1
|
Harris M, Kim BY, Garud N. Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species. Genetics 2024; 226:iyae019. [PMID: 38366786 PMCID: PMC10990427 DOI: 10.1093/genetics/iyae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
The X chromosome, being hemizygous in males, is exposed one-third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across 6 commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.
Collapse
Affiliation(s)
- Mariana Harris
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bernard Y Kim
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Nandita Garud
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
2
|
Nunez JCB, Lenhart BA, Bangerter A, Murray CS, Mazzeo GR, Yu Y, Nystrom TL, Tern C, Erickson PA, Bergland AO. A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila. Genetics 2024; 226:iyad207. [PMID: 38051996 PMCID: PMC10847723 DOI: 10.1093/genetics/iyad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
Fluctuations in the strength and direction of natural selection through time are a ubiquitous feature of life on Earth. One evolutionary outcome of such fluctuations is adaptive tracking, wherein populations rapidly adapt from standing genetic variation. In certain circumstances, adaptive tracking can lead to the long-term maintenance of functional polymorphism despite allele frequency change due to selection. Although adaptive tracking is likely a common process, we still have a limited understanding of aspects of its genetic architecture and its strength relative to other evolutionary forces such as drift. Drosophila melanogaster living in temperate regions evolve to track seasonal fluctuations and are an excellent system to tackle these gaps in knowledge. By sequencing orchard populations collected across multiple years, we characterized the genomic signal of seasonal demography and identified that the cosmopolitan inversion In(2L)t facilitates seasonal adaptive tracking and shows molecular footprints of selection. A meta-analysis of phenotypic studies shows that seasonal loci within In(2L)t are associated with behavior, life history, physiology, and morphological traits. We identify candidate loci and experimentally link them to phenotype. Our work contributes to our general understanding of fluctuating selection and highlights the evolutionary outcome and dynamics of contemporary selection on inversions.
Collapse
Affiliation(s)
- Joaquin C B Nunez
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Vermont, 109 Carrigan Drive, Burlington, VT 05405, USA
| | - Benedict A Lenhart
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Alyssa Bangerter
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Connor S Murray
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Giovanni R Mazzeo
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Yang Yu
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Taylor L Nystrom
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Courtney Tern
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Priscilla A Erickson
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Alan O Bergland
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| |
Collapse
|
3
|
Harris M, Kim B, Garud N. Enrichment of hard sweeps on the X chromosome compared to autosomes in six Drosophila species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.21.545888. [PMID: 38106201 PMCID: PMC10723260 DOI: 10.1101/2023.06.21.545888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The X chromosome, being hemizygous in males, is exposed one third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enrichment of hard selective sweeps over soft selective sweeps on the X chromosome relative to the autosomes in a North American population of Drosophila melanogaster. To understand whether this enrichment is a universal feature of evolution on the X chromosome, we analyze diversity patterns across six commonly studied Drosophila species. We find an increased proportion of regions with steep reductions in diversity and elevated homozygosity on the X chromosome compared to autosomes. To assess if these signatures are consistent with positive selection, we simulate a wide variety of evolutionary scenarios spanning variations in demography, mutation rate, recombination rate, background selection, hard sweeps, and soft sweeps, and find that the diversity patterns observed on the X are most consistent with hard sweeps. Our findings highlight the importance of sex chromosomes in driving evolutionary processes and suggest that hard sweeps have played a significant role in shaping diversity patterns on the X chromosome across multiple Drosophila species.
Collapse
Affiliation(s)
- Mariana Harris
- Department of Computational Medicine, University of California Los Angeles, Los Angeles California, United States of America
| | - Bernard Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Nandita Garud
- Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles California, United States of America
- Department of Human Genetics, University of California, Los Angeles, California, United States of America
| |
Collapse
|
4
|
Signor S, Vedanayagam J, Kim BY, Wierzbicki F, Kofler R, Lai EC. Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species. PLoS Genet 2023; 19:e1010914. [PMID: 37643184 PMCID: PMC10495008 DOI: 10.1371/journal.pgen.1010914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/11/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Suppression of transposable elements (TEs) is paramount to maintain genomic integrity and organismal fitness. In D. melanogaster, the flamenco locus is a master suppressor of TEs, preventing the mobilization of certain endogenous retrovirus-like TEs from somatic ovarian support cells to the germline. It is transcribed by Pol II as a long (100s of kb), single-stranded, primary transcript, and metabolized into ~24-32 nt Piwi-interacting RNAs (piRNAs) that target active TEs via antisense complementarity. flamenco is thought to operate as a trap, owing to its high content of recent horizontally transferred TEs that are enriched in antisense orientation. Using newly-generated long read genome data, which is critical for accurate assembly of repetitive sequences, we find that flamenco has undergone radical transformations in sequence content and even copy number across simulans clade Drosophilid species. Drosophila simulans flamenco has duplicated and diverged, and neither copy exhibits synteny with D. melanogaster beyond the core promoter. Moreover, flamenco organization is highly variable across D. simulans individuals. Next, we find that D. simulans and D. mauritiana flamenco display signatures of a dual-stranded cluster, with ping-pong signals in the testis and/or embryo. This is accompanied by increased copy numbers of germline TEs, consistent with these regions operating as functional dual-stranded clusters. Overall, the physical and functional diversity of flamenco orthologs is testament to the extremely dynamic consequences of TE arms races on genome organization, not only amongst highly related species, but even amongst individuals.
Collapse
Affiliation(s)
- Sarah Signor
- Biological Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Jeffrey Vedanayagam
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, Texas, United States of America
| | - Bernard Y. Kim
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Eric C. Lai
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
| |
Collapse
|
5
|
A high throughput method for egg size measurement in Drosophila. Sci Rep 2023; 13:3791. [PMID: 36882448 PMCID: PMC9992389 DOI: 10.1038/s41598-023-30472-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
Life-history traits are used as proxies of fitness in insects including Drosophila. Egg size is an adaptive and ecologically important trait potentially with genetic variation across different populations. However, the low throughput of manual measurement of egg size has hampered the widespread use of this trait in evolutionary biology and population genetics. We established a method for accurate and high throughput measurement of Drosophila egg size using large particle flow cytometry (LPFC). The size estimates using LPFC are accurate and highly correlated with the manual measurements. The measurement of egg size is high throughput (average of 214 eggs measured per minute) and viable eggs of a specific size can be sorted rapidly (average of 70 eggs per minute). Sorting by LPFC does not reduce the survival of eggs making it a suitable approach for sorting eggs for downstream analyses. This protocol can be applied to any organism within the detectable size range (10-1500 µm) of the large particle flow cytometers. We discuss the potential applications of this method and provide recommendations for optimizing the protocol for other organisms.
