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Dearden PK. Evolution: Hidden homologies may underpin the diversity of arthropods. Curr Biol 2022; 32:R916-R918. [PMID: 36099895 DOI: 10.1016/j.cub.2022.07.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Arthropods are remarkable for the diversity of their exoskeletons. A new study shows that these structures, from crustacean carapaces to insect wings, may be homologous and derived from hidden developmental structures preserved through arthropod evolution.
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Affiliation(s)
- Peter K Dearden
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, Aotearoa-New Zealand.
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2
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Bruce HS, Patel NH. The Daphnia carapace and other novel structures evolved via the cryptic persistence of serial homologs. Curr Biol 2022; 32:3792-3799.e3. [PMID: 35858617 DOI: 10.1016/j.cub.2022.06.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/13/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022]
Abstract
Understanding how novel structures arise is a central question in evolution. Novel structures are often defined as structures that are not derived from (homologous to) any structure in the ancestor.1 The carapace of the crustacean Daphnia magna is a bivalved "cape" of exoskeleton. Shiga et al.2 proposed that the carapace of crustaceans like Daphnia and many other plate-like outgrowths in arthropods are novel structures that arose through the repeated co-option of genes like vestigial that also pattern insect wings.2-4 To determine whether the Daphnia carapace is a novel structure, we compare previous functional work2 with the expression of genes known to pattern the proximal leg region (pannier, araucan, and vestigial)5,6 between Daphnia, Parhyale, and Tribolium. Our results suggest that the Daphnia carapace did not arise by co-option but instead derived from an exite (lateral leg lobe) that emerges from an ancestral proximal leg segment that was incorporated into the Daphnia body wall. The Daphnia carapace, therefore, appears to be homologous to the Parhyale tergal plate and the insect wing.5 Remarkably, the vestigial-positive tissue that gives rise to the Daphnia carapace appears to be present in Parhyale7 and Tribolium as a small, inconspicuous protrusion. Thus, rather than a novel structure resulting from gene co-option, the Daphnia carapace appears to have arisen from a shared, ancestral tissue (morphogenetic field) that persists in a cryptic state in other arthropod lineages. Cryptic persistence of unrecognized serial homologs may thus be a general solution for the origin of novel structures.
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Affiliation(s)
- Heather S Bruce
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
| | - Nipam H Patel
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA; University of Chicago, Organismal Biology & Anatomy, 1027 E 57(th) Street, Chicago, IL 60637, USA
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3
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Melicher D, Bowsher JH, Rinehart JP. Fluctuating temperatures extend longevity in pupae and adult stages of the sepsid Themira biloba. J Therm Biol 2021; 99:102959. [PMID: 34420614 DOI: 10.1016/j.jtherbio.2021.102959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 11/16/2022]
Abstract
Fluctuating Thermal Regimes (FTR), where organisms are held at low temperatures with a brief, daily warm pulse, have been shown to increase longevity in adult insects and improve pupa survival while reducing sublethal effects. We used FTR to extend the longevity and thus generation time of the fly species Themira biloba (Diptera: Sepsidae). T. biloba can be maintained in continuous culture and requires an insecticide-free dung substrate for larval growth and development. Our objective was to decrease labor and consumable materials required to maintain insect species in critical scientific collections using FTR. We extended pupation time from 4 days up to 8 weeks with no increase in mortality, and mean adult longevity was increased from 12 days to 50 days. FTR is a valuable tool for reducing the investment required to maintain rare and exotic insects.
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Affiliation(s)
- Dacotah Melicher
- Bioscience Research Laboratory, U.S. Department of Agriculture/Agricultural Research Station, 1605 Albrecht Boulevard, Fargo, ND, 58105, USA.
| | - Julia H Bowsher
- Department of Biological Sciences, North Dakota State University, 1340 Bolley Drive, 218 Stevens Hall, Fargo, ND, 58102, USA
| | - Joseph P Rinehart
- Bioscience Research Laboratory, U.S. Department of Agriculture/Agricultural Research Station, 1605 Albrecht Boulevard, Fargo, ND, 58105, USA
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4
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Blanckenhorn WU, Baur J, Roy J, Puniamoorthy N, Busso JP, Schäfer MA, Rohner PT. Comparative sexual selection in field and laboratory in a guild of sepsid dung flies. Anim Behav 2021. [DOI: 10.1016/j.anbehav.2021.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Temporal flexibility of gene regulatory network underlies a novel wing pattern in flies. Proc Natl Acad Sci U S A 2020; 117:11589-11596. [PMID: 32393634 PMCID: PMC7261121 DOI: 10.1073/pnas.2002092117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Developmental genes can be coopted to generate evolutionary novelties by changing their spatial regulation. However, developmental genes seldom act independently, but rather work in a gene regulatory network (GRN). How is it possible to recruit a single gene from a whole GRN? What are the properties that allow parallel cooptions of the same genes during evolution? Here, we show that a novel engrailed gene expression underlies a novel wing color pattern in flies. We show that cooption is facilitated 1) because of GRN flexibility over development and 2) because every single gene of the GRN has its own functional time window. We suggest these two temporal properties could explain why the same gene can be independently recruited several times during evolution. Organisms have evolved endless morphological, physiological, and behavioral novel traits during the course of evolution. Novel traits were proposed to evolve mainly by orchestration of preexisting genes. Over the past two decades, biologists have shown that cooption of gene regulatory networks (GRNs) indeed underlies numerous evolutionary novelties. However, very little is known about the actual GRN properties that allow such redeployment. Here we have investigated the generation and evolution of the complex wing pattern of the fly Samoaia leonensis. We show that the transcription factor Engrailed is recruited independently from the other players of the anterior–posterior specification network to generate a new wing pattern. We argue that partial cooption is made possible because 1) the anterior–posterior specification GRN is flexible over time in the developing wing and 2) this flexibility results from the fact that every single gene of the GRN possesses its own functional time window. We propose that the temporal flexibility of a GRN is a general prerequisite for its possible cooption during the course of evolution.
