1
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Qi L, Zhang N, Xu B, Xu Q, Han X, Kong L, Li Q. Increased microgastropoda sampling give new insights into the phylogenetic relationships of Littorinoidea (Littorinimorpha). Mol Phylogenet Evol 2024; 199:108139. [PMID: 38986757 DOI: 10.1016/j.ympev.2024.108139] [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: 03/26/2024] [Revised: 06/14/2024] [Accepted: 06/30/2024] [Indexed: 07/12/2024]
Abstract
Littorinoidea is one of the most diverse radiations and the most successful group that evolutionary transitions from marine to terrestrial within Littorinimorpha. With such an unmatched diversity, few phylogenetic investigations have attempted to understand their evolutionary relationships, and existing research has primarily focused on typical intertidal species. To address this gap, we conducted the first phylogenomic analysis of the Littorinoidea, leveraging 35 transcriptomes to investigate their internal relationships. Our analyses revealed significant revisions necessary within the Littorinoidea: 1) Pomatias appears distantly related to Littorinidae, suggesting a potential ancestral origin outside of Littorinoidea, challenging traditional classification. The homology of penial innervation within Littorinoidea warrants reevaluation. 2) Lacuna's placement indicates a close relationship with Naticidae, prompting consideration for its removal from Littorinidae. 3) Based on the current phylogenetic research, Peasiella may belong to a distinct family separate from Littorinidae. 4) Our findings support revising the placement of Pteropods within the Littorinimorpha, which is situated phylogenetically between the families Littorinoidea and Naticoidea. Additionally, we highlight the impact of site heterogeneity and evolutionary rate variation on phylogenetic inference. Our study provides a robust phylogenomic framework for the Littorinoidea, emphasizing the importance of including microgastropoda taxa in molecular phylogenetic reconstructions of gastropod subgroups.
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Affiliation(s)
- Lu Qi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Ning Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Biyang Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Qinzeng Xu
- Key Laboratory of Science and Engineering for Marine Ecology and Environment, The First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Xiao Han
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Sanya Oceanographic Institution, Ocean University of China, Sanya,572000, China.
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China; Sanya Oceanographic Institution, Ocean University of China, Sanya,572000, China
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2
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Shin S, Baker AJ, Enk J, McKenna DD, Foquet B, Vandergast AG, Weissman DB, Song H. Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales. Sci Rep 2024; 14:21377. [PMID: 39271747 PMCID: PMC11399444 DOI: 10.1038/s41598-024-72622-6] [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: 02/01/2024] [Accepted: 09/09/2024] [Indexed: 09/15/2024] Open
Abstract
Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.
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Affiliation(s)
- Seunggwan Shin
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
| | - Austin J Baker
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
- Entomology Department, Natural History Museum of Los Angeles County, Los Angeles, CA, USA
| | - Jacob Enk
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Duane D McKenna
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
| | - Bert Foquet
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Amy G Vandergast
- San Diego Field Station, Western Ecological Research Center, U.S. Geological Survey, San Diego, CA, USA
| | - David B Weissman
- Department of Entomology, California Academy of Sciences, Golden Gate Park, San Francisco, CA, USA
| | - Hojun Song
- Department of Entomology, Texas A&M University, College Station, TX, USA.
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3
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Li Y, Moritz C, Brennan IG, Zwick A, Nicholls J, Grealy A, Slipinski A. Evolution across the adaptive landscape in a hyperdiverse beetle radiation. Curr Biol 2024; 34:3685-3697.e6. [PMID: 39067451 DOI: 10.1016/j.cub.2024.06.080] [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: 04/02/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
The extraordinary diversification of beetles on Earth is a textbook example of adaptive evolution. Yet, the tempo and drivers of this super-radiation remain largely unclear. Here, we address this problem by investigating macroevolutionary dynamics in darkling beetles (Coleoptera: Tenebrionidae), one of the most ecomorphologically diverse beetle families (with over 30,000 species). Using multiple genomic datasets and analytical approaches, we resolve the long-standing inconsistency over deep relationships in the family. In conjunction with a landmark-based dataset of body shape morphology, we show that the evolutionary history of darkling beetles is marked by ancient rapid radiations, frequent ecological transitions, and rapid bursts of morphological diversification. On a global scale, our analyses uncovered a significant pulse of phenotypic diversification proximal to the Cretaceous-Palaeogene (K/Pg) mass extinction and convergence of body shape associated with recurrent ecological specializations. On a regional scale, two major Australasian radiations, the Adeliini and the Heleine clade, exhibited contrasting patterns of ecomorphological diversification, representing phylogenetic niche conservatism versus adaptive radiation. Our findings align with the Simpsonian model of adaptive evolution across the macroevolutionary landscape and highlight a significant role of ecological opportunity in driving the immense ecomorphological diversity in a hyperdiverse beetle group.
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Affiliation(s)
- Yun Li
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia.
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - James Nicholls
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - Alicia Grealy
- Australian National Herbarium, CSIRO, Canberra, ACT 2601, Australia
| | - Adam Slipinski
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
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4
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Frandsen PB, Holzenthal RW, Espeland M, Breinholt J, Thomas Thorpe JA, Simon S, Kawahara AY, Plotkin D, Hotaling S, Li Y, Nelson CR, Niehuis O, Mayer C, Podsiadlowski L, Donath A, Misof B, Moriarty Lemmon E, Lemmon A, Morse JC, Liu S, Pauls SU, Zhou X. Phylogenomics recovers multiple origins of portable case making in caddisflies (Insecta: Trichoptera), nature's underwater architects. Proc Biol Sci 2024; 291:20240514. [PMID: 38955232 PMCID: PMC11285404 DOI: 10.1098/rspb.2024.0514] [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: 03/05/2024] [Revised: 05/11/2024] [Accepted: 06/10/2024] [Indexed: 07/04/2024] Open
Abstract
Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16 000 described species. They play a fundamental role in freshwater ecology and environmental engineering in streams, rivers and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programmes. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case making, remain unanswered owing to the lack of a well-resolved phylogeny. Here, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 207 species, representing 48 of 52 extant families and 174 genera. We calibrated and dated the tree with 33 carefully selected fossils. The first caddisflies originated approximately 295 million years ago in the Permian, and major suborders began to diversify in the Triassic. Furthermore, we show that portable case making evolved in three separate lineages, and shifts in diversification occurred in concert with key evolutionary innovations beyond case making.
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Affiliation(s)
- Paul B. Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | - Marianne Espeland
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | | | | | - Sabrina Simon
- Rosenheim University of Applied Sciences, Rosenheim, Germany
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - David Plotkin
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Scott Hotaling
- Department of Watershed Sciences, Utah State University, Logan, UT, USA
| | - Yiyuan Li
- Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang Province, People’s Republic of China
| | - C. Riley Nelson
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, Freiburg, Germany
| | - Christoph Mayer
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Lars Podsiadlowski
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Alexander Donath
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Bernhard Misof
- Museum Koenig Bonn, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
- Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Alan Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, USA
| | - John C. Morse
- Department of Plant & Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, People’s Republic of China
| | - Steffen U. Pauls
- LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
- Department of Insect Biotechnology, Justus-Liebig-University Gießen, Gießen, Germany
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, People’s Republic of China
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5
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Delic S, Shuman B, Lee S, Bahmanyar S, Momany M, Onishi M. The evolutionary origins and ancestral features of septins. Front Cell Dev Biol 2024; 12:1406966. [PMID: 38994454 PMCID: PMC11238149 DOI: 10.3389/fcell.2024.1406966] [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: 03/25/2024] [Accepted: 05/08/2024] [Indexed: 07/13/2024] Open
Abstract
Septins are a family of membrane-associated cytoskeletal guanine-nucleotide binding proteins that play crucial roles in various cellular processes, such as cell division, phagocytosis, and organelle fission. Despite their importance, the evolutionary origins and ancestral function of septins remain unclear. In opisthokonts, septins form five distinct groups of orthologs, with subunits from multiple groups assembling into heteropolymers, thus supporting their diverse molecular functions. Recent studies have revealed that septins are also conserved in algae and protists, indicating an ancient origin from the last eukaryotic common ancestor. However, the phylogenetic relationships among septins across eukaryotes remained unclear. Here, we expanded the list of non-opisthokont septins, including previously unrecognized septins from glaucophyte algae. Constructing a rooted phylogenetic tree of 254 total septins, we observed a bifurcation between the major non-opisthokont and opisthokont septin clades. Within the non-opisthokont septins, we identified three major subclades: Group 6 representing chlorophyte green algae (6A mostly for species with single septins, 6B for species with multiple septins), Group 7 representing algae in chlorophytes, heterokonts, haptophytes, chrysophytes, and rhodophytes, and Group 8 representing ciliates. Glaucophyte and some ciliate septins formed orphan lineages in-between all other septins and the outgroup. Combining ancestral-sequence reconstruction and AlphaFold predictions, we tracked the structural evolution of septins across eukaryotes. In the GTPase domain, we identified a conserved GAP-like arginine finger within the G-interface of at least one septin in most algal and ciliate species. This residue is required for homodimerization of the single Chlamydomonas septin, and its loss coincided with septin duplication events in various lineages. The loss of the arginine finger is often accompanied by the emergence of the α0 helix, a known NC-interface interaction motif, potentially signifying the diversification of septin-septin interaction mechanisms from homo-dimerization to hetero-oligomerization. Lastly, we found amphipathic helices in all septin groups, suggesting that membrane binding is an ancestral trait. Coiled-coil domains were also broadly distributed, while transmembrane domains were found in some septins in Group 6A and 7. In summary, this study advances our understanding of septin distribution and phylogenetic groupings, shedding light on their ancestral features, potential function, and early evolution.
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Affiliation(s)
- Samed Delic
- Department of Biology, Duke University, Durham, NC, United States
| | - Brent Shuman
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, GA, United States
| | - Shoken Lee
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Shirin Bahmanyar
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Michelle Momany
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, GA, United States
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, NC, United States
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6
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Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [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: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
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Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
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7
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Delic S, Shuman B, Lee S, Bahmanyar S, Momany M, Onishi M. The Evolutionary Origins and Ancestral Features of Septins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586683. [PMID: 38585751 PMCID: PMC10996617 DOI: 10.1101/2024.03.25.586683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Septins are a family of membrane-associated cytoskeletal GTPases that play crucial roles in various cellular processes, such as cell division, phagocytosis, and organelle fission. Despite their importance, the evolutionary origins and ancestral function of septins remain unclear. In opisthokonts, septins form five distinct groups of orthologs, with subunits from multiple groups assembling into heteropolymers, thus supporting their diverse molecular functions. Recent studies have revealed that septins are also conserved in algae and protists, indicating an ancient origin from the last eukaryotic common ancestor. However, the phylogenetic relationships among septins across eukaryotes remained unclear. Here, we expanded the list of non-opisthokont septins, including previously unrecognized septins from rhodophyte red algae and glaucophyte algae. Constructing a rooted phylogenetic tree of 254 total septins, we observed a bifurcation between the major non-opisthokont and opisthokont septin clades. Within the non-opisthokont septins, we identified three major subclades: Group 6 representing chlorophyte green algae (6A mostly for species with single septins, 6B for species with multiple septins), Group 7 representing algae in chlorophytes, heterokonts, haptophytes, chrysophytes, and rhodophytes, and Group 8 representing ciliates. Glaucophyte and some ciliate septins formed orphan lineages in-between all other septins and the outgroup. Combining ancestral-sequence reconstruction and AlphaFold predictions, we tracked the structural evolution of septins across eukaryotes. In the GTPase domain, we identified a conserved GAP-like arginine finger within the G-interface of at least one septin in most algal and ciliate species. This residue is required for homodimerization of the single Chlamydomonas septin, and its loss coincided with septin duplication events in various lineages. The loss of the arginine finger is often accompanied by the emergence of the α0 helix, a known NC-interface interaction motif, potentially signifying the diversification of septin-septin interaction mechanisms from homo-dimerization to hetero-oligomerization. Lastly, we found amphipathic helices in all septin groups, suggesting that curvature-sensing is an ancestral trait of septin proteins. Coiled-coil domains were also broadly distributed, while transmembrane domains were found in some septins in Group 6A and 7. In summary, this study advances our understanding of septin distribution and phylogenetic groupings, shedding light on their ancestral features, potential function, and early evolution.