Collapse
|
6
|
Wierzbicki F, Kofler R, Signor S. Evolutionary dynamics of piRNA clusters in Drosophila. Mol Ecol 2023; 32:1306-1322. [PMID: 34878692 DOI: 10.1111/mec.16311] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/24/2021] [Accepted: 12/01/2021] [Indexed: 12/21/2022]
Abstract
Small RNAs produced from transposable element (TE)-rich sections of the genome, termed piRNA clusters, are a crucial component in the genomic defence against selfish DNA. In animals, it is thought the invasion of a TE is stopped when a copy of the TE inserts into a piRNA cluster, triggering the production of cognate small RNAs that silence the TE. Despite this importance for TE control, little is known about the evolutionary dynamics of piRNA clusters, mostly because these repeat-rich regions are difficult to assemble and compare. Here, we establish a framework for studying the evolution of piRNA clusters quantitatively. Previously introduced quality metrics and a newly developed software for multiple alignments of repeat annotations (Manna) allow us to estimate the level of polymorphism segregating in piRNA clusters and the divergence among homologous piRNA clusters. By studying 20 conserved piRNA clusters in multiple assemblies of four Drosophila species, we show that piRNA clusters are evolving rapidly. While 70%-80% of the clusters are conserved within species, the clusters share almost no similarity between species as closely related as D. melanogaster and D. simulans. Furthermore, abundant insertions and deletions are segregating within the Drosophila species. We show that the evolution of clusters is mainly driven by large insertions of recently active TEs and smaller deletions mostly in older TEs. The effect of these forces is so rapid that homologous clusters often do not contain insertions from the same TE families.
Collapse
Affiliation(s)
- Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
| | - Sarah Signor
- Biological Sciences, North Dakota State University, Fargo, North Dakota, USA
| |
Collapse
|
7
|
Ding SD, Leitão AB, Day JP, Arunkumar R, Phillips M, Zhou SO, Jiggins FM. Trans-regulatory changes underpin the evolution of the Drosophila immune response. PLoS Genet 2022; 18:e1010453. [PMID: 36342922 PMCID: PMC9671443 DOI: 10.1371/journal.pgen.1010453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/17/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022] Open
Abstract
When an animal is infected, the expression of a large suite of genes is changed, resulting in an immune response that can defend the host. Despite much evidence that the sequence of proteins in the immune system can evolve rapidly, the evolution of gene expression is comparatively poorly understood. We therefore investigated the transcriptional response to parasitoid wasp infection in Drosophila simulans and D. sechellia. Although these species are closely related, there has been a large scale divergence in the expression of immune-responsive genes in their two main immune tissues, the fat body and hemocytes. Many genes, including those encoding molecules that directly kill pathogens, have cis regulatory changes, frequently resulting in large differences in their expression in the two species. However, these changes in cis regulation overwhelmingly affected gene expression in immune-challenged and uninfected animals alike. Divergence in the response to infection was controlled in trans. We argue that altering trans-regulatory factors, such as signalling pathways or immune modulators, may allow natural selection to alter the expression of large numbers of immune-responsive genes in a coordinated fashion.
Collapse
Affiliation(s)
| | - Alexandre B. Leitão
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Champalimaud Foundation, Lisbon, Portugal
| | - Jonathan P. Day
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ramesh Arunkumar
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Morgan Phillips
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Shuyu Olivia Zhou
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
8
|
Copy number changes in co-expressed odorant receptor genes enable selection for sensory differences in drosophilid species. Nat Ecol Evol 2022; 6:1343-1353. [PMID: 35864227 DOI: 10.1038/s41559-022-01830-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/15/2022] [Indexed: 11/09/2022]
Abstract
Despite numerous examples of chemoreceptor gene family expansions and contractions, how these relate to modifications in the sensory neuron populations in which they are expressed remains unclear. Drosophila melanogaster's odorant receptor (Or) family is ideal for addressing this question because most Ors are expressed in distinct olfactory sensory neuron (OSN) types. Between-species changes in Or copy number may therefore indicate increases or reductions in the number of OSN populations. Here we investigated the Or67a subfamily, which exhibits copy number variation in D. melanogaster and its closest relatives: D. simulans, D. sechellia and D. mauritiana. These species' common ancestor had three Or67a paralogues that had already diverged adaptively. Following speciation, two Or67a paralogues were lost independently in D. melanogaster and D. sechellia, with ongoing positive selection shaping the intact genes. Unexpectedly, the functionally diverged Or67a paralogues in D. simulans are co-expressed in a single neuron population, which projects to a glomerulus homologous to that innervated by Or67a neurons in D. melanogaster. Thus, while sensory pathway neuroanatomy is conserved, independent selection on co-expressed receptors has contributed to species-specific peripheral coding. This work reveals a type of adaptive change largely overlooked for olfactory evolution, raising the possibility that similar processes influence other cases of insect Or co-expression.
Collapse
|
9
|
Bubnell JE, Ulbing CKS, Fernandez Begne P, Aquadro CF. Functional Divergence of the bag-of-marbles Gene in the Drosophila melanogaster Species Group. Mol Biol Evol 2022; 39:6609986. [PMID: 35714266 PMCID: PMC9250105 DOI: 10.1093/molbev/msac137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In Drosophila melanogaster, a key germline stem cell (GSC) differentiation factor, bag of marbles (bam) shows rapid bursts of amino acid fixations between sibling species D. melanogaster and Drosophila simulans, but not in the outgroup species Drosophila ananassae. Here, we test the null hypothesis that bam's differentiation function is conserved between D. melanogaster and four additional Drosophila species in the melanogaster species group spanning approximately 30 million years of divergence. Surprisingly, we demonstrate that bam is not necessary for oogenesis or spermatogenesis in Drosophila teissieri nor is bam necessary for spermatogenesis in D. ananassae. Remarkably bam function may change on a relatively short time scale. We further report tests of neutral sequence evolution at bam in additional species of Drosophila and find a positive, but not perfect, correlation between evidence for positive selection at bam and its essential role in GSC regulation and fertility for both males and females. Further characterization of bam function in more divergent lineages will be necessary to distinguish between bam's critical gametogenesis role being newly derived in D. melanogaster, D. simulans, Drosophila yakuba, and D. ananassae females or it being basal to the genus and subsequently lost in numerous lineages.
