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Rice G, Gaitan-Escudero T, Charles-Obi K, Zeitlinger J, Rebeiz M. Gene regulatory network co-option is sufficient to induce a morphological novelty in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.584840. [PMID: 38585823 PMCID: PMC10996490 DOI: 10.1101/2024.03.22.584840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Identifying the molecular origins by which new morphological structures evolve is one of the long standing problems in evolutionary biology. To date, vanishingly few examples provide a compelling account of how new morphologies were initially formed, thereby limiting our understanding of how diverse forms of life derived their complex features. Here, we provide evidence that the large projections on the Drosophila eugracilis phallus that are implicated in sexual conflict have evolved through co-option of the trichome genetic network. These unicellular apical projections on the phallus postgonal sheath are reminiscent of trichomes that cover the Drosophila body but are up to 20-fold larger in size. During their development, they express the transcription factor Shavenbaby, the master regulator of the trichome network. Consistent with the co-option of the Shavenbaby network during the evolution of the D. eugracilis projections, somatic mosaic CRISPR/Cas9 mutagenesis shows that shavenbaby is necessary for their proper length. Moreover, mis-expression of Shavenbaby in the sheath of D. melanogaster , a naïve species that lacks these extensions, is sufficient to induce small trichomes. These induced extensions rely on a genetic network that is shared to a large extent with the D. eugracilis projections, indicating its co-option but also some genetic rewiring. Thus, by leveraging a genetically tractable evolutionarily novelty, our work shows that the trichome-forming network is flexible enough that it can be co-opted in a new context, and subsequently refined to produce unique apical projections that are barely recognizable compared to their simpler ancestral beginnings.
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2
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Gleason JM, Danborno B, Nigro M, Escobar H, Cobbs MJ. Mating dynamics of a sperm-limited drosophilid, Zaprionus indianus. PLoS One 2024; 19:e0300426. [PMID: 38526998 PMCID: PMC10962835 DOI: 10.1371/journal.pone.0300426] [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: 09/14/2023] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
When males have large sperm, they may become sperm limited and mating dynamics may be affected. One such species is Zaprionus indianus, a drosophilid that is an introduced pest species in the Americas. We examined aspects of mating behavior in Z. indianus to determine the senses necessary for mating and measure female and male remating habits. We found that vision is necessary for successful copulation, but wings, which produce courtship song, are not needed. Males need their foretarsi to successfully copulate and although the foretarsi may be needed for chemoreception, their role in hanging on to the female during copulation may be more important for successful mating. Females that mate once run out of sperm in approximately five days, although mating a second time greatly increases offspring production. Females do not seem to exert pre-mating choice among males with respect to mating with a familiar versus a novel male. Males are not capable of mating continuously and fail to produce offspring in many copulations. Overall, females of this species benefit from polyandry, providing an opportunity to study sexual selection in females. In addition, the dynamics of male competition for fertilizing eggs needs to be studied.
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Affiliation(s)
- Jennifer M. Gleason
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Barnabas Danborno
- Department of Anatomy, Faculty of Basic Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Marena Nigro
- Undergraduate Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Henry Escobar
- Undergraduate Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Micalea J. Cobbs
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
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3
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Seto Y, Iwasaki Y, Ogawa Y, Tamura K, Toda MJ. Skeleton phylogeny reconstructed with transcriptomes for the tribe Drosophilini (Diptera: Drosophilidae). Mol Phylogenet Evol 2024; 191:107978. [PMID: 38013068 DOI: 10.1016/j.ympev.2023.107978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 10/30/2023] [Accepted: 11/23/2023] [Indexed: 11/29/2023]
Abstract
The family Drosophilidae is one of the most important model systems in evolutionary biology. Thanks to advances in high-throughput sequencing technology, a number of molecular phylogenetic analyses have been undertaken by using large data sets of many genes and many species sampled across this family. Especially, recent analyses using genome sequences have depicted the family-wide skeleton phylogeny with high confidence. However, the taxon sampling is still insufficient for minor lineages and non-Drosophila genera. In this study, we carried out phylogenetic analyses using a large number of transcriptome-based nucleotide sequences, focusing on the largest, core tribe Drosophilini in the Drosophilidae. In our analyses, some noise factors against phylogenetic reconstruction were taken into account by removing putative paralogy from the datasets and examining the effects of missing data, i.e. gene occupancy and site coverage, and incomplete lineage sorting. The inferred phylogeny has newly resolved the following phylogenetic positions/relationships at the genomic scale: (i) the monophyly of the subgenus Siphlodora including Zaprionus flavofasciatus to be transferred therein; (ii) the paraphyly of the robusta and melanica species groups within a clade comprised of the robusta, melanica and quadrisetata groups and Z. flavofasciatus; (iii) Drosophila curviceps (representing the curviceps group), D. annulipes (the quadrilineata subgroup of the immigrans group) and D. maculinotata clustered into a clade sister to the Idiomyia + Scaptomyza clade, forming together the expanded Hawaiian drosophilid lineage; (iv) Dichaetophora tenuicauda (representing the lineage comprised of the Zygothrica genus group and Dichaetophora) placed as the sister to the clade of the expanded Hawaiian drosophilid lineage and Siphlodora; and (v) relationships of the subgenus Drosophila and the genus Zaprionus as follows: (Zaprionus, (the quadrilineata subgroup, ((D. sternopleuralis, the immigrans group proper), (the quinaria radiation, the tripunctata radiation)))). These results are to be incorporated into the so-far published phylogenomic tree as a backbone (constraint) tree for grafting much more species based on sequences of a limited number of genes. Such a comprehensive, highly confident phylogenetic tree with extensive and dense taxon sampling will provide an essential framework for comparative studies of the Drosophilidae.
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Affiliation(s)
- Yosuke Seto
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan; Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
| | - Yuma Iwasaki
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan.
| | - Yoshitaka Ogawa
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan.
| | - Koichiro Tamura
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan; Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan.
| | - Masanori J Toda
- Hokkaido University Museum, Hokkaido University, Sapporo, Japan.
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4
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Hopkins BR, Angus-Henry A, Kim BY, Carlisle JA, Thompson A, Kopp A. Decoupled evolution of the Sex Peptide gene family and Sex Peptide Receptor in Drosophilidae. Proc Natl Acad Sci U S A 2024; 121:e2312380120. [PMID: 38215185 PMCID: PMC10801855 DOI: 10.1073/pnas.2312380120] [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: 07/31/2023] [Accepted: 11/16/2023] [Indexed: 01/14/2024] Open
Abstract
Across internally fertilising species, males transfer ejaculate proteins that trigger wide-ranging changes in female behaviour and physiology. Much theory has been developed to explore the drivers of ejaculate protein evolution. The accelerating availability of high-quality genomes now allows us to test how these proteins are evolving at fine taxonomic scales. Here, we use genomes from 264 species to chart the evolutionary history of Sex Peptide (SP), a potent regulator of female post-mating responses in Drosophila melanogaster. We infer that SP first evolved in the Drosophilinae subfamily and has since followed markedly different evolutionary trajectories in different lineages. Outside of the Sophophora-Lordiphosa, SP exists largely as a single-copy gene with independent losses in several lineages. Within the Sophophora-Lordiphosa, the SP gene family has repeatedly and independently expanded. Up to seven copies, collectively displaying extensive sequence variation, are present in some species. Despite these changes, SP expression remains restricted to the male reproductive tract. Alongside, we document considerable interspecific variation in the presence and morphology of seminal microcarriers that, despite the critical role SP plays in microcarrier assembly in D. melanogaster, appears to be independent of changes in the presence/absence or sequence of SP. We end by providing evidence that SP's evolution is decoupled from that of its receptor, Sex Peptide Receptor, in which we detect no evidence of correlated diversifying selection. Collectively, our work describes the divergent evolutionary trajectories that a novel gene has taken following its origin and finds a surprisingly weak coevolutionary signal between a supposedly sexually antagonistic protein and its receptor.
