Life Sciences, Ahmedabad University, Ahmedabad, India
| | - Esra Durmaz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Daniel K. Fabian
- Department of Genetics, University of Cambridge, Cambridge, UK
- European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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5
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Bogaerts‐Márquez M, Guirao‐Rico S, Gautier M, González J. Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster. Mol Ecol 2021; 30:938-954. [PMID: 33350518 PMCID: PMC7986194 DOI: 10.1111/mec.15783] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
While several studies in a diverse set of species have shed light on the genes underlying adaptation, our knowledge on the selective pressures that explain the observed patterns lags behind. Drosophila melanogaster is a valuable organism to study environmental adaptation because this species originated in Southern Africa and has recently expanded worldwide, and also because it has a functionally well-annotated genome. In this study, we aimed to decipher which environmental variables are relevant for adaptation of D. melanogaster natural populations in Europe and North America. We analysed 36 whole-genome pool-seq samples of D. melanogaster natural populations collected in 20 European and 11 North American locations. We used the BayPass software to identify single nucleotide polymorphisms (SNPs) and transposable elements (TEs) showing signature of adaptive differentiation across populations, as well as significant associations with 59 environmental variables related to temperature, rainfall, evaporation, solar radiation, wind, daylight hours, and soil type. We found that in addition to temperature and rainfall, wind related variables are also relevant for D. melanogaster environmental adaptation. Interestingly, 23%-51% of the genes that showed significant associations with environmental variables were not found overly differentiated across populations. In addition to SNPs, we also identified 10 reference transposable element insertions associated with environmental variables. Our results showed that genome-environment association analysis can identify adaptive genetic variants that are undetected by population differentiation analysis while also allowing the identification of candidate environmental drivers of adaptation.
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Affiliation(s)
- María Bogaerts‐Márquez
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
| | - Sara Guirao‐Rico
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
| | - Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Josefa González
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
- The European Drosophila Population Genomics Consortium (DrosEU)Université de MontpellierMontpellierFrance
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6
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Flatt T. Life-History Evolution and the Genetics of Fitness Components in Drosophila melanogaster. Genetics 2020; 214:3-48. [PMID: 31907300 PMCID: PMC6944413 DOI: 10.1534/genetics.119.300160] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/03/2019] [Indexed: 12/28/2022] Open
Abstract
Life-history traits or "fitness components"-such as age and size at maturity, fecundity and fertility, age-specific rates of survival, and life span-are the major phenotypic determinants of Darwinian fitness. Analyzing the evolution and genetics of these phenotypic targets of selection is central to our understanding of adaptation. Due to its simple and rapid life cycle, cosmopolitan distribution, ease of maintenance in the laboratory, well-understood evolutionary genetics, and its versatile genetic toolbox, the "vinegar fly" Drosophila melanogaster is one of the most powerful, experimentally tractable model systems for studying "life-history evolution." Here, I review what has been learned about the evolution and genetics of life-history variation in D. melanogaster by drawing on numerous sources spanning population and quantitative genetics, genomics, experimental evolution, evolutionary ecology, and physiology. This body of work has contributed greatly to our knowledge of several fundamental problems in evolutionary biology, including the amount and maintenance of genetic variation, the evolution of body size, clines and climate adaptation, the evolution of senescence, phenotypic plasticity, the nature of life-history trade-offs, and so forth. While major progress has been made, important facets of these and other questions remain open, and the D. melanogaster system will undoubtedly continue to deliver key insights into central issues of life-history evolution and the genetics of adaptation.
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Affiliation(s)
- Thomas Flatt
- Department of Biology, University of Fribourg, CH-1700, Switzerland
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7
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Durmaz E, Rajpurohit S, Betancourt N, Fabian DK, Kapun M, Schmidt P, Flatt T. A clinal polymorphism in the insulin signaling transcription factor foxo contributes to life-history adaptation in Drosophila. Evolution 2019; 73:1774-1792. [PMID: 31111462 PMCID: PMC6771989 DOI: 10.1111/evo.13759] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 05/04/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
Abstract
A fundamental aim of adaptation genomics is to identify polymorphisms that underpin variation in fitness traits. In Drosophila melanogaster, latitudinal life-history clines exist on multiple continents and make an excellent system for dissecting the genetics of adaptation. We have previously identified numerous clinal single-nucleotide polymorphism in insulin/insulin-like growth factor signaling (IIS), a pathway known from mutant studies to affect life history. However, the effects of natural variants in this pathway remain poorly understood. Here we investigate how two clinal alternative alleles at foxo, a transcriptional effector of IIS, affect fitness components (viability, size, starvation resistance, fat content). We assessed this polymorphism from the North American cline by reconstituting outbred populations, fixed for either the low- or high-latitude allele, from inbred DGRP lines. Because diet and temperature modulate IIS, we phenotyped alleles across two temperatures (18°C, 25°C) and two diets differing in sugar source and content. Consistent with clinal expectations, the high-latitude allele conferred larger body size and reduced wing loading. Alleles also differed in starvation resistance and expression of insulin-like receptor, a transcriptional target of FOXO. Allelic reaction norms were mostly parallel, with few GxE interactions. Together, our results suggest that variation in IIS makes a major contribution to clinal life-history adaptation.
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Affiliation(s)
- Esra Durmaz
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Subhash Rajpurohit
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19140
- Division of Biological and Life SciencesAhmedabad UniversityAhmedabadIndia
| | - Nicolas Betancourt
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19140
| | - Daniel K. Fabian
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteWellcome Genome Campus, HinxtonCambridgeUnited Kingdom
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population, GeneticsViennaAustria
| | - Martin Kapun
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Paul Schmidt
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19140
| | - Thomas Flatt
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
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8
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Hardy CM, Burke MK, Everett LJ, Han MV, Lantz KM, Gibbs AG. Genome-Wide Analysis of Starvation-Selected Drosophila melanogaster-A Genetic Model of Obesity. Mol Biol Evol 2019; 35:50-65. [PMID: 29309688 DOI: 10.1093/molbev/msx254] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Experimental evolution affords the opportunity to investigate adaptation to stressful environments. Studies combining experimental evolution with whole-genome resequencing have provided insight into the dynamics of adaptation and a new tool to uncover genes associated with polygenic traits. Here, we selected for starvation resistance in populations of Drosophila melanogaster for over 80 generations. In response, the starvation-selected lines developed an obese condition, storing nearly twice the level of total lipids than their unselected controls. Although these fats provide a ∼3-fold increase in starvation resistance, the imbalance in lipid homeostasis incurs evolutionary cost. Some of these tradeoffs resemble obesity-associated pathologies in mammals including metabolic depression, low activity levels, dilated cardiomyopathy, and disrupted sleeping patterns. To determine the genetic basis of these traits, we resequenced genomic DNA from the selected lines and their controls. We found 1,046,373 polymorphic sites, many of which diverged between selection treatments. In addition, we found a wide range of genetic heterogeneity between the replicates of the selected lines, suggesting multiple mechanisms of adaptation. Genome-wide heterozygosity was low in the selected populations, with many large blocks of SNPs nearing fixation. We found candidate loci under selection by using an algorithm to control for the effects of genetic drift. These loci were mapped to a set of 382 genes, which associated with many processes including nutrient response, catabolic metabolism, and lipid droplet function. The results of our study speak to the evolutionary origins of obesity and provide new targets to understand the polygenic nature of obesity in a unique model system.