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6
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Blanckenhorn WU, Baur J, Busso JP, Giesen A, Gourgoulianni N, van Koppenhagen N, Roy J, Schäfer MA, Wegmann A, Rohner PT. Sexual size dimorphism is associated with reproductive life history trait differentiation in coexisting sepsid flies. OIKOS 2020. [DOI: 10.1111/oik.07036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Wolf U. Blanckenhorn
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstrasse 190 CH‐8057 Zürich Switzerland
| | - Julian Baur
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstrasse 190 CH‐8057 Zürich Switzerland
| | - Juan Pablo Busso
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstrasse 190 CH‐8057 Zürich Switzerland
| | - Athene Giesen
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstrasse 190 CH‐8057 Zürich Switzerland
| | - Natalia Gourgoulianni
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstrasse 190 CH‐8057 Zürich Switzerland
| | - Nicola van Koppenhagen
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstrasse 190 CH‐8057 Zürich Switzerland
| | - Jeannine Roy
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstrasse 190 CH‐8057 Zürich Switzerland
| | - Martin A. Schäfer
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstrasse 190 CH‐8057 Zürich Switzerland
| | - Alexandra Wegmann
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstrasse 190 CH‐8057 Zürich Switzerland
| | - Patrick T. Rohner
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Winterthurerstrasse 190 CH‐8057 Zürich Switzerland
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7
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Rajaratnam G, Supeinthiran A, Meier R, Su KFY. CRISPR/Cas9 deletions in a conserved exon of Distal-less generates gains and losses in a recently acquired morphological novelty in flies. iScience 2018; 10:222-233. [PMID: 30553946 PMCID: PMC6297884 DOI: 10.1016/j.isci.2018.11.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 01/23/2023] Open
Abstract
Distal-less has been repeatedly co-opted for the development of many novel traits. Here, we document its curious role in the development of a novel abdominal appendage (“sternite brushes”) in sepsid flies. CRISPR/Cas9 deletions in the homeodomain result in losses of sternite brushes, demonstrating that Distal-less is necessary for their development. However, deletions in the upstream coding exon (Exon 2) produce losses or gains of brushes. A dissection of Exon 2 reveals that the likely mechanism for gains involves a deletion in an exon-splicing enhancer site that leads to exon skipping. Such contradictory phenotypes are also observed in butterflies, suggesting that mutations in the conserved upstream regions have the potential to generate phenotypic variability in insects that diverged 300 million years ago. Our results demonstrate the importance of Distal-less for the development of a novel abdominal appendage in insects and highlight how site-specific mutations in the same exon can produce contradictory phenotypes. Distal-less is necessary for the development of a novel abdominal appendage CRISPR/Cas9 editing produced both losses and gains of novel abdominal appendages Gains of appendages result from mutations in exonic splicing enhancer (ESEs) sites ESE mutations likely led to exon skipping and an altered Distal-less protein
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Affiliation(s)
- Gowri Rajaratnam
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | | | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Lee Kong Chian Natural History Museum, Singapore, Singapore.
| | - Kathy F Y Su
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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8
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Melicher D, Su KFY, Meier R, Bowsher JH. Comparative analysis reveals the complex role of histoblast nest size in the evolution of novel insect abdominal appendages in Sepsidae (Diptera). BMC Evol Biol 2018; 18:151. [PMID: 30314458 PMCID: PMC6186081 DOI: 10.1186/s12862-018-1265-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/26/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The males of some sepsid species (Sepsidae: Diptera) have abdominal appendages that are remarkable in several ways. They are sexually dimorphic, have a complex evolutionary history of gain and loss, and can be jointed and thus highly mobile. The sternite brushes are used extensively in complex courtship behaviors that differ considerably between species and during mating. The abdominal appendages have a novel developmental pathway developing from histoblast nests rather than imaginal discs. RESULTS We focus on the evolution of cell number, nest area, and segment length in both sexes to understand how this tissue relates to the formation of novel abdominal appendages. We map histoblast nest size of wandering-phase larvae of 17 species across 10 genera to a phylogenetic tree of Sepsidae and demonstrate that abdominal appendages require significant increases of histoblast nest size and cell number in most species while one species produces small appendages even without such modifications. In species with particularly large appendages, not only the nests on the fourth, but nests in neighboring segments are enlarged (Themira biloba, Themira putris). The loss of abdominal appendages corresponds to the loss of an enlarged fourth histoblast nest, although one species showed an exception to this pattern. One species that constitutes an independent origin of abdominal appendages (Perochaeta dikowi) uses an unusual developmental mechanism in that the histoblast nest sizes are not sexually dimorphic. CONCLUSIONS The surprisingly high diversity in histoblast size and degree of sexual dimorphism suggests that the developmental mechanism used for abdominal appendage formation in sepsids is highly adaptable. The presence of appendages usually correlate with increased histoblast cell number and in most cases appendage loss results in a return to ancestral histoblast morphology. However, we also identify several exceptions that indicate the abdominal appendages have a malleable developmental origin that is responsive to selection.