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Affiliation(s)
- Ben R. Hopkins
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Aidan Angus-Henry
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Bernard Y. Kim
- Department of Biology, Stanford University, Stanford, CA94305
| | - Jolie A. Carlisle
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
| | - Ammon Thompson
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California, Davis, CA95616
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5
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Erlenbach T, Haynes L, Fish O, Beveridge J, Giambrone S, Reed LK, Dyer KA, Scott Chialvo CH. Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila. Ecol Evol 2023; 13:e10736. [PMID: 38099137 PMCID: PMC10719611 DOI: 10.1002/ece3.10736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 12/17/2023] Open
Abstract
Understanding how and when key novel adaptations evolved is a central goal of evolutionary biology. Within the immigrans-tripunctata radiation of Drosophila, many mushroom-feeding species are tolerant of host toxins, such as cyclopeptides, that are lethal to nearly all other eukaryotes. In this study, we used phylogenetic and functional approaches to investigate the evolution of cyclopeptide tolerance in the immigrans-tripunctata radiation of Drosophila. First, we inferred the evolutionary relationships among 48 species in this radiation using 978 single copy orthologs. Our results resolved previous incongruities within species groups across the phylogeny. Second, we expanded on previous studies of toxin tolerance by assaying 16 of these species for tolerance to α-amanitin and found that six of them could develop on diet with toxin. Finally, we asked how α-amanitin tolerance might have evolved across the immigrans-tripunctata radiation, and inferred that toxin tolerance was ancestral in mushroom-feeding Drosophila and subsequently lost multiple times. Our findings expand our understanding of toxin tolerance across the immigrans-tripunctata radiation and emphasize the uniqueness of toxin tolerance in this adaptive radiation and the complexity of biochemical adaptations.
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Affiliation(s)
| | - Lauren Haynes
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Olivia Fish
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Jordan Beveridge
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | | | - Laura K. Reed
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Kelly A. Dyer
- Department of GeneticsUniversity of GeorgiaAthensGeorgiaUSA
| | - Clare H. Scott Chialvo
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
- Department of BiologyAppalachian State UniversityBooneNorth CarolinaUSA
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6
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Hopkins BR, Angus-Henry A, Kim BY, Carlisle JA, Thompson A, Kopp A. Decoupled evolution of the Sex Peptide gene family and Sex Peptide Receptor in Drosophilidae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547128. [PMID: 37425821 PMCID: PMC10327216 DOI: 10.1101/2023.06.29.547128] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Across internally fertilising species, males transfer ejaculate proteins that trigger wide-ranging changes in female behaviour and physiology. Much theory has been developed to explore the drivers of ejaculate protein evolution. The accelerating availability of high-quality genomes now allows us to test how these proteins are evolving at fine taxonomic scales. Here, we use genomes from 264 species to chart the evolutionary history of Sex Peptide (SP), a potent regulator of female post-mating responses in Drosophila melanogaster. We infer that SP first evolved in the Drosophilinae subfamily and has followed markedly different evolutionary trajectories in different lineages. Outside of the Sophophora-Lordiphosa, SP exists largely as a single-copy gene with independent losses in several lineages. Within the Sophophora-Lordiphosa, the SP gene family has repeatedly and independently expanded. Up to seven copies, collectively displaying extensive sequence variation, are present in some species. Despite these changes, SP expression remains restricted to the male reproductive tract. Alongside, we document considerable interspecific variation in the presence and morphology of seminal microcarriers that, despite the critical role SP plays in microcarrier assembly in D. melanogaster, appear to be independent of changes in the presence/absence or sequence of SP. We end by providing evidence that SP's evolution is decoupled from that of its receptor, SPR, in which we detect no evidence of correlated diversifying selection. Collectively, our work describes the divergent evolutionary trajectories that a novel gene has taken following its origin and finds a surprisingly weak coevolutionary signal between a supposedly sexually antagonistic protein and its receptor.
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Affiliation(s)
- Ben R. Hopkins
- Department of Evolution and Ecology, University of California – Davis, CA, USA
| | - Aidan Angus-Henry
- Department of Evolution and Ecology, University of California – Davis, CA, USA
| | | | - Jolie A. Carlisle
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Ammon Thompson
- Department of Evolution and Ecology, University of California – Davis, CA, USA
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California – Davis, CA, USA
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7
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van Lopik J, Alizada A, Trapotsi MA, Hannon GJ, Bornelöv S, Czech Nicholson B. Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus. Nat Commun 2023; 14:7337. [PMID: 37957172 PMCID: PMC10643416 DOI: 10.1038/s41467-023-42787-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway prevents endogenous genomic parasites, i.e. transposable elements, from damaging the genetic material of animal gonadal cells. Specific regions in the genome, called piRNA clusters, are thought to define each species' piRNA repertoire and therefore its capacity to recognize and silence specific transposon families. The unistrand cluster flamenco (flam) is essential in the somatic compartment of the Drosophila ovary to restrict Gypsy-family transposons from infecting the neighbouring germ cells. Disruption of flam results in transposon de-repression and sterility, yet it remains unknown whether this silencing mechanism is present more widely. Here, we systematically characterise 119 Drosophila species and identify five additional flam-like clusters separated by up to 45 million years of evolution. Small RNA-sequencing validated these as bona-fide unistrand piRNA clusters expressed in somatic cells of the ovary, where they selectively target transposons of the Gypsy family. Together, our study provides compelling evidence of a widely conserved transposon silencing mechanism that co-evolved with virus-like Gypsy-family transposons.
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Affiliation(s)
- Jasper van Lopik
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Azad Alizada
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Maria-Anna Trapotsi
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Susanne Bornelöv
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
| | - Benjamin Czech Nicholson
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
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8
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Kim BY, Gellert HR, Church SH, Suvorov A, Anderson SS, Barmina O, Beskid SG, Comeault AA, Crown KN, Diamond SE, Dorus S, Fujichika T, Hemker JA, Hrcek J, Kankare M, Katoh T, Magnacca KN, Martin RA, Matsunaga T, Medeiros MJ, Miller DE, Pitnick S, Simoni S, Steenwinkel TE, Schiffer M, Syed ZA, Takahashi A, Wei KHC, Yokoyama T, Eisen MB, Kopp A, Matute D, Obbard DJ, O'Grady PM, Price DK, Toda MJ, Werner T, Petrov DA. Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560517. [PMID: 37873137 PMCID: PMC10592941 DOI: 10.1101/2023.10.02.560517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.
