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Züger S, Krings W, Gorb SN, Büscher TH, Sombke A. Material composition and mechanical properties of the venom-injecting forcipules in centipedes. Front Zool 2024; 21:21. [PMID: 39180121 PMCID: PMC11342574 DOI: 10.1186/s12983-024-00543-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024] Open
Abstract
BACKGROUND Centipedes are terrestrial and predatory arthropods that possess an evolutionary transformed pair of appendages used for venom injection-the forcipules. Many arthropods incorporate reinforcing elements into the cuticle of their piercing or biting structures to enhance hardness, elasticity or resistance to wear and structural failure. Given their frequent exposure to high mechanical stress, we hypothesise that the cuticle of the centipede forcipule might be mechanically reinforced. With a combination of imaging, analytical techniques and mechanical testing, we explore the centipede forcipule in detail to shed light on its morphology and performance. Additionally, we compare these data to characteristics of the locomotory leg to infer evolutionary processes. RESULTS We examined sclerotization patterns using confocal laser-scanning microscopy based on autofluorescence properties of the cuticle (forcipule and leg) and elemental composition by energy-dispersive X-ray spectroscopy in representative species from all five centipede lineages. These experiments revealed gradually increasing sclerotization towards the forcipular tarsungulum and a stronger sclerotization of joints in taxa with condensed podomeres. Depending on the species, calcium, zinc or chlorine are present with a higher concentration towards the distal tarsungulum. Interestingly, these characteristics are more or less mirrored in the locomotory leg's pretarsal claw in Epimorpha. To understand how incorporated elements affect mechanical properties, we tested resistance to structural failure, hardness (H) and Young's modulus (E) in two representative species, one with high zinc and one with high calcium content. Both species, however, exhibit similar properties and no differences in mechanical stress the forcipule can withstand. CONCLUSIONS Our study reveals similarities in the material composition and properties of the forcipules in centipedes. The forcipules transformed from an elongated leg-like appearance into rigid piercing structures. Our data supports their serial homology to the locomotory leg and that the forcipule's tarsungulum is a fusion of tarsus and pretarsal claw. Calcium or zinc incorporation leads to comparable mechanical properties like in piercing structures of chelicerates and insects, but the elemental incorporation does not increase H and E in centipedes, suggesting that centipedes followed their own pathways in the evolutionary transformation of piercing tools.
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Affiliation(s)
- Simon Züger
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Department of Functional Morphology and Biomechanics, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
| | - Wencke Krings
- Department of Functional Morphology and Biomechanics, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
- Department of Cariology, Endodontology and Periodontology, Universität Leipzig, Liebigstrasse 12, 04103, Leipzig, Germany
| | - Stanislav N Gorb
- Department of Functional Morphology and Biomechanics, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Thies H Büscher
- Department of Functional Morphology and Biomechanics, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Andy Sombke
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Center for Anatomy and Cell Biology, Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, 1090, Vienna, Austria
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2
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Zhang L, Zhang K, Yang F, Dayananda B, Cao Y, Hu Z, Liu Y. Chromosome-level genome of Scolopendra mutilans provides insights into its evolution. Integr Zool 2024. [PMID: 39075924 DOI: 10.1111/1749-4877.12871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Report the first chromosome level genome of myriapod Scolopendra mutilans. Reveal gene expansions for importance to adapt. Annotate nine Hox cluster genes in this genome.
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Affiliation(s)
- Lin Zhang
- Hubei Shizhen Laboratory, Hubei Key Laboratory of Theory and Application Research of Liver and Kidney in Traditional Chinese Medicine, School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, China
| | - Kai Zhang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Fang Yang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Buddhi Dayananda
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Yunpeng Cao
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Yifei Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
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Fleming J, Eriksen PM, Struck TH. Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric. F1000Res 2024; 12:945. [PMID: 38799242 PMCID: PMC11128044 DOI: 10.12688/f1000research.139356.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/05/2024] [Indexed: 05/29/2024] Open
Abstract
Background: The phylogenetic bootstrap, first proposed by Felsenstein in 1985, is a critically important statistical method in assessing the robusticity of phylogenetic datasets. Core to its concept was the use of pseudo sampling - assessing the data by generating new replicates derived from the initial dataset that was used to generate the phylogeny. In this way, phylogenetic support metrics could overcome the lack of perfect, infinite data. With infinite data, however, it is possible to sample smaller replicates directly from the data to obtain both the phylogeny and its statistical robusticity in the same analysis. Due to the growth of whole genome sequencing, the depth and breadth of our datasets have greatly expanded and are set to only expand further. With genome-scale datasets comprising thousands of genes, we can now obtain a proxy for infinite data. Accordingly, we can potentially abandon the notion of pseudo sampling and instead randomly sample small subsets of genes from the thousands of genes in our analyses. Methods: We introduce Scoutknife, a jackknife-style subsampling implementation that generates 100 datasets by randomly sampling a small number of genes from an initial large-gene dataset to jointly establish both a phylogenetic hypothesis and assess its robusticity. We assess its effectiveness by using 18 previously published datasets and 100 simulation studies. Results: We show that Scoutknife is conservative and informative as to conflicts and incongruence across the whole genome, without the need for subsampling based on traditional model selection criteria. Conclusions: Scoutknife reliably achieves comparable results to selecting the best genes on both real and simulation datasets, while being resistant to the potential biases caused by selecting for model fit. As the amount of genome data grows, it becomes an even more exciting option to assess the robusticity of phylogenetic hypotheses.