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Affiliation(s)
- Samed Delic
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Brent Shuman
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, Georgia, USA
| | - Shoken Lee
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Shirin Bahmanyar
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Michelle Momany
- Fungal Biology Group and Plant Biology Department, University of Georgia, Athens, Georgia, USA
| | - Masayuki Onishi
- Department of Biology, Duke University, Durham, North Carolina, USA
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8
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Li X, Breinholt JW, Martinez JI, Keegan K, Ellis EA, Homziak NT, Zwick A, Storer CG, McKenna D, Kawahara AY. Large-scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea). Cladistics 2024; 40:21-33. [PMID: 37787424 DOI: 10.1111/cla.12559] [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: 04/21/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 10/04/2023] Open
Abstract
The owlet moths (Noctuoidea; ~43-45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal-likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large-scale genomic data.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Jesse W Breinholt
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Precision Genomics, Intermountain Healthcare, St George, UT, 84790, USA
| | - Jose I Martinez
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
| | - Kevin Keegan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06268, USA
- Section of Invertebrate Zoology, Carnegie Museum of Natural History, 4400 Forbes Ave, Pittsburgh, PA, 15213-4080, USA
| | - Emily A Ellis
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Nicholas T Homziak
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Caroline G Storer
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Duane McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
- Center for Biodiversity Research, University of Memphis, Memphis, TN, 38152, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
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9
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Young LA, Maughan PJ, Jarvis DE, Hunt SP, Warner HC, Durrant KK, Kohlert T, Curti RN, Bertero D, Filippi GA, Pospíšilíková T, Krak K, Mandák B, Jellen EN. A chromosome-scale reference of Chenopodium watsonii helps elucidate relationships within the North American A-genome Chenopodium species and with quinoa. THE PLANT GENOME 2023; 16:e20349. [PMID: 37195017 DOI: 10.1002/tpg2.20349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 05/18/2023]
Abstract
Quinoa (Chenopodium quinoa), an Andean pseudocereal, attained global popularity beginning in the early 2000s due to its protein quality, glycemic index, and high fiber, vitamin, and mineral contents. Pitseed goosefoot (Chenopodium berlandieri), quinoa's North American free-living sister species, grows on disturbed and sandy substrates across the North America, including saline coastal sands, southwestern deserts, subtropical highlands, the Great Plains, and boreal forests. Together with South American avian goosefoot (Chenopodium hircinum) they comprise the American tetraploid goosefoot complex (ATGC). Superimposed on pitseed goosefoot's North American range are approximately 35 AA diploids, most of which are adapted to a diversity of niche environments. We chose to assemble a reference genome for Sonoran A-genome Chenopodium watsonii due to fruit morphological and high (>99.3%) preliminary sequence-match similarities with quinoa, along with its well-established taxonomic status. The genome was assembled into 1377 scaffolds spanning 547.76 Mb (N50 = 55.14 Mb, L50 = 5), with 94% comprised in nine chromosome-scale scaffolds and 93.9% Benchmarking Universal Single-Copy Orthologs genes identified as single copy and 3.4% as duplicated. A high degree of synteny, with minor and mostly telomeric rearrangements, was found when comparing this taxon with the previously reported genome of South American C. pallidicaule and the A-subgenome chromosomes of C. quinoa. Phylogenetic analysis was performed using 10,588 single-nucleotide polymorphisms generated by resequencing a panel of 41 New World AA diploid accessions and the Eurasian H-genome diploid Chenopodium vulvaria, along with three AABB tetraploids previously sequenced. Phylogenetic analysis of these 32 taxa positioned the psammophyte Chenopodium subglabrum on the branch containing A-genome sequences from the ATGC. We also present evidence for long-range dispersal of Chenopodium diploids between North and South America.
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Affiliation(s)
- Lauren A Young
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | | | - David E Jarvis
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Spencer P Hunt
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Heather C Warner
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Kristin K Durrant
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Tyler Kohlert
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
| | - Ramiro N Curti
- Facultad de Ciencias Naturales, Universidad Nacional de Salta, CCT-CONICET, Salta, Argentina
| | - Daniel Bertero
- Cátedra de Producción Vegetal, Facultad de Agronomía, Universidad de Buenos Aires and IFEVA-CONICET, Buenos Aires, Argentina
| | - Gabrielle A Filippi
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Tereza Pospíšilíková
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Karol Krak
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Bohumil Mandák
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Eric N Jellen
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, USA
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10
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Flury JM, Meusemann K, Martin S, Hilgers L, Spanke T, Böhne A, Herder F, Mokodongan DF, Altmüller J, Wowor D, Misof B, Nolte AW, Schwarzer J. Potential Contribution of Ancient Introgression to the Evolution of a Derived Reproductive Strategy in Ricefishes. Genome Biol Evol 2023; 15:evad138. [PMID: 37493080 PMCID: PMC10465105 DOI: 10.1093/gbe/evad138] [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: 07/05/2022] [Revised: 06/28/2023] [Accepted: 07/13/2023] [Indexed: 07/27/2023] Open
Abstract
Transitions from no parental care to extensive care are costly and involve major changes in life history, behavior, and morphology. Nevertheless, in Sulawesi ricefishes, pelvic brooding evolved from transfer brooding in two distantly related lineages within the genera Adrianichthys and Oryzias, respectively. Females of pelvic brooding species carry their eggs attached to their belly until the fry hatches. Despite their phylogenetic distance, both pelvic brooding lineages share a set of external morphological traits. A recent study found no direct gene flow between pelvic brooding lineages, suggesting independent evolution of the derived reproductive strategy. Convergent evolution can, however, also rely on repeated sorting of preexisting variation of an admixed ancestral population, especially when subjected to similar external selection pressures. We thus used a multispecies coalescent model and D-statistics to identify gene-tree-species-tree incongruencies, to evaluate the evolution of pelvic brooding with respect to interspecific gene flow not only between pelvic brooding lineages but also between pelvic brooding lineages and other Sulawesi ricefish lineages. We found a general network-like evolution in Sulawesi ricefishes, and as previously reported, we detected no gene flow between the pelvic brooding lineages. Instead, we found hybridization between the ancestor of pelvic brooding Oryzias and the common ancestor of the Oryzias species from the Lake Poso area. We further detected signs of introgression within the confidence interval of a quantitative trait locus associated with pelvic brooding in O. eversi. Our results hint toward a contribution of ancient standing genetic variation to the evolution of pelvic brooding in Oryzias.
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Affiliation(s)
- Jana M Flury
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Karen Meusemann
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Sebastian Martin
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Leon Hilgers
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Tobias Spanke
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Astrid Böhne
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Fabian Herder
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Daniel F Mokodongan
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, West Java, Indonesia
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Cologne University, Cologne, Germany
| | - Daisy Wowor
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, West Java, Indonesia
| | - Bernhard Misof
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
| | - Arne W Nolte
- Department of Ecological Genomics, Carl von Ossietzky Universität, Oldenburg, Germany
| | - Julia Schwarzer
- Leibniz-Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig Bonn, Bonn, Germany
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11
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Liu JL, Zhang JW, Han W, Wang YS, He SL, Wang ZQ. Advances in the understanding of Blattodea evolution: Insights from phylotranscriptomics and spermathecae. Mol Phylogenet Evol 2023; 182:107753. [PMID: 36898488 DOI: 10.1016/j.ympev.2023.107753] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023]
Abstract
Cockroaches, an ancient and diverse group of insects on earth that originated in the Carboniferous, displays a wide array of morphology or biology diversity. The spermatheca is an organ of the insect reproductive system; the diversity of spermathecae might be the adaption to different mating and sperm storage strategies. Yet a consensus about the phylogenetic relationships among the main lineages of Blattodea and the evolution of spermatheca has not been reached until now. Here we added the transcriptome data of Anaplectidae for the first time and supplemented other family level groups (such as Blaberidae, Corydiidae) to address the pending issues. Our results showed that Blattoidea was recovered as sister to Corydioidea, which was strongly supported by molecular evidence. In Blattoidea, (Lamproblattidae + Anaplectidae) + (Cryptocercidae + Termitoidae) was strongly supported by our molecular data. In Blaberoidea, Pseudophyllodromiidae and Blaberidae were recovered to be monophyletic, while Blattellidae was found to be paraphyletic with respect to Malaccina. Ectobius sylvestris + Malaccina discoidalis formed the sister group to other Blaberoidea; Blattellidae (except Malaccina discoidalis) + Nyctiboridae was found as the sister of Blaberidae. Corydiidae was recovered to be non-monophyletic due to the embedding of Nocticola sp. Our ASR analysis of spermatheca suggested that primary spermathecae were present in the common ancestor, and it transformed at least six times during the evolutionary history of Blattodea. The evolution of spermatheca could be described as a unidirectional trend: the increased size to accommodate more sperm. Furthermore, major splits within the existing genera of cockroaches occurred in the Upper Paleogene to Neogene. Our study provides strong support for the relationship among three superfamilies and offers some new insights into the phylogeny of cockroaches. Meanwhile, this study also provides basic knowledge on the evolution of spermathecae and reproductive patterns.
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Affiliation(s)
- Jin-Lin Liu
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China
| | - Jia-Wei Zhang
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China
| | - Wei Han
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China
| | - Yi-Shu Wang
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China
| | - Shu-Lin He
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing 401331, China
| | - Zong-Qing Wang
- Institute of Entomology, College of Plant Protection, Southwest University, Beibei, Chongqing 400715, China; Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China.
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12
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Xuan JL, Scheffer SJ, Lewis M, Cassel BK, Liu WX, Wiegmann BM. The phylogeny and divergence times of leaf-mining flies (Diptera: Agromyzidae) from anchored phylogenomics. Mol Phylogenet Evol 2023; 184:107778. [PMID: 37030415 DOI: 10.1016/j.ympev.2023.107778] [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: 10/17/2022] [Revised: 02/24/2023] [Accepted: 03/31/2023] [Indexed: 04/10/2023]
Abstract
Leaf-mining flies (Diptera: Agromyzidae) are a diverse clade of phytophagous Diptera known largely for their economic impact as leaf- or stem-miners on vegetable and ornamental plants. Higher-level phylogenetic relationships of Agromyzidae have remained uncertain because of challenges in sampling of both taxa and characters for morphology and PCR-based Sanger-era molecular systematics. Here, we used hundreds of orthologous single-copy nuclear loci obtained from anchored hybrid enrichment (AHE) to reconstruct phylogenetic relationships among the major lineages of leaf-mining flies. The resulting phylogenetic trees are highly congruent and well-supported, except for a few deep nodes, when using different molecular data types and phylogenetic methods. Based on divergence time dating using a relaxed clock and model-based historical biogeography analysis, leaf-mining flies are shown to have diversified in multiple lineages since the early Paleocene, approximately 65 million years ago. Our study not only reveals a revised classification system of leaf-mining flies, but also provides a new phylogenetic framework to understand their macroevolution.
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Affiliation(s)
- Jing-Li Xuan
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA; Anhui Bio-breeding Engineering Research Center for Water melon and Melon, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, P. R. China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Sonja J Scheffer
- Systematic Entomology Laboratory, USDA, Beltsville Agricultural Research Station, Beltsville, MD, 20705, USA.
| | - Matt Lewis
- Systematic Entomology Laboratory, USDA, Beltsville Agricultural Research Station, Beltsville, MD, 20705, USA
| | - Brian K Cassel
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Wan-Xue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Brian M Wiegmann
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA.
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13
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Reginato M. A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use. PeerJ 2022; 10:e14525. [PMID: 36523475 PMCID: PMC9745922 DOI: 10.7717/peerj.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Background Genome skimming is a popular method in plant phylogenomics that do not include a biased enrichment step, relying on random shallow sequencing of total genomic DNA. From these data the plastome is usually readily assembled and constitutes the bulk of phylogenetic information generated in these studies. Despite a few attempts to use genome skims to recover low copy nuclear loci for direct phylogenetic use, such endeavor remains neglected. Causes might include the trade-off between libraries with few reads and species with large genomes (i.e., missing data caused by low coverage), but also might relate to the lack of pipelines for data assembling. Methods A pipeline and its companion R package designed to automate the recovery of low copy nuclear markers from genome skimming libraries are presented. Additionally, a series of analyses aiming to evaluate the impact of key assembling parameters, reference selection and missing data are presented. Results A substantial amount of putative low copy nuclear loci was assembled and proved useful to base phylogenetic inference across the libraries tested (4 to 11 times more data than previously assembled plastomes from the same libraries). Discussion Critical aspects of assembling low copy nuclear markers from genome skims include the minimum coverage and depth of a sequence to be used. More stringent values of these parameters reduces the amount of assembled data and increases the relative amount of missing data, which can compromise phylogenetic inference, in turn relaxing the same parameters might increase sequence error. These issues are discussed in the text, and parameter tuning through multiple comparisons tracking their effects on support and congruence is highly recommended when using this pipeline. The skimmingLoci pipeline (https://github.com/mreginato/skimmingLoci) might stimulate the use of genome skims to recover nuclear loci for direct phylogenetic use, increasing the power of genome skimming data to resolve phylogenetic relationships, while reducing the amount of sequenced DNA that is commonly wasted.