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Affiliation(s)
| | | | - Samuel H Church
- Department of Ecology and Evolutionary Biology, Yale University, USA
| | - Anton Suvorov
- Department of Biological Sciences, Virginia Tech, USA
| | - Sean S Anderson
- Department of Biology, University of North Carolina Chapel Hill, USA
| | - Olga Barmina
- Department of Evolution and Ecology, University of California Davis, USA
| | | | - Aaron A Comeault
- School of Environmental and Natural Sciences, Bangor University, UK
| | - K Nicole Crown
- Department of Biology, Case Western Reserve University, USA
| | | | - Steve Dorus
- Center for Reproductive Evolution, Department of Biology, Syracuse University, USA
| | - Takako Fujichika
- Department of Biological Sciences, Tokyo Metropolitan University, Japan
| | - James A Hemker
- Department of Developmental Biology, Stanford University, USA
| | - Jan Hrcek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, Czechia
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Toru Katoh
- Department of Biological Sciences, Hokkaido University, Japan
| | - Karl N Magnacca
- Hawaii Invertebrate Program, Division of Forestry & Wildlife, State of Hawaii, USA
| | - Ryan A Martin
- Department of Biology, Case Western Reserve University, USA
| | - Teruyuki Matsunaga
- Department of Complexity Science and Engineering, The University of Tokyo, Japan
| | | | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics; Department of Laboratory Medicine and Pathology, University of Washington, USA
| | - Scott Pitnick
- Center for Reproductive Evolution, Department of Biology, Syracuse University, USA
| | - Sara Simoni
- Department of Biology, Stanford University, USA
| | | | - Michele Schiffer
- Daintree Rainforest Observatory, James Cook University, Australia
| | - Zeeshan A Syed
- Center for Reproductive Evolution, Department of Biology, Syracuse University, USA
| | - Aya Takahashi
- Department of Biological Sciences, Tokyo Metropolitan University, Japan
| | - Kevin H-C Wei
- Department of Zoology, The University of British Columbia
| | | | - Michael B Eisen
- Department of Cell and Molecular Biology, University of California Berkeley, United States
- Howard Hughes Medical Institute,University of California Berkeley, United States
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California Davis, USA
| | - Daniel Matute
- Department of Biology, University of North Carolina Chapel Hill, USA
| | - Darren J Obbard
- Institute of Ecology and Evolution, University of Edinburgh, UK
| | | | - Donald K Price
- School of Life Sciences, University of Nevada Las Vegas, USA
| | | | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, USA
- CZ Biohub, Investigator
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9
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Leung W, Torosin N, Cao W, Reed LK, Arrigo C, Elgin SCR, Ellison CE. Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai, Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae. G3 (BETHESDA, MD.) 2023; 13:jkad191. [PMID: 37611223 PMCID: PMC10542312 DOI: 10.1093/g3journal/jkad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/25/2023]
Abstract
Flow cytometry estimates of genome sizes among species of Drosophila show a 3-fold variation, ranging from ∼127 Mb in Drosophila mercatorum to ∼400 Mb in Drosophila cyrtoloma. However, the assembled portion of the Muller F element (orthologous to the fourth chromosome in Drosophila melanogaster) shows a nearly 14-fold variation in size, ranging from ∼1.3 Mb to >18 Mb. Here, we present chromosome-level long-read genome assemblies for 4 Drosophila species with expanded F elements ranging in size from 2.3 to 20.5 Mb. Each Muller element is present as a single scaffold in each assembly. These assemblies will enable new insights into the evolutionary causes and consequences of chromosome size expansion.
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Affiliation(s)
- Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicole Torosin
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Weihuan Cao
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Laura K Reed
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Cindy Arrigo
- Department of Biology, New Jersey City University, Jersey City, NJ 07305, USA
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Christopher E Ellison
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
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10
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Wang Z, Pu J, Richards C, Giannetti E, Cong H, Lin Z, Chung H. Evolution of a fatty acyl-CoA elongase underlies desert adaptation in Drosophila. SCIENCE ADVANCES 2023; 9:eadg0328. [PMID: 37647401 PMCID: PMC10468142 DOI: 10.1126/sciadv.adg0328] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Traits that allow species to survive in extreme environments such as hot-arid deserts have independently evolved in multiple taxa. However, the genetic and evolutionary mechanisms underlying these traits have thus far not been elucidated. Here, we show that Drosophila mojavensis, a desert-adapted fruit fly species, has evolved high desiccation resistance by producing long-chain methyl-branched cuticular hydrocarbons (mbCHCs) that contribute to a cuticular lipid layer reducing water loss. We show that the ability to synthesize these longer mbCHCs is due to evolutionary changes in a fatty acyl-CoA elongase (mElo). mElo knockout in D. mojavensis led to loss of longer mbCHCs and reduction of desiccation resistance at high temperatures but did not affect mortality at either high temperatures or desiccating conditions individually. Phylogenetic analysis showed that mElo is a Drosophila-specific gene, suggesting that while the physiological mechanisms underlying desert adaptation may be similar between species, the genes involved in these mechanisms may be species or lineage specific.
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Affiliation(s)
- Zinan Wang
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Jian Pu
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
- College of Agriculture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Cole Richards
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Elaina Giannetti
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Haosu Cong
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO 63104, USA
| | - Henry Chung
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
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11
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Peláez JN, Gloss AD, Goldman-Huertas B, Kim B, Lapoint RT, Pimentel-Solorio G, Verster KI, Aguilar JM, Nelson Dittrich AC, Singhal M, Suzuki HC, Matsunaga T, Armstrong EE, Charboneau JLM, Groen SC, Hembry DH, Ochoa CJ, O’Connor TK, Prost S, Zaaijer S, Nabity PD, Wang J, Rodas E, Liang I, Whiteman NK. Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae. G3 (BETHESDA, MD.) 2023; 13:jkad133. [PMID: 37317982 PMCID: PMC10411586 DOI: 10.1093/g3journal/jkad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 03/19/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023]
Abstract
Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genomic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families-genes directly mediating interactions with plant chemical defenses-underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many insect lineages are ancient (>150 million years ago (mya)), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several nonherbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza has among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant-binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on living plants (bitter or electrophilic phytotoxins) or their ancestral diet (fermenting plant volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight gene candidates that have also been linked to other dietary transitions in Drosophila.
