1
|
Lovejoy PC, Foley KE, Conti MM, Meadows SM, Bishop C, Fiumera AC. Genetic basis of susceptibility to low-dose paraquat and variation between the sexes in Drosophila melanogaster. Mol Ecol 2021; 30:2040-2053. [PMID: 33710693 DOI: 10.1111/mec.15878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 02/23/2021] [Indexed: 12/18/2022]
Abstract
Toxicant resistance is a complex trait, affected both by genetics and the environment. Like most complex traits, it can exhibit sexual dimorphism, yet sex is often overlooked as a factor in studies of toxicant resistance. Paraquat, one such toxicant, is a commonly used herbicide and is known to produce mitochondrial oxidative stress, decrease dopaminergic neurons and dopamine (DA) levels, and decrease motor ability. While the main effects of paraquat are well-characterized, less is known about the naturally occurring variation in paraquat susceptibility. The purpose of this study was to map the genes contributing to low-dose paraquat susceptibility in Drosophila melanogaster, and to determine if susceptibility differs between the sexes. One hundred of the Drosophila Genetic Reference Panel (DGRP) lines were scored for susceptibility via climbing ability and used in a genome-wide association study (GWAS). Variation in seventeen genes in females and thirty-five genes in males associated with paraquat susceptibility. Only two candidate genes overlapped between the sexes despite a significant positive correlation between male and female susceptibilities. Many associated polymorphisms had significant interactions with sex, with most having conditionally neutral effects. Conditional neutrality between the sexes probably stems from sex-biased expression which may result from partial resolution of sexual conflict. Candidate genes were verified with RNAi knockdowns, gene expression analyses, and DA quantification. Several of these genes are novel associations with paraquat susceptibility. This research highlights the importance of assessing both sexes when studying toxicant susceptibility.
Collapse
Affiliation(s)
- Pamela C Lovejoy
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA.,Department of Biology, St. Joseph's College, Brooklyn, NY, USA
| | - Kate E Foley
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| | - Melissa M Conti
- Department of Psychology, Binghamton University, Binghamton, NY, USA
| | | | | | - Anthony C Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| |
Collapse
|
2
|
Ruzicka F, Dutoit L, Czuppon P, Jordan CY, Li X, Olito C, Runemark A, Svensson EI, Yazdi HP, Connallon T. The search for sexually antagonistic genes: Practical insights from studies of local adaptation and statistical genomics. Evol Lett 2020; 4:398-415. [PMID: 33014417 PMCID: PMC7523564 DOI: 10.1002/evl3.192] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/13/2020] [Accepted: 07/28/2020] [Indexed: 12/16/2022] Open
Abstract
Sexually antagonistic (SA) genetic variation-in which alleles favored in one sex are disfavored in the other-is predicted to be common and has been documented in several animal and plant populations, yet we currently know little about its pervasiveness among species or its population genetic basis. Recent applications of genomics in studies of SA genetic variation have highlighted considerable methodological challenges to the identification and characterization of SA genes, raising questions about the feasibility of genomic approaches for inferring SA selection. The related fields of local adaptation and statistical genomics have previously dealt with similar challenges, and lessons from these disciplines can therefore help overcome current difficulties in applying genomics to study SA genetic variation. Here, we integrate theoretical and analytical concepts from local adaptation and statistical genomics research-including F ST and F IS statistics, genome-wide association studies, pedigree analyses, reciprocal transplant studies, and evolve-and-resequence experiments-to evaluate methods for identifying SA genes and genome-wide signals of SA genetic variation. We begin by developing theoretical models for between-sex F ST and F IS, including explicit null distributions for each statistic, and using them to critically evaluate putative multilocus signals of sex-specific selection in previously published datasets. We then highlight new statistics that address some of the limitations of F ST and F IS, along with applications of more direct approaches for characterizing SA genetic variation, which incorporate explicit fitness measurements. We finish by presenting practical guidelines for the validation and evolutionary analysis of candidate SA genes and discussing promising empirical systems for future work.