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14
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Lukhtanov VA, Gagarina AV. Molecular Phylogeny and Taxonomy of the Butterfly Subtribe Scolitantidina with Special Focus on the Genera Pseudophilotes, Glaucopsyche and Iolana (Lepidoptera, Lycaenidae). INSECTS 2022; 13:1110. [PMID: 36555020 PMCID: PMC9782982 DOI: 10.3390/insects13121110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The Palearctic blue butterfly genus Pseudophilotes Beuret, 1958 is not homogenous regarding the morphology of its genital structures. For this reason, some of its species have been considered to be representatives of other genera of the subtribe Scolitantidina (subfamily Polyommatinae). Here, we address these taxonomic problems by analyzing the phylogenetic relationships between the genera, subgenera, and species of this subtribe inferred via the analysis of five nuclear and two mitochondrial DNA sequences. We demonstrate that the enigmatic Asian species P. panope (Eversmann, 1851) belongs to the genus Pseudophilotes but not to Praephilotes Forster, 1938 or Palaeophilotes Forster, 1938 and does not represent the independent genus Inderskia Korshunov, 2000, as hypothesized previously. We synonymize P. svetlana Yakovlev, 2003 (syn. nov.) and P. marina Zhdanko, 2004 (syn. nov.) with P. panope. We demonstrate a deep genetic divergence between lineages that were previously considered as subspecies of the single species Iolana iolas (Ochsenheimer, 1816). As a result, we confirm the multispecies concept of the genus Iolana Bethune-Baker, 1914. We show that the Holarctic genus Glaucopsyche can be divided into four subgenera: Glaucopsyche Scudder, 1872 (=Shijimiaeoides Beuret, 1958), Apelles Hemming, 1931, Bajluana Korshunov and Ivonin, 1990, and Phaedrotes Scudder, 1876.
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15
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Trinca V, Uliana JVC, Ribeiro GKS, Torres TT, Monesi N. Characterization of the mitochondrial genomes of Bradysia hygida, Phytosciara flavipes and Trichosia splendens (Diptera: Sciaridae) and novel insights on the control region of sciarid mitogenomes. INSECT MOLECULAR BIOLOGY 2022; 31:482-496. [PMID: 35332955 DOI: 10.1111/imb.12774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Sciarids, also called "fungus gnats" are small, almost entirely dark-coloured insects. Sciarid larvae feed on different substrates and can infest agricultural crops and mushroom nurseries, causing economic losses. Of the 2174 Diptera mitogenome sequences currently available in GenBank, only eight are from the Sciaridae family, none of which are complete circular molecules. Here we describe the mitogenome sequences of three sciarid species: Phytosciara flavipes, Trichosia splendens and Bradysia hygida and provide novel insights on the control region of sciarid mitogenomes. The assembled mitogenomes range from 16,062 bp in P. flavipes to 17,095 bp in B. hygida. All 13 protein coding genes, 22 tRNAs and 2 rRNAs characteristic of insect mitogenomes were identified, but the sequence of the control region could not be determined. Experimental results suggest that the B. hygida control region is about 21 kb long resulting in a 37 kb long mitogenome which constitutes the largest insect mitochondrial genome described so far. Phylogenetic analysis using all Bibionomorpha mitogenome sequences available in GenBank strongly supports the Sciaridae monophyly and led to the identification of species and subfamily specific gene rearrangements. Our study extends the knowledge of this large and diverse insect family that includes agricultural pest species.
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Affiliation(s)
- Vitor Trinca
- Programa de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - João Vitor Cardoso Uliana
- Programa de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Geyza Katrinny Sousa Ribeiro
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Tatiana Teixeira Torres
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Nadia Monesi
- Programa de Biologia Celular e Molecular, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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16
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Out of chaos: Phylogenomics of Asian Sonerileae. Mol Phylogenet Evol 2022; 175:107581. [PMID: 35810973 DOI: 10.1016/j.ympev.2022.107581] [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: 01/05/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 11/22/2022]
Abstract
Sonerileae is a diverse Melastomataceae lineage comprising ca. 1000 species in 44 genera, with >70% of genera and species distributed in Asia. Asian Sonerileae are taxonomically intractable with obscure generic circumscriptions. The backbone phylogeny of this group remains poorly resolved, possibly due to complexity caused by rapid species radiation in early and middle Miocene, which hampers further systematic study. Here, we used genome resequencing data to reconstruct the phylogeny of Asian Sonerileae. Three parallel datasets, viz. single-copy ortholog (SCO), genomic SNPs, and whole plastome, were assembled from genome resequencing data of 205 species for this purpose. Based on these genome-scale data, we provided the first well resolved phylogeny of Asian Sonerileae, with 34 major clades identified and 74% of the interclade relationships consistently resolved by both SCO and genomic data. Meanwhile, widespread phylogenetic discordance was detected among SCO gene trees as well as species trees reconstructed using different tree estimation methods (concatenation/site-based coalescent method/summary method) or different datasets (SCO/genomic/plastome). We explored sources of discordance using multiple approaches and found that the observed discordance in Asian Sonerileae was mainly caused by a combination of biased distribution of missing data, random noise from uninformative genes, incomplete lineage sorting, and hybridization/introgression. Exploration of these sources can enable us to generate hypotheses for future testing, which is the first step towards understanding the evolution of Asian Sonerileae. We also detected high levels of homoplasy for some characters traditionally used in taxonomy, which explains current chaotic generic delimitations. The backbone phylogeny of Asian Sonerileae revealed in this study offers a solid basis for future taxonomic revision at the generic level.
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17
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Woodyard ET, Bierman AE, Edwards JJ, Finney JC, Rosser TG, Griffin MJ, Marancik DP. Kudoa hypoepicardialis and associated cardiac lesions in invasive red lionfish Pterois volitans in Grenada, West Indies. DISEASES OF AQUATIC ORGANISMS 2022; 149:97-108. [PMID: 35678355 DOI: 10.3354/dao03663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Invasive red lionfish Pterois volitans (Linnaeus, 1758) represent an ongoing ecological threat within temperate and tropical waters. Relatively little is known regarding the overall health of P. volitans and their potential for spreading pathogens in non-native regions. Lionfish collected from inshore reefs of Grenada, West Indies, in 2019 and 2021 were identified as P. volitans based on cytochrome c oxidase subunit 1 barcoding. Gross and microscopic examination of tissues revealed myxozoan plasmodia in the hearts of 24/76 (31.6%) lionfish by histopathology or wet mount cytology. Further histopathologic examination revealed severe granulomatous inflammation and myofiber necrosis associated with developing plasmodia and presporogonic life stages. Fresh myxospores were morphologically and molecularly consistent with Kudoa hypoepicardialis, being quadrate in apical view with 4 valves and 4 equal polar capsules. The spore body was 5.1-7.9 (mean: 6.0) µm long, 8.1-9.8 (8.7) µm wide, and 6.9-8.5 (7.7) µm thick. Polar capsules were 2.3-2.7 (2.5) µm long and 0.9-1.6 (1.3) µm wide. 18S small subunit rDNA sequences were 99.81-99.87% similar to sequence data from the original description of the species. Novel 28S large subunit rDNA and elongation factor 2 data, which did not match any previously reported species, were provided. This is the first account of a myxozoan parasite of P. volitans, a new host record and locality for K. hypoepicardialis, and one of few reports describing pathogen-associated lesions in invasive lionfish.
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Affiliation(s)
- Ethan T Woodyard
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762, USA
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Jin M, Shin S, Ashman LG, Leschen RAB, Zwick A, de Keyzer R, McKenna DD, Ślipiński A. Phylogenomics resolves timing and patterns in the evolution of Australasian Cerambycinae (Coleoptera: Cerambycidae), and reveals new insights into the subfamily-level classification and historical biogeography of longhorn beetles. Mol Phylogenet Evol 2022; 172:107486. [PMID: 35469917 DOI: 10.1016/j.ympev.2022.107486] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/12/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022]
Abstract
Cerambycinae is the second-largest subfamily of longhorn beetles in the Southern Hemisphere. The phylogeny of Cerambycinae is poorly known, resulting in a highly artificial tribal-level classification and a largely speculative evolutionary history. We reconstructed the phylogenetic relationships of Cerambycinae at the generic level using anchored hybrid enrichment data from hundreds of nuclear genes, with a primary focus on the extraordinarily diverse faunas of Australia and New Zealand. We also estimated divergence times by incorporating fossil calibrations in our analyses. We identified two main clades within Cerambycinae, which can also be separated morphologically by a distinct type of antennal foramen. We recovered a Late Jurassic origin of crown Cerambycinae. Dorcasominae, which was newly found to have representatives in Australia, was notably derived from within Cerambycinae. We recovered two independent origins of Australian Cerambycinae: one clade originated in the Early Cretaceous and is likely endemic to the Southern Hemisphere, while the other clade appears to have immigrated to Australia, perhaps from the Northern Hemisphere. Within the Australian lineages were multiple independent origins of New Zealand taxa, all of which are relative host-plant generalists. Tribal relationships and assignments are discussed, and based on our results, the following major nomenclatural acts were made: Dorcasominae Lacordaire, 1868 is downgraded to a tribe Dorcasomini of Cerambycinae Latreille, 1804; Neostenini Lacordaire, 1868syn. nov. is treated as a junior synonym of Uracanthini Blanchard, 1851.
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Affiliation(s)
- Mengjie Jin
- Australian National Insect Collection, CSIRO, Canberra, ACT, Australia; State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Seunggwan Shin
- Department of Biological Sciences, University of Memphis, Memphis, TN, U.S.A; Center for Biodiversity Research, University of Memphis, Memphis, TN, USA; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Lauren G Ashman
- Australian National Insect Collection, CSIRO, Canberra, ACT, Australia; Research School of Biology, Australian National University, Canberra 2601, Australia
| | - Richard A B Leschen
- New Zealand Arthropod Collection, Manaaki Whenua - Landcare Research, Auckland, New Zealand
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, Canberra, ACT, Australia
| | - Roger de Keyzer
- Research Associate, Entomology, Australian Museum, Sydney, New South Wales, Australia
| | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, TN, U.S.A; Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, Canberra, ACT, Australia
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Zheng B, Han Y, Yuan R, Liu J, van Achterberg C, Tang P, Chen X. Comparative Mitochondrial Genomics of 104 Darwin Wasps (Hymenoptera: Ichneumonidae) and Its Implication for Phylogeny. INSECTS 2022; 13:insects13020124. [PMID: 35206698 PMCID: PMC8874624 DOI: 10.3390/insects13020124] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary Nearly a hundred mitochondrial genomes of ichneumonid wasps are newly reported. Comparative mitogenomics of 104 mitochondrial genomes representing 33 subfamilies of Ichneumonidae, as well as its implications for phylogeny, were studied. We found that the mitochondrial genomes of ichneumonid wasps were highly conserved in their base composition and had low evolutionary rates, but were diverse in gene order. There are 38 types of gene rearrangement events in 104 ichneumonid mitochondrial genomes, of which 30 novel rearrangement types (R3-6, R8-R10, R12-R15, R17-R18, R20-R35 and R38) and a hot spot rearrangement around R1, with a shuffled tRNA cluster trnW-trnY-trnC and trnI-trnQ-trnM, were detected. The relationships among these subfamilies are firstly discussed based on mitochondrial genomes at a large scale. We suggest five subfamily groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively. Abstract Ichneumonidae is one of the largest families of insects with a mega-diversity of specialized morphological and biological characteristics. We newly sequenced 92 mitochondrial genomes of ichneumonid wasps and found that they have a conserved base composition and a lower evolutionary rate than that of other families of parasitic Hymenoptera. There are 38 types of gene order in the ichneumonid mitochondrial genome, with 30 novel types identified in 104 ichneumonids. We also found that the rearrangement events occur more frequently in Ophioniformes than in Ichneumoniformes and Pimpliformes. Furthermore, the higher Ophioniformes and their relative lineages shared the transposition of trnL2 to trnI-trnQ-trnM tRNA cluster. We confirmed five higher-level groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively. The results will improve our understanding of the diversity and evolution of Ichneumonidae.