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Affiliation(s)
- Julianne N Peláez
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Andrew D Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Benjamin Goldman-Huertas
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Bernard Kim
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Richard T Lapoint
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Kirsten I Verster
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Jessica M Aguilar
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Anna C Nelson Dittrich
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Malvika Singhal
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Chemistry & Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Hiromu C Suzuki
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Teruyuki Matsunaga
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Ellie E Armstrong
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Joseph L M Charboneau
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Simon C Groen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Department of Nematology, University of California Riverside, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
- Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, USA
| | - David H Hembry
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology, University of Texas Permian Basin, Odessa, TX 79762, USA
| | - Christopher J Ochoa
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy K O’Connor
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Stefan Prost
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Sophie Zaaijer
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Jacobs Institute, Cornell Tech, New York, NY 10044, USA
- FIND Genomics, New York, NY 10044, USA
| | - Paul D Nabity
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Jiarui Wang
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
| | - Esteban Rodas
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Irene Liang
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Noah K Whiteman
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
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12
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Erlenbach T, Haynes L, Fish O, Beveridge J, Bingolo E, Giambrone SA, Kropelin G, Rudisill S, Chialvo P, Reed LK, Dyer KA, Chialvo CS. Investigating the phylogenetic history of toxin tolerance in mushroom-feeding Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551872. [PMID: 37577671 PMCID: PMC10418198 DOI: 10.1101/2023.08.03.551872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Understanding how and when key novel adaptations evolved is a central goal of evolutionary biology. Within the immigrans-tripunctata radiation of Drosophila , many mushroom-feeding species are tolerant of host toxins, such as cyclopeptides, that are lethal to nearly all other eukaryotes. In this study, we used phylogenetic and functional approaches to investigate the evolution of cyclopeptide tolerance in the immigrans-tripunctata radiation of Drosophila . We first inferred the evolutionary relationships among 48 species in this radiation using 978 single copy orthologs. Our results resolved previous incongruities within species groups across the phylogeny. Second, we expanded on previous studies of toxin tolerance by assaying 16 of these species for tolerance to α-amanitin and found that six of these species could develop on diet with toxin. Third, we examined fly development on a diet containing a natural mix of toxins extracted from the Death Cap Amanita phalloides mushroom. Both tolerant and susceptible species developed on diet with this mix, though tolerant species survived at significantly higher concentrations. Finally, we asked how cyclopeptide tolerance might have evolved across the immigrans-tripunctata radiation and inferred that toxin tolerance was ancestral and subsequently lost multiple times. Our results suggest the evolutionary history of cyclopeptide tolerance is complex, and simply describing this trait as present or absent does not fully capture the occurrence or impact on this adaptive radiation. More broadly, the evolution of novelty can be more complex than previously thought, and that accurate descriptions of such novelties are critical in studies examining their evolution.
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13
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Leung W, Torosin N, Cao W, Reed LK, Arrigo C, Elgin SCR, Ellison CE. Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai , Drosophila takahashii , Drosophila bipectinata , and Drosophila ananassae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541758. [PMID: 37292993 PMCID: PMC10245892 DOI: 10.1101/2023.05.22.541758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Flow cytometry estimates of genome sizes among species of Drosophila show a 3-fold variation, ranging from ∼127 Mb in Drosophila mercatorum to ∼400 Mb in Drosophila cyrtoloma . However, the assembled portion of the Muller F Element (orthologous to the fourth chromosome in Drosophila melanogaster ) shows a nearly 14-fold variation in size, ranging from ∼1.3 Mb to > 18 Mb. Here, we present chromosome-level long read genome assemblies for four Drosophila species with expanded F Elements ranging in size from 2.3 Mb to 20.5 Mb. Each Muller Element is present as a single scaffold in each assembly. These assemblies will enable new insights into the evolutionary causes and consequences of chromosome size expansion.
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Affiliation(s)
- Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicole Torosin
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Weihuan Cao
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Laura K Reed
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, 35487, USA
| | - Cindy Arrigo
- Department of Biology, New Jersey City University, Jersey City, NJ 07305, USA
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Christopher E Ellison
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
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14
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Pelaez JN, Gloss AD, Goldman-Huertas B, Kim B, Lapoint RT, Pimentel-Solorio G, Verster KI, Aguilar JM, Dittrich ACN, Singhal M, Suzuki HC, Matsunaga T, Armstrong EE, Charboneau JL, Groen SC, Hembry DH, Ochoa CJ, O’Connor TK, Prost S, Zaaijer S, Nabity PD, Wang J, Rodas E, Liang I, Whiteman NK. Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532987. [PMID: 36993186 PMCID: PMC10055167 DOI: 10.1101/2023.03.16.532987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genetic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that expansions and contractions of chemosensory and detoxification gene families - genes directly mediating interactions with plant chemical defenses - underlie successful plant colonization. However, this hypothesis has been challenging to test because the origins of herbivory in many lineages are ancient (>150 million years ago [mya]), obscuring genomic evolutionary patterns. Here, we characterized chemosensory and detoxification gene family evolution across Scaptomyza, a genus nested within Drosophila that includes a recently derived (<15 mya) herbivore lineage of mustard (Brassicales) specialists and carnation (Caryophyllaceae) specialists, and several non-herbivorous species. Comparative genomic analyses revealed that herbivorous Scaptomyza have among the smallest chemosensory and detoxification gene repertoires across 12 drosophilid species surveyed. Rates of gene turnover averaged across the herbivore clade were significantly higher than background rates in over half of the surveyed gene families. However, gene turnover was more limited along the ancestral herbivore branch, with only gustatory receptors and odorant binding proteins experiencing strong losses. The genes most significantly impacted by gene loss, duplication, or changes in selective constraint were those involved in detecting compounds associated with feeding on plants (bitter or electrophilic phytotoxins) or their ancestral diet (yeast and fruit volatiles). These results provide insight into the molecular and evolutionary mechanisms of plant-feeding adaptations and highlight strong gene candidates that have also been linked to other dietary transitions in Drosophila .
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Affiliation(s)
- Julianne N. Pelaez
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Andrew D. Gloss
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Benjamin Goldman-Huertas
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Bernard Kim
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Richard T. Lapoint
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- National Center for Biotechnology Information, Bethesda, MD 20894, USA
| | | | - Kirsten I. Verster
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Jessica M. Aguilar
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Anna C. Nelson Dittrich
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Boyce Thompson Institute, Ithaca NY 14853 USA
| | - Malvika Singhal
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Chemistry & Biochemistry, University of Oregon, OR, CA 97403, USA
| | - Hiromu C. Suzuki
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Teruyuki Matsunaga
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | | | - Joseph L.M. Charboneau
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Simon C. Groen
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Department of Nematology, University of California-Riverside, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA 92521, USA
- Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA
| | - David H. Hembry
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Biology, University of Texas Permian Basin, Odessa, TX 79762, USA
| | - Christopher J. Ochoa
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy K. O’Connor
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Stefan Prost
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Sophie Zaaijer
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Jacobs Institute, Cornell Tech, New York, NY 10044, USA
- FIND Genomics, New York, NY 10044, USA
| | - Paul D. Nabity
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, CA 92521, USA
| | - Jiarui Wang
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90007, USA
| | - Esteban Rodas
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Irene Liang
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Noah K. Whiteman
- Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
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15
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Wang Z, Receveur JP, Pu J, Cong H, Richards C, Liang M, Chung H. Desiccation resistance differences in Drosophila species can be largely explained by variations in cuticular hydrocarbons. eLife 2022; 11:e80859. [PMID: 36473178 PMCID: PMC9757832 DOI: 10.7554/elife.80859] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Maintaining water balance is a universal challenge for organisms living in terrestrial environments, especially for insects, which have essential roles in our ecosystem. Although the high surface area to volume ratio in insects makes them vulnerable to water loss, insects have evolved different levels of desiccation resistance to adapt to diverse environments. To withstand desiccation, insects use a lipid layer called cuticular hydrocarbons (CHCs) to reduce water evaporation from the body surface. It has long been hypothesized that the water-proofing capability of this CHC layer, which can confer different levels of desiccation resistance, depends on its chemical composition. However, it is unknown which CHC components are important contributors to desiccation resistance and how these components can determine differences in desiccation resistance. In this study, we used machine-learning algorithms, correlation analyses, and synthetic CHCs to investigate how different CHC components affect desiccation resistance in 50 Drosophila and related species. We showed that desiccation resistance differences across these species can be largely explained by variation in CHC composition. In particular, length variation in a subset of CHCs, the methyl-branched CHCs (mbCHCs), is a key determinant of desiccation resistance. There is also a significant correlation between the evolution of longer mbCHCs and higher desiccation resistance in these species. Given that CHCs are almost ubiquitous in insects, we suggest that evolutionary changes in insect CHC components can be a general mechanism for the evolution of desiccation resistance and adaptation to diverse and changing environments.