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Affiliation(s)
- Christopher M Hardy
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
| | - Molly K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, OR
| | - Logan J Everett
- Department of Biological Sciences, North Carolina State University, Raleigh, NC
| | - Mira V Han
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
| | - Kathryn M Lantz
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
| | - Allen G Gibbs
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV.,Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
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9
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Durmaz E, Benson C, Kapun M, Schmidt P, Flatt T. An inversion supergene in Drosophila underpins latitudinal clines in survival traits. J Evol Biol 2018; 31:1354-1364. [PMID: 29904977 DOI: 10.1111/jeb.13310] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/09/2018] [Accepted: 06/04/2018] [Indexed: 01/18/2023]
Abstract
Chromosomal inversions often contribute to local adaptation across latitudinal clines, but the underlying selective mechanisms remain poorly understood. We and others have previously shown that a clinal inversion polymorphism in Drosophila melanogaster, In(3R)Payne, underpins body size clines along the North American and Australian east coasts. Here, we ask whether this polymorphism also contributes to clinal variation in other fitness-related traits, namely survival traits (lifespan, survival upon starvation and survival upon cold shock). We generated homokaryon lines, either carrying the inverted or standard chromosomal arrangement, isolated from populations approximating the endpoints of the North American cline (Florida, Maine) and phenotyped the flies at two growth temperatures (18 °C, 25 °C). Across both temperatures, high-latitude flies from Maine lived longer and were more stress resistant than low-latitude flies from Florida, as previously observed. Interestingly, we find that this latitudinal pattern is partly explained by the clinal distribution of the In(3R)P polymorphism, which is at ~ 50% frequency in Florida but absent in Maine: inverted karyotypes tended to be shorter-lived and less stress resistant than uninverted karyotypes. We also detected an interaction between karyotype and temperature on survival traits. As In(3R)P influences body size and multiple survival traits, it can be viewed as a 'supergene', a cluster of tightly linked loci affecting multiple complex phenotypes. We conjecture that the inversion cline is maintained by fitness trade-offs and balancing selection across geography; elucidating the mechanisms whereby this inversion affects alternative, locally adapted phenotypes across the cline is an important task for future work.
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Affiliation(s)
- Esra Durmaz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Clare Benson
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,School of Biological Sciences, University of Manchester, Manchester, UK
| | - Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
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10
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Abstract
Longevity varies among individuals, but how natural genetic variation contributes to variation in lifespan is poorly understood. Drosophila melanogaster presents an advantageous model system to explore the genetic underpinnings of longevity, since its generation time is brief and both the genetic background and rearing environment can be precisely controlled. The bellwether (blw) gene encodes the α subunit of mitochondrial ATP synthase. Since metabolic rate may influence lifespan, we investigated whether alternative haplotypes in the blw promoter affect lifespan when expressed in a co-isogenic background. We amplified 521 bp upstream promoter sequences containing alternative haplotypes and assessed promoter activity both in vitro and in vivo using a luciferase reporter system. The AG haplotype showed significantly greater expression of luciferase than the GT haplotype. We then overexpressed a blw cDNA construct driven by either the AG or GT haplotype promoter in transgenic flies and showed that the AG haplotype also results in greater blw cDNA expression and a significant decrease in lifespan relative to the GT promoter haplotype, in male flies only. Thus, our results show that naturally occurring regulatory variants of blw affect lifespan in a sex-specific manner.
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Affiliation(s)
- Júlia Frankenberg Garcia
- Program in Genetics, W. M. Keck Center for Behavioral Biology, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.,School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Mary Anna Carbone
- Program in Genetics, W. M. Keck Center for Behavioral Biology, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Robert R H Anholt
- Program in Genetics, W. M. Keck Center for Behavioral Biology, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA.
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11
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Machado HE, Bergland AO, O'Brien KR, Behrman EL, Schmidt PS, Petrov DA. Comparative population genomics of latitudinal variation in Drosophila simulans and Drosophila melanogaster. Mol Ecol 2016; 25:723-40. [PMID: 26523848 DOI: 10.1111/mec.13446] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/15/2022]
Abstract
Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here, we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and Drosophila melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple time points over 2 years. Consistent with phenotypic studies, we find less clinal variation in D. simulans than D. melanogaster, particularly for the autosomes. Moreover, we find that clinally varying loci in D. simulans are less stable over multiple years than comparable clines in D. melanogaster. D. simulans shows a significantly weaker pattern of isolation by distance than D. melanogaster and we find evidence for a stronger contribution of migration to D. simulans population genetic structure. While population bottlenecks and migration can plausibly explain the differences in stability of clinal variation between the two species, we also observe a significant enrichment of shared clinal genes, suggesting that the selective forces associated with climate are acting on the same genes and phenotypes in D. simulans and D. melanogaster.
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Affiliation(s)
- Heather E Machado
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, USA
| | - Alan O Bergland
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, USA
| | - Katherine R O'Brien
- School of Biological Sciences, University of Nebraska-Lincoln, 348 Manter Hall, Lincoln, NE, 68588, USA.,Department of Biology, University of Pennsylvania, 102 Leidy Laboratories, Philadelphia, PA, 19104-6313, USA
| | - Emily L Behrman
- Department of Biology, University of Pennsylvania, 102 Leidy Laboratories, Philadelphia, PA, 19104-6313, USA
| | - Paul S Schmidt
- Department of Biology, University of Pennsylvania, 102 Leidy Laboratories, Philadelphia, PA, 19104-6313, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305-5020, USA
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12
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Stallard E. Underlying and Multiple Case Mortality Advanced Ages: United States 1980-1998. ACTA ACUST UNITED AC 2014. [DOI: 10.1080/10920277.2002.11073999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Li C, Zhang Y, Yun X, Wang Y, Sang M, Liu X, Hu X, Li B. Methuselah-like genes affect development, stress resistance, lifespan and reproduction in Tribolium castaneum. INSECT MOLECULAR BIOLOGY 2014; 23:587-597. [PMID: 24924269 DOI: 10.1111/imb.12107] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Methuselah (Mth) is associated with lifespan, stress resistance and reproduction in Drosophila melanogaster, but Mth is not present in nondrosophiline insects. A number of methuselah-likes (mthls) have been identified in nondrosophiline insects, but it is unknown whether the functions of mth are shared by mthls or are divergent from them. Five mthls have been identified in Tribolium castaneum. Although they have different developmental expression patterns, they all enhance resistance to starvation. Only mthl1 and mthl2 enhance resistance to high temperature, whereas mthl4 and mthl5 negatively regulate oxidative stress in T. castaneum. Unlike in the fly with mth mutation, knockdown of mthls, except mthl3, shortens the lifespan of T. castaneum. Moreover, mthl1 and mthl2 are critical for Tribolium development. mthl1 plays important roles in larval and pupal development and adult eclosion, while mthl2 is required for eclosion. Moreover, mthl1 and mthl2 silencing reduces the fertility of T. castaneum, and mthl1 and mthl4 are also essential for embryo development. In conclusion, mthls have a significant effect on insect development, lifespan, stress resistance and reproduction. These results provide experimental evidence for functional divergence among mthls/mth and clues for the signal transduction of Mthls.
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Affiliation(s)
- Chengjun Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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14
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A recent global selective sweep on the age-1 phosphatidylinositol 3-OH kinase regulator of the insulin-like signaling pathway within Caenorhabditis remanei. G3-GENES GENOMES GENETICS 2014; 4:1123-33. [PMID: 24727287 PMCID: PMC4065255 DOI: 10.1534/g3.114.010629] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The discovery that genetic pathways can be manipulated to extend lifespan has revolutionized our understanding of aging, yet their function within natural populations remains poorly characterized. In particular, evolutionary theories of aging predict tradeoffs in resource investment toward somatic maintenance vs. reproductive output that should impose strong natural selection on genetic components that influence this balance. To explore such selective pressure at the molecular level, we examine population genetic variation in the insulin-like signaling pathway of the nematode Caenorhabditis remanei. We document a recent global selective sweep on the phosphoinositide-3-kinase pathway regulator, age-1, the first life-extension gene to have been identified. In particular, we find that age-1 has 5−20 times less genetic variation than any other insulin-like signaling pathway components and that evolutionary signatures of selection center on the age-1 locus within its genomic environment. These results demonstrate that critical components of aging-related pathways can be subject to shifting patterns of strong selection, as predicted by theory. This highly polymorphic outcrossing species offers high-resolution, population-level analyses of molecular variation as a complement to functional genetic studies within the self-reproducing C. elegans model system.
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15
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Savory FR, Benton TG, Varma V, Hope IA, Sait SM. Stressful environments can indirectly select for increased longevity. Ecol Evol 2014; 4:1176-85. [PMID: 24772292 PMCID: PMC3997331 DOI: 10.1002/ece3.1013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/30/2014] [Indexed: 01/15/2023] Open
Abstract
Longevity is modulated by a range of conserved genes in eukaryotes, but it is unclear how variation in these genes contributes to the evolution of longevity in nature. Mutations that increase life span in model organisms typically induce trade-offs which lead to a net reduction in fitness, suggesting that such mutations are unlikely to become established in natural populations. However, the fitness consequences of manipulating longevity have rarely been assessed in heterogeneous environments, in which stressful conditions are encountered. Using laboratory selection experiments, we demonstrate that long-lived, stress-resistant Caenorhabditis elegans age-1(hx546) mutants have higher fitness than the wild-type genotype if mixed genotype populations are periodically exposed to high temperatures when food is not limited. We further establish, using stochastic population projection models, that the age-1(hx546) mutant allele can confer a selective advantage if temperature stress is encountered when food availability also varies over time. Our results indicate that heterogeneity in environmental stress may lead to altered allele frequencies over ecological timescales and indirectly drive the evolution of longevity. This has important implications for understanding the evolution of life-history strategies.