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Affiliation(s)
- James Fleming
- Natural History Museum, Universitetet i Oslo, Oslo, Oslo, 0562, Norway
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Schendel V, Müller CHG, Kenning M, Maxwell M, Jenner RA, Undheim EAB, Sombke A. The venom and telopodal defence systems of the centipede Lithobius forficatus are functionally convergent serial homologues. BMC Biol 2024; 22:135. [PMID: 38867210 PMCID: PMC11170834 DOI: 10.1186/s12915-024-01925-x] [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: 11/07/2023] [Accepted: 05/22/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Evolution of novelty is a central theme in evolutionary biology, yet studying the origins of traits with an apparently discontinuous origin remains a major challenge. Venom systems are a well-suited model for the study of this phenomenon because they capture several aspects of novelty across multiple levels of biological complexity. However, while there is some knowledge on the evolution of individual toxins, not much is known about the evolution of venom systems as a whole. One way of shedding light on the evolution of new traits is to investigate less specialised serial homologues, i.e. repeated traits in an organism that share a developmental origin. This approach can be particularly informative in animals with repetitive body segments, such as centipedes. RESULTS Here, we investigate morphological and biochemical aspects of the defensive telopodal glandular organs borne on the posterior legs of venomous stone centipedes (Lithobiomorpha), using a multimethod approach, including behavioural observations, comparative morphology, proteomics, comparative transcriptomics and molecular phylogenetics. We show that the anterior venom system and posterior telopodal defence system are functionally convergent serial homologues, where one (telopodal defence) represents a model for the putative early evolutionary state of the other (venom). Venom glands and telopodal glandular organs appear to have evolved from the same type of epidermal gland (four-cell recto-canal type) and while the telopodal defensive secretion shares a great degree of compositional overlap with centipede venoms in general, these similarities arose predominantly through convergent recruitment of distantly related toxin-like components. Both systems are composed of elements predisposed to functional innovation across levels of biological complexity that range from proteins to glands, demonstrating clear parallels between molecular and morphological traits in the properties that facilitate the evolution of novelty. CONCLUSIONS The evolution of the lithobiomorph telopodal defence system provides indirect empirical support for the plausibility of the hypothesised evolutionary origin of the centipede venom system, which occurred through functional innovation and gradual specialisation of existing epidermal glands. Our results thus exemplify how continuous transformation and functional innovation can drive the apparent discontinuous emergence of novelties on higher levels of biological complexity.
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Affiliation(s)
- Vanessa Schendel
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD, 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Carsten H G Müller
- Zoological Institute and Museum, University of Greifswald, Loitzer Strasse 26, Greifswald, 17489, Germany
| | - Matthes Kenning
- Zoological Institute and Museum, University of Greifswald, Loitzer Strasse 26, Greifswald, 17489, Germany
| | - Michael Maxwell
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | | | - Eivind A B Undheim
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD, 4072, Australia.
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, 0316, Norway.
| | - Andy Sombke
- Centre for Anatomy and Cell Biology, Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Vienna, 1090, Austria.
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Djerassiplatz 1, 1030, Austria.
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Chikami Y, Yahata K. The structural and functional modularity of ovarian follicle epithelium in the pill-millipede Hyleoglomeris japonica Verhoeff, 1936 (Diplopoda: Glomerida: Glomeridae). Tissue Cell 2024; 88:102372. [PMID: 38598872 DOI: 10.1016/j.tice.2024.102372] [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: 11/30/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Ovarian somatic tissues typically surround developing oocytes and play a crucial role in oogenesis across various metazoans, often displaying structural properties specific to their functions. However, there is an absence of evident structural modularity in the follicle epithelium of Myriapoda. We report here two structurally and developmentally distinct domains within the follicle epithelium of the Japanese pill millipede, Hyleoglomeris japonica. The follicle epithelium of H. japonica exhibits a thick cell mass at the apex of the follicle. These cells harbor abundant rough endoplasmic reticulum, mitochondria, Golgi complexes, and numerous microvilli, indicative of synthetic/secretory activities. Moreover, their height increases as oogenesis progresses. In contrast, another region of the epithelium lacks these features. Our findings highlight the presence of structural and functional modularity in the follicle epithelium of H. japonica. We suggest classifying the follicle epithelium of Myriapoda into three types: homogenous epithelia with enhanced synthetic activities, homogenous epithelia with diminished such activities, and heterogeneous epithelia with varying synthetic activities. These findings prompt a reevaluation of the nature of ovarian somatic tissues in Myriapoda as well as in Arthropoda.
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Affiliation(s)
- Yasuhiko Chikami
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
| | - Kensuke Yahata
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.