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Affiliation(s)
- Boying Zheng
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Han
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ruizhong Yuan
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jingxian Liu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China;
| | - Cornelis van Achterberg
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Pu Tang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Correspondence:
| | - Xuexin Chen
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
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20
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Woodyard ET, Rosser TG, Stilwell JM, Camus AC, Khoo LH, Waldbieser G, Lorenz WW, Griffin MJ. New data on Henneguya postexilis Minchew, 1977, a parasite of channel catfish Ictalurus punctatus, with notes on resolution of molecular markers for myxozoan phylogeny. Syst Parasitol 2022; 99:41-62. [PMID: 35028798 DOI: 10.1007/s11230-021-10015-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/15/2021] [Indexed: 11/27/2022]
Abstract
Previous morphological and histological data are supplemented with molecular and ultrastructural data for a Henneguya sp. isolated from farm-raised channel catfish Ictalurus punctatus in Mississippi, USA. Myxospores were cryptic, encapsulated within a thin layer of epithelium in the gill lamellae with spore measurements consistent with the original description of Henneguya postexilis Minchew, 1977. Myxospores were 42.7-49.1 µm in total length with spore bodies 12.1-17.2 × 3.6-4.8 × 2.9-3 µm. Polar capsules were of unequal length, with the longer capsule being 4.4-6.7 × 1.1-1.6 µm and the shorter capsule being 4.4-6.4 × 1.1-1.6 µm. Polar tubules had 6-8 turns. Caudal processes were 25.7-38.1 µm in length. Spores were encapsulated in a thin layer of epithelium in the gill lamellae. Molecular data from the most commonly used markers for myxozoan identification and phylogeny, partial 18S small subunit ribosomal gene (SSU), partial 28S large subunit ribosomal gene (LSU), and elongation factor 2 (EF2) were generated for H. postexilis. Additionally, novel data for LSU and EF2 were generated for archived myxozoan specimens from farm-raised catfish (H. mississippiensis, H. ictaluri, H. exilis, H. adiposa, H. sutherlandi, H. bulbosus, Unicauda fimbrethilae), as well as archived specimens from wild fish (H. laseeae [from Pylodictis olivaris], Hennegoides flockae [from Aphredoderus sayanus], Myxobolus cloutmani [from Cycleptus elongatus]. These include the first EF2 sequence data for the genera Hennegoides and Unicauda. Phylogenetic analyses using these data placed H. postexilis in well supported clades with other ictalurid-infecting Henneguya species. Phylogenetic signal assessments on these analyses suggest that while SSU provided the greatest phylogenetic signal, LSU yielded comparable signal, supporting previous work implying this region may be underutilised in reconstructing myxobolid phylogenies.
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Affiliation(s)
- Ethan T Woodyard
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39759, USA.
| | - Thomas G Rosser
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39759, USA
| | - Justin M Stilwell
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Alvin C Camus
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Lester H Khoo
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39759, USA
| | - Geoffrey Waldbieser
- USDA-ARS Warmwater Aquaculture Research Unit, Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS, 38776, USA
| | - W Walter Lorenz
- Georgia Genomics and Bioinformatics Core, University of Georgia, Athens, GA, 30602, USA
| | - Matt J Griffin
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, 39759, USA
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21
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Breeschoten T, van der Linden CFH, Ros VID, Schranz ME, Simon S. Expanding the Menu: Are Polyphagy and Gene Family Expansions Linked across Lepidoptera? Genome Biol Evol 2022; 14:6482744. [PMID: 34951642 PMCID: PMC8725640 DOI: 10.1093/gbe/evab283] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2021] [Indexed: 12/31/2022] Open
Abstract
Evolutionary expansions and contractions of gene families are often correlated with key innovations and/or ecological characteristics. In butterflies and moths (Lepidoptera), expansions of gene families involved in detoxification of plant specialized metabolites are hypothesized to facilitate a polyphagous feeding style. However, analyses supporting this hypothesis are mostly based on a limited number of lepidopteran species. We applied a phylogenomics approach, using 37 lepidopteran genomes, to analyze if gene family evolution (gene gain and loss) is associated with the evolution of polyphagy. Specifically, we compared gene counts and evolutionary gene gain and loss rates of gene families involved in adaptations with plant feeding. We correlated gene evolution to host plant family range (phylogenetic diversity) and specialized metabolite content of plant families (functional metabolite diversity). We found a higher rate for gene loss than gene gain in Lepidoptera, a potential consequence of genomic rearrangements and deletions after (potentially small-scale) duplication events. Gene family expansions and contractions varied across lepidopteran families, and were associated to host plant use and specialization levels. Within the family Noctuidae, a higher expansion rate for gene families involved in detoxification can be related to the large number of polyphagous species. However, gene family expansions are observed in both polyphagous and monophagous lepidopteran species and thus seem to be species-specific in the taxa sampled. Nevertheless, a significant positive correlation of gene counts of the carboxyl- and choline esterase and glutathione-S-transferase detoxification gene families with the level of polyphagy was identified across Lepidoptera.
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Affiliation(s)
| | | | - Vera I D Ros
- Laboratory of Virology, Wageningen University & Research, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, The Netherlands
| | - Sabrina Simon
- Biosystematics Group, Wageningen University & Research, The Netherlands
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22
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Karmeinski D, Meusemann K, Goodheart JA, Schroedl M, Martynov A, Korshunova T, Wägele H, Donath A. Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia. BMC Ecol Evol 2021; 21:226. [PMID: 34963462 PMCID: PMC8895541 DOI: 10.1186/s12862-021-01944-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/23/2021] [Indexed: 11/24/2022] Open
Abstract
Background The soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as targets for drug discovery), the evolutionary history of cladobranch sea slugs is not yet fully understood. Results To enlarge the current knowledge on the phylogenetic relationships, we generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa (Berthella plumula and Polycera quadrilineata). We complemented our taxon sampling with previously published transcriptome data, resulting in a final data set covering 56 species from all but one accepted cladobranch superfamilies. We assembled all transcriptomes using six different assemblers, selecting those assemblies that provided the largest amount of potentially phylogenetically informative sites. Quality-driven compilation of data sets resulted in four different supermatrices: two with full coverage of genes per species (446 and 335 single-copy protein-coding genes, respectively) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximal statistical support for all major splits and phylogenetic relationships at the family level. Besides the questionable position of Noumeaella rubrofasciata, rendering the Facelinidae as polyphyletic, the only notable discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. Conclusions Our data matrices and the inferred trees can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The placement of E. pulchra, however, proves challenging, even with large data sets and various optimization strategies. Moreover, quartet mapping results show that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01944-0.
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Affiliation(s)
- Dario Karmeinski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Karen Meusemann
- Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany.,Australian National Insect Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO), National Facilities and Collections, Clunies Ross Street, Acton, Canberra, ACT, 2601, Australia
| | - Jessica A Goodheart
- Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, 92037, USA
| | - Michael Schroedl
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247, Munich, Germany.,GeoBioCenter LMU und Biozentrum, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Alexander Martynov
- Zoological Museum of the Moscow State University, Bolshaya Nikitskaya Str. 6, 125009, Moscow, Russia
| | - Tatiana Korshunova
- Koltzov Institute of Developmental Biology, Vavilova Str. 26, 119334, Moscow, Russia
| | - Heike Wägele
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany.
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23
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Montes de Oca L, Indicatti RP, Opatova V, Almeida M, Pérez-Miles F, Bond JE. Phylogenomic analysis, reclassification, and evolution of South American nemesioid burrowing mygalomorph spiders. Mol Phylogenet Evol 2021; 168:107377. [PMID: 34954378 DOI: 10.1016/j.ympev.2021.107377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/30/2022]
Abstract
The family Nemesiidae was once among the most species-rich of mygalomorph spider families. However, over the past few decades both morphological and molecular studies focusing on mygalomorph phylogeny have recovered the group as paraphyletic. Hence, the systematics of the family Nemesiidae has more recently been controversial, with numerous changes at the family-group level and the recognition of the supra-familial clade Nemesioidina. Indeed, in a recent study by Opatova and collaborators, six nemesiid genera were transferred to the newly re-established family Pycnothelidae. Despite these changes, 12 South American nemesiid genera remained unplaced, and classified as incertae sedis due to shortcomings in taxon sampling. Accordingly, we evaluate the phylogenetic relationships of South American nemesioid species and genera with the principle aim of resolving their family level placement. Our work represents the most exhaustive phylogenomic sampling for South American Nemesiidae by including nine of the 12 genera described for the continent. Phylogenetic relationships were reconstructed using 457 loci obtained using the spider Anchored Hybrid Enrichment probe set. Based on these results Nemesiidae, Pycnothelidae, Microstigmatidae and Cyrtaucheniidae are not considered monophyletic. Our study also indicates that the lineage including the genus Fufius requires elevation to the family level (Rhytidicolidae Simon, 1903 (NEW RANK)). In Pycnothelidae, we recognize/delimit five subfamilies (Diplothelopsinae, Pionothelinae NEW SUBFAMILY, Prorachiinae NEW SUBFAMILY, Pselligminae NEW RANK, Pycnothelinae). We also transfer all the 12 South American nemesiid genera to Pycnothelidae: Chaco, Chilelopsis, Diplothelopsis, Flamencopsis, Hermachura, Longistylus, Lycinus, Neostothis, Prorachias, Psalistopoides, Pselligmus, Rachias. Additionally, we transferred the microstigmatid genus Xenonemesia to Pycnothelidae, and we propose the following generic synonymies and species transfers: Neostothis and Bayana are junior synonyms of Pycnothele (NEW SYNONYMY), as P. gigas and P. labordai, respectively (NEW COMBINATIONS); Hermachura is a junior synonym of Stenoterommata (NEW SYNONYMY), as S. luederwaldti (NEW COMBINATION); Flamencopsis is a junior synonym of Chilelopsis (NEW SYNONYMY), as C. minima (NEW COMBINATION); and Diplothelopsis is a junior synonym of Lycinus (NEW SYNONYMY), as L. ornatus and L. bonariensis (NEW COMBINATIONS). Considering the transferred genera and synonymies, Pycnothelidae now includes 15 described genera and 137 species. Finally, these results provide a robust phylogenetic framework that includes enhanced taxonomic sampling, for further resolving the biogeography and evolutionary time scale for the family Pycnothelidae.
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Affiliation(s)
- Laura Montes de Oca
- Sección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225, 11400, Montevideo, Uruguay; Instituto de Investigaciones Biológicas Clemente Estable, Ministerio de Educación y Cultura. Av. Italia 3318, 11600, Montevideo, Uruguay.
| | - Rafael P Indicatti
- Laboratório de Coleções Zoológicas, Instituto Butantan. Av. Vital Brazil, 1500 05503-900, São Paulo, São Paulo, Brazil; Departamento de Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista, Av. 24A, 1515, CEP: 13.506-900, Rio Claro, São Paulo, Brazil.
| | - Vera Opatova
- Department of Zoology, Charles University, Faculty of Science, Viničná 7, 128 44 Prague, Czech Republic.
| | - Marlus Almeida
- Instituto Nacional de Pesquisas da Amazônia, Laboratório de Sistemática e Ecologia de Invertebrados do Solo, Av. André Araújo, 2936 - Petrópolis - Manaus, Amazonas, Brazil.
| | - Fernando Pérez-Miles
- Sección Entomología, Facultad de Ciencias, Universidad de la República. Iguá 4225, 11400, Montevideo, Uruguay
| | - Jason E Bond
- Department of Entomology and Nematology, University of California Davis, Academic Surge Building 1282, Davis, CA 95616, USA.
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24
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Kohli M, Letsch H, Greve C, Béthoux O, Deregnaucourt I, Liu S, Zhou X, Donath A, Mayer C, Podsiadlowski L, Gunkel S, Machida R, Niehuis O, Rust J, Wappler T, Yu X, Misof B, Ware J. Evolutionary history and divergence times of Odonata (dragonflies and damselflies) revealed through transcriptomics. iScience 2021; 24:103324. [PMID: 34805787 PMCID: PMC8586788 DOI: 10.1016/j.isci.2021.103324] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 05/14/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022] Open
Abstract
Dragonflies and damselflies are among the earliest flying insects with extant representatives. However, unraveling details of their long evolutionary history, such as egg laying (oviposition) strategies, is impeded by unresolved phylogenetic relationships, particularly in damselflies. Here we present a transcriptome-based phylogenetic reconstruction of Odonata, analyzing 2,980 protein-coding genes in 105 species representing nearly all the order's families. All damselfly and most dragonfly families are recovered as monophyletic. Our data suggest a sister relationship between dragonfly families of Gomphidae and Petaluridae. According to our divergence time estimates, both crown-Zygoptera and -Anisoptera arose during the late Triassic. Egg-laying with a reduced ovipositor apparently evolved in dragonflies during the late Jurassic/early Cretaceous. Lastly, we also test the impact of fossil choice and placement, particularly, of the extinct fossil species, †Triassolestodes asiaticus, and †Proterogomphus renateae on divergence time estimates. We find placement of †Proterogomphus renateae to be much more impactful than †Triassolestodes asiaticus.