Collapse
Affiliation(s)
| | - Cynthia K S Ulbing
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | | |
Collapse
|
10
|
Chang CH, Gregory LE, Gordon KE, Meiklejohn CD, Larracuente AM. Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes. eLife 2022; 11:e75795. [PMID: 34989337 PMCID: PMC8794474 DOI: 10.7554/elife.75795] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/18/2021] [Indexed: 02/06/2023] Open
Abstract
Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long-read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism contributes to the convergent evolution of Y chromosome organization across organisms.
Collapse
Affiliation(s)
- Ching-Ho Chang
- Department of Biology, University of RochesterRochesterUnited States
| | - Lauren E Gregory
- Department of Biology, University of RochesterRochesterUnited States
| | - Kathleen E Gordon
- School of Biological Sciences, University of Nebraska-LincolnLincolnUnited States
| | - Colin D Meiklejohn
- School of Biological Sciences, University of Nebraska-LincolnLincolnUnited States
| | | |
Collapse
|
11
|
Prieto-Godino LL, Schmidt HR, Benton R. Molecular reconstruction of recurrent evolutionary switching in olfactory receptor specificity. eLife 2021; 10:69732. [PMID: 34677122 PMCID: PMC8575457 DOI: 10.7554/elife.69732] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
Olfactory receptor repertoires exhibit remarkable functional diversity, but how these proteins have evolved is poorly understood. Through analysis of extant and ancestrally reconstructed drosophilid olfactory receptors from the Ionotropic receptor (Ir) family, we investigated evolution of two organic acid-sensing receptors, Ir75a and Ir75b. Despite their low amino acid identity, we identify a common ‘hotspot’ in their ligand-binding pocket that has a major effect on changing the specificity of both Irs, as well as at least two distinct functional transitions in Ir75a during evolution. Moreover, we show that odor specificity is refined by changes in additional, receptor-specific sites, including those outside the ligand-binding pocket. Our work reveals how a core, common determinant of ligand-tuning acts within epistatic and allosteric networks of substitutions to lead to functional evolution of olfactory receptors.
Collapse
Affiliation(s)
- Lucia L Prieto-Godino
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,The Francis Crick Institute, London, United Kingdom
| | - Hayden R Schmidt
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
12
|
Kim BY, Wang JR, Miller DE, Barmina O, Delaney E, Thompson A, Comeault AA, Peede D, D'Agostino ERR, Pelaez J, Aguilar JM, Haji D, Matsunaga T, Armstrong EE, Zych M, Ogawa Y, Stamenković-Radak M, Jelić M, Veselinović MS, Tanasković M, Erić P, Gao JJ, Katoh TK, Toda MJ, Watabe H, Watada M, Davis JS, Moyle LC, Manoli G, Bertolini E, Košťál V, Hawley RS, Takahashi A, Jones CD, Price DK, Whiteman N, Kopp A, Matute DR, Petrov DA. Highly contiguous assemblies of 101 drosophilid genomes. eLife 2021; 10:e66405. [PMID: 34279216 PMCID: PMC8337076 DOI: 10.7554/elife.66405] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022] Open
Abstract
Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.
Collapse
Affiliation(s)
- Bernard Y Kim
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Jeremy R Wang
- Department of Genetics, University of North CarolinaChapel HillUnited States
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s HospitalSeattleUnited States
| | - Olga Barmina
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Emily Delaney
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Ammon Thompson
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Aaron A Comeault
- School of Natural Sciences, Bangor UniversityBangorUnited Kingdom
| | - David Peede
- Biology Department, University of North CarolinaChapel HillUnited States
| | | | - Julianne Pelaez
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Jessica M Aguilar
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Diler Haji
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Teruyuki Matsunaga
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | | | - Molly Zych
- Molecular and Cellular Biology Program, University of WashingtonSeattleUnited States
| | - Yoshitaka Ogawa
- Department of Biological Sciences, Tokyo Metropolitan UniversityHachiojiJapan
| | | | - Mihailo Jelić
- Faculty of Biology, University of BelgradeBelgradeSerbia
| | | | - Marija Tanasković
- University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of SerbiaBelgradeSerbia
| | - Pavle Erić
- University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of SerbiaBelgradeSerbia
| | - Jian-Jun Gao
- School of Ecology and Environmental Science, Yunnan UniversityKunmingChina
| | - Takehiro K Katoh
- School of Ecology and Environmental Science, Yunnan UniversityKunmingChina
| | | | - Hideaki Watabe
- Biological Laboratory, Sapporo College, Hokkaido University of EducationSapporoJapan
| | - Masayoshi Watada
- Graduate School of Science and Engineering, Ehime UniversityMatsuyamaJapan
| | - Jeremy S Davis
- Department of Biology, University of KentuckyLexingtonUnited States
| | - Leonie C Moyle
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Giulia Manoli
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of WürzburgWürzburgGermany
| | - Enrico Bertolini
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of WürzburgWürzburgGermany
| | - Vladimír Košťál
- Institute of Entomology, Biology Centre, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - R Scott Hawley
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Stowers Institute for Medical ResearchKansas CityUnited States
| | - Aya Takahashi
- Department of Biological Sciences, Tokyo Metropolitan UniversityHachiojiJapan
| | - Corbin D Jones
- Biology Department, University of North CarolinaChapel HillUnited States
| | - Donald K Price
- School of Life Science, University of NevadaLas VegasUnited States
| | - Noah Whiteman
- Department of Integrative Biology, University of California, BerkeleyBerkeleyUnited States
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California DavisDavisUnited States
| | - Daniel R Matute
- Biology Department, University of North CarolinaChapel HillUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
| |
Collapse
|
13
|
Dai A, Wang Y, Greenberg A, Liufu Z, Tang T. Rapid Evolution of Autosomal Binding Sites of the Dosage Compensation Complex in Drosophila melanogaster and Its Association With Transcription Divergence. Front Genet 2021; 12:675027. [PMID: 34194473 PMCID: PMC8238462 DOI: 10.3389/fgene.2021.675027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/19/2021] [Indexed: 11/25/2022] Open
Abstract
How pleiotropy influences evolution of protein sequence remains unclear. The male-specific lethal (MSL) complex in Drosophila mediates dosage compensation by 2-fold upregulation of the X chromosome in males. Nevertheless, several MSL proteins also bind autosomes and likely perform functions not related to dosage compensation. Here, we study the evolution of MOF, MSL1, and MSL2 biding sites in Drosophila melanogaster and its close relative Drosophila simulans. We found pervasive expansion of the MSL binding sites in D. melanogaster, particularly on autosomes. The majority of these newly-bound regions are unlikely to function in dosage compensation and associated with an increase in expression divergence between D. melanogaster and D. simulans. While dosage-compensation related sites show clear signatures of adaptive evolution, these signatures are even more marked among autosomal regions. Our study points to an intriguing avenue of investigation of pleiotropy as a mechanism promoting rapid protein sequence evolution.