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Affiliation(s)
- Dacotah Melicher
- U.S. Department of Agriculture/Agricultural Research Station, Bioscience Research Laboratory, 1605 Albrecht Boulevard, Fargo, ND 58102 USA
| | - Kathy F Y Su
- Department of Biological Sciences, National University of Singapore, 14 Science Dr 4, Singapore, 117543 Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, 14 Science Dr 4, Singapore, 117543 Singapore
| | - Julia H Bowsher
- Department of Biological Sciences, North Dakota State University, 1340 Bolley Drive, 218 Stevens Hall, Fargo, ND 58102 USA
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9
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Thompson KJ. Oviposition-like central pattern generators in pregenital segments of male and female grasshoppers. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2018; 204:419-433. [PMID: 29423751 DOI: 10.1007/s00359-018-1249-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/27/2018] [Accepted: 01/31/2018] [Indexed: 10/18/2022]
Abstract
Grasshoppers produce an extraordinary oviposition behavior that is associated with multiple specializations of the skeletal and neuromuscular systems in the posterior abdomen, including a central pattern generator (CPG) in the female's terminal abdominal ganglion. Two pairs of shovel-shaped appendages, the ovipositor valves on the abdomen tip, excavate the soil for deposition of eggs. By contrast, the sexually monomorphic pregenital region of the abdomen is without appendages. Morphological homologues of ovipositor muscles and efferent neurons in the eighth abdominal segment are nevertheless present in pregenital segments of males and females. In both sexes, a robust rhythmic motor program was induced in pregenital segments by the same experimental methods used to elicit oviposition digging. The activity, recorded extracellularly, was oviposition-like in burst period (5-6 s) and homologous muscle phase relationships, and it persisted after sensory inputs were removed, indicating the presence of pregenital CPGs. The abdomen exhibited posterior-going waves of activity with an intersegmental phase delay of approximately 1 s. These results indicate that serially homologous motor systems, including functional CPGs, provided the foundation for the evolution of oviposition behavior.
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Affiliation(s)
- Karen J Thompson
- Department of Biology, Agnes Scott College, 141 E College Ave., Decatur, 30030, GA, USA.
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10
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Herath B, Dochtermann NA, Johnson JI, Leonard Z, Bowsher JH. Selection on bristle length has the ability to drive the evolution of male abdominal appendages in the sepsid fly Themira biloba. J Evol Biol 2015; 28:2308-17. [PMID: 26356143 DOI: 10.1111/jeb.12755] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 09/01/2015] [Accepted: 09/07/2015] [Indexed: 11/30/2022]
Abstract
Many exaggerated and novel traits are strongly influenced by sexual selection. Although sexual selection is a powerful evolutionary force, underlying genetic interactions can constrain evolutionary outcomes. The relative strength of selection vs. constraint has been a matter of debate for the evolution of male abdominal appendages in sepsid flies. These abdominal appendages are involved in courtship and mating, but their function has not been directly tested. We performed mate choice experiments to determine whether sexual selection acts on abdominal appendages in the sepsid Themira biloba. We tested whether appendage bristle length influenced successful insemination by surgically trimming the bristles. Females paired with males that had shortened bristles laid only unfertilized eggs, indicating that long bristles are necessary for successful insemination. We also tested whether the evolution of bristle length was constrained by phenotypic correlations with other traits. Analyses of phenotypic covariation indicated that bristle length was highly correlated with other abdominal appendage traits, but was not correlated with abdominal sternite size. Thus, abdominal appendages are not exaggerated traits like many sexual ornaments, but vary independently from body size. At the same time, strong correlations between bristle length and appendage length suggest that selection on bristle length is likely to result in a correlated increase in appendage length. Bristle length is under sexual selection in T. biloba and has the potential to evolve independently from abdomen size.