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Porta AO, Giribet G. A new genus of scutigerid centipede from southern South America with the description of two new species and an updated molecular phylogeny of the myriapod order Scutigeromorpha (Myriapoda: Chilopoda). INVERTEBR SYST 2024; 38:IS24006. [PMID: 38744498 DOI: 10.1071/is24006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/12/2024] [Indexed: 05/16/2024]
Abstract
Scutigeromorph centipedes are conspicuous, yet often ignored myriapods for which little work has been conducted in southern South America. After examining recent and museum collections from Chile and Argentina, two new species of generic uncertainty were identified. A new genus of scutigerid centipede, Edgethreua , is therefore described with two new species, E. chilensis from Central Chile (type species of the genus) and E. goloboffi from Argentinian Patagonia. The new genus is characterised by the presence of scattered setiform bristles with short paired spines and the absence of simple spinulae and spines on all stomatotergites, the presence of a single spine-bristle in the prefemur of the second maxilla, a patch of cuticular ridges and pores surrounding the sensilla of the proximal labral portion of the epipharynx, the morphology of the sensilla of the distal patch of the hypopharynx and the morphology of the female gonopods. A phylogenetic analysis of the new species using two nuclear ribosomal RNA genes (18S and 28S rRNA), two mitochondrial ribosomal RNA genes (12S and 16S rRNA) and the mitochondrial protein-encoding gene cytochrome c oxidase subunit I show that the new genus does not cluster with any other described genus of scutigeromorph represented in molecular phylogenies. The data indicate that the new genus is probably sister group to a clade including the genera Lassophora , Ballonema and the subfamily Thereuoneminae, although one analysis suggests a position as sister group to Scutigerinae. ZooBank: urn:lsid:zoobank.org:pub:A4D453F3-9031-4E21-84C7-87F16C07AD51.
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Affiliation(s)
- Andrés O Porta
- División de Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Avenida Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina; and Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA, UBA-CONICET), Pabellón II, Ciudad Universitaria, Buenos Aires, C1428EGA, Argentina; and Departamento de Ciencias Exactas, Universidad Nacional del Oeste, Belgrano 369 C1718, San Antonio de Padua, Buenos Aires, Argentina
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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7
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Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol 2024; 42:139-147. [PMID: 37081138 PMCID: PMC10791578 DOI: 10.1038/s41587-023-01753-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/16/2023] [Indexed: 04/22/2023]
Abstract
Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly and annotation quality, especially for large datasets. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes and bypasses traditional steps in phylogeny inference, such as genome assembly, annotation and all-versus-all sequence comparisons, while retaining accuracy. In a benchmark encompassing a broad variety of datasets, Read2Tree is 10-100 times faster than assembly-based approaches and in most cases more accurate-the exception being when sequencing coverage is high and reference species very distant. Here, to illustrate the broad applicability of the tool, we reconstruct a yeast tree of life of 435 species spanning 590 million years of evolution. We also apply Read2Tree to >10,000 Coronaviridae samples, accurately classifying highly diverse animal samples and near-identical severe acute respiratory syndrome coronavirus 2 sequences on a single tree. The speed, accuracy and versatility of Read2Tree enable comparative genomics at scale.
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Affiliation(s)
- David Dylus
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- F. Hoffmann-La Roche Ltd, Immunology, Infectious Disease, and Ophthalmology (I2O), Roche Pharmaceutical Research and Early Development (pRED), Basel, Switzerland
| | - Adrian Altenhoff
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Computer Science, ETH, Zurich, Switzerland
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Department of Computer Science, University College London, London, UK.
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
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Su YT, Cai CY, Huang DIY. A new species of Polydesmidae (Myriapoda, Diplopoda, Polydesmida) from the mid-Cretaceous Burmese amber. Zootaxa 2023; 5396:112-123. [PMID: 38220976 DOI: 10.11646/zootaxa.5396.1.16] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Indexed: 01/16/2024]
Abstract
A new species of the flat-backed millipede family Polydesmidae, Propolydesmus cretaceus sp. nov., is described from the mid-Cretaceous Burmese amber. Detailed morphological characters are provided on the basis of 3 well-preserved adults (2 males and 1 females), 2 female subadults, and 14 additional specimens, using confocal laser scanning microscopy (CLSM) and X-ray micro-computed tomography (CT) with computer-aided 3D-reconstructions. The new species can be placed in the extant genus Propolydesmus. It majorly differs from other congeners due to the stronger gonopod acropodite and the presence of a bipartite gonopod exomerite.
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Affiliation(s)
- Yi-Tong Su
- State Key Laboratory of Palaeobiology and Stratigraphy; Center for Excellence in Life and Paleoenvironment; Nanjing Institute of Geology and Palaeontology; Chinese Academy of Sciences; Nanjing 210008; China.
| | - Chen-Yang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy; Center for Excellence in Life and Paleoenvironment; Nanjing Institute of Geology and Palaeontology; Chinese Academy of Sciences; Nanjing 210008; China.
| | - DI-Ying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy; Center for Excellence in Life and Paleoenvironment; Nanjing Institute of Geology and Palaeontology; Chinese Academy of Sciences; Nanjing 210008; China.