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Affiliation(s)
- Manpreet Kohli
- Department of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Harald Letsch
- Department for Animal Biodiversity, Universität Wien, Vienna, Austria
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Olivier Béthoux
- CR2P (Centre de Recherche en Paléontologie – Paris), MNHN – CNRS – Sorbonne Université, Paris, France
| | - Isabelle Deregnaucourt
- CR2P (Centre de Recherche en Paléontologie – Paris), MNHN – CNRS – Sorbonne Université, Paris, France
| | - Shanlin Liu
- Department of Entomology, China Agricultural University,Beijing 100193, People’s Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University,Beijing 100193, People’s Republic of China
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Simon Gunkel
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Research Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano, Japan
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, Freiburg, Germany
| | - Jes Rust
- Palaeontology Section, Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn 53115, Germany
| | - Torsten Wappler
- Palaeontology Section, Institute of Geosciences, Rheinische Friedrich-Wilhelms Universität Bonn, Bonn 53115, Germany
| | - Xin Yu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Bernhard Misof
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Jessica Ware
- Department of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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25
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Li X, St Laurent R, Earl C, Doorenweerd C, van Nieukerken EJ, Davis DR, Johns CA, Kawakita A, Kobayashi S, Zwick A, Lopez-Vaamonde C, Ohshima I, Kawahara AY. Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data. Cladistics 2021; 38:277-300. [PMID: 34710244 DOI: 10.1111/cla.12490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/27/2022] Open
Abstract
Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially among subfamilies, remain uncertain. Genomic data (83 taxa, 589 loci) were integrated with Sanger data (130 taxa, 22 loci), to reconstruct a phylogeny of Gracillariidae. Based on analyses of both datasets combined and analyzed separately, monophyly of Gracillariidae and all its subfamilies, monophyly of the clade "LAMPO" (subfamilies: Lithocolletinae, Acrocercopinae, Marmarinae, Phyllocnistinae, and Oecophyllembiinae) and relationships of its subclade "AMO" (subfamilies: Acrocercopinae, Marmarinae, and Oecophyllembiinae) were strongly supported. A sister-group relationship of Ornixolinae to the remainder of the family, and a monophyletic leaf roller lineage (Callicercops Vári + Parornichinae) + Gracillariinae, as sister to the "LAMPO" clade were supported by the most likely tree. Dating analyses indicate a mid-Cretaceous (105.3 Ma) origin of the family, followed by a rapid diversification into the nine subfamilies predating the Cretaceous-Palaeogene extinction. We hypothesize that advanced larval behaviours, such as making keeled or tentiform blotch mines, rolling leaves and galling, allowed gracillariids to better avoid larval parasitoids allowing them to further diversify. Finally, we stabilize the classification by formally re-establishing the subfamily ranks of Marmarinae stat.rev., Oecophyllembiinae stat.rev. and Parornichinae stat.rev., and erect a new subfamily, Callicercopinae Li, Ohshima and Kawahara to accommodate the enigmatic genus Callicercops.
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Affiliation(s)
- Xuankun Li
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Ryan St Laurent
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Chandra Earl
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Camiel Doorenweerd
- Department of Plant and Environmental Protection Services, University of Hawaii, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
| | | | - Donald R Davis
- Department of Entomology, NHB 105, Smithsonian Institution, Washington, DC, USA
| | - Chris A Johns
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Atsushi Kawakita
- The Botanical Gardens, Graduate School of Science, The University of Tokyo, Tokyo, 112-0001, Japan
| | - Shigeki Kobayashi
- Entomological Laboratory, Graduate School of life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Andreas Zwick
- Australian National Insect Collection, National Research Collections Australia, CSIRO, Canberra, ACT, 2601, Australia
| | - Carlos Lopez-Vaamonde
- INRAE, URZF, Orléans, France.,IRBI, UMR 7261, CNRS-Université de Tours, Tours, France
| | - Issei Ohshima
- Department of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan.,Center for Frontier Natural History, Kyoto Prefectural University, Sakyo, Kyoto, 606-8522, Japan
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Entomology and Nematology Department, University of Florida, Gainesville, FL, 32608, USA
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26
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Yan L, Pape T, Meusemann K, Kutty SN, Meier R, Bayless KM, Zhang D. Monophyletic blowflies revealed by phylogenomics. BMC Biol 2021; 19:230. [PMID: 34706743 PMCID: PMC8555136 DOI: 10.1186/s12915-021-01156-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 09/23/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Blowflies are ubiquitous insects, often shiny and metallic, and the larvae of many species provide important ecosystem services (e.g., recycling carrion) and are used in forensics and debridement therapy. Yet, the taxon has repeatedly been recovered to be para- or polyphyletic, and the lack of a well-corroborated phylogeny has prevented a robust classification. RESULTS We here resolve the relationships between the different blowfly subclades by including all recognized subfamilies in a phylogenomic analysis using 2221 single-copy nuclear protein-coding genes of Diptera. Maximum likelihood (ML), maximum parsimony (MP), and coalescent-based phylogeny reconstructions all support the same relationships for the full data set. Based on this backbone phylogeny, blowflies are redefined as the most inclusive monophylum within the superfamily Oestroidea not containing Mesembrinellidae, Mystacinobiidae, Oestridae, Polleniidae, Sarcophagidae, Tachinidae, and Ulurumyiidae. The constituent subfamilies are re-classified as Ameniinae (including the Helicoboscinae, syn. nov.), Bengaliinae, Calliphorinae (including Aphyssurinae, syn. nov., Melanomyinae, syn. nov., and Toxotarsinae, syn. nov.), Chrysomyinae, Luciliinae, Phumosiinae, Rhiniinae stat. rev., and Rhinophorinae stat. rev. Metallic coloration in the adult is shown to be widespread but does not emerge as the most likely ground plan feature. CONCLUSIONS Our study provides the first phylogeny of oestroid calyptrates including all blowfly subfamilies. This allows settling a long-lasting controversy in Diptera by redefining blowflies as a well-supported monophylum, and blowfly classification is adjusted accordingly. The archetypical blowfly trait of carrion-feeding maggots most likely evolved twice, and the metallic color may not belong to the blowfly ground plan.
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Affiliation(s)
- Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Thomas Pape
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Karen Meusemann
- Evolutionary Biology & Ecology, University of Freiburg, Freiburg, Germany
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Canberra, Australia
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Berlin, Germany
| | - Keith M Bayless
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Canberra, Australia
- Department of Entomology, California Academy of Sciences, San Francisco, USA
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
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Simon S, Breeschoten T, Jansen HJ, Dirks RP, Schranz ME, Ros VID. Genome and transcriptome analysis of the beet armyworm Spodoptera exigua reveals targets for pest control. G3 (BETHESDA, MD.) 2021; 11:jkab311. [PMID: 34557910 PMCID: PMC8527508 DOI: 10.1093/g3journal/jkab311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/19/2021] [Indexed: 12/13/2022]
Abstract
The genus Spodoptera (Lepidoptera: Noctuidae) includes some of the most infamous insect pests of cultivated plants including Spodoptera frugiperda, Spodoptera litura, and Spodoptera exigua. To effectively develop targeted pest control strategies for diverse Spodoptera species, genomic resources are highly desired. To this aim, we provide the genome assembly and developmental transcriptome comprising all major life stages of S. exigua, the beet armyworm. Spodoptera exigua is a polyphagous herbivore that can feed on > 130 host plants, including several economically important crops. The 419 Mb beet armyworm genome was sequenced from a female S. exigua pupa. Using a hybrid genome sequencing approach (Nanopore long-read data and Illumina short read), a high-quality genome assembly was achieved (N50 = 1.1 Mb). An official gene set (18,477 transcripts) was generated by automatic annotation and by using transcriptomic RNA-seq datasets of 18 S. exigua samples as supporting evidence. In-depth analyses of developmental stage-specific expression combined with gene tree analyses of identified homologous genes across Lepidoptera genomes revealed four potential genes of interest (three of them Spodoptera-specific) upregulated during first- and third-instar larval stages for targeted pest-outbreak management. The beet armyworm genome sequence and developmental transcriptome covering all major developmental stages provide critical insights into the biology of this devastating polyphagous insect pest species worldwide. In addition, comparative genomic analyses across Lepidoptera significantly advance our knowledge to further control other invasive Spodoptera species and reveals potential lineage-specific target genes for pest control strategies.
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Affiliation(s)
- Sabrina Simon
- Biosystematics Group, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Thijmen Breeschoten
- Biosystematics Group, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Hans J Jansen
- Future Genomics Technologies, Leiden, The Netherlands
| | - Ron P Dirks
- Future Genomics Technologies, Leiden, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Vera I D Ros
- Laboratory of Virology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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28
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Yan L, Buenaventura E, Pape T, Narayanan Kutty S, Bayless KM, Zhang D. A phylotranscriptomic framework for flesh fly evolution (Diptera, Calyptratae, Sarcophagidae). Cladistics 2021; 37:540-558. [PMID: 34570937 DOI: 10.1111/cla.12449] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 11/28/2022] Open
Abstract
The Sarcophagidae (flesh flies) comprise a large and widely distributed radiation within the Calyptratae (Diptera). Larval feeding habits are ecologically diverse and include sarcosaprophagy, coprophagy, herbivory, invertebrate and vertebrate predation, and kleptoparasitism. To elucidate the geographic origin and evolution of flesh fly life-history, we inferred a backbone phylogeny based on transcriptomic data from 26 sarcophagid species covering all three subfamilies plus 15 outgroups. The phylogeny was inferred using maximum parsimony and maximum likelihood methods based on a series of supermatrices, one set with overall information content improved by MARE (2290 loci), one set with 100% gene coverage for all included species (587 loci), and the last set including mitochondrial and nuclear genes (589 loci) and additional taxa. In order to obtain a more detailed hypothesis, we utilized the supertree approach to combine results from the present study with previously published hypotheses. This resulted supertree covers 84 of the one hundred currently recognized sarcophagid genera and formed the basis for the ancestral state reconstructions. The monophyletic Sarcophagidae is well-supported as sister to {Mystacinobiidae + Oestridae}, and relationships at the subfamily level are inferred as {Sarcophaginae, (Paramacronychiinae + Miltogramminae)}. The Sarcophagidae and each subfamily originated in the Americas, with Sarcophaginae diversifying mainly in the Neotropics, whereas the major radiation of both Miltogramminae and Paramacronychiinae occurred in the Palaearctic. Sarcosaprophagy is reconstructed as the ancestral larval feeding habit of the family Sarcophagidae and each subfamily. The ancestral sarcophagid larva probably utilized dead invertebrates as food, and the food spectrum expanded together with the diversification of breeding strategies. Particularly, kleptoparasitism in Miltogramminae is derived from sarcosaprophagy and may be seen as having derived from the breeding biology of 'lower' miltogrammines, the larvae of which feed on buried vertebrate carrion.
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Affiliation(s)
- Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
| | - Eliana Buenaventura
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Berlin, 10115, Germany
| | - Thomas Pape
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, 14 Science Dr 4, Singapore, 117543, Singapore.,Tropical Marine Science Institute, National University of Singapore, 18 Kent Ridge Road, Singapore, 119227, Singapore
| | - Keith M Bayless
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Acton, Canberra, ACT, 2601, Australia.,Department of Entomology, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, 100083, China
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29
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Pazoki S, Rahimian H, Struck TH. Genetic diversity and population structure of three Hydroides species (Sedentaria, Serpulidae) in the Persian Gulf and Gulf of Oman, with the possible indication of heteroplasmy. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1965668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Samaneh Pazoki
- Department of Animal Biology, Faculty of Biology, College of Sciences, University of Tehran, Tehran, Iran
| | - Hassan Rahimian
- Department of Animal Biology, Faculty of Biology, College of Sciences, University of Tehran, Tehran, Iran
| | - Torsten H. Struck
- Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, Oslo, NO-0318, Norway
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30
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Li X, Teasdale LC, Bayless KM, Ellis AG, Wiegmann BM, Lamas CJE, Lambkin CL, Evenhuis NL, Nicholls JA, Hartley D, Shin S, Trautwein M, Zwick A, Lessard BD, Yeates DK. Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae). Cladistics 2021; 37:276-297. [PMID: 34478201 DOI: 10.1111/cla.12436] [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: 12/23/2019] [Revised: 07/07/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023] Open
Abstract
Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the main lineages in our AHE tree to build a data set with more genes (550 loci versus 216 loci) and higher support levels. Our overall results show strong congruence with the current classification of the family, with 11 out of 14 included subfamilies recovered as monophyletic. Heterotropinae and Mythicomyiinae are successive sister groups to the remainder of the family. We examined the evolution of key morphological characters through our phylogenetic hypotheses and show that neither the "sand chamber subfamilies" nor the "Tomophthalmae" are monophyletic in our phylogenomic analyses. Based on our results, we reinstate two tribes at the subfamily level (Phthiriinae stat. rev. and Ecliminae stat. rev.) and we include the genus Sericosoma Macquart (previously incertae sedis) in the subfamily Oniromyiinae, bringing the total number of bee fly subfamilies to 19. Our dating analyses indicate a Jurassic origin of the family (165-194 Ma), with the sand chamber evolving early in bee fly evolution, in the late Jurassic or mid-Cretaceous (100-165 Ma). We hypothesize that the angiosperm radiation and the hothouse climate established during the late Cretaceous accelerated the diversification of bee flies, by providing an expanded range of resources for the parasitoid larvae and nectarivorous adults.