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Affiliation(s)
- B Herath
- Department of Biological Sciences, NDSU Dept 2715, North Dakota State University, Fargo, ND, USA
| | - N A Dochtermann
- Department of Biological Sciences, NDSU Dept 2715, North Dakota State University, Fargo, ND, USA
| | - J I Johnson
- Department of Biological Sciences, NDSU Dept 2715, North Dakota State University, Fargo, ND, USA
| | - Z Leonard
- Department of Biological Sciences, NDSU Dept 2715, North Dakota State University, Fargo, ND, USA
| | - J H Bowsher
- Department of Biological Sciences, NDSU Dept 2715, North Dakota State University, Fargo, ND, USA
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11
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Smith FW, Angelini DR, Gaudio MS, Jockusch EL. Metamorphic labral axis patterning in the beetle Tribolium castaneum requires multiple upstream, but few downstream, genes in the appendage patterning network. Evol Dev 2014; 16:78-91. [PMID: 24617987 DOI: 10.1111/ede.12066] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The arthropod labrum is an anterior appendage-like structure that forms the dorsal side of the preoral cavity. Conflicting interpretations of fossil, nervous system, and developmental data have led to a proliferation of scenarios for labral evolution. The best supported hypothesis is that the labrum is a novel structure that shares development with appendages as a result of co-option. Here, we use RNA interference in the red flour beetle Tribolium castaneum to compare metamorphic patterning of the labrum to previously published data on ventral appendage patterning. As expected under the co-option hypothesis, depletion of several genes resulted in similar defects in the labrum and ventral appendages. These include proximal deletions and proximal-to-distal transformations resulting from depletion of the leg gap genes homothorax and extradenticle, large-scale deletions resulting from depletion of the leg gap gene Distal-less, and smaller distal deletions resulting from knockdown of the EGF ligand Keren. However, depletion of dachshund and many of the genes that function downstream of the leg gap genes in the ventral appendages had either subtle or no effects on labral axis patterning. This pattern of partial similarity suggests that upstream genes act through different downstream targets in the labrum. We also discovered that many appendage axis patterning genes have roles in patterning the epipharyngeal sensillum array, suggesting that they have become integrated into a novel regulatory network. These genes include Notch, Delta, and decapentaplegic, and the transcription factors abrupt, bric à brac, homothorax, extradenticle and the paralogs apterous a and apterous b.
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Affiliation(s)
- Frank W Smith
- Department of Ecology & Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd., U-3043, Storrs, CT, 06269-3043, USA
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12
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Cerretti P, Di Giulio A, Romani R, Inclan DJ, Whitmore D, Di Giovanni F, Scalici M, Minelli A. First report of exocrine epithelial glands in oestroid flies: the tachinid sexual patches (Diptera: Oestroidea: Tachinidae). ACTA ZOOL-STOCKHOLM 2014. [DOI: 10.1111/azo.12085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pierfilippo Cerretti
- DAFNAE-Entomologia; Università degli Studi di Padova; Viale dell'Università 16 Legnaro I 35020 Italy
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’; ‘Sapienza’ Università di Roma; Piazzale A. Moro 5 Rome I 00185 Italy
| | - Andrea Di Giulio
- Dipartimento di Scienze; Università degli Studi ‘Roma Tre’; Viale G. Marconi 446 Rome I 00146 Italy
| | - Roberto Romani
- Dipartimento di Scienze Agrarie Alimentari e Ambientali; Università degli Studi di Perugia; Borgo XX Giugno 74 Perugia I 06121 Italy
| | - Diego J. Inclan
- DAFNAE-Entomologia; Università degli Studi di Padova; Viale dell'Università 16 Legnaro I 35020 Italy
| | - Daniel Whitmore
- Department of Life Sciences; Natural History Museum; Cromwell Road London SW7 5BD UK
| | - Filippo Di Giovanni
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’; ‘Sapienza’ Università di Roma; Piazzale A. Moro 5 Rome I 00185 Italy
| | - Massimiliano Scalici
- Dipartimento di Scienze; Università degli Studi ‘Roma Tre’; Viale G. Marconi 446 Rome I 00146 Italy
| | - Alessandro Minelli
- Dipartimento di Biologia; Università degli Studi di Padova; Via Ugo Bassi 58B Padova I 35131 Italy
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13
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Melicher D, Torson AS, Dworkin I, Bowsher JH. A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach. BMC Genomics 2014; 15:188. [PMID: 24621177 PMCID: PMC4008362 DOI: 10.1186/1471-2164-15-188] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 03/03/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Sepsidae family of flies is a model for investigating how sexual selection shapes courtship and sexual dimorphism in a comparative framework. However, like many non-model systems, there are few molecular resources available. Large-scale sequencing and assembly have not been performed in any sepsid, and the lack of a closely related genome makes investigation of gene expression challenging. Our goal was to develop an automated pipeline for de novo transcriptome assembly, and to use that pipeline to assemble and analyze the transcriptome of the sepsid Themira biloba. RESULTS Our bioinformatics pipeline uses cloud computing services to assemble and analyze the transcriptome with off-site data management, processing, and backup. It uses a multiple k-mer length approach combined with a second meta-assembly to extend transcripts and recover more bases of transcript sequences than standard single k-mer assembly. We used 454 sequencing to generate 1.48 million reads from cDNA generated from embryo, larva, and pupae of T. biloba and assembled a transcriptome consisting of 24,495 contigs. Annotation identified 16,705 transcripts, including those involved in embryogenesis and limb patterning. We assembled transcriptomes from an additional three non-model organisms to demonstrate that our pipeline assembled a higher-quality transcriptome than single k-mer approaches across multiple species. CONCLUSIONS The pipeline we have developed for assembly and analysis increases contig length, recovers unique transcripts, and assembles more base pairs than other methods through the use of a meta-assembly. The T. biloba transcriptome is a critical resource for performing large-scale RNA-Seq investigations of gene expression patterns, and is the first transcriptome sequenced in this Dipteran family.