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Affiliation(s)
- Fiona R Savory
- Faculty of Biological Sciences, School of Biology, University of Leeds Leeds, LS2 9JT, U.K ; National Centre for Biological Sciences, TATA Institute of Fundamental Research Bangalore, 560 065, India
| | - Timothy G Benton
- Faculty of Biological Sciences, School of Biology, University of Leeds Leeds, LS2 9JT, U.K
| | - Varun Varma
- Faculty of Biological Sciences, School of Biology, University of Leeds Leeds, LS2 9JT, U.K ; National Centre for Biological Sciences, TATA Institute of Fundamental Research Bangalore, 560 065, India
| | - Ian A Hope
- Faculty of Biological Sciences, School of Biology, University of Leeds Leeds, LS2 9JT, U.K
| | - Steven M Sait
- Faculty of Biological Sciences, School of Biology, University of Leeds Leeds, LS2 9JT, U.K
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16
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Sgrò CM, van Heerwaarden B, Kellermann V, Wee CW, Hoffmann AA, Lee SF. Complexity of the genetic basis of ageing in nature revealed by a clinal study of lifespan and methuselah, a gene for ageing, in Drosophila from eastern Australia. Mol Ecol 2014; 22:3539-51. [PMID: 23802551 DOI: 10.1111/mec.12353] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 03/12/2013] [Accepted: 03/16/2013] [Indexed: 11/29/2022]
Abstract
Clinal studies are a powerful tool for understanding the genetic basis of climatic adaptation. However, while clines in quantitative traits and genetic polymorphisms have been observed within and across continents, few studies have attempted to demonstrate direct links between them. The gene methuselah in Drosophila has been shown to have a major effect on stress response and longevity phenotypes based largely on laboratory studies of induced mutations in the mth gene. Clinal patterns in the most common mth haplotype and for lifespan (both increasing with latitude) have been observed in North American populations of D. melanogaster, implicating climatic selection. While these clinal patterns have led some to suggest that mth influences ageing in natural populations, limited evidence on the association between the two has so far been collected. Here, we describe a significant cline in the mth haplotype in eastern Australian D. melanogaster populations that parallel the cline in North America. We also describe a cline in mth gene expression. These findings further support the idea that mth is itself under selection. In contrast, we show that lifespan has a strong nonlinear clinal pattern, increasing southwards from the tropics, but then decreasing again from mid-latitudes. Furthermore, in association studies, we find no evidence for a direct link between mth haplotype and lifespan. Thus, while our data support a role for mth variation being under natural selection, we found no link to naturally occurring variation in lifespan and ageing in Australian populations of D. melanogaster. Our results indicate that the mth locus likely has genetic background and environment-specific effects.
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Affiliation(s)
- Carla M Sgrò
- Department of Biological Sciences, Monash University, Clayton, Vic., 3800, Australia.
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17
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Araújo AR, Reis M, Rocha H, Aguiar B, Morales-Hojas R, Macedo-Ribeiro S, Fonseca NA, Reboiro-Jato D, Reboiro-Jato M, Fdez-Riverola F, Vieira CP, Vieira J. The Drosophila melanogaster methuselah gene: a novel gene with ancient functions. PLoS One 2013; 8:e63747. [PMID: 23696853 PMCID: PMC3655951 DOI: 10.1371/journal.pone.0063747] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/05/2013] [Indexed: 01/10/2023] Open
Abstract
The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth), has been described as a novel gene that is less than 10 million years old. Nevertheless, it shows a highly specific expression pattern in embryos, larvae, and adults, and has been implicated in larval development, stress resistance, and in the setting of adult lifespan, among others. Although mth belongs to a gene subfamily with 16 members in D. melanogaster, there is no evidence for functional redundancy in this subfamily. Therefore, it is surprising that a novel gene influences so many traits. Here, we explore the alternative hypothesis that mth is an old gene. Under this hypothesis, in species distantly related to D. melanogaster, there should be a gene with features similar to those of mth. By performing detailed phylogenetic, synteny, protein structure, and gene expression analyses we show that the D. virilis GJ12490 gene is the orthologous of mth in species distantly related to D. melanogaster. We also show that, in D. americana (a species of the virilis group of Drosophila), a common amino acid polymorphism at the GJ12490 orthologous gene is significantly associated with developmental time, size, and lifespan differences. Our results imply that GJ12490 orthologous genes are candidates for developmental time and lifespan differences in Drosophila in general.
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Affiliation(s)
- Ana Rita Araújo
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Micael Reis
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Helder Rocha
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Bruno Aguiar
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Ramiro Morales-Hojas
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Nuno A. Fonseca
- Center of Research in Advanced Computing Systems (CRACS-INESC Porto), Universidade do Porto, Porto, Portugal
- EMBL-European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | | | | | | | - Cristina P. Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- * E-mail:
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18
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Alcedo J, Flatt T, Pasyukova EG. Neuronal inputs and outputs of aging and longevity. Front Genet 2013; 4:71. [PMID: 23653632 PMCID: PMC3644678 DOI: 10.3389/fgene.2013.00071] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/13/2013] [Indexed: 12/14/2022] Open
Abstract
An animal’s survival strongly depends on its ability to maintain homeostasis in response to the changing quality of its external and internal environment. This is achieved through intracellular and intercellular communication within and among different tissues. One of the organ systems that plays a major role in this communication and the maintenance of homeostasis is the nervous system. Here we highlight different aspects of the neuronal inputs and outputs of pathways that affect aging and longevity. Accordingly, we discuss how sensory inputs influence homeostasis and lifespan through the modulation of different types of neuronal signals, which reflects the complexity of the environmental cues that affect physiology. We also describe feedback, compensatory, and feed-forward mechanisms in these longevity-modulating pathways that are necessary for homeostasis. Finally, we consider the temporal requirements for these neuronal processes and the potential role of natural genetic variation in shaping the neurobiology of aging.
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Affiliation(s)
- Joy Alcedo
- Friedrich Miescher Institute for Biomedical Research Basel, Switzerland ; Department of Biological Sciences, Wayne State University Detroit, MI, USA
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19
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Li C, Chen M, Sang M, Liu X, Wu W, Li B. Comparative genomic analysis and evolution of family-B G protein-coupled receptors from six model insect species. Gene 2013; 519:1-12. [PMID: 23428791 DOI: 10.1016/j.gene.2013.01.061] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/21/2012] [Accepted: 01/30/2013] [Indexed: 10/27/2022]
Abstract
Family-B G protein-coupled receptors (GPCR-Bs) play vital roles in many biological processes, including growth, development and reproduction. However, the evolution and function of GPCR-Bs have been poorly understood in insects. We have identified 87 GPCR-Bs from six model insect species, 20 from Tribolium castaneum, 9 from Apis mellifera, 11 from Bombyx mori, 9 from Acyrthosiphon pisum, 14 from Anopheles gambiae and 24 from Drosophila melanogaster. 22 of them were reported in this study for the first time. Phylogenetic analysis revealed that there are three kinds of evolutionary patterns that occurred among GPCR-Bs during insect evolution: one-to-one orthologous relationships, species-specific expansion and episodic duplication or loss in certain insect lineages. A striking finding was the discovery of a parathyroid hormone receptor like gene (pthrl) in invertebrates, which was independently duplicated in vertebrates and invertebrates, whereas this gene was lost at least twice during insect evolution. These results indicate that PTHRL is possibly divergent in the functions between mammals and insects. The information of family-B GPCRs in nondrosophiline insects has been established, and will promote the further study on the function of these GPCRs and deorphanization of them. On the other hand, this study provides us with multiple function of GPCR-Bs in differential organisms, which will be also the potential attacking targets for new pesticides and drugs.