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Yuan ML, Chen WT, Zhang QL, Li M, Zhang L, Tang PA. Transcriptomic data recover a new superfamily-level phylogeny of Cucujiformia (Coleoptera, Polyphaga). Mol Phylogenet Evol 2023; 179:107679. [PMID: 36539017 DOI: 10.1016/j.ympev.2022.107679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/30/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Cucujiformia, the largest taxon in the order Coleoptera, exhibits extraordinary morphological, ecological, and behavioral diversity. This infraorder is currently divided into seven superfamilies, but considerably incongruent relationships among superfamilies have been reported by recent phylogenomic studies. Here, we combined the 21 newly sequenced transcriptomes representing six superfamilies with nine previously published cucujiform genomes/transcriptomes to elucidate the phylogeny and evolution of Cucujiformia. The monophyly of each of five superfamilies were consistently supported by all phylogenetic analyses based on the twelve datasets (matrix occupancy, amino acid and nucleotide data) and the two analytical methods (maximum likelihood method and Bayesian inference). Both the amino acid datasets and the RY recoded nucleotide datasets recovered the monophyly of Cucujoidea. Topology test results statistically supported the following robust superfamily-level phylogeny in Cucujiformia: (Coccinelloidea, (Cleroidea, (Tenebrionoidea, (Cucujoidea, (Chrysomeloidea, Curculionoidea))))). Our divergence time analyses recovered a Permian origin of Cucujiformia and a Jurassic-Cretaceous origin of most superfamilies. The diversification of phytophagous beetles that occurred in the Cretaceous can be attributed to its co-evolution with angiosperms, supporting the hypothesis of a Cretaceous Terrestrial Revolution.
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Affiliation(s)
- Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China.
| | - Wen-Ting Chen
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Min Li
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Li Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Pei-An Tang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, People's Republic of China.
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10
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Benavides LR, Edgecombe GD, Giribet G. Re-evaluating and dating myriapod diversification with phylotranscriptomics under a regime of dense taxon sampling. Mol Phylogenet Evol 2023; 178:107621. [PMID: 36116731 DOI: 10.1016/j.ympev.2022.107621] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022]
Abstract
Recent transcriptomic studies of myriapod phylogeny have been based on relatively small datasets with <40 myriapod terminals and variably supported or contradicted the traditional morphological groupings of Progoneata and Dignatha. Here we amassed a large dataset of 104 myriapod terminals, including multiple species for each of the four myriapod classes. Across the tree, most nodes are stable and well supported. Most analyses across a range of gene occupancy levels provide moderate to strong support for a deep split of Myriapoda into Symphyla + Pauropoda (=Edafopoda) and an uncontradicted grouping of Chilopoda + Diplopoda (=Pectinopoda nov.), as in other recent transcriptome-based analyses; no analysis recovers Progoneata or Dignatha as clades. As in all recent multi-locus and phylogenomic studies, chilopod interrelationships resolve with Craterostigmus excluded from Amalpighiata rather than uniting with other centipedes with maternal brood care in Phylactometria. Diplopod ordinal interrelationships are largely congruent with morphology-based classifications. Chilognathan clades that are not invariably advocated by morphologists include Glomerida + Glomeridesmida, such that the volvation-related characters of pill millipedes may be convergent, and Stemmiulida + Polydesmida more closely allied to Juliformia than to Callipodida + Chordeumatida. The latter relationship implies homoplasy in spinnerets and contradicts Nematophora. A time-tree with nodes calibrated by 25 myriapod and six outgroup fossil terminals recovers Cambrian-Ordovician divergences for the deepest splits in Myriapoda, Edafopoda and Pectinopoda, predating the terrestrial fossil record of myriapods as in other published chronograms, whereas age estimates within Chilopoda and Diplopoda overlap with or do not appreciably predate the calibration fossils. The grouping of Chilopoda and Diplopoda is recovered in all our analyses and is formalized as Pectinopoda nov., named for the shared presence of mandibular comb lamellae. New taxonomic proposals for Chilopoda based on uncontradicted clades are Tykhepoda nov. for the three blind families of Scolopendromorpha that share a "sieve-type" gizzard, and Taktikospina nov. for Scolopendromorpha to the exclusion of Mimopidae.
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Affiliation(s)
- Ligia R Benavides
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | | | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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11
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Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Read2Tree: scalable and accurate phylogenetic trees from raw reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.04.18.488678. [PMID: 36561179 PMCID: PMC9774205 DOI: 10.1101/2022.04.18.488678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The inference of phylogenetic trees is foundational to biology. However, state-of-the-art phylogenomics requires running complex pipelines, at significant computational and labour costs, with additional constraints in sequencing coverage, assembly and annotation quality. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes. In a benchmark encompassing a broad variety of datasets, our assembly-free approach was 10-100x faster than conventional approaches, and in most cases more accurate-the exception being when sequencing coverage was high and reference species very distant. To illustrate the broad applicability of the tool, we reconstructed a yeast tree of life of 435 species spanning 590 million years of evolution. Applied to Coronaviridae samples, Read2Tree accurately classified highly diverse animal samples and near-identical SARS-CoV-2 sequences on a single tree-thereby exhibiting remarkable breadth and depth. The speed, accuracy, and versatility of Read2Tree enables comparative genomics at scale.