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Affiliation(s)
- Dacotah Melicher
- />Department of Biological Sciences, North Dakota State University, 1340 Bolley Drive, 218 Stevens Hall, Fargo, ND 58102 USA
| | - Alex S Torson
- />Department of Biological Sciences, North Dakota State University, 1340 Bolley Drive, 218 Stevens Hall, Fargo, ND 58102 USA
| | - Ian Dworkin
- />Department of Zoology, Michigan State University, 328 Giltner Hall, East Lansing, MI 48823 USA
| | - Julia H Bowsher
- />Department of Biological Sciences, North Dakota State University, 1340 Bolley Drive, 218 Stevens Hall, Fargo, ND 58102 USA
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14
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Zhao L, Annie ASH, Amrita S, Yi SKF, Rudolf M. Does better taxon sampling help? A new phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha) based on 50 new taxa and the same old mitochondrial and nuclear markers. Mol Phylogenet Evol 2013; 69:153-64. [PMID: 23707858 DOI: 10.1016/j.ympev.2013.05.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 05/05/2013] [Accepted: 05/14/2013] [Indexed: 11/19/2022]
Abstract
We here present a phylogenetic hypothesis for Sepsidae (Diptera: Cyclorrhapha), a group of schizophoran flies with ca. 320 described species that is widely used in sexual selection research. The hypothesis is based on five nuclear and five mitochondrial markers totaling 8813 bp for ca. 30% of the diversity (105 sepsid taxa) and - depending on analysis - six or nine outgroup species. Maximum parsimony (MP), maximum likelihood (ML), and Bayesian inferences (BI) yield overall congruent, well-resolved, and supported trees that are largely unaffected by three different ways to partition the data in BI and ML analyses. However, there are also five areas of uncertainty that affect suprageneric relationships where different analyses yield alternate topologies and MP and ML trees have significant conflict according to Shimodaira-Hasegawa tests. Two of these were already affected by conflict in a previous analysis that was based on the same genes and a subset of 69 species. The remaining three involve newly added taxa or genera whose relationships were previously resolved with low support. We thus find that the denser taxon sample in the present analysis does not reduce the topological conflict that had been identified previously. The present study nevertheless presents a significant contribution to the understanding of sepsid relationships in that 50 additional taxa from 18 genera are added to the Tree-of-Life of Sepsidae and that the placement of most taxa is well supported and robust to different tree reconstruction techniques.
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Affiliation(s)
- Lei Zhao
- Department of Biological Sciences, National University of Singapore, 14 Science Dr 4, Singapore 117543, Singapore
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15
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Bowsher JH, Ang Y, Ferderer T, Meier R. Deciphering the evolutionary history and developmental mechanisms of a complex sexual ornament: the abdominal appendages of Sepsidae (Diptera). Evolution 2012; 67:1069-80. [PMID: 23550756 DOI: 10.1111/evo.12006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Male abdomen appendages are a novel trait found within Sepsidae (Diptera). Here we demonstrate that they are likely to have evolved once, were lost three times, and then secondarily gained in one lineage. The developmental basis of these appendages was investigated by counting the number of histoblast cells in each abdominal segment in four species: two that represented the initial instance of appendage evolution, one that has secondarily gained appendages, and one species that did not have appendages. Males of all species with appendages have elevated cell counts for the fourth segment, which gives rise to the appendages. In Perochaeta dikowi, which reacquired the trait, the females also have elevated cell count on the fourth segment despite the fact that females do not develop appendages. The species without appendages has similar cell counts in all segments regardless of sex. These results suggest that the basis for appendage development is shared in males across all species, but the sexual dimorphism is regulated differently in P. dikowi.
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Affiliation(s)
- Julia H Bowsher
- Department of Biological Sciences, North Dakota State University, NDSU Dept 2715, PO Box 6050, Fargo, North Dakota 58108, USA.