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Affiliation(s)
- Chengjun Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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20
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Gimenez LED, Ghildyal P, Fischer KE, Hu H, Ja WW, Eaton BA, Wu Y, Austad SN, Ranjan R. Modulation of methuselah expression targeted to Drosophila insulin-producing cells extends life and enhances oxidative stress resistance. Aging Cell 2013; 12:121-9. [PMID: 23121290 DOI: 10.1111/acel.12027] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2012] [Indexed: 01/14/2023] Open
Abstract
Ubiquitously reduced signaling via Methuselah (MTH), a G-protein-coupled receptor (GPCR) required for neurosecretion, has previously been reported to extend life and enhance stress resistance in flies. Whether these effects are due to reduced MTH signalling in specific tissues remains unknown. We determined that reduced expression of mth targeted to the insulin-producing cells (IPCs) of the fly brain was sufficient to extend life and enhance oxidative stress resistance. Paradoxically, we discovered that overexpression of mth targeted to the same cells has similar phenotypic effects to reduced expression due to MTH's interaction with β-arrestin, which uncouples GPCRs from their G-proteins. We confirmed the functional relationship between MTH and β-arrestin by finding that IPC-targeted overexpression of β-arrestin alone mimics the longevity phenotype of reduced MTH signaling. As reduced MTH signaling also inhibits insulin secretion from the IPCs, the most parsimonious mechanistic explanation of its longevity and stress-resistance enhancement might be through reduced insulin/IGF signaling (IIS). However, examination of phenotypic features of long-lived IPC-mth modulated flies as well as several downstream IIS targets implicates enhanced activity of the JNK stress-resistance pathway more directly than insulin signaling in the longevity and stress-resistance phenotypes.
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Affiliation(s)
- Luis E. D. Gimenez
- Department of Pharmacology; University of Texas Health Science Center San Antonio; San Antonio; TX; 78245; USA
| | - Parakashtha Ghildyal
- Department of Pharmacology; University of Texas Health Science Center San Antonio; San Antonio; TX; 78245; USA
| | - Kathleen E. Fischer
- Department of Physiology; University of Texas Health Science Center San Antonio; San Antonio; TX; 78229; USA
| | - Hongxiang Hu
- Department of Pharmacology; University of Texas Health Science Center San Antonio; San Antonio; TX; 78245; USA
| | - William W. Ja
- Department of Metabolism & Aging; The Scripps Research Institute; Jupiter; FL; 33458; USA
| | - Benjamin A. Eaton
- Department of Physiology; University of Texas Health Science Center San Antonio; San Antonio; TX; 78229; USA
| | - Yimin Wu
- Department of Physiology; University of Texas Health Science Center San Antonio; San Antonio; TX; 78229; USA
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21
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22
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Patel MV, Hallal DA, Jones JW, Bronner DN, Zein R, Caravas J, Husain Z, Friedrich M, Vanberkum MFA. Dramatic expansion and developmental expression diversification of the methuselah gene family during recent Drosophila evolution. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2012; 318:368-87. [PMID: 22711569 DOI: 10.1002/jez.b.22453] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Functional studies of the methuselah/methuselah-like (mth/mthl) gene family have focused on the founding member mth, but little is known regarding the developmental functions of this receptor or any of its paralogs. We undertook a comprehensive analysis of developmental expression and sequence divergence in the mth/mthl gene family. Using in situ hybridization techniques, we detect expression of six genes (mthl1, 5, 9, 11, 13, and 14) in the embryo during gastrulation and development of the gut, heart, and lymph glands. Four receptors (mthl3, 4, 6, and 8) are expressed in the larval central nervous system, imaginal discs, or both, and two receptors (mthl10 and mth) are expressed in both embryos and larvae. Phylogenetic analysis of all mth/mthl genes in five Drosophila species, mosquito and flour beetle structured the mth/mthl family into several subclades. mthl1, 5, and 14 are present in most species, each forming a separate clade. A newly identified Drosophila mthl gene (CG31720; herein mthl15) formed another ancient clade. The remaining Drosophila receptors, including mth, are members of a large "superclade" that diversified relatively recently during dipteran evolution, in many cases within the melanogaster subgroup. Comparing the expression patterns of the mth/mthl "superclade" paralogs to the embryonic expression of the singleton ortholog in Tribolium suggests both subfunctionalization and acquisition of novel functionalities. Taken together, our findings shed novel light on mth as a young member of an adaptively evolving developmental gene family.
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Affiliation(s)
- Meghna V Patel
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
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23
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Fabian DK, Kapun M, Nolte V, Kofler R, Schmidt PS, Schlötterer C, Flatt T. Genome-wide patterns of latitudinal differentiation among populations of Drosophila melanogaster from North America. Mol Ecol 2012; 21:4748-69. [PMID: 22913798 PMCID: PMC3482935 DOI: 10.1111/j.1365-294x.2012.05731.x] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/29/2012] [Accepted: 07/04/2012] [Indexed: 01/18/2023]
Abstract
Understanding the genetic underpinnings of adaptive change is a fundamental but largely unresolved problem in evolutionary biology. Drosophila melanogaster, an ancestrally tropical insect that has spread to temperate regions and become cosmopolitan, offers a powerful opportunity for identifying the molecular polymorphisms underlying clinal adaptation. Here, we use genome-wide next-generation sequencing of DNA pools ('pool-seq') from three populations collected along the North American east coast to examine patterns of latitudinal differentiation. Comparing the genomes of these populations is particularly interesting since they exhibit clinal variation in a number of important life history traits. We find extensive latitudinal differentiation, with many of the most strongly differentiated genes involved in major functional pathways such as the insulin/TOR, ecdysone, torso, EGFR, TGFβ/BMP, JAK/STAT, immunity and circadian rhythm pathways. We observe particularly strong differentiation on chromosome 3R, especially within the cosmopolitan inversion In(3R)Payne, which contains a large number of clinally varying genes. While much of the differentiation might be driven by clinal differences in the frequency of In(3R)P, we also identify genes that are likely independent of this inversion. Our results provide genome-wide evidence consistent with pervasive spatially variable selection acting on numerous loci and pathways along the well-known North American cline, with many candidates implicated in life history regulation and exhibiting parallel differentiation along the previously investigated Australian cline.
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Affiliation(s)
- Daniel K Fabian
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, A-1210, Vienna, Austria
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24
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Poelchau MF, Reynolds JA, Denlinger DL, Elsik CG, Armbruster PA. A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation. BMC Genomics 2011; 12:619. [PMID: 22185595 PMCID: PMC3258294 DOI: 10.1186/1471-2164-12-619] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Accepted: 12/20/2011] [Indexed: 12/12/2022] Open
Abstract
Background Many temperate insects survive the harsh conditions of winter by undergoing photoperiodic diapause, a pre-programmed developmental arrest initiated by short day lengths. Despite the well-established ecological significance of photoperiodic diapause, the molecular basis of this crucial adaptation remains largely unresolved. The Asian tiger mosquito, Aedes albopictus (Skuse), represents an outstanding emerging model to investigate the molecular basis of photoperiodic diapause in a well-defined ecological and evolutionary context. Ae. albopictus is a medically significant vector and is currently considered the most invasive mosquito in the world. Traits related to diapause appear to be important factors contributing to the rapid spread of this mosquito. To generate novel sequence information for this species, as well as to discover transcripts involved in diapause preparation, we sequenced the transcriptome of Ae. albopictus oocytes destined to become diapausing or non-diapausing pharate larvae. Results 454 GS-FLX transcriptome sequencing yielded >1.1 million quality-filtered reads, which we assembled into 69,474 contigs (N50 = 1,009 bp). Our contig filtering approach, where we took advantage of strong sequence similarity to the fully sequenced genome of Aedes aegypti, as well as other reference organisms, resulted in 11,561 high-quality, conservative ESTs. Differential expression estimates based on normalized read counts revealed 57 genes with higher expression, and 257 with lower expression under diapause-inducing conditions. Analysis of expression by qPCR for 47 of these genes indicated a high correlation of expression levels between 454 sequence data and qPCR, but congruence of statistically significant differential expression was low. Seven genes identified as differentially expressed based on qPCR have putative functions that are consistent with the insect diapause syndrome; three genes have unknown function and represent novel candidates for the transcriptional basis of diapause. Conclusions Our transcriptome database provides a rich resource for the comparative genomics and functional genetics of Ae. albopictus, an invasive and medically important mosquito. Additionally, the identification of differentially expressed transcripts related to diapause enriches the limited knowledge base for the molecular basis of insect diapause, in particular for the preparatory stage. Finally, our analysis illustrates a useful approach that draws from a closely related reference genome to generate high-confidence ESTs in a non-model organism.