Collapse
Affiliation(s)
- Aimei Dai
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yushuai Wang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | | | - Zhongqi Liufu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tian Tang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
14
|
Abstract
Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus Pseudocercospora fijiensis, a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from P. fijiensis populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of P. fijiensis isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance.IMPORTANCE Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus Pseudocercospora fijiensis causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.
Collapse
|
15
|
Wallace MA, Coffman KA, Gilbert C, Ravindran S, Albery GF, Abbott J, Argyridou E, Bellosta P, Betancourt AJ, Colinet H, Eric K, Glaser-Schmitt A, Grath S, Jelic M, Kankare M, Kozeretska I, Loeschcke V, Montchamp-Moreau C, Ometto L, Onder BS, Orengo DJ, Parsch J, Pascual M, Patenkovic A, Puerma E, Ritchie MG, Rota-Stabelli O, Schou MF, Serga SV, Stamenkovic-Radak M, Tanaskovic M, Veselinovic MS, Vieira J, Vieira CP, Kapun M, Flatt T, González J, Staubach F, Obbard DJ. The discovery, distribution, and diversity of DNA viruses associated with Drosophila melanogaster in Europe. Virus Evol 2021; 7:veab031. [PMID: 34408913 PMCID: PMC8363768 DOI: 10.1093/ve/veab031] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described from the family Drosophilidae. This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of the Drosophila virome. Here, we report fourteen DNA viruses detected in a metagenomic analysis of 6668 pool-sequenced Drosophila, sampled from forty-seven European locations between 2014 and 2016. These include three new nudiviruses, a new and divergent entomopoxvirus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of galbut virus, a double-stranded RNA partitivirus, segregating at very low frequency. Remarkably, we find that Drosophila Vesanto virus, a small DNA virus previously described as a bidnavirus, may be composed of up to twelve segments and thus represent a new lineage of segmented DNA viruses. Two of the DNA viruses, Drosophila Kallithea nudivirus and Drosophila Vesanto virus are relatively common, found in 2 per cent or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly available datasets, with Drosophila Kallithea nudivirus and Drosophila Vesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses in D.melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses.
Collapse
Affiliation(s)
- Megan A Wallace
- The European Drosophila Population Genomics Consortium (DrosEU)
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Kelsey A Coffman
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Clément Gilbert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Sanjana Ravindran
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Gregory F Albery
- Department of Biology, Georgetown University, Washington, DC, USA
| | - Jessica Abbott
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Section for Evolutionary Ecology, Lund University, Sölvegatan 37, Lund 223 62, Sweden
| | - Eliza Argyridou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Paola Bellosta
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Cellular, Computational and Integrative Biology, CIBIO University of Trento, Via Sommarive 9, Trento 38123, Italy
- Department of Medicine & Endocrinology, NYU Langone Medical Center, 550 First Avenue, New York, NY 10016, USA
| | - Andrea J Betancourt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Hervé Colinet
- The European Drosophila Population Genomics Consortium (DrosEU)
- UMR CNRS 6553 ECOBIO, Université de Rennes1, Rennes, France
| | - Katarina Eric
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute for Biological Research “Sinisa Stankovic”, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia
| | - Amanda Glaser-Schmitt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Sonja Grath
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Mihailo Jelic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia
| | - Maaria Kankare
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Iryna Kozeretska
- The European Drosophila Population Genomics Consortium (DrosEU)
- National Antarctic Scientific Center of Ukraine, 16 Shevchenko Avenue, Kyiv, 01601, Ukraine
| | - Volker Loeschcke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Genetics, Ecology and Evolution, Aarhus University, Ny Munkegade 116, Aarhus C DK-8000, Denmark
| | - Catherine Montchamp-Moreau
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Lino Ometto
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy
| | - Banu Sebnem Onder
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Dorcas J Orengo
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - John Parsch
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Marta Pascual
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Aleksandra Patenkovic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute for Biological Research “Sinisa Stankovic”, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia
| | - Eva Puerma
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Michael G Ritchie
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, St Andrews University, St Andrews HY15 4SS, UK
| | - Omar Rota-Stabelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Research and Innovation Center, Fondazione E. Mach, San Michele all’Adige (TN) 38010, Italy
- Centre Agriculture Food Environment, University of Trento, San Michele all’Adige (TN) 38010, Italy
| | - Mads Fristrup Schou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Section for Evolutionary Ecology, Lund University, Sölvegatan 37, Lund 223 62, Sweden
- Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Svitlana V Serga
- The European Drosophila Population Genomics Consortium (DrosEU)
- National Antarctic Scientific Center of Ukraine, 16 Shevchenko Avenue, Kyiv, 01601, Ukraine
- Taras Shevchenko National University of Kyiv, 64 Volodymyrska str, Kyiv 01601, Ukraine
| | - Marina Stamenkovic-Radak
- The European Drosophila Population Genomics Consortium (DrosEU)
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia
| | - Marija Tanaskovic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute for Biological Research “Sinisa Stankovic”, National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia
| | - Marija Savic Veselinovic
- The European Drosophila Population Genomics Consortium (DrosEU)
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, Serbia
| | - Jorge Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, i3S, Porto, Portugal
| | - Cristina P Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, i3S, Porto, Portugal
| | - Martin Kapun
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Division of Cell & Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Thomas Flatt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Fribourg, Fribourg CH-1700, Switzerland
| | - Josefa González
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Fabian Staubach
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolution and Ecology, University of Freiburg, Freiburg 79104, Germany
| | - Darren J Obbard
- The European Drosophila Population Genomics Consortium (DrosEU)
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| |
Collapse
|
16
|
Ellison CE, Kagda MS, Cao W. Telomeric TART elements target the piRNA machinery in Drosophila. PLoS Biol 2020; 18:e3000689. [PMID: 33347429 PMCID: PMC7785250 DOI: 10.1371/journal.pbio.3000689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 01/05/2021] [Accepted: 12/10/2020] [Indexed: 11/23/2022] Open
Abstract
Coevolution between transposable elements (TEs) and their hosts can be antagonistic, where TEs evolve to avoid silencing and the host responds by reestablishing TE suppression, or mutualistic, where TEs are co-opted to benefit their host. The TART-A TE functions as an important component of Drosophila telomeres but has also reportedly inserted into the Drosophila melanogaster nuclear export factor gene nxf2. We find that, rather than inserting into nxf2, TART-A has actually captured a portion of nxf2 sequence. We show that TART-A produces abundant Piwi-interacting small RNAs (piRNAs), some of which are antisense to the nxf2 transcript, and that the TART-like region of nxf2 is evolving rapidly. Furthermore, in D. melanogaster, TART-A is present at higher copy numbers, and nxf2 shows reduced expression, compared to the closely related species Drosophila simulans. We propose that capturing nxf2 sequence allowed TART-A to target the nxf2 gene for piRNA-mediated repression and that these 2 elements are engaged in antagonistic coevolution despite the fact that TART-A is serving a critical role for its host genome. Co-evolution between transposable elements (TEs) and their hosts can be antagonistic, where TEs evolve to avoid silencing and the host responds by re-establishing TE suppression, or mutualistic, where TEs are co-opted to benefit their host. This study shows that a specialized Drosophila retrotransposon that functions as a telomere has captured a portion of a host piRNA gene which may allow it to evade silencing.