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Affiliation(s)
- Zinan Wang
- Department of Entomology, Michigan State UniversityEast LansingUnited States
- Ecology, Evolution, and Behavior Program, Michigan State UniversityEast LansingUnited States
| | - Joseph P Receveur
- Department of Entomology, Michigan State UniversityEast LansingUnited States
- Ecology, Evolution, and Behavior Program, Michigan State UniversityEast LansingUnited States
- Institute for Genome Sciences, University of MarylandBaltimoreUnited States
| | - Jian Pu
- Department of Entomology, Michigan State UniversityEast LansingUnited States
- College of Agriculture, Sichuan Agricultural UniversitySichuanChina
| | - Haosu Cong
- Department of Entomology, Michigan State UniversityEast LansingUnited States
| | - Cole Richards
- Department of Entomology, Michigan State UniversityEast LansingUnited States
| | - Muxuan Liang
- Department of Biostatistics, University of FloridaGainesvilleUnited States
| | - Henry Chung
- Department of Entomology, Michigan State UniversityEast LansingUnited States
- Ecology, Evolution, and Behavior Program, Michigan State UniversityEast LansingUnited States
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16
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Tanaka KM, Takahashi K, Rice G, Rebeiz M, Kamimura Y, Takahashi A. Trichomes on female reproductive tract: rapid diversification and underlying gene regulatory network in Drosophila suzukii and its related species. BMC Ecol Evol 2022; 22:93. [PMID: 35902820 PMCID: PMC9331688 DOI: 10.1186/s12862-022-02046-1] [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] [Received: 01/24/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
Background The ovipositors of some insects are external female genitalia, which have their primary function to deliver eggs. Drosophila suzukii and its sibling species D. subpulchrella are known to have acquired highly sclerotized and enlarged ovipositors upon their shifts in oviposition sites from rotting to ripening fruits. Inside the ovipositor plates, there are scale-like polarized protrusions termed “oviprovector scales” that are likely to aid the mechanical movement of the eggs. The size and spatial distribution of the scales need to be rearranged following the divergence of the ovipositors. In this study, we examined the features of the oviprovector scales in D. suzukii and its closely related species. We also investigated whether the scales are single-cell protrusions comprised of F-actin under the same conserved gene regulatory network as the well-characterized trichomes on the larval cuticular surface. Results The oviprovector scales of D. suzukii and D. subpulchrella were distinct in size and spatial arrangement compared to those of D. biarmipes and other closely related species. The scale numbers also varied greatly among these species. The comparisons of the size of the scales suggested a possibility that the apical cell area of the oviprovector has expanded upon the elongation of the ovipositor plates in these species. Our transcriptome analysis revealed that 43 out of the 46 genes known to be involved in the trichome gene regulatory network are expressed in the developing female genitalia of D. suzukii and D. subpulchrella. The presence of Shavenbaby (Svb) or svb was detected in the inner cavity of the developing ovipositors of D. melanogaster, D. suzukii, and D. subpulchrella. Also, shavenoid (sha) was expressed in the corresponding patterns in the developing ovipositors and showed differential expression levels between D. suzukii and D. subpulchrella at 48 h APF. Conclusions The oviprovector scales have divergent size and spatial arrangements among species. Therefore, these scales may represent a rapidly diversifying morphological trait of the female reproductive tract reflecting ecological contexts. Furthermore, our results showed that the gene regulatory network underlying trichome formation is also utilized to develop the rapidly evolving trichomes on the oviprovectors of these flies. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02046-1.
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17
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Peláez JN, Gloss AD, Ray JF, Chaturvedi S, Haji D, Charboneau JLM, Verster KI, Whiteman NK. Evolution and genomic basis of the plant-penetrating ovipositor: a key morphological trait in herbivorous Drosophilidae. Proc Biol Sci 2022; 289:20221938. [PMID: 36350206 PMCID: PMC9653217 DOI: 10.1098/rspb.2022.1938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Herbivorous insects are extraordinarily diverse, yet are found in only one-third of insect orders. This skew may result from barriers to plant colonization, coupled with phylogenetic constraint on plant-colonizing adaptations. The plant-penetrating ovipositor, however, is one trait that surmounts host plant physical defences and may be evolutionarily labile. Ovipositors densely lined with hard bristles have evolved repeatedly in herbivorous lineages, including within the Drosophilidae. However, the evolution and genetic basis of this innovation has not been well studied. Here, we focused on the evolution of this trait in Scaptomyza, a genus sister to Hawaiian Drosophila, that contains a herbivorous clade. Our phylogenetic approach revealed that ovipositor bristle number increased as herbivory evolved in the Scaptomyza lineage. Through a genome-wide association study, we then dissected the genomic architecture of variation in ovipositor bristle number within S. flava. Top-associated variants were enriched for transcriptional repressors, and the strongest associations included genes contributing to peripheral nervous system development. Individual genotyping supported the association at a variant upstream of Gαi, a neural development gene, contributing to a gain of 0.58 bristles/major allele. These results suggest that regulatory variation involving conserved developmental genes contributes to this key morphological trait involved in plant colonization.
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Affiliation(s)
- Julianne N. Peláez
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | - Andrew D. Gloss
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10012, USA,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Julianne F. Ray
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Samridhi Chaturvedi
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | - Diler Haji
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | | | - Kirsten I. Verster
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | - Noah K. Whiteman
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA,Department of Molecular and Cell Biology, University of California, Berkeley, 94720 CA, USA
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18
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Winkler IS, Kirk-Spriggs AH, Bayless KM, Soghigian J, Meier R, Pape T, Yeates DK, Carvalho AB, Copeland RS, Wiegmann BM. Phylogenetic resolution of the fly superfamily Ephydroidea-Molecular systematics of the enigmatic and diverse relatives of Drosophilidae. PLoS One 2022; 17:e0274292. [PMID: 36197946 PMCID: PMC9534441 DOI: 10.1371/journal.pone.0274292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/26/2022] [Indexed: 11/05/2022] Open
Abstract
The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes eight families, ranging from the well-known vinegar flies (Drosophilidae) and shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematists. An extraordinary diversity in life histories, feeding habits and morphology are a hallmark of fly biology, and the Ephydroidea are no exception. Extreme specialization can lead to "orphaned" taxa with no clear evidence for their phylogenetic position. To resolve relationships among a diverse sample of Ephydroidea, including the highly modified flies in the families Braulidae and Mormotomyiidae, we conducted phylogenomic sampling. Using exon capture from Anchored Hybrid Enrichment and transcriptomics to obtain 320 orthologous nuclear genes sampled for 32 species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic hypothesis for representatives of the superfamily. These data strongly support monophyly of Ephydroidea with Ephydridae as an early branching radiation and the placement of Mormotomyiidae as a family-level lineage sister to all remaining families. We confirm placement of Cryptochetidae as sister taxon to a large clade containing both Drosophilidae and Braulidae-the latter a family of honeybee ectoparasites. Our results reaffirm that sampling of both taxa and characters is critical in hyperdiverse clades and that these factors have a major influence on phylogenomic reconstruction of the history of the schizophoran fly radiation.