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Affiliation(s)
- Monica F Poelchau
- Department of Biology, Georgetown University, 37th and O Streets NW, Washington, DC, USA.
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25
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Hancock AM, Witonsky DB, Alkorta-Aranburu G, Beall CM, Gebremedhin A, Sukernik R, Utermann G, Pritchard JK, Coop G, Di Rienzo A. Adaptations to climate-mediated selective pressures in humans. PLoS Genet 2011; 7:e1001375. [PMID: 21533023 PMCID: PMC3080864 DOI: 10.1371/journal.pgen.1001375] [Citation(s) in RCA: 197] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 03/15/2011] [Indexed: 02/07/2023] Open
Abstract
Humans inhabit a remarkably diverse range of environments, and adaptation through natural selection has likely played a central role in the capacity to survive and thrive in extreme climates. Unlike numerous studies that used only population genetic data to search for evidence of selection, here we scan the human genome for selection signals by identifying the SNPs with the strongest correlations between allele frequencies and climate across 61 worldwide populations. We find a striking enrichment of genic and nonsynonymous SNPs relative to non-genic SNPs among those that are strongly correlated with these climate variables. Among the most extreme signals, several overlap with those from GWAS, including SNPs associated with pigmentation and autoimmune diseases. Further, we find an enrichment of strong signals in gene sets related to UV radiation, infection and immunity, and cancer. Our results imply that adaptations to climate shaped the spatial distribution of variation in humans. Classical studies that examined the global distributions of human physiological traits such as pigmentation, basal metabolic rate, and body shape and size suggested that natural selection related to climate has been important during recent human evolutionary history. We scanned the human genome using data for about 650,000 variants in 61 worldwide populations to look for correlations between allele frequencies and 9 climate variables and found evidence for adaptations to climate at the genome-wide level. In addition, we detected compelling signals for individual SNPs involved in pigmentation and immune response, as well as for pathways related to UV radiation, infection and immunity, and cancer. A particularly appealing aspect of this approach is that we identify a set of candidate advantageous SNPs associated with specific biological hypotheses, which will be useful for follow-up testing. We developed an online resource to browse the results of our data analyses, allowing researchers to quickly assess evidence for selection in a particular genomic region and to compare it across several studies.
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Affiliation(s)
- Angela M. Hancock
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - David B. Witonsky
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Gorka Alkorta-Aranburu
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Cynthia M. Beall
- Department of Anthropology, Case Western Research University, Cleveland, Ohio, United States of America
| | - Amha Gebremedhin
- Department of Internal Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Rem Sukernik
- Laboratory of Human Molecular Genetics, Department of Molecular and Cellular Biology, Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Novosibirsk, Russia
| | - Gerd Utermann
- Institute for Medical Biology and Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Jonathan K. Pritchard
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Graham Coop
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Evolution and Ecology and Center for Population Biology, University of California Davis, Davis, California, United States of America
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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26
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Eanes WF. Molecular population genetics and selection in the glycolytic pathway. ACTA ACUST UNITED AC 2011; 214:165-71. [PMID: 21177937 DOI: 10.1242/jeb.046458] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this review, I discuss the evidence for differential natural selection acting across enzymes in the glycolytic pathway in Drosophila. Across the genome, genes evolve at very different rates and possess markedly varying levels of molecular polymorphism, codon bias and expression variation. Discovering the underlying causes of this variation has been a challenge in evolutionary biology. It has been proposed that both the intrinsic properties of enzymes and their pathway position have direct effects on their molecular evolution, and with the genomic era the study of adaptation has been taken to the level of pathways and networks of genes and their products. Of special interest have been the energy-producing pathways. Using both population genetic and experimental approaches, our laboratory has been engaged in a study of molecular variation across the glycolytic pathway in Drosophila melanogaster and its close relatives. We have observed a pervasive pattern in which genes at the top of the pathway, especially around the intersection at glucose 6-phosphate, show evidence for both contemporary selection, in the form of latitudinal allele clines, and inter-specific selection, in the form of elevated levels of amino acid substitutions between species. To further explore this question, future work will require corroboration in other species, expansion into tangential pathways, and experimental work to better characterize metabolic control through the pathway and to examine the pleiotropic effects of these genes on other traits and fitness components.
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Affiliation(s)
- Walter F Eanes
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11790, USA.
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27
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Strotmann R, Schröck K, Böselt I, Stäubert C, Russ A, Schöneberg T. Evolution of GPCR: change and continuity. Mol Cell Endocrinol 2011; 331:170-8. [PMID: 20708652 DOI: 10.1016/j.mce.2010.07.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 06/28/2010] [Accepted: 07/13/2010] [Indexed: 12/26/2022]
Abstract
Once introduced into the very early eukaryotic blueprint, seven-transmembrane receptors soon became the central and versatile components of the evolutionary highly successful G protein-coupled transmembrane signaling mechanism. In contrast to all other components of this signal transduction pathway, G protein-coupled receptors (GPCR) evolved in various structural families, eventually comprising hundreds of members in vertebrate genomes. Their functional diversity is in contrast to the conserved transmembrane core and the invariant set of intracellular signaling mechanisms, and it may be the interplay of these properties that is the key to the evolutionary success of GPCR. The GPCR repertoires retrieved from extant vertebrate genomes are the recent endpoints of this long evolutionary process. But the shaping of the fine structure and the repertoire of GPCR is still ongoing, and signatures of recent selection acting on GPCR genes can be made visible by modern population genetic methods. The very dynamic evolution of GPCR can be analyzed from different perspectives: at the levels of sequence comparisons between species from different families, orders and classes, and at the level of populations within a species. Here, we summarize the main conclusions from studies at these different levels with a specific focus on the more recent evolutionary dynamics of GPCR.
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Affiliation(s)
- Rainer Strotmann
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Germany.
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28
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Kolaczkowski B, Kern AD, Holloway AK, Begun DJ. Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics 2011; 187:245-60. [PMID: 21059887 PMCID: PMC3018305 DOI: 10.1534/genetics.110.123059] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 11/03/2010] [Indexed: 11/18/2022] Open
Abstract
Determining the genetic basis of environmental adaptation is a central problem of evolutionary biology. This issue has been fruitfully addressed by examining genetic differentiation between populations that are recently separated and/or experience high rates of gene flow. A good example of this approach is the decades-long investigation of selection acting along latitudinal clines in Drosophila melanogaster. Here we use next-generation genome sequencing to reexamine the well-studied Australian D. melanogaster cline. We find evidence for extensive differentiation between temperate and tropical populations, with regulatory regions and unannotated regions showing particularly high levels of differentiation. Although the physical genomic scale of geographic differentiation is small--on the order of gene sized--we observed several larger highly differentiated regions. The region spanned by the cosmopolitan inversion polymorphism In(3R)P shows higher levels of differentiation, consistent with the major difference in allele frequencies of Standard and In(3R)P karyotypes in temperate vs. tropical Australian populations. Our analysis reveals evidence for spatially varying selection on a number of key biological processes, suggesting fundamental biological differences between flies from these two geographic regions.
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Affiliation(s)
- Bryan Kolaczkowski
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 and Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Andrew D. Kern
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 and Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Alisha K. Holloway
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 and Department of Evolution and Ecology, University of California, Davis, California 95616
| | - David J. Begun
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755 and Department of Evolution and Ecology, University of California, Davis, California 95616
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Pijpe J, Pul N, van Duijn S, Brakefield PM, Zwaan BJ. Changed gene expression for candidate ageing genes in long-lived Bicyclus anynana butterflies. Exp Gerontol 2010; 46:426-34. [PMID: 21118714 DOI: 10.1016/j.exger.2010.11.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 10/26/2010] [Accepted: 11/22/2010] [Indexed: 01/13/2023]
Abstract
Candidate genes for the regulation of lifespan have emerged from studies that use mutants and genetically manipulated model organisms. However, it is rarely addressed whether these genes contribute to lifespan variation in populations of these species that capture natural standing genetic variation. Here, we explore expression variation in three candidate ageing genes, Indy, sod2, and catalase, in Bicyclus anynana, a butterfly with well understood ecology. We used lines established from natural populations and artificially selected for increased adult starvation resistance. They show a considerable increase in adult lifespan under both starvation and optimal food conditions. We measured adult butterflies of various ages, under a range of optimal and starvation diets, from two selected populations and one unselected control population. In all lines, Indy and catalase are up-regulated in response to starvation while this is not evident for sod2. Under starvation, Indy and catalase are up-regulated in, while this is not evident for sod2. Under optimal food conditions, Indy is down-regulated at a later age, with Indy expression showing relatively high inter-individual variation. We find differences between the selected lines and the unselected line. Under starvation conditions, expression is higher for catalase in one, and for sod2 in both selected lines. Importantly, sod2 expression is also higher in the selected populations under optimal food conditions. We conclude that sod2, but not Indy, is involved in the response to artificial selection for increased starvation resistance. The role of catalase is less clear because of the differences between the two selected lines. Moreover, sod2 appears to be a candidate gene that underpins the genetic correlation between starvation resistance and longevity. Our study indicates that some, but not all, genes identified through mutant screens in other organisms may underpin standing genetic variation for ageing-related traits in stocks of Bicyclus butterflies established from natural populations. Clearly, this needs to be investigated in other organisms as well, especially in the organisms to which mutants screens were applied. This information will narrow down the list of genes that underpin variation in lifespan and ageing in extant populations of organisms, and which may serve as candidate genes in humans.