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McCauley BS, Wright EP, Exner C, Kitazawa C, Hinman VF. Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms. EvoDevo 2012; 3:17. [PMID: 22877149 PMCID: PMC3482387 DOI: 10.1186/2041-9139-3-17] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 06/22/2012] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The mechanisms by which the conserved genetic "toolkit" for development generates phenotypic disparity across metazoans is poorly understood. Echinoderm larvae provide a great resource for understanding how developmental novelty arises. The sea urchin pluteus larva is dramatically different from basal echinoderm larval types, which include the auricularia-type larva of its sister taxon, the sea cucumbers, and the sea star bipinnaria larva. In particular, the pluteus has a mesodermally-derived larval skeleton that is not present in sea star larvae or any outgroup taxa. To understand the evolutionary origin of this structure, we examined the molecular development of mesoderm in the sea cucumber, Parastichopus parvimensis. RESULTS By comparing gene expression in sea urchins, sea cucumbers and sea stars, we partially reconstructed the mesodermal regulatory state of the echinoderm ancestor. Surprisingly, we also identified expression of the transcription factor alx1 in a cryptic skeletogenic mesenchyme lineage in P. parvimensis. Orthologs of alx1 are expressed exclusively within the sea urchin skeletogenic mesenchyme, but are not expressed in the mesenchyme of the sea star, which suggests that alx1+ mesenchyme is a synapomorphy of at least sea urchins and sea cucumbers. Perturbation of Alx1 demonstrates that this protein is necessary for the formation of the sea cucumber spicule. Overexpression of the sea star alx1 ortholog in sea urchins is sufficient to induce additional skeleton, indicating that the Alx1 protein has not evolved a new function during the evolution of the larval skeleton. CONCLUSIONS The proposed echinoderm ancestral mesoderm state is highly conserved between the morphologically similar, but evolutionarily distant, auricularia and bipinnaria larvae. However, the auricularia, but not bipinnaria, also develops a simple skelotogenic cell lineage. Our data indicate that the first step in acquiring these novel cell fates was to re-specify the ancestral mesoderm into molecularly distinct territories. These new territories likely consisted of only a few cells with few regulatory differences from the ancestral state, thereby leaving the remaining mesoderm to retain its original function. The new territories were then free to take on a new fate. Partitioning of existing gene networks was a necessary pre-requisite to establish novelty in this system.
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Affiliation(s)
- Brenna S McCauley
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Avenue, Pittsburgh, PA, 15213, USA
| | - Erin P Wright
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Avenue, Pittsburgh, PA, 15213, USA
| | - Cameron Exner
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Avenue, Pittsburgh, PA, 15213, USA
| | - Chisato Kitazawa
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Avenue, Pittsburgh, PA, 15213, USA
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Avenue, Pittsburgh, PA, 15213, USA
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Shirai LT, Saenko SV, Keller RA, Jerónimo MA, Brakefield PM, Descimon H, Wahlberg N, Beldade P. Evolutionary history of the recruitment of conserved developmental genes in association to the formation and diversification of a novel trait. BMC Evol Biol 2012; 12:21. [PMID: 22335999 PMCID: PMC3361465 DOI: 10.1186/1471-2148-12-21] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 02/15/2012] [Indexed: 12/31/2022] Open
Abstract
Background The origin and modification of novel traits are important aspects of biological diversification. Studies combining concepts and approaches of developmental genetics and evolutionary biology have uncovered many examples of the recruitment, or co-option, of genes conserved across lineages for the formation of novel, lineage-restricted traits. However, little is known about the evolutionary history of the recruitment of those genes, and of the relationship between them -for example, whether the co-option involves whole or parts of existing networks, or whether it occurs by redeployment of individual genes with de novo rewiring. We use a model novel trait, color pattern elements on butterfly wings called eyespots, to explore these questions. Eyespots have greatly diversified under natural and sexual selection, and their formation involves genetic circuitries shared across insects. Results We investigated the evolutionary history of the recruitment and co-recruitment of four conserved transcription regulators to the larval wing disc region where circular pattern elements develop. The co-localization of Antennapedia, Notch, Distal-less, and Spalt with presumptive (eye)spot organizers was examined in 13 butterfly species, providing the largest comparative dataset available for the system. We found variation between families, between subfamilies, and between tribes. Phylogenetic reconstructions by parsimony and maximum likelihood methods revealed an unambiguous evolutionary history only for Antennapedia, with a resolved single origin of eyespot-associated expression, and many homoplastic events for Notch, Distal-less, and Spalt. The flexibility in the (co-)recruitment of the targeted genes includes cases where different gene combinations are associated with morphologically similar eyespots, as well as cases where identical protein combinations are associated with very different phenotypes. Conclusions The evolutionary history of gene (co-)recruitment is consistent with both divergence from a recruited putative ancestral network, and with independent co-option of individual genes. The diversity in the combinations of genes expressed in association with eyespot formation does not parallel diversity in characteristics of the adult phenotype. We discuss these results in the context of inferring homology. Our study underscores the importance of widening the representation of phylogenetic, morphological, and genetic diversity in order to establish general principles about the mechanisms behind the evolution of novel traits.
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Affiliation(s)
- Leila T Shirai
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, P-2780-156 Oeiras, Portugal
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Monteiro A. Gene regulatory networks reused to build novel traits: co-option of an eye-related gene regulatory network in eye-like organs and red wing patches on insect wings is suggested by optix expression. Bioessays 2012; 34:181-6. [PMID: 22223407 DOI: 10.1002/bies.201100160] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Co-option of the eye developmental gene regulatory network may have led to the appearance of novel functional traits on the wings of flies and butterflies. The first trait is a recently described wing organ in a species of extinct midge resembling the outer layers of the midge's own compound eye. The second trait is red pigment patches on Heliconius butterfly wings connected to the expression of an eye selector gene, optix. These examples, as well as others, are discussed regarding the type of empirical evidence and burden of proof that have been used to infer gene network co-option underlying the origin of novel traits. A conceptual framework describing increasing confidence in inference of network co-option is proposed. Novel research directions to facilitate inference of network co-option are also highlighted, especially in cases where the pre-existent and novel traits do not resemble each other.