Collapse
Affiliation(s)
- Christopher E. Ellison
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
- * E-mail:
| | - Meenakshi S. Kagda
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Weihuan Cao
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| |
Collapse
|
17
|
Langmüller AM, Nolte V, Galagedara R, Poupardin R, Dolezal M, Schlötterer C. Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature. BMC Biol 2020; 18:157. [PMID: 33121485 PMCID: PMC7597021 DOI: 10.1186/s12915-020-00882-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/28/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Insect pest control programs often use periods of insecticide treatment with intermittent breaks, to prevent fixing of mutations conferring insecticide resistance. Such mutations are typically costly in an insecticide-free environment, and their frequency is determined by the balance between insecticide treatment and cost of resistance. Ace, a key gene in neuronal signaling, is a prominent target of many insecticides and across several species, three amino acid replacements (I161V, G265A, and F330Y) provide resistance against several insecticides. Because temperature disturbs neuronal signaling homeostasis, we reasoned that the cost of insecticide resistance could be modulated by ambient temperature. RESULTS Experimental evolution of a natural Drosophila simulans population at hot and cold temperature regimes uncovered a surprisingly strong effect of ambient temperature. In the cold temperature regime, the resistance mutations were strongly counter selected (s = - 0.055), but in a hot environment, the fitness costs of resistance mutations were reduced by almost 50% (s = - 0.031). We attribute this unexpected observation to the advantage of the reduced enzymatic activity of resistance mutations in hot environments. CONCLUSION We show that fitness costs of insecticide resistance genes are temperature-dependent and suggest that the duration of insecticide-free periods need to be adjusted for different climatic regions to reflect these costs. We suggest that such environment-dependent fitness effects may be more common than previously assumed and pose a major challenge for modeling climate change.
Collapse
Affiliation(s)
- Anna Maria Langmüller
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Ruwansha Galagedara
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Rodolphe Poupardin
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
- Present Address: Paracelsus Medical University Salzburg, Strubergasse 21, 5020, Salzburg, Austria
| | - Marlies Dolezal
- Plattform Bioinformatik und Biostatistik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.
| |
Collapse
|
18
|
Signor SA. Evolution of Plasticity in Response to Ethanol between Sister Species with Different Ecological Histories ( Drosophila melanogaster and D. simulans). Am Nat 2020; 196:620-633. [PMID: 33064591 DOI: 10.1086/710763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractWhen populations evolve adaptive reaction norms in response to novel environments, it can occur through a process termed genetic accommodation. Under this model, the initial response to the environment is widely variable between genotypes as a result of cryptic genetic variation, which is then refined by selection to a single adaptive response. Here, I empirically test these predictions from genetic accommodation by measuring reaction norms in individual genotypes and across several time points. I compare two species of Drosophila that differ in their adaptation to ethanol (D. melanogaster and D. simulans). Both species are human commensals with a recent cosmopolitan expansion, but only D. melanogaster is adapted to ethanol exposure. Using gene expression as a phenotype and an approach that combines information about expression and alternative splicing, I find that D. simulans exhibits cryptic genetic variation in the response to ethanol, while D. melanogaster has almost no genotype-specific variation in reaction norm. This is evidence for adaptation to ethanol through genetic accommodation, suggesting that the evolution of phenotypic plasticity could be an important contributor to the ability to exploit novel resources.
Collapse
|
19
|
Buffalo V, Coop G. Estimating the genome-wide contribution of selection to temporal allele frequency change. Proc Natl Acad Sci U S A 2020; 117:20672-20680. [PMID: 32817464 PMCID: PMC7456072 DOI: 10.1073/pnas.1919039117] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rapid phenotypic adaptation is often observed in natural populations and selection experiments. However, detecting the genome-wide impact of this selection is difficult since adaptation often proceeds from standing variation and selection on polygenic traits, both of which may leave faint genomic signals indistinguishable from a noisy background of genetic drift. One promising signal comes from the genome-wide covariance between allele frequency changes observable from temporal genomic data (e.g., evolve-and-resequence studies). These temporal covariances reflect how heritable fitness variation in the population leads changes in allele frequencies at one time point to be predictive of the changes at later time points, as alleles are indirectly selected due to remaining associations with selected alleles. Since genetic drift does not lead to temporal covariance, we can use these covariances to estimate what fraction of the variation in allele frequency change through time is driven by linked selection. Here, we reanalyze three selection experiments to quantify the effects of linked selection over short timescales using covariance among time points and across replicates. We estimate that at least 17 to 37% of allele frequency change is driven by selection in these experiments. Against this background of positive genome-wide temporal covariances, we also identify signals of negative temporal covariance corresponding to reversals in the direction of selection for a reasonable proportion of loci over the time course of a selection experiment. Overall, we find that in the three studies we analyzed, linked selection has a large impact on short-term allele frequency dynamics that is readily distinguishable from genetic drift.