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Affiliation(s)
- Jeroen Pijpe
- Institute of Biology, Leiden University, P.O.-Box 9505, 2300 RA Leiden, The Netherlands.
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Rybina OY, Pasyukova EG. A naturally occurring polymorphism at Drosophila melanogaster Lim3 Locus, a homolog of human LHX3/4, affects Lim3 transcription and fly lifespan. PLoS One 2010; 5:e12621. [PMID: 20838645 PMCID: PMC2935391 DOI: 10.1371/journal.pone.0012621] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Accepted: 08/05/2010] [Indexed: 11/18/2022] Open
Abstract
Lim3 encodes an RNA polymerase II transcription factor with a key role in neuron specification. It was also identified as a candidate gene that affects lifespan. These pleiotropic effects indicate the fundamental significance of the potential interplay between neural development and lifespan control. The goal of this study was to analyze the causal relationships between Lim3 structural variations, and gene expression and lifespan changes, and to provide insights into regulatory pathways controlling lifespan. Fifty substitution lines containing second chromosomes from a Drosophila natural population were used to analyze the association between lifespan and sequence variation in the 5'-regulatory region, and first exon and intron of Lim3A, in which we discovered multiple transcription start sites (TSS). The core and proximal promoter organization for Lim3A and a previously unknown mRNA named Lim3C were described. A haplotype of two markers in the Lim3A regulatory region was significantly associated with variation in lifespan. We propose that polymorphisms in the regulatory region affect gene transcription, and consequently lifespan. Indeed, five polymorphic markers located within 380 to 680 bp of the Lim3A major TSS, including two markers associated with lifespan variation, were significantly associated with the level of Lim3A transcript, as evaluated by real time RT-PCR in embryos, adult heads, and testes. A naturally occurring polymorphism caused a six-fold change in gene transcription and a 25% change in lifespan. Markers associated with long lifespan and intermediate Lim3A transcription were present in the population at high frequencies. We hypothesize that polymorphic markers associated with Lim3A expression are located within the binding sites for proteins that regulate gene function, and provide general rather than tissue-specific regulation of transcription, and that intermediate levels of Lim3A expression confer a selective advantage and longer lifespan.
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31
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Hughes KA. Mutation and the evolution of ageing: from biometrics to system genetics. Philos Trans R Soc Lond B Biol Sci 2010; 365:1273-9. [PMID: 20308103 DOI: 10.1098/rstb.2009.0265] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A notable success for evolutionary genetics during the past century was to generate a coherent, quantitative explanation for an apparent evolutionary paradox: the tendency for multicellular organisms to show declining fitness with age (senescence, often referred to simply as 'ageing'). This general theory is now widely accepted and explains most of the features of senescence that are observed in natural and laboratory populations, but specific instantiations of that theory have been more controversial. To date, most of the empirical tests of these models have relied on data generated from biometric experiments. Modern population genetics and genomics provide new, and probably more powerful, ways to test ideas that are still controversial more than half a century after the original theory was developed. System-genetic experiments have the potential to address both evolutionary and mechanistic questions about ageing by identifying causal loci and the genetic networks with which they interact. Both the biometrical approaches and the newer approaches are reviewed here, with an emphasis on the challenges and limitations that each method faces.
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Affiliation(s)
- Kimberly A Hughes
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA.
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32
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Flatt T, Schmidt PS. Integrating evolutionary and molecular genetics of aging. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1790:951-62. [PMID: 19619612 PMCID: PMC2972575 DOI: 10.1016/j.bbagen.2009.07.010] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Revised: 07/07/2009] [Accepted: 07/10/2009] [Indexed: 12/25/2022]
Abstract
Aging or senescence is an age-dependent decline in physiological function, demographically manifest as decreased survival and fecundity with increasing age. Since aging is disadvantageous it should not evolve by natural selection. So why do organisms age and die? In the 1940s and 1950s evolutionary geneticists resolved this paradox by positing that aging evolves because selection is inefficient at maintaining function late in life. By the 1980s and 1990s this evolutionary theory of aging had received firm empirical support, but little was known about the mechanisms of aging. Around the same time biologists began to apply the tools of molecular genetics to aging and successfully identified mutations that affect longevity. Today, the molecular genetics of aging is a burgeoning field, but progress in evolutionary genetics of aging has largely stalled. Here we argue that some of the most exciting and unresolved questions about aging require an integration of molecular and evolutionary approaches. Is aging a universal process? Why do species age at different rates? Are the mechanisms of aging conserved or lineage-specific? Are longevity genes identified in the laboratory under selection in natural populations? What is the genetic basis of plasticity in aging in response to environmental cues and is this plasticity adaptive? What are the mechanisms underlying trade-offs between early fitness traits and life span? To answer these questions evolutionary biologists must adopt the tools of molecular biology, while molecular biologists must put their experiments into an evolutionary framework. The time is ripe for a synthesis of molecular biogerontology and the evolutionary biology of aging.
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Affiliation(s)
- Thomas Flatt
- Institut für Populationsgenetik, Veterinärmedizinische Universität Wien, Josef Baumann Gasse 1, A-1210 Wien, Austria
| | - Paul S. Schmidt
- University of Pennsylvania, Department of Biology, 433 South University Avenue, Philadelphia, PA 19104-6018, USA.
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Schmidt PS, Serrão EA, Pearson GA, Riginos C, Rawson PD, Hilbish TJ, Brawley SH, Trussell GC, Carrington E, Wethey DS, Grahame JW, Bonhomme F, Rand DM. Ecological genetics in the North Atlantic: environmental gradients and adaptation at specific loci. Ecology 2009; 89:S91-107. [PMID: 19097487 DOI: 10.1890/07-1162.1] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The North Atlantic intertidal community provides a rich set of organismal and environmental material for the study of ecological genetics. Clearly defined environmental gradients exist at multiple spatial scales: there are broad latitudinal trends in temperature, meso-scale changes in salinity along estuaries, and smaller scale gradients in desiccation and temperature spanning the intertidal range. The geology and geography of the American and European coasts provide natural replication of these gradients, allowing for population genetic analyses of parallel adaptation to environmental stress and heterogeneity. Statistical methods have been developed that provide genomic neutrality tests of population differentiation and aid in the process of candidate gene identification. In this paper, we review studies of marine organisms that illustrate associations between an environmental gradient and specific genetic markers. Such highly differentiated markers become candidate genes for adaptation to the environmental factors in question, but the functional significance of genetic variants must be comprehensively evaluated. We present a set of predictions about locus-specific selection across latitudinal, estuarine, and intertidal gradients that are likely to exist in the North Atlantic. We further present new data and analyses that support and contradict these simple selection models. Some taxa show pronounced clinal variation at certain loci against a background of mild clinal variation at many loci. These cases illustrate the procedures necessary for distinguishing selection driven by internal genomic vs. external environmental factors. We suggest that the North Atlantic intertidal community provides a model system for identifying genes that matter in ecology due to the clarity of the environmental stresses and an extensive experimental literature on ecological function. While these organisms are typically poor genetic and genomic models, advances in comparative genomics have provided access to molecular tools that can now be applied to taxa with well-defined ecologies. As many of the organisms we discuss have tight physiological limits driven by climatic factors, this synthesis of molecular population genetics with marine ecology could provide a sensitive means of assessing evolutionary responses to climate change.