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Affiliation(s)
- Isaac S. Winkler
- Department of Biology, Cornell College, Mount Vernon, Iowa, United States of America
| | | | - Keith M. Bayless
- Australian National Insect Collection, CSIRO National Research Collection, Australia (NRCA), Acton, Canberra, ACT, Australia
| | - John Soghigian
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Thomas Pape
- Natural History Museum of Denmark, Copenhagen, Denmark
| | - David K. Yeates
- Australian National Insect Collection, CSIRO National Research Collection, Australia (NRCA), Acton, Canberra, ACT, Australia
| | - A. Bernardo Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Robert S. Copeland
- International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Brian M. Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
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19
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Kopp A, Barmina O. Interspecific variation in sex-specific gustatory organs in Drosophila. J Comp Neurol 2022; 530:2439-2450. [PMID: 35603778 PMCID: PMC9339527 DOI: 10.1002/cne.25340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/08/2022]
Abstract
Drosophila males use leg gustatory bristles to discriminate between male and female cuticular pheromones as an important part of courtship behavior. In Drosophila melanogaster, several male-specific gustatory bristles are present on the anterior surface of the first tarsal segment of the prothoracic leg, in addition to a larger set of gustatory bristles found in both sexes. These bristles are thought to be specialized for pheromone detection. Here, we report the number and location of sex-specific gustatory bristles in 27 other Drosophila species. Although some species have a pattern similar to D. melanogaster, others lack anterior male-specific bristles but have many dorsal male-specific gustatory bristles instead. Some species have both anterior and dorsal male-specific bristles, while others lack sexual dimorphism entirely. In several distantly related species, the number of gustatory bristles is much greater in males than in females due to a male-specific transformation of ancestrally mechanosensory bristles to a chemosensory identity. This variation in the extent and pattern of sexual dimorphism may affect the formation and function of neuronal circuits that control Drosophila courtship and contribute to the evolution of mating behavior.
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Affiliation(s)
- Artyom Kopp
- Department of Evolution and Ecology, University of California Davis
| | - Olga Barmina
- Department of Evolution and Ecology, University of California Davis
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20
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Hultmark D, Andó I. Hematopoietic plasticity mapped in Drosophila and other insects. eLife 2022; 11:78906. [PMID: 35920811 PMCID: PMC9348853 DOI: 10.7554/elife.78906] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/20/2022] [Indexed: 12/12/2022] Open
Abstract
Hemocytes, similar to vertebrate blood cells, play important roles in insect development and immunity, but it is not well understood how they perform their tasks. New technology, in particular single-cell transcriptomic analysis in combination with Drosophila genetics, may now change this picture. This review aims to make sense of recently published data, focusing on Drosophila melanogaster and comparing to data from other drosophilids, the malaria mosquito, Anopheles gambiae, and the silkworm, Bombyx mori. Basically, the new data support the presence of a few major classes of hemocytes: (1) a highly heterogenous and plastic class of professional phagocytes with many functions, called plasmatocytes in Drosophila and granular cells in other insects. (2) A conserved class of cells that control melanin deposition around parasites and wounds, called crystal cells in D. melanogaster, and oenocytoids in other insects. (3) A new class of cells, the primocytes, so far only identified in D. melanogaster. They are related to cells of the so-called posterior signaling center of the larval hematopoietic organ, which controls the hematopoiesis of other hemocytes. (4) Different kinds of specialized cells, like the lamellocytes in D. melanogaster, for the encapsulation of parasites. These cells undergo rapid evolution, and the homology relationships between such cells in different insects are uncertain. Lists of genes expressed in the different hemocyte classes now provide a solid ground for further investigation of function.
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Affiliation(s)
- Dan Hultmark
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - István Andó
- Biological Research Centre, Institute of Genetics, Innate Immunity Group, Eötvös Loránd Research Network, Szeged, Hungary
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21
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Xiao L, Li NN, Yang LK, Li JL, Gao JJ. Evolution of the Colocasiomyia gigantea Species Group (Diptera: Drosophilidae): Phylogeny, Biogeography and Shift of Host Use. INSECTS 2022; 13:insects13070647. [PMID: 35886823 PMCID: PMC9319340 DOI: 10.3390/insects13070647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/03/2022] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
Abstract
Simple Summary All the species in the Colocasiomyia gigantea group breed on monsteroid host plants (aroids in the subfamily Monsteroideae). So far, we have not resolved the phylogenetic relationship among these fly species, making it difficult to trace the origin and history of the species diversification, biogeography and host plant selection. In this study, we reconstructed the evolutionary relationships between these species using multilocus DNA sequence data, and we inferred their ancestral areas and host plants. According to the results, this group diverged from its sister taxon through a split between the northeastern Oriental region and Sundaland + Wallacea, with the subsequent diversification occurring largely in the first region. We inferred the most likely ancestral host genus of this group to be Rhaphidophora Hassk, with possible subsequent shifts to Scindapsus Schott and/or Epipremnum Schott. We discuss the potential of the group as a model system for studies in evolutionary ecology and developmental genetics. Abstract The gigantea species group of the genus Colocasiomyia de Meijere (Diptera: Drosophilidae) is among the four aroid-breeding species groups in this genus; however, it differs from the remaining three groups in the host use: all the flies in this group use plants from the subfamily Monsteroideae instead of from the subfamily Aroideae. So far, we have not resolved the phylogenetic relationship within this group, making it difficult to trace its geographical origin, pattern of species diversification and history of host plant use. In this study, we reconstructed the phylogenetic relationships within the C. gigantea group using DNA sequences of eight (two mitochondrial and six nuclear) gene markers, and we inferred the ancestral areas and host plants of the group based on the resulting phylogeny. According to the results, the C. gigantea group may have diverged from its sister group (i.e., the C. cristata group) through vicariance between the northeastern Oriental region and Sundaland + Wallacea, and the subsequent diversification of the C. gigantea group occurred mostly in the northeastern Oriental region, although an Oriental-to-Sundaland dispersal was followed by vicariance between these two areas, which finally gave rise to the C. gigantea-C. scindapsae lineage in the latter area. We inferred the most likely ancestral host plant of the C. gigantea group to be of the genus Rhaphidophora Hassk, with possible subsequent shifts to Scindapsus Schott and/or Epipremnum Schott plants. We discuss the potential for the egg filaments in the C. gigantea group to be used as a model system for comparative studies in pollination mutualism and developmental genetics concerning tubulogenesis.