Collapse
Affiliation(s)
- Vince Buffalo
- Population Biology Graduate Group, University of California, Davis, CA 95616;
- Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, CA 95616
| | - Graham Coop
- Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, CA 95616
| |
Collapse
|
20
|
Godinho DP, Cruz MA, Charlery de la Masselière M, Teodoro‐Paulo J, Eira C, Fragata I, Rodrigues LR, Zélé F, Magalhães S. Creating outbred and inbred populations in haplodiploids to measure adaptive responses in the laboratory. Ecol Evol 2020; 10:7291-7305. [PMID: 32760529 PMCID: PMC7391545 DOI: 10.1002/ece3.6454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Laboratory studies are often criticized for not being representative of processes occurring in natural populations. One reason for this is the fact that laboratory populations generally do not capture enough of the genetic variation of natural populations. This can be mitigated by mixing the genetic background of several field populations when creating laboratory populations. From these outbred populations, it is possible to generate inbred lines, thereby freezing and partitioning part of their variability, allowing each genotype to be characterized independently. Many studies addressing adaptation of organisms to their environment, such as those involving quantitative genetics or experimental evolution, rely on inbred or outbred populations, but the methodology underlying the generation of such biological resources is usually not explicitly documented. Here, we developed different procedures to circumvent common pitfalls of laboratory studies, and illustrate their application using two haplodiploid species, the spider mites Tetranychus urticae and Tetranychus evansi. First, we present a method that increases the chance of capturing high amounts of variability when creating outbred populations, by performing controlled crosses between individuals from different field-collected populations. Second, we depict the creation of inbred lines derived from such outbred populations, by performing several generations of sib-mating. Third, we outline an experimental evolution protocol that allows the maintenance of a constant population size at the beginning of each generation, thereby preventing bottlenecks and diminishing extinction risks. Finally, we discuss the advantages of these procedures and emphasize that sharing such biological resources and combining them with available genetic tools will allow consistent and comparable studies that greatly contribute to our understanding of ecological and evolutionary processes.
Collapse
Affiliation(s)
- Diogo P. Godinho
- Centre for Ecology, Evolution and Environmental Changes – cE3cFaculdade de Ciências da Universidade de LisboaLisboaPortugal
| | - Miguel A. Cruz
- Centre for Ecology, Evolution and Environmental Changes – cE3cFaculdade de Ciências da Universidade de LisboaLisboaPortugal
| | - Maud Charlery de la Masselière
- Centre for Ecology, Evolution and Environmental Changes – cE3cFaculdade de Ciências da Universidade de LisboaLisboaPortugal
| | - Jéssica Teodoro‐Paulo
- Centre for Ecology, Evolution and Environmental Changes – cE3cFaculdade de Ciências da Universidade de LisboaLisboaPortugal
| | - Cátia Eira
- Centre for Ecology, Evolution and Environmental Changes – cE3cFaculdade de Ciências da Universidade de LisboaLisboaPortugal
| | - Inês Fragata
- Centre for Ecology, Evolution and Environmental Changes – cE3cFaculdade de Ciências da Universidade de LisboaLisboaPortugal
| | - Leonor R. Rodrigues
- Centre for Ecology, Evolution and Environmental Changes – cE3cFaculdade de Ciências da Universidade de LisboaLisboaPortugal
| | - Flore Zélé
- Centre for Ecology, Evolution and Environmental Changes – cE3cFaculdade de Ciências da Universidade de LisboaLisboaPortugal
| | - Sara Magalhães
- Centre for Ecology, Evolution and Environmental Changes – cE3cFaculdade de Ciências da Universidade de LisboaLisboaPortugal
| |
Collapse
|
21
|
Signor S. Transposable elements in individual genotypes of Drosophila simulans. Ecol Evol 2020; 10:3402-3412. [PMID: 32273997 PMCID: PMC7141027 DOI: 10.1002/ece3.6134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/25/2020] [Accepted: 02/04/2020] [Indexed: 11/17/2022] Open
Abstract
Transposable elements are abundant, dynamic components of the genome that affect organismal phenotypes and fitness. In Drosophila melanogaster, they have increased in abundance as the species spread out of Africa, and different populations differ in their transposable element content. However, very little is currently known about how transposable elements differ between individual genotypes, and how that relates to the population dynamics of transposable elements overall. The sister species of D. melanogaster, D. simulans, has also recently become cosmopolitan, and panels of inbred genotypes exist from cosmopolitan and African flies. Therefore, we can determine whether the differences in colonizing populations are repeated in D. simulans, what the dynamics of transposable elements are in individual genotypes, and how that compares to wild flies. After estimating copy number in cosmopolitan and African D. simulans, I find that transposable element load is higher in flies from cosmopolitan populations. In addition, transposable element load varies considerably between populations, between genotypes, but not overall between wild and inbred lines. Certain genotypes either contain active transposable elements or are more permissive of transposition and accumulate copies of particular transposable elements. Overall, it is important to quantify genotype-specific transposable element dynamics as well as population averages to understand the dynamics of transposable element accumulation over time.
Collapse
Affiliation(s)
- Sarah Signor
- Department of Biological SciencesNorth Dakota State UniversityFargoNDUSA
| |
Collapse
|
22
|
Auer TO, Khallaf MA, Silbering AF, Zappia G, Ellis K, Álvarez-Ocaña R, Arguello JR, Hansson BS, Jefferis GSXE, Caron SJC, Knaden M, Benton R. Olfactory receptor and circuit evolution promote host specialization. Nature 2020. [PMID: 32132713 DOI: 10.1038/s41586-020–2073-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The evolution of animal behaviour is poorly understood1,2. Despite numerous correlations between interspecific divergence in behaviour and nervous system structure and function, demonstrations of the genetic basis of these behavioural differences remain rare3-5. Here we develop a neurogenetic model, Drosophila sechellia, a species that displays marked differences in behaviour compared to its close cousin Drosophila melanogaster6,7, which are linked to its extreme specialization on noni fruit (Morinda citrifolia)8-16. Using calcium imaging, we identify olfactory pathways in D. sechellia that detect volatiles emitted by the noni host. Our mutational analysis indicates roles for different olfactory receptors in long- and short-range attraction to noni, and our cross-species allele-transfer experiments demonstrate that the tuning of one of these receptors is important for species-specific host-seeking. We identify the molecular determinants of this functional change, and characterize their evolutionary origin and behavioural importance. We perform circuit tracing in the D. sechellia brain, and find that receptor adaptations are accompanied by increased sensory pooling onto interneurons as well as species-specific central projection patterns. This work reveals an accumulation of molecular, physiological and anatomical traits that are linked to behavioural divergence between species, and defines a model for investigating speciation and the evolution of the nervous system.