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Affiliation(s)
- Xuankun Li
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia.,Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Luisa C Teasdale
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Keith M Bayless
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Allan G Ellis
- Botany and Zoology Department, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Carlos José E Lamas
- Museu de Zoologia da Universidade de São Paulo. Avenida Nazaré, 481 Ipiranga 04263-000, São Paulo, SP, Brazil
| | | | - Neal L Evenhuis
- J. Linsley Gressitt Center for Research in Entomology, Bishop Museum, 1525 Bernice Street, Honolulu, HI, 96817, USA
| | - James A Nicholls
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Diana Hartley
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Seunggwan Shin
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA.,School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Michelle Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - Bryan D Lessard
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
| | - David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT, 2601, Australia
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31
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Gene Flow and Diversification in Himalopsyche martynovi Species Complex (Trichoptera: Rhyacophilidae) in the Hengduan Mountains. BIOLOGY 2021; 10:biology10080816. [PMID: 34440048 PMCID: PMC8389565 DOI: 10.3390/biology10080816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022]
Abstract
The Hengduan Mountains are one of the most species-rich mountainous areas in the world. The origin and evolution of such a remarkable biodiversity are likely to be associated with geological or climatic dynamics, as well as taxon-specific biotic processes (e.g., hybridization, polyploidization, etc.). Here, we investigate the mechanisms fostering the diversification of the endemic Himalopsyche martynovi complex, a poorly known group of aquatic insects. We used multiple allelic datasets generated from 691 AHE loci to reconstruct species and RaxML phylogenetic trees. We selected the most reliable phylogenetic tree to perform network and gene flow analyses. The phylogenetic reconstructions and network analysis identified three clades, including H. epikur, H. martynovi sensu stricto and H. cf. martynovi. Himalopsyche martynovi sensu stricto and H. cf. martynovi present an intermediate morphology between H. epikur and H. viteceki, the closest known relative to the H. martynovi-complex. The gene flow analysis revealed extensive gene flow among these lineages. Our results suggest that H. viteceki and H. epikur are likely to have contributed to the evolution of H. martynovi sensu stricto and H. cf. martynovi via gene flow, and thus, our study provides insights in the diversification process of a lesser-known ecological group, and hints at the potential role of gene flow in the emergence of biological novelty in the Hengduan Mountains.
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32
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Suvorov A, Scornavacca C, Fujimoto MS, Bodily P, Clement M, Crandall KA, Whiting MF, Schrider DR, Bybee SM. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies. Syst Biol 2021; 71:526-546. [PMID: 34324671 PMCID: PMC9017697 DOI: 10.1093/sysbio/syab063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.
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Affiliation(s)
- Anton Suvorov
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Celine Scornavacca
- Institut des Sciences de l'Evolution Université de Montpellier, CNRS, IRD, EPHE CC 064, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - M Stanley Fujimoto
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Paul Bodily
- Department of Computer Science, Idaho State University, Pocatello, ID, United States
| | - Mark Clement
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
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33
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Tessens B, Monnens M, Backeljau T, Jordaens K, Van Steenkiste N, Breman FC, Smeets K, Artois T. Is ‘everything everywhere’? Unprecedented cryptic diversity in the cosmopolitan flatworm
Gyratrix hermaphroditus. ZOOL SCR 2021. [DOI: 10.1111/zsc.12507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Bart Tessens
- Research Group Zoology: Biodiversity and Toxicology Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Marlies Monnens
- Research Group Zoology: Biodiversity and Toxicology Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Thierry Backeljau
- Department of Biology Evolutionary Ecology Group University of Antwerp Antwerp Belgium
- Royal Belgian Institute of Natural Sciences (RBINS: Taxonomy and Phylogeny & JEMU) Brussels Belgium
| | - Kurt Jordaens
- Royal Museum for Central Africa (RMCA: Entomology Section & JEMU) Tervuren Belgium
| | - Niels Van Steenkiste
- Research Group Zoology: Biodiversity and Toxicology Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
- Departments of Botany and Zoology University of British Columbia Vancouver BC Canada
| | - Floris C. Breman
- Royal Belgian Institute of Natural Sciences (RBINS: Taxonomy and Phylogeny & JEMU) Brussels Belgium
| | - Karen Smeets
- Research Group Zoology: Biodiversity and Toxicology Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Tom Artois
- Research Group Zoology: Biodiversity and Toxicology Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
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34
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McAllister CT, Woodyard ET, Stilwell JM, Rosser TG, Fayton TJ, Camus AJ, Griffin MJ, Robison HW. A NEW SPECIES OF MYXOBOLUS (CNIDARIA: MYXOSPOREA: MYXOBOLIDAE) FROM THE BLUE SUCKER, CYCLEPTUS ELONGATUS (LESUEUR) (CYPRINIFORMES: CATOSTOMIDAE: CYCLEPTINAE), FROM ARKANSAS. J Parasitol 2021; 107:582-592. [PMID: 34314485 DOI: 10.1645/20-125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
During 9-10 February 2018 and 21-22 February 2020, 7 adult Blue Suckers, Cycleptus elongatus, were collected by hoop nets from the Red River, Little River County (n = 3), and the Black River, Lawrence County (n = 4), Arkansas, and their gills, gallbladders, fins, integument, other major organs, and musculature were examined for myxozoans. All 7 (100%) were infected with an unknown species of gill-infecting Myxobolus sp. Twenty formalin-fixed plasmodia (cysts) of Myxobolus cloutmani n. sp. were elliptoidal, 407 μm long × 270 μm wide. Formalin-fixed myxospores were orbicular to broadly elliptoidal, 8.7 μm long × 7.8 μm wide. Two polar capsules were pyriform and subequal in size, extending over halfway in the myxospore. The larger polar capsule was 5.5 μm long × 3.1 μm wide, while the shorter was 5.1 × 2.9 μm. A coiled polar filament possessed 5 or 6 coils. The myxospore was 3.7 μm thick in sutural view, with a distinct sutural ridge. Qualitative and quantitative morphological data were from formalin-fixed as well as ethanol-preserved spores, while molecular data consisted of a 2,010 base pair sequence of the partial 18S ribosomal RNA gene and a 2,502 base pair sequence of the partial 28S ribosomal RNA gene. Phylogenetic analysis grouped M. cloutmani n. sp. with the other catostomid-infecting myxobolids. This is the first myxozoan reported from C. elongatus.
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Affiliation(s)
- Chris T McAllister
- Science and Mathematics Division, Eastern Oklahoma State College, Idabel, Oklahoma 74745
| | - Ethan T Woodyard
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762
| | - Justin M Stilwell
- Department of Pathology, University of Georgia, Athens, Georgia 30602
| | - Thomas G Rosser
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762
| | - Thomas J Fayton
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853
| | - Alvin J Camus
- Department of Pathology, University of Georgia, Athens, Georgia 30602
| | - Matt J Griffin
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi 39762
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Abstract
The Antarctic environment is famously inhospitable to most terrestrial biodiversity, traditionally viewed as a driver of species extinction. Combining population- and species-level molecular data, we show that beetles on islands along the Antarctic Polar Front diversified in response to major climatic events over the last 50 Ma in surprising synchrony with the region’s marine organisms. Unique algae- and moss-feeding habits enabled beetles to capitalize on cooling conditions, which resulted in a decline in flowering plants—the typical hosts for beetles elsewhere. Antarctica’s cooling paleoclimate thus fostered the diversification of both terrestrial and marine life. Climatically driven evolutionary processes since the Miocene may underpin much of the region’s diversity, are still ongoing, and should be further investigated among Antarctic biota. Global cooling and glacial–interglacial cycles since Antarctica’s isolation have been responsible for the diversification of the region’s marine fauna. By contrast, these same Earth system processes are thought to have played little role terrestrially, other than driving widespread extinctions. Here, we show that on islands along the Antarctic Polar Front, paleoclimatic processes have been key to diversification of one of the world’s most geographically isolated and unique groups of herbivorous beetles—Ectemnorhinini weevils. Combining phylogenomic, phylogenetic, and phylogeographic approaches, we demonstrate that these weevils colonized the sub-Antarctic islands from Africa at least 50 Ma ago and repeatedly dispersed among them. As the climate cooled from the mid-Miocene, diversification of the beetles accelerated, resulting in two species-rich clades. One of these clades specialized to feed on cryptogams, typical of the polar habitats that came to prevail under Miocene conditions yet remarkable as a food source for any beetle. This clade’s most unusual representative is a marine weevil currently undergoing further speciation. The other clade retained the more common weevil habit of feeding on angiosperms, which likely survived glaciation in isolated refugia. Diversification of Ectemnorhinini weevils occurred in synchrony with many other Antarctic radiations, including penguins and notothenioid fishes, and coincided with major environmental changes. Our results thus indicate that geo-climatically driven diversification has progressed similarly for Antarctic marine and terrestrial organisms since the Miocene, potentially constituting a general biodiversity paradigm that should be sought broadly for the region’s taxa.
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Iritani D, Banks JC, Webb SC, Fidler A, Horiguchi T, Wakeman KC. New gregarine species (Apicomplexa) from tunicates show an evolutionary history of host switching and suggest a problem with the systematics of Lankesteria and Lecudina. J Invertebr Pathol 2021; 183:107622. [PMID: 34043973 DOI: 10.1016/j.jip.2021.107622] [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: 03/03/2020] [Revised: 05/13/2021] [Accepted: 05/18/2021] [Indexed: 11/28/2022]
Abstract
Apicomplexa (sensu stricto) are a diverse group of obligate parasites to a variety of animal species. Gregarines have been the subject of particular interest due to their diversity, phylogenetically basal position, and more recently, their symbiotic relationships with their hosts. In the present study, four new species of marine eugregarines infecting ascidian hosts (Lankesteria kaiteriteriensis sp. nov., L. dolabra sp. nov., L. savignyii sp. nov., and L. pollywoga sp. nov.) were described using a combination of morphological and molecular data. Phylogenetic analysis using small subunit rDNA sequences suggested that gregarines that parasitize ascidians and polychaetes share a common origin as traditionally hypothesized by predecessors in the discipline. However, Lankesteria and Lecudina species did not form clades as expected, but were instead intermixed amongst each other and their respective type species in the phylogeny. These two major genera are therefore taxonomically problematic. We hypothesize that the continued addition of new species from polychaete and tunicate hosts as well as the construction of multigene phylogenies that include type-material will further dissolve the currently accepted distinction between Lankesteria and Lecudina. The species discovered and described in the current study add new phylogenetic and taxonomic data to the knowledge of marine gregarine parasitism in ascidian hosts.
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Affiliation(s)
- Davis Iritani
- Graduate School of Science, Hokkaido University, North 10, West 8, Sapporo 060-0810, Japan
| | - Jonathan C Banks
- Cawthron Institute, 98 Halifax Street East, Nelson 7010, New Zealand
| | - Stephen C Webb
- Cawthron Institute, 98 Halifax Street East, Nelson 7010, New Zealand
| | | | - Takeo Horiguchi
- Faculty of Science, Hokkaido University, North 10, West 8, Sapporo 060-0810, Japan
| | - Kevin C Wakeman
- Institute for the Advancement of Higher Education, Hokkaido University, Sapporo 060-0815, Japan.
