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Wutke S, Blank SM, Boevé JL, Faircloth BC, Koch F, Linnen CR, Malm T, Niu G, Prous M, Schiff NM, Schmidt S, Taeger A, Vilhelmsen L, Wahlberg N, Wei M, Nyman T. Phylogenomics and biogeography of sawflies and woodwasps (Hymenoptera, Symphyta). Mol Phylogenet Evol 2024; 199:108144. [PMID: 38972494 DOI: 10.1016/j.ympev.2024.108144] [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: 03/11/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
Phylogenomic approaches have recently helped elucidate various insect relationships, but large-scale comprehensive analyses on relationships within sawflies and woodwasps are still lacking. Here, we infer the relationships and long-term biogeographic history of these hymenopteran groups using a large dataset of 354 UCE loci collected from 385 species that represent all major lineages. Early Hymenoptera started diversifying during the Early Triassic ∼249 Ma and spread all over the ancient supercontinent Pangaea. We recovered Xyeloidea as a monophyletic sister group to other Hymenoptera and Pamphilioidea as sister to Unicalcarida. Within the diverse family Tenthredinidae, our taxonomically and geographically expanded taxon sampling highlights the non-monophyly of several traditionally defined subfamilies. In addition, the recent removal of Athalia and related genera from the Tenthredinidae into the separate family Athaliidae is supported. The deep historical biogeography of the group is characterised by independent dispersals and re-colonisations between the northern (Laurasia) and southern (Gondwana) palaeocontinents. The breakup of these landmasses led to ancient vicariance in several Gondwanan lineages, while interchange across the Northern Hemisphere has continued until the Recent. The little-studied African sawfly fauna is likewise a diverse mixture of groups with varying routes of colonization. Our results reveal interesting parallels in the evolution and biogeography of early hymenopterans and other ancient insect groups.
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Affiliation(s)
- Saskia Wutke
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.
| | - Stephan M Blank
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Jean-Luc Boevé
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Frank Koch
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Tobias Malm
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Marko Prous
- Museum of Natural History, University of Tartu, Estonia
| | - Nathan M Schiff
- Formerly with the USDA Forest Service, Southern Research Station, Center for Bottomland Hardwoods Research, Stoneville, MS, USA
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany
| | - Andreas Taeger
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Lars Vilhelmsen
- Natural History Museum of Denmark, SCIENCE, University of Copenhagen, Denmark
| | | | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
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Vertacnik KL, Herrig DK, Godfrey RK, Hill T, Geib SM, Unckless RL, Nelson DR, Linnen CR. Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae). Ecol Evol 2023; 13:e10506. [PMID: 37791292 PMCID: PMC10542623 DOI: 10.1002/ece3.10506] [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: 06/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 10/05/2023] Open
Abstract
A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.
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Affiliation(s)
- Kim L. Vertacnik
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | | | - R. Keating Godfrey
- McGuire Center for Lepidoptera and Biodiversity, University of FloridaGainesvilleFloridaUSA
| | - Tom Hill
- National Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research UnitUnited States Department of Agriculture: Agriculture Research Service Pacific Basin Agricultural Research CenterHiloHawaiiUSA
| | - Robert L. Unckless
- Department of Molecular BiosciencesUniversity of KansasLawrenceKansasUSA
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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Michell CT, Wagner N, Mutanen M, Lee KM, Nyman T. Genomic evidence for contrasting patterns of host-associated genetic differentiation across shared host-plant species in leaf- and bud-galling sawflies. Mol Ecol 2023; 32:1791-1809. [PMID: 36626108 DOI: 10.1111/mec.16844] [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: 08/02/2021] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Resource specialization and ecological speciation arising through host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary timescales. We applied genome-wide single nucleotide polymorphism and mitochondrial DNA sequence data obtained through genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae) collected from seven shared willow (Salicaceae: Salix) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their Salix hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species compared with most bud gallers. In contrast to bud gallers, leaf gallers also exhibited statistically significant cophylogenetic signal with their Salix hosts. The observed discordant patterns of resource specialization and host shifts in two related galler groups that have radiated in parallel across a shared resource base indicate a lack of evolutionary repeatability in the focal system, and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.
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Affiliation(s)
- Craig T Michell
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Natascha Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
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Bell EA, Butler CL, Oliveira C, Marburger S, Yant L, Taylor MI. Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines. Mol Ecol Resour 2021; 22:823-833. [PMID: 34407282 DOI: 10.1111/1755-0998.13489] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022]
Abstract
Transposable elements (TEs) are significant genomic components which can be detected either through sequence homology against existing databases or de novo, with the latter potentially reducing the risk of underestimating TE abundance. Here, we describe the semi-automated generation of a de novo TE library using the newly developed EDTA pipeline and DeepTE classifier in a non-model teleost (Corydoras fulleri). Using both genomic and transcriptomic data, we assess this de novo pipeline's performance across four TE based metrics: (i) abundance, (ii) composition, (iii) fragmentation, and (iv) age distributions. We then compare the results to those found when using a curated teleost library (Danio rerio). We identify quantitative differences in these metrics and highlight how TE library choice can have major impacts on TE-based estimates in non-model species.
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Affiliation(s)
- Ellen A Bell
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | | | - Claudio Oliveira
- Department of Structural and Functional Biology, Institute of Biosciences/UNESP, Rua Professor Doutor Antonio Celso Wagner Zanin, Botucatu, São Paulo, Brazil
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, Norfolk, UK
| | - Levi Yant
- Future Food Beacon of Excellence and the School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
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