Collapse
Affiliation(s)
- Thomas O Auer
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| | - Mohammed A Khallaf
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ana F Silbering
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Giovanna Zappia
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Kaitlyn Ellis
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Raquel Álvarez-Ocaña
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - J Roman Arguello
- Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Bill S Hansson
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Sophie J C Caron
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Markus Knaden
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
23
|
Auer TO, Khallaf MA, Silbering AF, Zappia G, Ellis K, Álvarez-Ocaña R, Arguello JR, Hansson BS, Jefferis GSXE, Caron SJC, Knaden M, Benton R. Olfactory receptor and circuit evolution promote host specialization. Nature 2020; 579:402-408. [PMID: 32132713 PMCID: PMC7100913 DOI: 10.1038/s41586-020-2073-7] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 01/31/2020] [Indexed: 11/09/2022]
Abstract
The evolution of animal behaviour is poorly understood1,2. Despite numerous correlations of behavioural and nervous system divergence, demonstration of the genetic basis of interspecific behavioural differences remains rare3–5. Here, we develop a novel neurogenetic model, Drosophila sechellia, a close cousin of D. melanogaster6,7 that displays profound behavioural changes linked to its extreme specialisation on noni fruit8–16. Using calcium imaging, we identify D. sechellia olfactory pathways detecting host volatiles. Mutational analysis indicates roles for different olfactory receptors in long- and short-range attraction to noni. Cross-species allele transfer demonstrates that tuning of one of these receptors is important for species-specific host-seeking. We identify the molecular determinants of this functional change, and characterise their evolutionary origin and behavioural significance. Through circuit tracing in the D. sechellia brain, we find that receptor adaptations are accompanied by increased sensory pooling onto interneurons and novel central projection patterns. This work reveals the accumulation of molecular, physiological and anatomical traits linked to behavioural divergence, and defines a powerful model for investigating nervous system evolution and speciation.
Collapse
Affiliation(s)
- Thomas O Auer
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| | - Mohammed A Khallaf
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ana F Silbering
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Giovanna Zappia
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Kaitlyn Ellis
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Raquel Álvarez-Ocaña
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - J Roman Arguello
- Department of Ecology and Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Bill S Hansson
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Sophie J C Caron
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Markus Knaden
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| |
Collapse
|
24
|
Ruzicka F, Hill MS, Pennell TM, Flis I, Ingleby FC, Mott R, Fowler K, Morrow EH, Reuter M. Genome-wide sexually antagonistic variants reveal long-standing constraints on sexual dimorphism in fruit flies. PLoS Biol 2019; 17:e3000244. [PMID: 31022179 PMCID: PMC6504117 DOI: 10.1371/journal.pbio.3000244] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/07/2019] [Accepted: 04/09/2019] [Indexed: 01/02/2023] Open
Abstract
The evolution of sexual dimorphism is constrained by a shared genome, leading to ‘sexual antagonism’, in which different alleles at given loci are favoured by selection in males and females. Despite its wide taxonomic incidence, we know little about the identity, genomic location, and evolutionary dynamics of antagonistic genetic variants. To address these deficits, we use sex-specific fitness data from 202 fully sequenced hemiclonal Drosophila melanogaster fly lines to perform a genome-wide association study (GWAS) of sexual antagonism. We identify approximately 230 chromosomal clusters of candidate antagonistic single nucleotide polymorphisms (SNPs). In contradiction to classic theory, we find no clear evidence that the X chromosome is a hot spot for sexually antagonistic variation. Characterising antagonistic SNPs functionally, we find a large excess of missense variants but little enrichment in terms of gene function. We also assess the evolutionary persistence of antagonistic variants by examining extant polymorphism in wild D. melanogaster populations and closely related species. Remarkably, antagonistic variants are associated with multiple signatures of balancing selection across the D. melanogaster distribution range and in their sister species D. simulans, indicating widespread and evolutionarily persistent (about 1 million years) genomic constraints on the evolution of sexual dimorphism. Based on our results, we propose that antagonistic variation accumulates because of constraints on the resolution of sexual conflict over protein coding sequences, thus contributing to the long-term maintenance of heritable fitness variation. This study characterises antagonistic loci across the genome of the fruit fly Drosophila melanogaster, finding them to be preferentially associated with variation in coding sequences and to be selectively maintained across worldwide populations of D. melanogaster, and even its sister species D. simulans.
Collapse
Affiliation(s)
- Filip Ruzicka
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Mark S. Hill
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- Department of Ecology and Evolutionary Biology, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tanya M. Pennell
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Ilona Flis
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Fiona C. Ingleby
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Richard Mott
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Kevin Fowler
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Edward H. Morrow
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
- * E-mail: (MR); (EHM)
| | - Max Reuter
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- * E-mail: (MR); (EHM)
| |
Collapse
|
25
|
Kelly JK, Hughes KA. Pervasive Linked Selection and Intermediate-Frequency Alleles Are Implicated in an Evolve-and-Resequencing Experiment of Drosophila simulans. Genetics 2019; 211:943-961. [PMID: 30593495 PMCID: PMC6404262 DOI: 10.1534/genetics.118.301824] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 12/15/2018] [Indexed: 11/18/2022] Open
Abstract
We develop analytical and simulation tools for evolve-and-resequencing experiments and apply them to a new study of rapid evolution in Drosophila simulans Likelihood test statistics applied to pooled population sequencing data suggest parallel evolution of 138 SNPs across the genome. This number is reduced by orders of magnitude from previous studies (thousands or tens of thousands), owing to differences in both experimental design and statistical analysis. Whole genome simulations calibrated from Drosophila genetic data sets indicate that major features of the genome-wide response could be explained by as few as 30 loci under strong directional selection with a corresponding hitchhiking effect. Smaller effect loci are likely also responding, but are below the detection limit of the experiment. Finally, SNPs showing strong parallel evolution in the experiment are intermediate in frequency in the natural population (usually 30-70%) indicative of balancing selection in nature. These loci also exhibit elevated differentiation among natural populations of D. simulans, suggesting environmental heterogeneity as a potential balancing mechanism.