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37
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Monroy Kuhn JM, Meusemann K, Korb J. Disentangling the aging gene expression network of termite queens. BMC Genomics 2021; 22:339. [PMID: 33975542 PMCID: PMC8114706 DOI: 10.1186/s12864-021-07649-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/22/2021] [Indexed: 02/07/2023] Open
Abstract
Background Most insects are relatively short-lived, with a maximum lifespan of a few weeks, like the aging model organism, the fruit-fly Drosophila melanogaster. By contrast, the queens of many social insects (termites, ants and some bees) can live from a few years to decades. This makes social insects promising models in aging research providing insights into how a long reproductive life can be achieved. Yet, aging studies on social insect reproductives are hampered by a lack of quantitative data on age-dependent survival and time series analyses that cover the whole lifespan of such long-lived individuals. We studied aging in queens of the drywood termite Cryptotermes secundus by determining survival probabilities over a period of 15 years and performed transcriptome analyses for queens of known age that covered their whole lifespan. Results The maximum lifespan of C. secundus queens was 13 years, with a median maximum longevity of 11.0 years. Time course and co-expression network analyses of gene expression patterns over time indicated a non-gradual aging pattern. It was characterized by networks of genes that became differentially expressed only late in life, namely after ten years, which associates well with the median maximum lifespan for queens. These old-age gene networks reflect processes of physiological upheaval. We detected strong signs of stress, decline, defense and repair at the transcriptional level of epigenetic control as well as at the post-transcriptional level with changes in transposable element activity and the proteostasis network. The latter depicts an upregulation of protein degradation, together with protein synthesis and protein folding, processes which are often down-regulated in old animals. The simultaneous upregulation of protein synthesis and autophagy is indicative of a stress-response mediated by the transcription factor cnc, a homolog of human nrf genes. Conclusions Our results show non-linear senescence with a rather sudden physiological upheaval at old-age. Most importantly, they point to a re-wiring in the proteostasis network and stress as part of the aging process of social insect queens, shortly before queens die. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07649-4.
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Affiliation(s)
- José Manuel Monroy Kuhn
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstr. 1, D-79104, Freiburg (i. Brsg.), Germany. .,Computational Discovery Research, Institute for Diabetes and Obesity, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, D-85764, Neuherberg, Germany.
| | - Karen Meusemann
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstr. 1, D-79104, Freiburg (i. Brsg.), Germany.,Australian National Insect Collection, CSIRO National Research Collections Australia, Clunies Ross Street, Acton, ACT 2601, Canberra, Australia
| | - Judith Korb
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstr. 1, D-79104, Freiburg (i. Brsg.), Germany.
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38
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Foley S, Krehenwinkel H, Cheng DQ, Piel WH. Phylogenomic analyses reveal a Gondwanan origin and repeated out of India colonizations into Asia by tarantulas (Araneae: Theraphosidae). PeerJ 2021; 9:e11162. [PMID: 33868819 PMCID: PMC8034372 DOI: 10.7717/peerj.11162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/04/2021] [Indexed: 12/23/2022] Open
Abstract
The study of biogeography seeks taxa that share a key set of characteristics, such as timescale of diversification, dispersal ability, and ecological lability. Tarantulas are ideal organisms for studying evolution over continental-scale biogeography given their time period of diversification, their mostly long-lived sedentary lives, low dispersal rate, and their nevertheless wide circumtropical distribution. In tandem with a time-calibrated transcriptome-based phylogeny generated by PhyloBayes, we estimate the ancestral ranges of ancient tarantulas using two methods, DEC+j and BBM, in the context of their evolution. We recover two ecologically distinct tarantula lineages that evolved on the Indian Plate before it collided with Asia, emphasizing the evolutionary significance of the region, and show that both lineages diversified across Asia at different times. The most ancestral tarantulas emerge on the Americas and Africa 120 Ma-105.5 Ma. We provide support for a dual colonization of Asia by two different tarantula lineages that occur at least 20 million years apart, as well as a Gondwanan origin for the group. We determine that their current distributions are attributable to a combination of Gondwanan vicariance, continental rafting, and geographic radiation. We also discuss emergent patterns in tarantula habitat preferences through time.
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Affiliation(s)
- Saoirse Foley
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biological Science, National University of Singapore, Singapore, Singapore
- Division of Science, Yale-NUS College, Singapore, Singapore
| | | | | | - William H. Piel
- Department of Biological Science, National University of Singapore, Singapore, Singapore
- Division of Science, Yale-NUS College, Singapore, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
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39
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Smith CH. A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). Genome Biol Evol 2021; 13:evab029. [PMID: 33570560 PMCID: PMC7937423 DOI: 10.1093/gbe/evab029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
From a genomics perspective, bivalves (Mollusca: Bivalvia) have been poorly explored with the exception for those of high economic value. The bivalve order Unionida, or freshwater mussels, has been of interest in recent genomic studies due to their unique mitochondrial biology and peculiar life cycle. However, genomic studies have been hindered by the lack of a high-quality reference genome. Here, I present a genome assembly of Potamilus streckersoni using Pacific Bioscience single-molecule real-time long reads and 10X Genomics-linked read sequencing. Further, I use RNA sequencing from multiple tissue types and life stages to annotate the reference genome. The final assembly was far superior to any previously published freshwater mussel genome and was represented by 2,368 scaffolds (2,472 contigs) and 1,776,755,624 bp, with a scaffold N50 of 2,051,244 bp. A high proportion of the assembly was comprised of repetitive elements (51.03%), aligning with genomic characteristics of other bivalves. The functional annotation returned 52,407 gene models (41,065 protein, 11,342 tRNAs), which was concordant with the estimated number of genes in other freshwater mussel species. This genetic resource, along with future studies developing high-quality genome assemblies and annotations, will be integral toward unraveling the genomic bases of ecologically and evolutionarily important traits in this hyper-diverse group.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, Texas, USA
- Biology Department, Baylor University, Waco, Texas, USA
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40
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Bayless KM, Trautwein MD, Meusemann K, Shin S, Petersen M, Donath A, Podsiadlowski L, Mayer C, Niehuis O, Peters RS, Meier R, Kutty SN, Liu S, Zhou X, Misof B, Yeates DK, Wiegmann BM. Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics. BMC Biol 2021; 19:23. [PMID: 33557827 PMCID: PMC7871583 DOI: 10.1186/s12915-020-00944-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 12/17/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The most species-rich radiation of animal life in the 66 million years following the Cretaceous extinction event is that of schizophoran flies: a third of fly diversity including Drosophila fruit fly model organisms, house flies, forensic blow flies, agricultural pest flies, and many other well and poorly known true flies. Rapid diversification has hindered previous attempts to elucidate the phylogenetic relationships among major schizophoran clades. A robust phylogenetic hypothesis for the major lineages containing these 55,000 described species would be critical to understand the processes that contributed to the diversity of these flies. We use protein encoding sequence data from transcriptomes, including 3145 genes from 70 species, representing all superfamilies, to improve the resolution of this previously intractable phylogenetic challenge. RESULTS Our results support a paraphyletic acalyptrate grade including a monophyletic Calyptratae and the monophyly of half of the acalyptrate superfamilies. The primary branching framework of Schizophora is well supported for the first time, revealing the primarily parasitic Pipunculidae and Sciomyzoidea stat. rev. as successive sister groups to the remaining Schizophora. Ephydroidea, Drosophila's superfamily, is the sister group of Calyptratae. Sphaeroceroidea has modest support as the sister to all non-sciomyzoid Schizophora. We define two novel lineages corroborated by morphological traits, the 'Modified Oviscapt Clade' containing Tephritoidea, Nerioidea, and other families, and the 'Cleft Pedicel Clade' containing Calyptratae, Ephydroidea, and other families. Support values remain low among a challenging subset of lineages, including Diopsidae. The placement of these families remained uncertain in both concatenated maximum likelihood and multispecies coalescent approaches. Rogue taxon removal was effective in increasing support values compared with strategies that maximise gene coverage or minimise missing data. CONCLUSIONS Dividing most acalyptrate fly groups into four major lineages is supported consistently across analyses. Understanding the fundamental branching patterns of schizophoran flies provides a foundation for future comparative research on the genetics, ecology, and biocontrol.
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Affiliation(s)
- Keith M Bayless
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Acton, Canberra, ACT, Australia.
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA.
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA.
| | - Michelle D Trautwein
- Department of Entomology, California Academy of Sciences, San Francisco, CA, USA
| | - Karen Meusemann
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Acton, Canberra, ACT, Australia
- Centre for Molecular Biodiversity Research (ZMB), Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstraße 1, Freiburg i. Br., Germany
| | - Seunggwan Shin
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Malte Petersen
- Max-Planck-Institut of Immunobiology and Epigenetics, Freiburg, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research (ZMB), Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research (ZMB), Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research (ZMB), Zoologisches Forschungsmuseum Alexander Koenig (ZFMK), Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology & Ecology, Institute of Biology I, Albert Ludwig University of Freiburg, Hauptstraße 1, Freiburg i. Br., Germany
| | - Ralph S Peters
- Centre of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore, Singapore
| | - Sujatha Narayanan Kutty
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, People's Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, People's Republic of China
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany
| | - David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Acton, Canberra, ACT, Australia
| | - Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA
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Van Steenkiste NWL, Rivlin N, Kahn P, Wakeman K, Leander BS. Grappleria corona gen. et sp. nov. (Platyhelminthes: Rhabdocoela: Jenseniidae fam. nov.) and an updated molecular phylogeny of ‘dalyelliid’ and temnocephalid microturbellarians. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2020.1841326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Niels W. L. Van Steenkiste
- Departments of Botany and Zoology, University of British Columbia, 3156-6270 University Blvd, Vancouver, V6T 1Z4, BC, Canada
| | - Natalie Rivlin
- Departments of Botany and Zoology, University of British Columbia, 3156-6270 University Blvd, Vancouver, V6T 1Z4, BC, Canada
| | - Penelope Kahn
- Departments of Botany and Zoology, University of British Columbia, 3156-6270 University Blvd, Vancouver, V6T 1Z4, BC, Canada
| | - Kevin Wakeman
- Institute for the Advancement of Higher Education, Hokkaido University, North 17, West 8, Kita-ku, Sapporo, 060-0808, Japan
- Graduate School of Science, Hokkaido University, North 10, West 8, Kita-ku, Sapporo, 060-0810, Japan
| | - Brian S. Leander
- Departments of Botany and Zoology, University of British Columbia, 3156-6270 University Blvd, Vancouver, V6T 1Z4, BC, Canada
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Schoville SD, Simon S, Bai M, Beethem Z, Dudko RY, Eberhard MJB, Frandsen PB, Küpper SC, Machida R, Verheij M, Willadsen PC, Zhou X, Wipfler B. Comparative transcriptomics of ice-crawlers demonstrates cold specialization constrains niche evolution in a relict lineage. Evol Appl 2021; 14:360-382. [PMID: 33664782 PMCID: PMC7896716 DOI: 10.1111/eva.13120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/25/2020] [Accepted: 08/17/2020] [Indexed: 12/26/2022] Open
Abstract
Key changes in ecological niche space are often critical to understanding how lineages diversify during adaptive radiations. However, the converse, or understanding why some lineages are depauperate and relictual, is more challenging, as many factors may constrain niche evolution. In the case of the insect order Grylloblattodea, highly conserved thermal breadth is assumed to be closely tied to their relictual status, but has not been formerly tested. Here, we investigate whether evolutionary constraints in the physiological tolerance of temperature can help explain relictualism in this lineage. Using a comparative transcriptomics approach, we investigate gene expression following acute heat and cold stress across members of Grylloblattodea and their sister group, Mantophasmatodea. We additionally examine patterns of protein evolution, to identify candidate genes of positive selection. We demonstrate that cold specialization in Grylloblattodea has been accompanied by the loss of the inducible heat shock response under both acute heat and cold stress. Additionally, there is widespread evidence of selection on protein-coding genes consistent with evolutionary constraints due to cold specialization. This includes positive selection on genes involved in trehalose transport, metabolic function, mitochondrial function, oxygen reduction, oxidative stress, and protein synthesis. These patterns of molecular adaptation suggest that Grylloblattodea have undergone evolutionary trade-offs to survive in cold habitats and should be considered highly vulnerable to climate change. Finally, our transcriptomic data provide a robust backbone phylogeny for generic relationships within Grylloblattodea and Mantophasmatodea. Major phylogenetic splits in each group relate to arid conditions driving biogeographical patterns, with support for a sister-group relationship between North American Grylloblatta and Altai-Sayan Grylloblattella, and a range disjunction in Namibia splitting major clades within Mantophasmatodea.