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Affiliation(s)
- Ling Xiao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming 650500, China;
| | - Nan-Nan Li
- School of Forestry, Southwest Forestry University, Kunming 650224, China; (N.-N.L.); (L.-K.Y.)
| | - Long-Kun Yang
- School of Forestry, Southwest Forestry University, Kunming 650224, China; (N.-N.L.); (L.-K.Y.)
| | - Jia-Ling Li
- Wuzhishan Division, National Park of Hainan Tropical Rainforest, Wuzhishan 572215, China;
| | - Jian-Jun Gao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming 650500, China;
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Correspondence:
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22
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Dietary Utilization Drives the Differentiation of Gut Bacterial Communities between Specialist and Generalist Drosophilid Flies. Microbiol Spectr 2022; 10:e0141822. [PMID: 35863034 PMCID: PMC9431182 DOI: 10.1128/spectrum.01418-22] [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: 11/28/2022] Open
Abstract
Gut bacteria play vital roles in the dietary detoxification, digestion, and nutrient supplementation of hosts during dietary specialization. The roles of gut bacteria in the host can be unveiled by comparing communities of specialist and generalist bacterial species. However, these species usually have a long evolutionary history, making it difficult to determine whether bacterial community differentiation is due to host dietary adaptation or phylogenetic divergence. In this regard, we investigated the bacterial communities from two Araceae-feeding Colocasiomyia species and further performed a meta-analysis by incorporating the published data from Drosophila bacterial community studies. The compositional and functional differentiation of bacterial communities was uncovered by comparing three (Araceae-feeding, mycophagous, and cactophilic) specialists with generalist flies. The compositional differentiation showed that Bacteroidetes and Firmicutes inhabited specialists, while more Proteobacteria lived in generalists. The functional prediction based on the bacterial community compositions suggested that amino acid metabolism and energy metabolism are overrepresented pathways in specialists and generalists, respectively. The differences were mainly associated with the higher utilization of structural complex carbohydrates, protein utilization, vitamin B12 acquisition, and demand for detoxification in specialists than in generalists. The complementary roles of bacteria reveal a connection between gut bacterial communities and fly dietary specialization. IMPORTANCE Gut bacteria may play roles in the dietary utilization of hosts, especially in specialist animals, during long-term host-microbe interaction. By comparing the gut bacterial communities between specialist and generalist drosophilid flies, we found that specialists harbor more bacteria linked to complex carbohydrate degradation, amino acid metabolism, vitamin B12 formation, and detoxification than do generalists. This study reveals the roles of gut bacteria in drosophilid species in dietary utilization.
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23
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Ishikawa Y, Kimura MT, Toda MJ. Biology and ecology of the Oriental flower-breeding Drosophila elegans and related species. Fly (Austin) 2022; 16:207-220. [PMID: 35499147 PMCID: PMC9067466 DOI: 10.1080/19336934.2022.2066953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Animals adapt to their environments in the course of evolution. One effective approach to elucidate mechanisms of adaptive evolution is to compare closely related species with model organisms in which knowledge of the molecular and physiological bases of various traits has been accumulated. Drosophila elegans and its close relatives, belonging to the same species group as the model organism D. melanogaster, exhibit various unique characteristics such as flower-breeding habit, courtship display, territoriality, sexual dimorphism, and colour polymorphism. Their ease of culturing and availability of genomic information makes them a useful model for understanding mechanisms of adaptive evolution. Here, we review the morphology, distribution, and phylogenetic relationships of D. elegans and related species, as well as their characteristic flower-dependent biology, food habits, and life-history traits. We also describe their unique mating and territorial behaviours and note their distinctive karyotype and the genetic mechanisms of morphological diversity that have recently been revealed.
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Affiliation(s)
- Yuki Ishikawa
- Graduate School of Science, Nagoya University, Nagoya, Japan
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24
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Grimaldi DA. The Drosophila funebris Species Group in North America (Diptera: Drosophilidae). AMERICAN MUSEUM NOVITATES 2022. [DOI: 10.1206/3988.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- David A. Grimaldi
- Division of Invertebrate Zoology, American Museum of Natural History
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25
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Wang WWY, Gunderson AR. The Physiological and Evolutionary Ecology of Sperm Thermal Performance. Front Physiol 2022; 13:754830. [PMID: 35399284 PMCID: PMC8987524 DOI: 10.3389/fphys.2022.754830] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 02/28/2022] [Indexed: 12/26/2022] Open
Abstract
Ongoing anthropogenic climate change has increased attention on the ecological and evolutionary consequences of thermal variation. Most research in this field has focused on the physiology and behavior of diploid whole organisms. The thermal performance of haploid gamete stages directly tied to reproductive success has received comparatively little attention, especially in the context of the evolutionary ecology of wild (i.e., not domesticated) organisms. Here, we review evidence for the effects of temperature on sperm phenotypes, emphasizing data from wild organisms whenever possible. We find that temperature effects on sperm are pervasive, and that above normal temperatures in particular are detrimental. That said, there is evidence that sperm traits can evolve adaptively in response to temperature change, and that adaptive phenotypic plasticity in sperm traits is also possible. We place results in the context of thermal performance curves, and encourage this framework to be used as a guide for experimental design to maximize ecological relevance as well as the comparability of results across studies. We also highlight gaps in our understanding of sperm thermal performance that require attention to more fully understand thermal adaptation and the consequences of global change.
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26
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Bertocchi NÁ, Oliveira TDD, Deprá M, Goñi B, Valente VLS. Interpopulation variation of transposable elements of the hAT superfamily in Drosophila willistoni (Diptera: Drosophilidae): in-situ approach. Genet Mol Biol 2022; 45:e20210287. [PMID: 35297941 PMCID: PMC8961557 DOI: 10.1590/1678-4685-gmb-2021-0287] [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] [Received: 09/10/2021] [Accepted: 01/31/2022] [Indexed: 11/22/2022] Open
Abstract
Transposable elements are abundant and dynamic part of the genome, influencing
organisms in different ways through their presence or mobilization, or by acting
directly on pre- and post-transcriptional regulatory regions. We compared and
evaluated the presence, structure, and copy number of three hAT
superfamily transposons (hobo, BuT2, and mar)
in five strains of Drosophila willistoni
species. These D. willistoni strains are
of different geographical origins, sampled across the north-south occurrence of
this species. We used sequenced clones of the hAT elements in
fluorescence in-situ hybridizations in the polytene chromosomes
of three strains of D. willistoni. We also analyzed the
structural characteristics and number of copies of these hAT
elements in the 10 currently available sequenced genomes of the
willistoni group. We found that hobo,
BuT2, and mar were widely distributed in
D. willistoni polytene chromosomes and sequenced genomes of
the willistoni group, except for mar, which is
restricted to the subgroup willistoni. Furthermore, the
elements hobo, BuT2, and mar have different
evolutionary histories. The transposon differences among D.
willistoni strains, such as variation in the number, structure, and
chromosomal distribution of hAT transposons, could reflect the
genomic and chromosomal plasticity of D. willistoni species in
adapting to highly variable environments.