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Affiliation(s)
- Antónia Monteiro
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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Abstract
Insect glia represents a conspicuous and diverse population of cells and plays a role in controlling neuronal progenitor proliferation, axonal growth, neuronal differentiation and maintenance, and neuronal function. Genetic studies in Drosophila have elucidated many aspects of glial structure, function, and development. Just as in vertebrates, it appears as if different classes of glial cells are specialized for different functions. On the basis of topology and cell shape, glial cells of the central nervous system fall into three classes (Fig. 1A-C): (i) surface glia that extend sheath-like processes to wrap around the entire brain; (ii) cortex glia (also called cell body-associated glia) that encapsulate neuronal somata and neuroblasts which form the outer layer (cortex) of the central nervous system; (iii) neuropile glia that are located at the interface between the cortex and the neuropile, the central domain of the nervous system formed by the highly branched neuronal processes and their synaptic contacts. Surface glia is further subdivided into an outer, perineurial layer, and an inner, subperineurial layer. Likewise, neuropile glia comprises a class of cells that remain at the surface of the neuropile (ensheathing glia), and a second class that forms profuse lamellar processes around nerve fibers within the neuropile (astrocyte-like or reticular glia). Glia also surrounds the peripheral nerves and sensory organs; here, one also recognizes perineurial and subperineurial glia, and a third type called "wrapping glia" that most likely corresponds to the ensheathing glia of the central nervous system. Much more experimental work is needed to determine how fundamental these differences between classes of glial cells are, or how and when during development they are specified. To aid in this work the following review will briefly summarize our knowledge of the classes of glial cells encountered in the Drosophila nervous system, and then survey their development from the embryo to adult.
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Affiliation(s)
- Volker Hartenstein
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA.
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Tanaka K, Barmina O, Sanders LE, Arbeitman MN, Kopp A. Evolution of sex-specific traits through changes in HOX-dependent doublesex expression. PLoS Biol 2011; 9:e1001131. [PMID: 21886483 PMCID: PMC3160335 DOI: 10.1371/journal.pbio.1001131] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 07/15/2011] [Indexed: 12/27/2022] Open
Abstract
Almost every animal lineage is characterized by unique sex-specific traits, implying that such traits are gained and lost frequently in evolution. However, the genetic mechanisms responsible for these changes are not understood. In Drosophila, the activity of the sex determination pathway is restricted to sexually dimorphic tissues, suggesting that spatial regulation of this pathway may contribute to the evolution of sex-specific traits. We examine the regulation and function of doublesex (dsx), the main transcriptional effector of the sex determination pathway, in the development and evolution of Drosophila sex combs. Sex combs are a recent evolutionary innovation and show dramatic diversity in the relatively few Drosophila species that have them. We show that dsx expression in the presumptive sex comb region is activated by the HOX gene Sex combs reduced (Scr), and that the male isoform of dsx up-regulates Scr so that both genes become expressed at high levels in this region in males but not in females. Precise spatial regulation of dsx is essential for defining sex comb position and morphology. Comparative analysis of Scr and dsx expression reveals a tight correlation between sex comb morphology and the expression patterns of both genes. In species that primitively lack sex combs, no dsx expression is observed in the homologous region, suggesting that the origin and diversification of this structure were linked to the gain of a new dsx expression domain. Two other, distantly related fly lineages that independently evolved novel male-specific structures show evolutionary gains of dsx expression in the corresponding tissues, where dsx may also be controlled by Scr. These findings suggest that changes in the spatial regulation of sex-determining genes are a key mechanism that enables the evolution of new sex-specific traits, contributing to some of the most dramatic examples of phenotypic diversification in nature.
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Affiliation(s)
- Kohtaro Tanaka
- Department of Evolution and Ecology, University of California–Davis, Davis, California, United States of America
| | - Olga Barmina
- Department of Evolution and Ecology, University of California–Davis, Davis, California, United States of America
| | - Laura E. Sanders
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Michelle N. Arbeitman
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California–Davis, Davis, California, United States of America
- * E-mail:
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21
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Tan DSH, Ng SR, Meier R. New information on the evolution of mating behaviour in Sepsidae (Diptera) and the cost of male copulations in Saltella sphondylii. ORG DIVERS EVOL 2011. [DOI: 10.1007/s13127-011-0054-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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22
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Saenko SV, Marialva MS, Beldade P. Involvement of the conserved Hox gene Antennapedia in the development and evolution of a novel trait. EvoDevo 2011; 2:9. [PMID: 21504568 PMCID: PMC3108338 DOI: 10.1186/2041-9139-2-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 04/19/2011] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Hox proteins specify segment identity during embryogenesis and have typical associated expression patterns. Changes in embryonic expression and activity of Hox genes were crucial in the evolution of animal body plans, but their role in the post-embryonic development of lineage-specific traits remains largely unexplored. Here, we focus on the insect Hox genes Ultrabithorax (Ubx) and Antennapedia (Antp), and implicate the latter in the formation and diversification of novel, butterfly-specific wing patterns. RESULTS First, we describe a conserved pattern of Ubx expression and a novel pattern of Antp expression in wing discs of Bicyclus anynana butterflies. The discrete, reiterated domains of Antp contrast with the typical expression of Hox genes in single continuous regions in arthropod embryos. Second, we show that this pattern is associated with the establishment of the organizing centres of eyespots. Antp upregulation is the earliest event in organizer development described to date, and in contrast to all genes implicated in eyespot formation, is exclusive to those centres. Third, our comparative analysis of gene expression across nymphalids reveals unexpected differences in organizer determination. CONCLUSIONS We show that the Antp's recruitment for the formation of novel traits in butterfly wing discs involved the evolution of new expression domains, and is restricted to a particular lineage. This study contributes novel insights into the evolution of Antp expression, as well as into the genetic mechanisms underlying morphological diversification. Our results also underscore how a wider representation of morphological and phylogenetic diversity is essential in evolutionary developmental biology.