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Affiliation(s)
| | - Sabrina Simon
- Biosystematics GroupWageningen University & ResearchPB WageningenThe Netherlands
| | - Ming Bai
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | - Zachary Beethem
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
Department of Biomedical SciencesSchool of Veterinary MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Roman Y. Dudko
- Institute of Systematics and Ecology of AnimalsSiberian Branch of the Russian Academy of SciencesNovosibirskRussia
- Tomsk State UniversityTomskRussia
| | - Monika J. B. Eberhard
- Zoological Institute and MuseumGeneral Zoology and Zoological SystematicsUniversity of GreifswaldGreifswaldGermany
| | - Paul B. Frandsen
- Department of Plant & Wildlife SciencesBrigham Young UniversityProvoUTUSA
- Data Science LabOffice of the Chief Information OfficerSmithsonian InstitutionWashingtonDCU.S.A
| | - Simon C. Küpper
- Zoological Institute and MuseumGeneral Zoology and Zoological SystematicsUniversity of GreifswaldGreifswaldGermany
| | - Ryuichiro Machida
- Sugadaira Research StationMountain Science CenterUniversity of TsukubaUeda, NaganoJapan
| | - Max Verheij
- Biosystematics GroupWageningen University & ResearchPB WageningenThe Netherlands
| | - Peter C. Willadsen
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
Department of Entomology and Plant PathologyNorth Carolina State UniversityCampus Box 7613RaleighNCUSA
| | - Xin Zhou
- Department of EntomologyCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
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Maletti S, Niehuis O, Mayer C, Sann M, Klopfstein S, Nottebrock G, Baur H, Peters RS. Phylogeny, taxonomics, and ovipositor length variation of the
Pteromalus albipennis
species group (Hymenoptera: Chalcidoidea: Pteromalidae: Pteromalinae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Sina Maletti
- Department of Invertebrates Natural History Museum Bern Bern Switzerland
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology, (Zoology) Albert Ludwig University Freiburg Freiburg Germany
| | - Christoph Mayer
- Center for Molecular Biodiversity Research Zoologisches Forschungsmuseum Alexander Koenig Bonn Germany
| | - Manuela Sann
- Department of Evolutionary Biology and Ecology, Institute of Biology, (Zoology) Albert Ludwig University Freiburg Freiburg Germany
| | | | - Gaby Nottebrock
- Arthropoda Department Zoologisches Forschungsmuseum Alexander Koenig Bonn Germany
| | - Hannes Baur
- Department of Invertebrates Natural History Museum Bern Bern Switzerland
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Ralph S. Peters
- Arthropoda Department Zoologisches Forschungsmuseum Alexander Koenig Bonn Germany
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Opatova V, Hamilton CA, Hedin M, De Oca LM, Král J, Bond JE. Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data. Syst Biol 2021; 69:671-707. [PMID: 31841157 DOI: 10.1093/sysbio/syz064] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022] Open
Abstract
The infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3000 nominal species. This ancient group has a worldwide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel-web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here, we present a comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae. We employ 472 loci obtained through anchored hybrid enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We sampled nearly all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing insights to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). Three families Entypesidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY), and one subfamily Australothelinae (NEW SUBFAMILY) are newly proposed. Such a major rearrangement in classification, recognizing nine newly established family-level rank taxa, is the largest the group has seen in over three decades. [Biogeography; molecular clocks; phylogenomics; spider web foraging; taxonomy.].
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Affiliation(s)
- Vera Opatova
- Department of Entomology and Nematology, University of California, 1282 Academic Surge, One Shields Avenue, Davis, CA 95616, USA
| | - Chris A Hamilton
- Department of Entomology, Plant Pathology & Nematology, University of Idaho, 875 Perimeter Dr. MS 2329, Moscow ID 83844-2329, USA
| | - Marshal Hedin
- Department of Biology, LSN 204E, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-4614, USA
| | - Laura Montes De Oca
- Departamento de Ecología y Biología Evolutiva, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, Montevideo 11600, Uruguay
| | - Jiři Král
- Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Viničná 5, Prague 2 128 44, Czech Republic
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, 1282 Academic Surge, One Shields Avenue, Davis, CA 95616, USA
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Zhang Z, Pan D, Hao X, Sun H. Two new species of freshwater crabs of the genera Eosamon Yeo & Ng, 2007 and Indochinamon Yeo & Ng, 2007 (Crustacea, Brachyura, Potamidae) from southern Yunnan, China. Zookeys 2020; 980:1-21. [PMID: 33192135 PMCID: PMC7642192 DOI: 10.3897/zookeys.980.52186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 09/14/2020] [Indexed: 11/28/2022] Open
Abstract
Two new species of potamid crabs, Eosamondaiaesp. nov. and Indochinamonmalipoensesp. nov. are described from the Sino-Burmese border, southwestern Yunnan and from the Sino-Vietnamese border, southeastern Yunnan, China. The two new species can be distinguished from their closest congeners by several characters, among which is the form of the first gonopod structures. Molecular analyses based on partial mitochondrial 16S rDNA sequences also support the systematic status of these new taxa.
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Affiliation(s)
- Zewei Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd, Nanjing 210023, China Nanjing Normal University Nanjing China
| | - Da Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd, Nanjing 210023, China Nanjing Normal University Nanjing China
| | - Xiyang Hao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd, Nanjing 210023, China Nanjing Normal University Nanjing China
| | - Hongying Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd, Nanjing 210023, China Nanjing Normal University Nanjing China
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Vasilikopoulos A, Misof B, Meusemann K, Lieberz D, Flouri T, Beutel RG, Niehuis O, Wappler T, Rust J, Peters RS, Donath A, Podsiadlowski L, Mayer C, Bartel D, Böhm A, Liu S, Kapli P, Greve C, Jepson JE, Liu X, Zhou X, Aspöck H, Aspöck U. An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola). BMC Evol Biol 2020; 20:64. [PMID: 32493355 PMCID: PMC7268685 DOI: 10.1186/s12862-020-01631-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The latest advancements in DNA sequencing technologies have facilitated the resolution of the phylogeny of insects, yet parts of the tree of Holometabola remain unresolved. The phylogeny of Neuropterida has been extensively studied, but no strong consensus exists concerning the phylogenetic relationships within the order Neuroptera. Here, we assembled a novel transcriptomic dataset to address previously unresolved issues in the phylogeny of Neuropterida and to infer divergence times within the group. We tested the robustness of our phylogenetic estimates by comparing summary coalescent and concatenation-based phylogenetic approaches and by employing different quartet-based measures of phylogenomic incongruence, combined with data permutations. RESULTS Our results suggest that the order Raphidioptera is sister to Neuroptera + Megaloptera. Coniopterygidae is inferred as sister to all remaining neuropteran families suggesting that larval cryptonephry could be a ground plan feature of Neuroptera. A clade that includes Nevrorthidae, Osmylidae, and Sisyridae (i.e. Osmyloidea) is inferred as sister to all other Neuroptera except Coniopterygidae, and Dilaridae is placed as sister to all remaining neuropteran families. Ithonidae is inferred as the sister group of monophyletic Myrmeleontiformia. The phylogenetic affinities of Chrysopidae and Hemerobiidae were dependent on the data type analyzed, and quartet-based analyses showed only weak support for the placement of Hemerobiidae as sister to Ithonidae + Myrmeleontiformia. Our molecular dating analyses suggest that most families of Neuropterida started to diversify in the Jurassic and our ancestral character state reconstructions suggest a primarily terrestrial environment of the larvae of Neuropterida and Neuroptera. CONCLUSION Our extensive phylogenomic analyses consolidate several key aspects in the backbone phylogeny of Neuropterida, such as the basal placement of Coniopterygidae within Neuroptera and the monophyly of Osmyloidea. Furthermore, they provide new insights into the timing of diversification of Neuropterida. Despite the vast amount of analyzed molecular data, we found that certain nodes in the tree of Neuroptera are not robustly resolved. Therefore, we emphasize the importance of integrating the results of morphological analyses with those of sequence-based phylogenomics. We also suggest that comparative analyses of genomic meta-characters should be incorporated into future phylogenomic studies of Neuropterida.
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Affiliation(s)
- Alexandros Vasilikopoulos
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Bernhard Misof
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany.
| | - Karen Meusemann
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
- Australian National Insect Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT 2601, Australia
| | - Doria Lieberz
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Tomáš Flouri
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743, Jena, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Torsten Wappler
- Natural History Department, Hessisches Landesmuseum Darmstadt, 64283, Darmstadt, Germany
| | - Jes Rust
- Steinmann-Institut für Geologie, Mineralogie und Paläontologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115, Bonn, Germany
| | - Ralph S Peters
- Centre for Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Christoph Mayer
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113, Bonn, Germany
| | - Daniela Bartel
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Alexander Böhm
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), 60325, Frankfurt, Germany
| | - James E Jepson
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, T23 N73K, Cork, Ireland
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Horst Aspöck
- Institute of Specific Prophylaxis and Tropical Medicine, Medical Parasitology, Medical University of Vienna (MUW), 1090, Vienna, Austria
| | - Ulrike Aspöck
- Department of Evolutionary Biology, University of Vienna, 1090, Vienna, Austria
- Zoological Department II, Natural History Museum of Vienna, 1010, Vienna, Austria
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Jermiin LS, Catullo RA, Holland BR. A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics. NAR Genom Bioinform 2020; 2:lqaa041. [PMID: 33575594 PMCID: PMC7671319 DOI: 10.1093/nargab/lqaa041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.
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Affiliation(s)
- Lars S Jermiin
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Biology & Environment Science, University College Dublin, Belfield, Dublin 4, Ireland
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Renee A Catullo
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Science and Health & Hawkesbury Institute of the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
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Morphological and Molecular Characterisation of Myxidium kudoi Meglitsch, 1937 from the Blue Catfish Ictalurus furcatus, Valenciennes in Oklahoma, USA. Acta Parasitol 2020; 65:388-395. [PMID: 32052241 DOI: 10.2478/s11686-020-00172-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/17/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND Myxidium kudoi Meglitsch, 1937 has been described from the type host, blue catfish Ictalurus furcatus, with no additional host records or molecular data available for this species. PURPOSE To provide molecular data and a novel host locality for this species and carry out phylogenetic analyses to infer the evolutionary relationship of the species to other members of the family Myxidiidae for which DNA sequence data is available. METHODS These data were collected using myxospores from the gallbladder of a blue catfish, Ictalurus furcatus collected from Lake Texoma, Oklahoma, USA. Myxospores were morphologically consistent with the only other account of this species and not any other Myxidium species described from siluriform fishes. RESULTS Myxospores were oblong with rounded ends and were 10.8-12.6 (11.6 ± 0.5) µm in length and 4.7-6.6 (5.7 ± 0.5) µm in width. Polar capsules were subspherical and 2.7-3.9 (3.4 ± 0.3) µm in length and 2.4-3.5 (3.1 ± 0.3) µm in diameter, with each capsule containing a polar filament with 3-4 coils. Molecular data consisted of a 2918-bp sequence of the partial 18S, complete ITS1, 5.8S, ITS2, and partial 28S ribosomal rRNA regions as well as a 2455-bp sequence of partial 28S ribosomal RNA. The partial 18S and 28S data was used in a concatenated Bayesian phylogenetic analysis to further infer the evolutionary relationships of the Myxidiidae. Additionally, the partial 18S data was used in a separate phylogenetic analysis. CONCLUSIONS The present work reports novel morphological and molecular data for Myxidium kudoi as well as a novel locality of occurrence for this species. In concatenated phylogenetic analysis using 18S and 28S data and other molecular data from Myxozoa, M. kudoi grouped with other freshwater Myxidiidae. In the single-locus, 18S analysis, M. kudoi grouped with Myxidium rhodei from Rutilus rutilus and Myxidium amazonense from Corydoras melini, the only other Myxidium species of catfish for which molecular data are available.
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Abstract
Knowing phylogenetic relationships among species is fundamental for many studies in biology. An accurate phylogenetic tree underpins our understanding of the major transitions in evolution, such as the emergence of new body plans or metabolism, and is key to inferring the origin of new genes, detecting molecular adaptation, understanding morphological character evolution and reconstructing demographic changes in recently diverged species. Although data are ever more plentiful and powerful analysis methods are available, there remain many challenges to reliable tree building. Here, we discuss the major steps of phylogenetic analysis, including identification of orthologous genes or proteins, multiple sequence alignment, and choice of substitution models and inference methodologies. Understanding the different sources of errors and the strategies to mitigate them is essential for assembling an accurate tree of life.
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Lucentini L, Plazzi F, Sfriso AA, Pizzirani C, Sfriso A, Chiesa S. Additional taxonomic coverage of the doubly uniparental inheritance in bivalves: Evidence of sex‐linked heteroplasmy in the razor clam
Solen marginatus
Pulteney, 1799, but not in the lagoon cockle
Cerastoderma glaucum
(Bruguière, 1789). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Livia Lucentini
- Department of Chemistry, Biology and Biotechnologies University of Perugia Perugia Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences University of Bologna Bologna Italy
| | - Andrea Augusto Sfriso
- Department of Chemical and Pharmaceuticals Sciences University of Ferrara Ferrara Italy
| | - Claudia Pizzirani
- Department of Chemistry, Biology and Biotechnologies University of Perugia Perugia Italy
| | - Adriano Sfriso
- Department of Environmental Sciences, Informatics and Statistics Ca' Foscari University of Venice Venice Italy
| | - Stefania Chiesa
- Department of Molecular Sciences and Nanosystems Ca' Foscari University of Venice Venice Italy
- ISPRA Institute for Environmental Protection and Research Rome Italy
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