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Affiliation(s)
- David Dylus
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- present address: F. Hoffmann-La Roche Ltd, Immunology, Infectious Disease, and Ophthalmology (I2O), Roche Pharmaceutical Research and Early Development (pRED), Basel, 4070, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Adrian Altenhoff
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Department of Computer Science, ETH, 8092 Zurich, Switzerland
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Department of Computer Science, University College London, London WC1E 6BT, UK
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E, UK
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An unknown segment number in centipedes: a new species of Scolopocryptops (Chilopoda: Scolopendromorpha) from Trinidad with 25 leg-bearing segments. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00591-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Tihelka E, Howard RJ, Cai C, Lozano-Fernandez J. Was There a Cambrian Explosion on Land? The Case of Arthropod Terrestrialization. BIOLOGY 2022; 11:biology11101516. [PMID: 36290419 PMCID: PMC9598930 DOI: 10.3390/biology11101516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 01/24/2023]
Abstract
Arthropods, the most diverse form of macroscopic life in the history of the Earth, originated in the sea. Since the early Cambrian, at least ~518 million years ago, these animals have dominated the oceans of the world. By the Silurian-Devonian, the fossil record attests to arthropods becoming the first animals to colonize land, However, a growing body of molecular dating and palaeontological evidence suggests that the three major terrestrial arthropod groups (myriapods, hexapods, and arachnids), as well as vascular plants, may have invaded land as early as the Cambrian-Ordovician. These dates precede the oldest fossil evidence of those groups and suggest an unrecorded continental "Cambrian explosion" a hundred million years prior to the formation of early complex terrestrial ecosystems in the Silurian-Devonian. We review the palaeontological, phylogenomic, and molecular clock evidence pertaining to the proposed Cambrian terrestrialization of the arthropods. We argue that despite the challenges posed by incomplete preservation and the scarcity of early Palaeozoic terrestrial deposits, the discrepancy between molecular clock estimates and the fossil record is narrower than is often claimed. We discuss strategies for closing the gap between molecular clock estimates and fossil data in the evolution of early ecosystems on land.
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Affiliation(s)
- Erik Tihelka
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Richard J. Howard
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Chenyang Cai
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jesus Lozano-Fernandez
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- Department of Genetics, Microbiology and Statistics & Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Spain
- Correspondence:
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14
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A Rearrangement of the Mitochondrial Genes of Centipedes (Arthropoda, Myriapoda) with a Phylogenetic Analysis. Genes (Basel) 2022; 13:genes13101787. [DOI: 10.3390/genes13101787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
Due to the limitations of taxon sampling and differences in results from the available data, the phylogenetic relationships of the Myriapoda remain contentious. Therefore, we try to reconstruct and analyze the phylogenetic relationships within the Myriapoda by examining mitochondrial genomes (the mitogenome). In this study, typical circular mitogenomes of Mecistocephalus marmoratus and Scolopendra subspinipes were sequenced by Sanger sequencing; they were 15,279 bp and 14,637 bp in length, respectively, and a control region and 37 typical mitochondrial genes were annotated in the sequences. The results showed that all 13 PCGs started with ATN codons and ended with TAR codons or a single T; what is interesting is that the gene orders of M. marmoratus have been extensively rearranged compared with most Myriapoda. Thus, we propose a simple duplication/loss model to explain the extensively rearranged genes of M. marmoratus, hoping to provide insights into mitogenome rearrangement events in Myriapoda. In addition, our mitogenomic phylogenetic analyses showed that the main myriapod groups are monophyletic and supported the combination of the Pauropoda and Diplopoda to form the Dignatha. Within the Chilopoda, we suggest that Scutigeromorpha is a sister group to the Lithobiomorpha, Geophilomorpha, and Scolopendromorpha. We also identified a close relationship between the Lithobiomorpha and Geophilomorpha. The results also indicate that the mitogenome can be used as an effective mechanism to understand the phylogenetic relationships within Myriapoda.
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15
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Lozano-Fernandez J. A Practical Guide to Design and Assess a Phylogenomic Study. Genome Biol Evol 2022; 14:evac129. [PMID: 35946263 PMCID: PMC9452790 DOI: 10.1093/gbe/evac129] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Over the last decade, molecular systematics has undergone a change of paradigm as high-throughput sequencing now makes it possible to reconstruct evolutionary relationships using genome-scale datasets. The advent of "big data" molecular phylogenetics provided a battery of new tools for biologists but simultaneously brought new methodological challenges. The increase in analytical complexity comes at the price of highly specific training in computational biology and molecular phylogenetics, resulting very often in a polarized accumulation of knowledge (technical on one side and biological on the other). Interpreting the robustness of genome-scale phylogenetic studies is not straightforward, particularly as new methodological developments have consistently shown that the general belief of "more genes, more robustness" often does not apply, and because there is a range of systematic errors that plague phylogenomic investigations. This is particularly problematic because phylogenomic studies are highly heterogeneous in their methodology, and best practices are often not clearly defined. The main aim of this article is to present what I consider as the ten most important points to take into consideration when planning a well-thought-out phylogenomic study and while evaluating the quality of published papers. The goal is to provide a practical step-by-step guide that can be easily followed by nonexperts and phylogenomic novices in order to assess the technical robustness of phylogenomic studies or improve the experimental design of a project.