Collapse
Affiliation(s)
- Filip Ruzicka
- School of Biological SciencesMonash UniversityClaytonVIC 3800Australia
| | - Ludovic Dutoit
- Department of ZoologyUniversity of OtagoDunedin9054New Zealand
| | - Peter Czuppon
- Institute of Ecology and Environmental Sciences, UPEC, CNRS, IRD, INRASorbonne UniversitéParis75252France
- Center for Interdisciplinary Research in Biology, CNRS, Collège de FrancePSL Research UniversityParis75231France
| | - Crispin Y. Jordan
- School of Biomedical SciencesUniversity of EdinburghEdinburghEH8 9XDUnited Kingdom
| | - Xiang‐Yi Li
- Institute of BiologyUniversity of NeuchâtelNeuchatelCH‐2000Switzerland
| | - Colin Olito
- Department of BiologyLund UniversityLundSE‐22362Sweden
| | - Anna Runemark
- Department of BiologyLund UniversityLundSE‐22362Sweden
| | | | | | - Tim Connallon
- School of Biological SciencesMonash UniversityClaytonVIC 3800Australia
| |
Collapse
|
3
|
Connallon T, Débarre F, Li XY. Linking local adaptation with the evolution of sex differences. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0414. [PMID: 30150215 DOI: 10.1098/rstb.2017.0414] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2018] [Indexed: 01/21/2023] Open
Abstract
Many conspicuous forms of evolutionary diversity occur within species. Two prominent examples include evolutionary divergence between populations differentially adapted to their local environments (local adaptation), and divergence between females and males in response to sex differences in selection (sexual dimorphism sensu lato). These two forms of diversity have inspired vibrant research programmes, yet these fields have largely developed in isolation from one another. Nevertheless, conceptual parallels between these research traditions are striking. Opportunities for local adaptation strike a balance between local selection, which promotes divergence, and gene flow-via dispersal and interbreeding between populations-which constrains it. Sex differences are similarly constrained by fundamental features of inheritance that mimic gene flow. Offspring of each sex inherit genes from same-sex and opposite-sex parents, leading to gene flow between each differentially selected half of the population, and raising the question of how sex differences arise and are maintained. This special issue synthesizes and extends emerging research at the interface between the research traditions of local adaptation and sex differences. Each field can promote understanding of the other, and interactions between local adaptation and sex differences can generate new empirical predictions about the evolutionary consequences of selection that varies across space, time, and between the sexes.This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.
Collapse
Affiliation(s)
- Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Florence Débarre
- CNRS, UMR 7241 Centre Interdisciplinaire de Recherche en Biologie (CIRB), Collège de France, Paris, France
| | - Xiang-Yi Li
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| |
Collapse
|
4
|
Jolly A, Bayram Y, Turan S, Aycan Z, Tos T, Abali ZY, Hacihamdioglu B, Coban Akdemir ZH, Hijazi H, Bas S, Atay Z, Guran T, Abali S, Bas F, Darendeliler F, Colombo R, Barakat TS, Rinne T, White JJ, Yesil G, Gezdirici A, Gulec EY, Karaca E, Pehlivan D, Jhangiani SN, Muzny DM, Poyrazoglu S, Bereket A, Gibbs RA, Posey JE, Lupski JR. Exome Sequencing of a Primary Ovarian Insufficiency Cohort Reveals Common Molecular Etiologies for a Spectrum of Disease. J Clin Endocrinol Metab 2019; 104:3049-3067. [PMID: 31042289 PMCID: PMC6563799 DOI: 10.1210/jc.2019-00248] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/25/2019] [Indexed: 12/15/2022]
Abstract
CONTEXT Primary ovarian insufficiency (POI) encompasses a spectrum of premature menopause, including both primary and secondary amenorrhea. For 75% to 90% of individuals with hypergonadotropic hypogonadism presenting as POI, the molecular etiology is unknown. Common etiologies include chromosomal abnormalities, environmental factors, and congenital disorders affecting ovarian development and function, as well as syndromic and nonsyndromic single gene disorders suggesting POI represents a complex trait. OBJECTIVE To characterize the contribution of known disease genes to POI and identify molecular etiologies and biological underpinnings of POI. DESIGN, SETTING, AND PARTICIPANTS We applied exome sequencing (ES) and family-based genomics to 42 affected female individuals from 36 unrelated Turkish families, including 31 with reported parental consanguinity. RESULTS This analysis identified likely damaging, potentially contributing variants and molecular diagnoses in 16 families (44%), including 11 families with likely damaging variants in known genes and five families with predicted deleterious variants in disease genes (IGSF10, MND1, MRPS22, and SOHLH1) not previously associated with POI. Of the 16 families, 2 (13%) had evidence for potentially pathogenic variants at more than one locus. Absence of heterozygosity consistent with identity-by-descent mediated recessive disease burden contributes to molecular diagnosis in 15 of 16 (94%) families. GeneMatcher allowed identification of additional families from diverse genetic backgrounds. CONCLUSIONS ES analysis of a POI cohort further characterized locus heterogeneity, reaffirmed the association of genes integral to meiotic recombination, demonstrated the likely contribution of genes involved in hypothalamic development, and documented multilocus pathogenic variation suggesting the potential for oligogenic inheritance contributing to the development of POI.