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Affiliation(s)
- Natasha Ávila Bertocchi
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Thays Duarte de Oliveira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Maríndia Deprá
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
| | - Beatriz Goñi
- Universidad de la República, Facultad de Ciencias, Montevideo, Uruguay
| | - Vera Lúcia S Valente
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Animal, Porto Alegre, RS, Brazil
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27
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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 E, 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. Correction: Highly contiguous assemblies of 101 drosophilid genomes. eLife 2022; 11:e78579. [PMID: 35302486 PMCID: PMC8933002 DOI: 10.7554/elife.78579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
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28
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Li F, Rane RV, Luria V, Xiong Z, Chen J, Li Z, Catullo RA, Griffin PC, Schiffer M, Pearce S, Lee SF, McElroy K, Stocker A, Shirriffs J, Cockerell F, Coppin C, Sgrò CM, Karger A, Cain JW, Weber JA, Santpere G, Kirschner MW, Hoffmann AA, Oakeshott JG, Zhang G. Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation. Mol Ecol Resour 2021; 22:1559-1581. [PMID: 34839580 PMCID: PMC9299920 DOI: 10.1111/1755-0998.13561] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/10/2021] [Indexed: 01/13/2023]
Abstract
Many Drosophila species differ widely in their distributions and climate niches, making them excellent subjects for evolutionary genomic studies. Here, we have developed a database of high‐quality assemblies for 46 Drosophila species and one closely related Zaprionus. Fifteen of the genomes were newly sequenced, and 20 were improved with additional sequencing. New or improved annotations were generated for all 47 species, assisted by new transcriptomes for 19. Phylogenomic analyses of these data resolved several previously ambiguous relationships, especially in the melanogaster species group. However, it also revealed significant phylogenetic incongruence among genes, mainly in the form of incomplete lineage sorting in the subgenus Sophophora but also including asymmetric introgression in the subgenus Drosophila. Using the phylogeny as a framework and taking into account these incongruences, we then screened the data for genome‐wide signals of adaptation to different climatic niches. First, phylostratigraphy revealed relatively high rates of recent novel gene gain in three temperate pseudoobscura and five desert‐adapted cactophilic mulleri subgroup species. Second, we found differing ratios of nonsynonymous to synonymous substitutions in several hundred orthologues between climate generalists and specialists, with trends for significantly higher ratios for those in tropical and lower ratios for those in temperate‐continental specialists respectively than those in the climate generalists. Finally, resequencing natural populations of 13 species revealed tropics‐restricted species generally had smaller population sizes, lower genome diversity and more deleterious mutations than the more widespread species. We conclude that adaptation to different climates in the genus Drosophila has been associated with large‐scale and multifaceted genomic changes.
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Affiliation(s)
- Fang Li
- BGI-Shenzhen, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rahul V Rane
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - Victor Luria
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Zijun Xiong
- BGI-Shenzhen, Shenzhen, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | - Renee A Catullo
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Division of Ecology and Evolution, Centre for Biodiversity Analysis, The Australian National University, Acton, ACT, Australia
| | - Philippa C Griffin
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - Michele Schiffer
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia.,Daintree Rainforest Observatory, James Cook University, Cape Tribulation, Qld, Australia
| | - Stephen Pearce
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Siu Fai Lee
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Applied BioSciences, Macquarie University, North Ryde, NSW, Australia
| | - Kerensa McElroy
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Ann Stocker
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - Jennifer Shirriffs
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - Fiona Cockerell
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Chris Coppin
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Amir Karger
- IT - Research Computing, Harvard Medical School, Boston, Massachusetts, USA
| | - John W Cain
- Department of Mathematics, Harvard University, Cambridge, Massachusetts, USA
| | - Jessica A Weber
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Gabriel Santpere
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences (DCEXS), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ary A Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, Parkville, Vic., Australia
| | - John G Oakeshott
- Commonwealth Scientific and Industrial Research Organisation, Acton, ACT, Australia.,Applied BioSciences, Macquarie University, North Ryde, NSW, Australia
| | - Guojie Zhang
- BGI-Shenzhen, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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29
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Ricchio J, Uno F, Carvalho AB. New Genes in the Drosophila Y Chromosome: Lessons from D. willistoni. Genes (Basel) 2021; 12:genes12111815. [PMID: 34828421 PMCID: PMC8623413 DOI: 10.3390/genes12111815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 01/05/2023] Open
Abstract
Y chromosomes play important roles in sex determination and male fertility. In several groups (e.g., mammals) there is strong evidence that they evolved through gene loss from a common X-Y ancestor, but in Drosophila the acquisition of new genes plays a major role. This conclusion came mostly from studies in two species. Here we report the identification of the 22 Y-linked genes in D. willistoni. They all fit the previously observed pattern of autosomal or X-linked testis-specific genes that duplicated to the Y. The ratio of gene gains to gene losses is ~25 in D. willistoni, confirming the prominent role of gene gains in the evolution of Drosophila Y chromosomes. We also found four large segmental duplications (ranging from 62 kb to 303 kb) from autosomal regions to the Y, containing ~58 genes. All but four of these duplicated genes became pseudogenes in the Y or disappeared. In the GK20609 gene the Y-linked copy remained functional, whereas its original autosomal copy degenerated, demonstrating how autosomal genes are transferred to the Y chromosome. Since the segmental duplication that carried GK20609 contained six other testis-specific genes, it seems that chance plays a significant role in the acquisition of new genes by the Drosophila Y chromosome.
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30
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Pu J, Wang Z, Cong H, Chin JSR, Justen J, Finet C, Yew JY, Chung H. Repression precedes independent evolutionary gains of a highly specific gene expression pattern. Cell Rep 2021; 37:109896. [PMID: 34706247 PMCID: PMC8578697 DOI: 10.1016/j.celrep.2021.109896] [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: 12/01/2020] [Revised: 08/24/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022] Open
Abstract
Highly specific expression patterns can be caused by the overlapping activities of activator and repressor sequences in enhancers. However, few studies illuminate how these sequences evolve in the origin of new enhancers. Here, we show that expression of the bond gene in the semicircular wall epithelium (swe) of the Drosophila melanogaster male ejaculatory bulb (EB) is controlled by an enhancer consisting of an activator region that requires Abdominal-B driving expression in the entire EB and a repressor region that restricts this expression to the EB swe. Although this expression pattern is independently gained in the distantly related Scaptodrosophila lebanonensis and does not require Abdominal-B, we show that functionally similar repressor sequences are present in Scaptodrosophila and also in species that do not express bond in the EB. We suggest that during enhancer evolution, repressor sequences can precede the evolution of activator sequences and may lead to similar but independently evolved expression patterns. Pu et al. show that the independent gain of a highly specific expression pattern across distantly related species may be because of the preexistence of repressor sequences that precedes the diversification of these species. This may reflect a general mechanism underlying the evolution of highly specific enhancers.
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Affiliation(s)
- Jian Pu
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA.
| | - Zinan Wang
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Haosu Cong
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Jacqueline S R Chin
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A(∗)STAR), Brenner Centre for Molecular Medicine, Singapore 117609, Singapore
| | - Jessa Justen
- Laboratory of Cellular and Molecular Biology, University of Wisconsin, Madison, WI 53706, USA
| | - Cédric Finet
- Yale-NUS College, 16 College Avenue West, Singapore 138527, Singapore
| | - Joanne Y Yew
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA
| | - Henry Chung
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA.
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31
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Marinotti O. Anopheles darlingi versus Nyssorhynchus darlingi, response to the discussion. Trends Parasitol 2021; 37:849. [PMID: 34420867 DOI: 10.1016/j.pt.2021.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 07/26/2021] [Indexed: 01/21/2023]
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32
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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: 57] [Impact Index Per Article: 19.0] [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.
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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
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