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Affiliation(s)
- Jesus Lozano-Fernandez
- Department of Genetics, Microbiology and Statistics, Biodiversity Research Institute (IRBio), University of Barcelona, Avd. Diagonal 643, 08028 Barcelona, Spain
- Institute of Evolutionary Biology (CSIC – Universitat Pompeu Fabra), Passeig marítim de la Barcelona 37-49, 08003 Barcelona, Spain
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16
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Ding J, Lan H, Xu W, Chen Y, Wu H, Jiang H, Wang J, Wu Y, Liu H. Two complete mitochondrial genomes in Scolopendra and a comparative analysis of tRNA rearrangements in centipedes. Mol Biol Rep 2022; 49:6173-6180. [PMID: 35411482 DOI: 10.1007/s11033-022-07409-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/21/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Centipedes are one of the oldest terrestrial arthropods belonging to the sub phylum Myriapoda. With the expansion of our understanding of the application of the two centipedes Scolopendra morsitans and Scolopendra hainanum, belonging to the order Scolopendromorpha, an exhaustive classification was required. Although consensus has been reached on the phylogeny of Chilopoda based on morphological traits, recent analyses based on molecular data exhibited differences in results. METHODS AND RESULTS The mitochondrial genome sequences of S. morsitans and S. hainanum were obtained by next-generation sequencing. S. morsitans contains 13 PCGs, two rRNAs, 11 tRNAs, and one CR. whereas S. hainanum contains 12 PCGs, of which ATP8 remains unpredicted, two rRNAs, 14 tRNAs, and one CR. An obvious tRNA rearrangement was found in the genus Scolopendra. S. morsitans exhibited a loss of trnW, trnC, trnI, trnK, trnD, trnA, trnN, trnQ, trnF, trnT, trnS, trnL, and trnV, and a repeat of trnR and trnL. S. hainanum exhibited a loss of trnQ, trnC, trnW, trnI, trnD, trnQ, trnP, and trnV. Phylogenetic analyses of centipedes based on 12 PCGs supported the sister relationship between the orders Geophilomorpha and Lithobiomorpha and a close relationship between Scolopendra dehaani and S. hainanum. CONCLUSIONS The new mitogenomes determined in this study provide new genomic resources for gene rearrangements and contribute to the understanding of the evolution of gene rearrangement in Chilopoda.
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Affiliation(s)
- Jiayu Ding
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Hong Lan
- Department of Agriculture, Zhejiang Open University, Hangzhou, 310030, China
| | - Wei Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Yining Chen
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Han Wu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Haoming Jiang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Jiachen Wang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Yongbo Wu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Hongyi Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China.
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17
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Uribe JE, González VL, Irisarri I, Kano Y, Herbert DG, Strong EE, Harasewych MG. A phylogenomic backbone for gastropod molluscs. Syst Biol 2022; 71:1271-1280. [PMID: 35766870 DOI: 10.1093/sysbio/syac045] [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: 06/29/2021] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Gastropods have survived several mass extinctions during their evolutionary history resulting in extraordinary diversity in morphology, ecology, and developmental modes, which complicate the reconstruction of a robust phylogeny. Currently, gastropods are divided into six subclasses: Caenogastropoda, Heterobranchia, Neomphaliones, Neritimorpha, Patellogastropoda, and Vetigastropoda. Phylogenetic relationships among these taxa historically lack consensus, despite numerous efforts using morphological and molecular information. We generated sequence data for transcriptomes derived from twelve taxa belonging to clades with little or no prior representation in previous studies in order to infer the deeper cladogenetic events within Gastropoda and, for the first time, infer the position of the deep-sea Neomphaliones using a phylogenomic approach. We explored the impact of missing data, homoplasy, and compositional heterogeneity on the inferred phylogenetic hypotheses. We recovered a highly supported backbone for gastropod relationships that is congruent with morphological and mitogenomic evidence, in which Patellogastropoda, true limpets, are the sister lineage to all other gastropods (Orthogastropoda) which are divided into two main clades (i) Vetigastropoda s.l. (including Pleurotomariida + Neomphaliones) and (ii) Neritimorpha + (Caenogastropoda + Heterobranchia). As such, our results support the recognition of five subclasses (or infraclasses) in Gastropoda: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda and Heterobranchia.
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Affiliation(s)
- Juan E Uribe
- Department of Invertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, P O Box 37012 Washington, DC 20013-7012, USA
| | - Vanessa L González
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, and Campus Institute Data Science (CIDAS), Göttingen, Germany.,Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Yasunori Kano
- Department of Marine Ecosystems Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - David G Herbert
- Department of Natural Sciences, National Museum Wales, Cathays Park, Cardiff, CF10 3NP, UK
| | - Ellen E Strong
- Department of Invertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, P O Box 37012 Washington, DC 20013-7012, USA
| | - M G Harasewych
- Department of Invertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, P O Box 37012 Washington, DC 20013-7012, USA
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18
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Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes. Nat Commun 2022; 13:3010. [PMID: 35637228 PMCID: PMC9151784 DOI: 10.1038/s41467-022-30690-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/12/2022] [Indexed: 01/08/2023] Open
Abstract
Animals display a fascinating diversity of body plans. Correspondingly, genomic analyses have revealed dynamic evolution of gene gains and losses among animal lineages. Here we sequence six new myriapod genomes (three millipedes, three centipedes) at key phylogenetic positions within this major but understudied arthropod lineage. We combine these with existing genomic resources to conduct a comparative analysis across all available myriapod genomes. We find that millipedes generally have considerably smaller genomes than centipedes, with the repeatome being a major contributor to genome size, driven by independent large gains of transposons in three centipede species. In contrast to millipedes, centipedes gained a large number of gene families after the subphyla diverged, with gains contributing to sensory and locomotory adaptations that facilitated their ecological shift to predation. We identify distinct horizontal gene transfer (HGT) events from bacteria to millipedes and centipedes, with no identifiable HGTs shared among all myriapods. Loss of juvenile hormone O-methyltransferase, a key enzyme in catalysing sesquiterpenoid hormone production in arthropods, was also revealed in all millipede lineages. Our findings suggest that the rapid evolution of distinct genomic pathways in centipede and millipede lineages following their divergence from the myriapod ancestor, was shaped by differing ecological pressures. Myriapods play an important ecological role in soil and forest ecosystems. Here the authors analyse nine myriapod genomes, showing rapid evolution of distinct genomic pathways in centipede and millipede lineages, shaped by differing ecological pressures.