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Affiliation(s)
- Paul S Schmidt
- Department of Biology, 433 South University Avenue, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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34
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Functional significance of allelic variation at methuselah, an aging gene in Drosophila. PLoS One 2008; 3:e1987. [PMID: 18414670 PMCID: PMC2288678 DOI: 10.1371/journal.pone.0001987] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 03/04/2008] [Indexed: 12/19/2022] Open
Abstract
Background Longevity and age-specific patterns of mortality are complex traits that vary within and among taxa. Multiple candidate genes for aging have been identified in model systems by extended longevity mutant phenotypes, including the G-protein coupled receptor methuselah (mth) in D. melanogaster. These genes offer important insights into the mechanisms of lifespan determination and have been major targets of interest in the biology of aging. However, it is largely unknown whether these genes contribute to genetic variance for lifespan in natural populations, and consequently contribute to lifespan evolution. Methodology/Principle Findings For a gene to contribute to genetic variance for a particular trait, it must meet two criteria: natural allelic variation and functional differences among variants. Previous work showed that mth varies significantly among wild populations; here we assess the functional significance of wild-derived mth alleles on lifespan, fecundity and stress resistance using a quantitative complementation scheme. Our results demonstrate that mth alleles segregating in nature have a functional effect on all three traits. Conclusions/Significance These results suggest that allelic variation at mth contributes to observed differences in lifespan and correlated phenotypes in natural populations, and that evaluation of genetic diversity at candidate genes for aging can be a fruitful approach to identifying loci contributing to lifespan evolution.
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35
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Evidence of spatially varying selection acting on four chromatin-remodeling loci in Drosophila melanogaster. Genetics 2008; 179:475-85. [PMID: 18245821 DOI: 10.1534/genetics.107.085423] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The packaging of DNA into proper chromatin structure contributes to transcriptional regulation. This packaging is environment sensitive, yet its role in adaptation to novel environmental conditions is completely unknown. We set out to identify candidate chromatin-remodeling loci that are differentiated between tropical and temperate populations in Drosophila melanogaster, an ancestrally equatorial African species that has recently colonized temperate environments around the world. Here we describe sequence variation at seven such chromatin-remodeling loci, four of which (chd1, ssrp, chm, and glu) exhibit strong differentiation between tropical and temperate populations. An in-depth analysis of chm revealed sequence differentiation restricted to a small portion of the gene, as well as evidence of clinal variation along the east coasts of both the United States and Australia. The functions of chd1, chm, ssrp, and glu point to several novel hypotheses for the role of chromatin-based transcriptional regulation in adaptation to a novel environment. Specifically, both stress-induced transcription and developmental homeostasis emerge as potential functional targets of environment-dependent selection.
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36
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Hancock AM, Witonsky DB, Gordon AS, Eshel G, Pritchard JK, Coop G, Di Rienzo A. Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genet 2008; 4:e32. [PMID: 18282109 PMCID: PMC2242814 DOI: 10.1371/journal.pgen.0040032] [Citation(s) in RCA: 216] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Accepted: 12/26/2007] [Indexed: 12/25/2022] Open
Abstract
Evolutionary pressures due to variation in climate play an important role in shaping phenotypic variation among and within species and have been shown to influence variation in phenotypes such as body shape and size among humans. Genes involved in energy metabolism are likely to be central to heat and cold tolerance. To test the hypothesis that climate shaped variation in metabolism genes in humans, we used a bioinformatics approach based on network theory to select 82 candidate genes for common metabolic disorders. We genotyped 873 tag SNPs in these genes in 54 worldwide populations (including the 52 in the Human Genome Diversity Project panel) and found correlations with climate variables using rank correlation analysis and a newly developed method termed Bayesian geographic analysis. In addition, we genotyped 210 carefully matched control SNPs to provide an empirical null distribution for spatial patterns of allele frequency due to population history alone. For nearly all climate variables, we found an excess of genic SNPs in the tail of the distributions of the test statistics compared to the control SNPs, implying that metabolic genes as a group show signals of spatially varying selection. Among our strongest signals were several SNPs (e.g., LEPR R109K, FABP2 A54T) that had previously been associated with phenotypes directly related to cold tolerance. Since variation in climate may be correlated with other aspects of environmental variation, it is possible that some of the signals that we detected reflect selective pressures other than climate. Nevertheless, our results are consistent with the idea that climate has been an important selective pressure acting on candidate genes for common metabolic disorders.
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Affiliation(s)
- Angela M Hancock
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - David B Witonsky
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Adam S Gordon
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Gidon Eshel
- Department of Geophysical Sciences, University of Chicago, Illinois, United States of America
| | - Jonathan K Pritchard
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Graham Coop
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
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37
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Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans. PLoS One 2007; 2:e1113. [PMID: 17971876 PMCID: PMC2040203 DOI: 10.1371/journal.pone.0001113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Accepted: 10/12/2007] [Indexed: 12/04/2022] Open
Abstract
Adaptive protein evolution is pervasive in Drosophila. Genomic studies, thus far, have analyzed each protein as a single entity. However, the targets of adaptive events may be localized to particular parts of proteins, such as protein domains or regions involved in protein folding. We compared the population genetic mechanisms driving sequence polymorphism and divergence in defined protein domains and non-domain regions. Interestingly, we find that non-domain regions of proteins are more frequent targets of directional selection. Protein domains are also evolving under directional selection, but appear to be under stronger purifying selection than non-domain regions. Non-domain regions of proteins clearly play a major role in adaptive protein evolution on a genomic scale and merit future investigations of their functional properties.
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38
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Schmidt PS, Matzkin L, Ippolito M, Eanes WF. GEOGRAPHIC VARIATION IN DIAPAUSE INCIDENCE, LIFE‐HISTORY TRAITS, AND CLIMATIC ADAPTATION INDROSOPHILA MELANOGASTER. Evolution 2007. [DOI: 10.1111/j.0014-3820.2005.tb01821.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Paul S. Schmidt
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794–5245
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104–6018
| | - Luciano Matzkin
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794–5245
| | - Michael Ippolito
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794–5245
| | - Walter F. Eanes
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794–5245
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39
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Baldal EA, Baktawar W, Brakefield PM, Zwaan BJ. Methuselah life history in a variety of conditions, implications for the use of mutants in longevity research. Exp Gerontol 2006; 41:1126-35. [PMID: 17064868 DOI: 10.1016/j.exger.2006.08.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Revised: 08/23/2006] [Accepted: 08/24/2006] [Indexed: 10/24/2022]
Abstract
The laboratory has yielded many long-lived mutants of several model-organisms in the past few years. Many of the resulting claims for extended longevity have been nuanced or shown to be restricted to specific conditions, including environments and genetic backgrounds. Here, we test whether the long-lived mutant fruit fly methuselah (mth(1)) displays its apparent superiority in longevity and stress resistance in different environments, at different ages and in correlated traits. The results demonstrate that stress resistance at different times in life is not consistently higher in the mutant relative to its progenitor strain (w(1118)). Furthermore, the mth(1) genotype only leads to an increase in longevity in an environment where reproduction is not stimulated. Also, virgin and mated life span were compared and showed that mating negatively affects life span, especially in the mth(1) individuals. This reduced the life span enhancing effect of the mutation to zero. This apparent environment and mating dependent trade-off between longevity and reproduction supports the disposable soma theory of ageing. We conclude that these data can only provide limited information on natural variation. The data show the need to uncover the full complexity of variation in such traits in natural environments.
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Affiliation(s)
- E A Baldal
- Institute of Biology, Leiden University, P.O. Box 9516, 2300 RA Leiden, The Netherlands
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40
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Norry FM, Sambucetti P, Scannapieco AC, Loeschcke V. Altitudinal patterns for longevity, fecundity and senescence in Drosophila buzzatii. Genetica 2006; 128:81-93. [PMID: 17028942 DOI: 10.1007/s10709-005-5537-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Accepted: 11/28/2005] [Indexed: 11/28/2022]
Abstract
We tested for variation in longevity, senescence rate and early fecundity of Drosophila buzzatii along an elevational transect in Argentina, using laboratory-reared flies in laboratory tests performed to avoid extrinsic mortality. At 25 degrees C, females from lowland populations lived longer and had a lower demographic rate of senescence than females from highland populations. Minimal instead of maximal temperature at the sites of origin of population best predicted this cline. A very different pattern was found at higher test temperature. At 29.5 degrees C, longevity of males increased with altitude of origin of population. No clinal trend was apparent for longevity of females at 29.5 degrees C. There was evidence for a trade-off between early fecundity and longevity at non-stressful temperature (25 degrees C) along the altitudinal gradient. This trait association is consistent with evolutionary theories of aging. Population-by-temperature and sex-by-temperature interactions indicate that senescence patterns are expressed in environment specific ways.