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Affiliation(s)
- Suzanne V Saenko
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
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23
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Hartenstein V. Morphological diversity and development of glia in Drosophila. Glia 2011; 59:1237-52. [PMID: 21438012 DOI: 10.1002/glia.21162] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 01/25/2011] [Indexed: 12/31/2022]
Abstract
Insect glia represents a conspicuous and diverse population of cells and plays a role in controlling neuronal progenitor proliferation, axonal growth, neuronal differentiation and maintenance, and neuronal function. Genetic studies in Drosophila have elucidated many aspects of glial structure, function, and development. Just as in vertebrates, it appears as if different classes of glial cells are specialized for different functions. On the basis of topology and cell shape, glial cells of the central nervous system fall into three classes (Fig. 1A-C): (i) surface glia that extend sheath-like processes to wrap around the entire brain; (ii) cortex glia (also called cell body-associated glia) that encapsulate neuronal somata and neuroblasts which form the outer layer (cortex) of the central nervous system; (iii) neuropile glia that are located at the interface between the cortex and the neuropile, the central domain of the nervous system formed by the highly branched neuronal processes and their synaptic contacts. Surface glia is further subdivided into an outer, perineurial layer, and an inner, subperineurial layer. Likewise, neuropile glia comprises a class of cells that remain at the surface of the neuropile (ensheathing glia), and a second class that forms profuse lamellar processes around nerve fibers within the neuropile (astrocyte-like or reticular glia). Glia also surrounds the peripheral nerves and sensory organs; here, one also recognizes perineurial and subperineurial glia, and a third type called "wrapping glia" that most likely corresponds to the ensheathing glia of the central nervous system. Much more experimental work is needed to determine how fundamental these differences between classes of glial cells are, or how and when during development they are specified. To aid in this work the following review will briefly summarize our knowledge of the classes of glial cells encountered in the Drosophila nervous system, and then survey their development from the embryo to adult.
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Affiliation(s)
- Volker Hartenstein
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California 90095, USA.
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Decapentaplegic (dpp) regulates the growth of a morphological novelty, beetle horns. Dev Genes Evol 2011; 221:17-27. [DOI: 10.1007/s00427-011-0355-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 02/17/2011] [Indexed: 12/13/2022]
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25
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Saenko SV, Brakefield PM, Beldade P. Single locus affects embryonic segment polarity and multiple aspects of an adult evolutionary novelty. BMC Biol 2010; 8:111. [PMID: 20796293 PMCID: PMC2940778 DOI: 10.1186/1741-7007-8-111] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 08/26/2010] [Indexed: 12/19/2022] Open
Abstract
Background The characterization of the molecular changes that underlie the origin and diversification of morphological novelties is a key challenge in evolutionary developmental biology. The evolution of such traits is thought to rely largely on co-option of a toolkit of conserved developmental genes that typically perform multiple functions. Mutations that affect both a universal developmental process and the formation of a novelty might shed light onto the genetics of traits not represented in model systems. Here we describe three pleiotropic mutations with large effects on a novel trait, butterfly eyespots, and on a conserved stage of embryogenesis, segment polarity. Results We show that three mutations affecting eyespot size and/or colour composition in Bicyclus anynana butterflies occurred in the same locus, and that two of them are embryonic recessive lethal. Using surgical manipulations and analysis of gene expression patterns in developing wings, we demonstrate that the effects on eyespot morphology are due to changes in the epidermal response component of eyespot induction. Our analysis of morphology and of gene expression in mutant embryos shows that they have a typical segment polarity phenotype, consistent with the mutant locus encoding a negative regulator of Wingless signalling. Conclusions This study characterizes the segregation and developmental effects of alleles at a single locus that controls the morphology of a lineage-specific trait (butterfly eyespots) and a conserved process (embryonic segment polarity and, specifically, the regulation of Wingless signalling). Because no gene with such function was found in the orthologous, highly syntenic genomic regions of two other lepidopterans, we hypothesize that our locus is a yet undescribed, possibly lineage-specific, negative regulator of the conserved Wnt/Wg pathway. Moreover, the fact that this locus interferes with multiple aspects of eyespot morphology and maps to a genomic region containing key wing pattern loci in different other butterfly species suggests it might correspond to a 'hotspot' locus in the diversification of this novel trait.
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Affiliation(s)
- Suzanne V Saenko
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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