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19
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Zuo Q, Zhang Z, Shen Y. Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS-2019 and phylogenetic analysis of the Myriapoda. Ecol Evol 2022; 12:e8764. [PMID: 35356579 PMCID: PMC8948135 DOI: 10.1002/ece3.8764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/29/2022] [Accepted: 03/10/2022] [Indexed: 11/29/2022] Open
Abstract
The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda, and Pauropoda). Due to the limitation of taxon sampling, the phylogenetic relationships within Myriapoda remained contentious, especially for Diplopoda. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS-2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT-skew (-0.236). Several genes rearrangements were detected and we propose a new rearrangement model: "TD (N\R) L + C" based on the genome-scale duplication + (non-random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.
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Affiliation(s)
- Qing Zuo
- Key Laboratory of Eco‐Environments in Three Gorges Reservoir Region (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Zhisheng Zhang
- Key Laboratory of Eco‐Environments in Three Gorges Reservoir Region (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Yanjun Shen
- Chongqing Key Laboratory of Animal BiologySchool of Life SciencesChongqing Normal UniversityChongqingChina
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20
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Cai C, Tihelka E, Giacomelli M, Lawrence JF, Ślipiński A, Kundrata R, Yamamoto S, Thayer MK, Newton AF, Leschen RAB, Gimmel ML, Lü L, Engel MS, Bouchard P, Huang D, Pisani D, Donoghue PCJ. Integrated phylogenomics and fossil data illuminate the evolution of beetles. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211771. [PMID: 35345430 PMCID: PMC8941382 DOI: 10.1098/rsos.211771] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/15/2022] [Indexed: 05/03/2023]
Abstract
Beetles constitute the most biodiverse animal order with over 380 000 described species and possibly several million more yet unnamed. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here, we use a dataset of 68 single-copy nuclear protein-coding (NPC) genes sampling 129 out of the 193 recognized extant families as well as the first comprehensive set of fully justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity, we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov. and Staphyliniformia sensu nov., and Erotyloidea stat. nov., Nitiduloidea stat. nov. and Cucujoidea sensu nov., alongside changes below the superfamily level. Our divergence time analyses recovered a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders and a Triassic-Jurassic origin of most extant families, while fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution.
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Affiliation(s)
- Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Erik Tihelka
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Mattia Giacomelli
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - John F. Lawrence
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Robin Kundrata
- Department of Zoology, Faculty of Science, Palacký University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Shûhei Yamamoto
- Hokkaido University Museum, Hokkaido University, Kita 8, Nishi 5, Kita-ku, Sapporo 060-0808, Japan
| | - Margaret K. Thayer
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Alfred F. Newton
- Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA
| | - Richard A. B. Leschen
- Manaaki Whenua Landcare Research, New Zealand Arthropod Collection, Private Bag 92170, Auckland, New Zealand
| | - Matthew L. Gimmel
- Invertebrate Zoology Department, Santa Barbara Museum of Natural History, 2559 Puesta del Sol Road, Santa Barbara, CA 93105, USA
| | - Liang Lü
- College of Life Science, Hebei Normal University, Shijiazhuang 050024, People's Republic of China
| | - Michael S. Engel
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, University of Kansas, 1501 Crestline Drive – Suite 140, Lawrence, KS 66045, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Patrice Bouchard
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, University of Kansas, 1501 Crestline Drive – Suite 140, Lawrence, KS 66045, USA
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C. J. Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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21
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Wang J, Bai Y, Zhao H, Mu R, Dong Y. Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective. PeerJ 2022; 9:e12691. [PMID: 35036164 PMCID: PMC8710254 DOI: 10.7717/peerj.12691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/05/2021] [Indexed: 11/20/2022] Open
Abstract
Background There have been extensive debates on the interrelationships among the four major classes of Myriapoda-Chilopoda, Symphyla, Diplopoda, and Pauropoda. The core controversy is the position of Pauropoda; that is, whether it should be grouped with Symphyla or Diplopoda as a sister group. Two recent phylogenomic studies separately investigated transcriptomic data from 14 and 29 Myriapoda species covering all four groups along with outgroups, and proposed two different topologies of phylogenetic relationships. Methods Building on these studies, we extended the taxon sampling by investigating 39 myriapods and integrating the previously available data with three new transcriptomic datasets generated in this study. Our analyses present the phylogenetic relationships among the four major classes of Myriapoda with a more abundant taxon sampling and provide a new perspective to investigate the above-mentioned question, where visual genes' identification were conducted. We compared the appearance pattern of genes, grouping them according to their classes and the visual pathways involved. Positive selection was detected for all identified visual genes between every pair of 39 myriapods, and 14 genes showed positive selection among 27 pairs. Results From the results of phylogenomic analyses, we propose that Symphyla is a sister group of Pauropoda. This stance has also received strong support from tree inference and topology tests.