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Affiliation(s)
- F M Norry
- Departamento de Ecología y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, (C-1428-EHA), Buenos Aires, Argentina.
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41
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Shmookler Reis RJ, Kang P, Ayyadevara S. Quantitative trait loci define genes and pathways underlying genetic variation in longevity. Exp Gerontol 2006; 41:1046-54. [PMID: 16919411 DOI: 10.1016/j.exger.2006.06.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2006] [Revised: 06/08/2006] [Accepted: 06/13/2006] [Indexed: 01/02/2023]
Abstract
Quantitative trait locus (QTL) mapping provides a means to discover and roughly position regions of the genome that harbor genes responsible for natural variation in a complex trait. QTL mapping has been utilized extensively in the pursuit of genes contributing to longevity, chiefly in two animal models, the nematode Caenorhabditis elegans and the dipteran insect Drosophila melanogaster. Research on both species has demonstrated that a relatively small set of loci accounts for most of their genetic variance in lifespan. QTL mapping complements the discovery of longevity genes by mutagenesis screens, because the two procedures are predicted to unveil overlapping but distinct types of genes. We argue that information gained from animal models, even invertebrates, can greatly facilitate the process of gene identification and testing of homologous genes in humans.
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42
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Schmidt PS, Conde DR. ENVIRONMENTAL HETEROGENEITY AND THE MAINTENANCE OF GENETIC VARIATION FOR REPRODUCTIVE DIAPAUSE IN DROSOPHILA MELANOGASTER. Evolution 2006. [DOI: 10.1111/j.0014-3820.2006.tb00505.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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43
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Abstract
The aging process is evolutionarily conserved and subject to quantitative modification by both genetic and environmental factors. Fundamental mechanisms of aging result in progressive deficits in the function of cells and organs, often leading to diseases that ultimately kill the organism such as cancers, cardiovascular disease and neurodegenerative disorders. Oxidative stress and damage to all of the major classes of molecules in cells are involved in aging and age-related diseases. The widely pursued approach of targeting disease-specific processes to develop therapeutic interventions has not had a major impact on healthspan. A more productive approach would be to target the fundamental mechanisms of aging throughout adult life so as to extend healthspan. Caloric restriction and regular exercise are two such approaches.
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Affiliation(s)
- Roy G Cutler
- Laboratory of Neurosciences, National Institute on Aging, Intramural Research Program, Baltimore, MD 21224, USA.
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44
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Vasemägi A. The adaptive hypothesis of clinal variation revisited: single-locus clines as a result of spatially restricted gene flow. Genetics 2006; 173:2411-4. [PMID: 16849603 PMCID: PMC1569722 DOI: 10.1534/genetics.106.059881] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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45
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Mockett RJ, Sohal RS. Temperature-dependent trade-offs between longevity and fertility in the Drosophila mutant, methuselah. Exp Gerontol 2006; 41:566-73. [PMID: 16677788 DOI: 10.1016/j.exger.2006.03.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Revised: 03/24/2006] [Accepted: 03/27/2006] [Indexed: 10/24/2022]
Abstract
Single gene, hypomorphic mutations which extend the life spans of cold-blooded animals, such as the methuselah (mth) mutation in the fruit fly, Drosophila melanogaster, may have additional, deleterious effects on overall fitness. The hypotheses tested here were: (i) that the extension of life span by mth might be temperature-dependent, and (ii) that it might be associated with depression of reproductive output, physical activity, or the rate of metabolism. The effect of mth on life span was smaller in magnitude than reported previously, and it was both sex-specific and temperature-dependent. Female longevity was increased only at 29 degrees C, whereas for male flies the extension of mean life span diminished progressively from 15-25% 25-29 degrees C to 2% at 18 degrees C, and the survival time at 4 degrees C was decreased by 22-39%. Conversely, the lifetime reproductive output of mth mutants was decreased at 29 degrees C, but increased at 18-22 degrees C. The walking speed of mth flies was significantly elevated, but mth had no effect on the rate of oxygen consumption at 25 degrees C. Collectively, the results demonstrate that where the life span is extended, there is an offsetting effect on reproductive output, suggesting that mth induces trade-off effects and is not a direct, mechanistic regulator of the aging process.
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Affiliation(s)
- Robin J Mockett
- Department of Molecular Pharmacology and Toxicology, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90033, USA
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46
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Schmidt PS, Conde DR. ENVIRONMENTAL HETEROGENEITY AND THE MAINTENANCE OF GENETIC VARIATION FOR REPRODUCTIVE DIAPAUSE IN DROSOPHILA MELANOGASTER. Evolution 2006. [DOI: 10.1554/05-430.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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47
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Schmidt PS, Paaby AB, Heschel MS. GENETIC VARIANCE FOR DIAPAUSE EXPRESSION AND ASSOCIATED LIFE HISTORIES IN DROSOPHILA MELANOGASTER. Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb00974.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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DuMont VB, Aquadro CF. Multiple signatures of positive selection downstream of notch on the X chromosome in Drosophila melanogaster. Genetics 2005; 171:639-53. [PMID: 16020794 PMCID: PMC1456778 DOI: 10.1534/genetics.104.038851] [Citation(s) in RCA: 34] [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
To identify genomic regions affected by the rapid fixation of beneficial mutations (selective sweeps), we performed a scan of microsatellite variability across the Notch locus region of Drosophila melanogaster. Nine microsatellites spanning 60 kb of the X chromosome were surveyed for variation in one African and three non-African populations of this species. The microsatellites identified an approximately 14-kb window for which we observed relatively low levels of variability and/or a skew in the frequency spectrum toward rare alleles, patterns predicted at regions linked to a selective sweep. DNA sequence polymorphism data were subsequently collected within this 14-kb region for three of the D. melanogaster populations. The sequence data strongly support the initial microsatellite findings; in the non-African populations there is evidence of a recent selective sweep downstream of the Notch locus near or within the open reading frames CG18508 and Fcp3C. In addition, we observe a significant McDonald-Kreitman test result suggesting too many amino acid fixations species wide, presumably due to positive selection, at the unannotated open reading frame CG18508. Thus, we observe within this small genomic region evidence for both recent (skew toward rare alleles in non-African populations) and recurring (amino acid evolution at CG18508) episodes of positive selection.
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Affiliation(s)
- Vanessa Bauer DuMont
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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Bessenyei B, Márka M, Urbán L, Zeher M, Semsei I. Single nucleotide polymorphisms: aging and diseases. Biogerontology 2005; 5:291-303. [PMID: 15547317 DOI: 10.1007/s10522-004-2567-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Differences of more than 3 million nucleotides can bee seen comparing the genomes of two individuals as a result of single nucleotide polymorphism (SNP). More and more SNPs can be identified and it seems that these alterations are behind of several biological phenomena. Personal differences in these nucleotides result for example in elevated disease susceptibilities, that is, certain nucleotides are more frequent in patients suffering from different diseases comparing to the healthy population. SNPs may cause substantial alterations in the cells, e.g. the enzyme activity of the respective gene changes, but in other cases the effects of the SNPs are not so pronounced. Later results indicate that SNPs can be rendered to individuals living a longer life than the average. Perhaps these results will not directly lead to the lengthening of the maximal life span; however, genes that play an important role in the aging process could be identified. In this respect SNPs are important factors in determining the information level of the cells of individuals which determines the maximal life span (I. Semsei On the nature of aging. Mech. Ageing Dev . 2000; 117: 93-108), in turn SNP is one of the factors that determine the aging process. Since there are certain age-related diseases, the discovery and the description of the SNPs as a function of age and diseases may result in a better understanding of the common roots of aging and those diseases.
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Affiliation(s)
- B Bessenyei
- Medical and Health Science Center, 3rd Department of Medicine, Molecular Biology Research Laboratory, University Medical School, Moricz Zs 22, H-4004 Debrecen, Hungary
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Schmidt PS, Matzkin L, Ippolito M, Eanes WF. GEOGRAPHIC VARIATION IN DIAPAUSE INCIDENCE, LIFE-HISTORY TRAITS, AND CLIMATIC ADAPTATION IN DROSOPHILA MELANOGASTER. Evolution 2005. [DOI: 10.1554/05-115.1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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