Collapse
Affiliation(s)
- John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045
| | - Kimberly A Hughes
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| |
Collapse
|
26
|
Ali S, Signor SA, Kozlov K, Nuzhdin SV. Novel approach to quantitative spatial gene expression uncovers genetic stochasticity in the developing Drosophila eye. Evol Dev 2019; 21:157-171. [PMID: 30756455 DOI: 10.1111/ede.12283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Robustness in development allows for the accumulation of genetically based variation in expression. However, this variation is usually examined in response to large perturbations, and examination of this variation has been limited to being spatial, or quantitative, but because of technical restrictions not both. Here we bridge these gaps by investigating replicated quantitative spatial gene expression using rigorous statistical models, in different genotypes, sexes, and species (Drosophila melanogaster and D. simulans). Using this type of quantitative approach with molecular developmental data allows for comparison among conditions, such as different genetic backgrounds. We apply this approach to the morphogenetic furrow, a wave of differentiation that patterns the developing eye disc. Within the morphogenetic furrow, we focus on four genes, hairy, atonal, hedgehog, and Delta. Hybridization chain reaction quantitatively measures spatial gene expression, co-staining for all four genes simultaneously. We find considerable variation in the spatial expression pattern of these genes in the eye between species, genotypes, and sexes. We also find that there has been evolution of the regulatory relationship between these genes, and that their spatial interrelationships have evolved between species. This variation has no phenotypic effect, and could be buffered by network thresholds or compensation from other genes. Both of these mechanisms could potentially be contributing to long term developmental systems drift.
Collapse
Affiliation(s)
- Sammi Ali
- Molecular and Computational Biology, University of Southern California, Los Angeles, California
| | - Sarah A Signor
- Molecular and Computational Biology, University of Southern California, Los Angeles, California
| | - Konstantin Kozlov
- Department of Applied Mathematics, St. Petersburg State Polytechnic University, St. Petersburg, Russia
| | - Sergey V Nuzhdin
- Molecular and Computational Biology, University of Southern California, Los Angeles, California.,Department of Applied Mathematics, St. Petersburg State Polytechnic University, St. Petersburg, Russia
| |
Collapse
|
27
|
Guirao-Rico S, González J. Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster. CURRENT OPINION IN INSECT SCIENCE 2019; 31:70-76. [PMID: 31109676 DOI: 10.1016/j.cois.2018.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/04/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
Drosophila melanogaster has long been used as an evolutionary model system. Its small genome size, well-annotated genome, and ease of sampling, also makes it a choice species for genome resequencing studies. Hundreds of genomic samples from populations worldwide are available and are currently being used to tackle a wide range of evolutionary questions. In this review, we focused on three insights that have increased our understanding of the evolutionary history of this species, and that have implications for the study of evolutionary processes in other species as well. Because of technical limitations, most of the studies so far have focused on SNP variants. However, long-read sequencing techniques should allow us in the near future to include other type of genomic variants that also influence genome evolution.
Collapse
Affiliation(s)
- Sara Guirao-Rico
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
| |
Collapse
|
28
|
Robin C, Battlay P, Fournier-Level A. What can genetic association panels tell us about evolutionary processes in insects? CURRENT OPINION IN INSECT SCIENCE 2019; 31:99-105. [PMID: 31109681 DOI: 10.1016/j.cois.2018.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
If we are to fully comprehend the evolution of insect diversity at a genomic level we need to understand how natural selection can alter genetically encoded characters within populations. Genetic association panels have the potential to be standard bearers in this endeavour. They enable the mapping of phenotypes to genotypes at unprecedented resolution while simultaneously providing population genomic samples that can be interrogated for the tell-tale signs of selection. Analyses of these panels promise to elucidate the entanglement of gene ontologies, pathways, developmental processes and evolutionary constraints, and inform how these are shaped by adaptation.
Collapse
Affiliation(s)
- Charles Robin
- The School of BioSciences, The University of Melbourne, Parkville 3010, Australia.
| | - Paul Battlay
- The School of BioSciences, The University of Melbourne, Parkville 3010, Australia
| | | |
Collapse
|
29
|
Structural Variants and Selective Sweep Foci Contribute to Insecticide Resistance in the Drosophila Genetic Reference Panel. G3-GENES GENOMES GENETICS 2018; 8:3489-3497. [PMID: 30190421 PMCID: PMC6222580 DOI: 10.1534/g3.118.200619] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Patterns of nucleotide polymorphism within populations of Drosophila melanogaster suggest that insecticides have been the selective agents driving the strongest recent bouts of positive selection. However, there is a need to explicitly link selective sweeps to the particular insecticide phenotypes that could plausibly account for the drastic selective responses that are observed in these non-target insects. Here, we screen the Drosophila Genetic Reference Panel with two common insecticides; malathion (an organophosphate) and permethrin (a pyrethroid). Genome-wide association studies map survival on malathion to two of the largest sweeps in the D. melanogaster genome; Ace and Cyp6g1. Malathion survivorship also correlates with lines which have high levels of Cyp12d1, Jheh1 and Jheh2 transcript abundance. Permethrin phenotypes map to the largest cluster of P450 genes in the Drosophila genome, however in contrast to a selective sweep driven by insecticide use, the derived allele seems to be associated with susceptibility. These results underscore previous findings that highlight the importance of structural variation to insecticide phenotypes: Cyp6g1 exhibits copy number variation and transposable element insertions, Cyp12d1 is tandemly duplicated, the Jheh loci are associated with a Bari1 transposable element insertion, and a Cyp6a17 deletion is associated with susceptibility.
Collapse
|
30
|
Signor S. Population genomics of Wolbachia and mtDNA in Drosophila simulans from California. Sci Rep 2017; 7:13369. [PMID: 29042606 PMCID: PMC5645465 DOI: 10.1038/s41598-017-13901-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/02/2017] [Indexed: 12/21/2022] Open
Abstract
Wolbachia pipientis is an intracellular endosymbiont infecting many arthropods and filarial nematodes. Little is known about the short-term evolution of Wolbachia or its interaction with its host. Wolbachia is maternally inherited, resulting in co-inheritance of mitochondrial organelles such as mtDNA. Here I explore the evolution of Wolbachia, and the relationship between Wolbachia and mtDNA, using a large inbred panel of Drosophila simulans. I compare this to the only other large population genomic Wolbachia dataset from D. melanogaster. I find reduced diversity relative to expectation in both Wolbachia and mtDNA, but only mtDNA shows evidence of a recent selective sweep or population bottleneck. I estimate Wolbachia and mtDNA titre in each genotype, and I find considerable variation in both phenotypes, despite low genetic diversity in Wolbachia and mtDNA. A phylogeny of Wolbachia and of mtDNA suggest a recent origin of the infection derived from a single origin. Using Wolbachia and mtDNA titre as a phenotype, I perform the first association analysis using this phenotype with the nuclear genome and find several implicated regions, including one which contains four CAAX-box protein processing genes. CAAX-box protein processing can be an important part of host-pathogen interactions in other systems, suggesting interesting directions for future research.
Collapse
Affiliation(s)
- Sarah Signor
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
| |
Collapse
|