Collapse
Affiliation(s)
- Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Serap Turan
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Zehra Aycan
- Department of Pediatric Endocrinology, Sami Ulus Children’s Hospital, Ankara, Turkey
| | - Tulay Tos
- Department of Medical Genetics, Sami Ulus Children’s Hospital, Ankara, Turkey
| | - Zehra Yavas Abali
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | | | | | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Serpil Bas
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Zeynep Atay
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Tulay Guran
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Saygin Abali
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Firdevs Bas
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Feyza Darendeliler
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Roberto Colombo
- Center for the Study of Rare Inherited Diseases (CeSMER), Niguarda Ca' Granda Metropolitan Hospital, Milan, Italy
- Faculty of Medicine, Catholic University, IRCCS Policlinico Gemelli University Hospital, Rome, Italy
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Gozde Yesil
- Department of Medical Genetics, Bezmialem University, Istanbul, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Ender Karaca
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | | | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Sukran Poyrazoglu
- Department of Pediatric Endocrinology, İstanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Abdullah Bereket
- Department of Pediatric Endocrinology and Diabetes, Marmara University School of Medicine, Istanbul, Turkey
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Correspondence and Reprint Requests: James R. Lupski, MD, PhD, DSc (Hon), FAAP, FACMG, FANA, FAAAS, FAAS, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, Texas 77030. E-mail: ; or Jennifer E. Posey, MD, PhD, FACMG, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room T603, Houston, Texas 77030. E-mail:
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Texas Children’s Hospital, Houston, Texas
- Correspondence and Reprint Requests: James R. Lupski, MD, PhD, DSc (Hon), FAAP, FACMG, FANA, FAAAS, FAAS, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, Texas 77030. E-mail: ; or Jennifer E. Posey, MD, PhD, FACMG, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room T603, Houston, Texas 77030. E-mail:
| |
Collapse
|
5
|
Connallon T, Hall MD. Genetic constraints on adaptation: a theoretical primer for the genomics era. Ann N Y Acad Sci 2018; 1422:65-87. [PMID: 29363779 DOI: 10.1111/nyas.13536] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/20/2017] [Accepted: 09/28/2017] [Indexed: 12/14/2022]
Abstract
Genetic constraints are features of inheritance systems that slow or prohibit adaptation. Several population genetic mechanisms of constraint have received sustained attention within the field since they were first articulated in the early 20th century. This attention is now reflected in a rich, and still growing, theoretical literature on the genetic limits to adaptive change. In turn, empirical research on constraints has seen a rapid expansion over the last two decades in response to changing interests of evolutionary biologists, along with new technologies, expanding data sets, and creative analytical approaches that blend mathematical modeling with genomics. Indeed, one of the most notable and exciting features of recent progress in genetic constraints is the close connection between theoretical and empirical research. In this review, we discuss five major population genetic contexts of genetic constraint: genetic dominance, pleiotropy, fitness trade-offs between types of individuals of a population, sign epistasis, and genetic linkage between loci. For each, we outline historical antecedents of the theory, specific contexts where constraints manifest, and their quantitative consequences for adaptation. From each of these theoretical foundations, we discuss recent empirical approaches for identifying and characterizing genetic constraints, each grounded and motivated by this theory, and outline promising areas for future work.
Collapse
Affiliation(s)
- Tim Connallon
- School of Biological Sciences, and Centre for Geometric Biology, Monash University, Clayton, Victoria, Australia
| | - Matthew D Hall
- School of Biological Sciences, and Centre for Geometric Biology, Monash University, Clayton, Victoria, Australia
| |
Collapse
|
6
|
Grieshop K, Berger D, Arnqvist G. Male-benefit sexually antagonistic genotypes show elevated vulnerability to inbreeding. BMC Evol Biol 2017; 17:134. [PMID: 28606137 PMCID: PMC5469140 DOI: 10.1186/s12862-017-0981-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/25/2017] [Indexed: 12/26/2022] Open
Abstract
Background There is theoretical and empirical evidence for strong sexual selection in males having positive effects on population viability by serving to purify the genome of its mutation load at a low demographic cost. However, there is also theoretical and empirical evidence for negative effects of sexual selection on female fitness, and therefore population viability, known as the gender load. This can take the form of sexually antagonistic (SA) genetic variation where alleles with a selective advantage in males pose a detriment to female fitness, and vice versa. Here, using seed beetles, we shed light on a previously unexplored manifestation of the gender load: the effect of SA genetic variation on tolerance to inbreeding. Results We found that genotypes encoding high male, but low female fitness exhibited significantly greater rates of extinction upon enforced inbreeding relative to genotypes encoding high female but low male fitness. Also, genotypes encoding low fitness in both sexes exhibited greater rates of extinction relative to generally high-fitness genotypes (though marginally non-significant), an expected finding attributable to variation in mutation load across genotypes. Despite follow-up investigations aiming to identify the mechanism(s) underlying these findings, it remains unclear whether the gender load and the mutation load have independent consequences for tolerance to inbreeding, or whether these two types of genetic architecture interact epistatically to render male-benefit genetic variation relatively intolerant to inbreeding. Conclusions Regardless of the underlying mechanism(s), our results show that male-benefit/female-detriment SA genetic variation poses a previously unseen detriment to population viability due to its elevated vulnerability to inbreeding/homozygosity. This suggests that sexual selection in the context of SA genetic variance for fitness may enhance the gender load on population viability more than previously appreciated, due to selecting for male-benefit SA genetic variation that engenders lineages to extinction upon inbreeding. We note that our results imply that SA alleles that are sexually selected for in males may be underrepresented or even lacking in panels of inbred lines. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0981-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Karl Grieshop
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
| | - David Berger
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Göran Arnqvist
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| |
Collapse
|