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Affiliation(s)
- Jiajia Wang
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, Anhui, China
| | - Yu Bai
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, Anhui, China
| | - Haifeng Zhao
- Key Laboratory of Space Utilization, Technology and Engineering Center for Space Utilization, Chinese Academy of Sciences, Beijing, China
| | - Ruinan Mu
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Dong
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, Anhui, China
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22
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Motyka M, Kusy D, Bocek M, Bilkova R, Bocak L. Phylogenomic and mitogenomic data can accelerate inventorying of tropical beetles during the current biodiversity crisis. eLife 2021; 10:71895. [PMID: 34927586 PMCID: PMC8798050 DOI: 10.7554/elife.71895] [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: 07/02/2021] [Accepted: 12/18/2021] [Indexed: 11/13/2022] Open
Abstract
Conservation efforts must be evidence-based, so rapid and economically feasible methods should be used to quantify diversity and distribution patterns. We have attempted to overcome current impediments to the gathering of biodiversity data by using integrative phylogenomic and three mtDNA fragment analyses. As a model, we sequenced the Metriorrhynchini beetle fauna, sampled from ~700 localities in three continents. The species-rich dataset included ~6,500 terminals, ~1,850 putative species delimited at 5% uncorrected pairwise threshold, possibly ~1,000 of them unknown to science. Neither type of data could alone answer our questions on biodiversity and phylogeny. The phylogenomic backbone enabled the integrative delimitation of robustly defined natural genus-group units that will inform future research. Using constrained mtDNA analysis, we identified the spatial structure of species diversity, very high species-level endemism, and a biodiversity hotspot in New Guinea. We suggest that focused field research and subsequent laboratory and bioinformatic workflow steps would substantially accelerate the inventorying of any hyperdiverse tropical group with several thousand species. The outcome would be a scaffold for the incorporation of further data from environmental sequencing and ecological studies. The database of sequences could set a benchmark for the spatiotemporal evaluation of biodiversity, would support evidence-based conservation planning, and would provide a robust framework for systematic, biogeographic, and evolutionary studies.
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Affiliation(s)
- Michal Motyka
- Laboratory of Biodiversity and Molecular Evolution, Czech Advanced Technology Research Institute, Olomouc, Czech Republic
| | - Dominik Kusy
- Laboratory of Biodiversity and Molecular Evolution, Czech Advanced Technology Research Institute, Olomouc, Czech Republic
| | - Matej Bocek
- Laboratory of Biodiversity and Molecular Evolution, Czech Advanced Technology Research Institute, Olomouc, Czech Republic
| | - Renata Bilkova
- Laboratory of Biodiversity and Molecular Evolution, Czech Advanced Technology Research Institute, Olomouc, Czech Republic
| | - Ladislav Bocak
- ZoologyLaboratory of Biodiversity and Molecular Evolution, Czech Advanced Technology Research Institute, Olomouc, Czech Republic
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23
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Benavides LR, Daniels SR, Giribet G. Understanding the real magnitude of the arachnid order Ricinulei through deep Sanger sequencing across its distribution range and phylogenomics, with the formalization of the first species from the Lesser Antilles. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ligia R. Benavides
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Savel R. Daniels
- Department of Botany and Zoology Stellenbosch University Matieland South Africa
| | - Gonzalo Giribet
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
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Benavides LR, Jiang C, Giribet G. Mimopidae is the sister group to all other scolopendromorph centipedes (Chilopoda, Scolopendromorpha): a phylotranscriptomic approach. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00502-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mongiardino Koch N. Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci. Mol Biol Evol 2021; 38:4025-4038. [PMID: 33983409 DOI: 10.1101/2021.02.13.431075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.
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Abstract
Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.
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Torres A, Goloboff PA, Catalano SA. Parsimony analysis of phylogenomic datasets (I): scripts and guidelines for using TNT (Tree Analysis using New Technology). Cladistics 2021; 38:103-125. [DOI: 10.1111/cla.12477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
- Ambrosio Torres
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
| | - Pablo A. Goloboff
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
- American Museum of Natural History 200 Central Park West New York NY 10024 USA
| | - Santiago A. Catalano
- Unidad Ejecutora Lillo Consejo Nacional de Investigaciones Científicas y Técnicas ‐ Fundación Miguel Lillo Miguel Lillo 251 S. M. de Tucumán Tucumán 4000 Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo Universidad Nacional de Tucumán Miguel Lillo 205 S. M. de Tucumán Tucumán 4000 Argentina
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Hopkins MJ, St John K. Incorporating Hierarchical Characters into Phylogenetic Analysis. Syst Biol 2021; 70:1163-1180. [PMID: 33560427 DOI: 10.1093/sysbio/syab005] [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: 06/25/2020] [Revised: 12/28/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
Popular optimality criteria for phylogenetic trees focus on sequences of characters that are applicable to all the taxa. As studies grow in breadth, it can be the case that some characters are applicable for a portion of the taxa and inapplicable for others. Past work has explored the limitations of treating inapplicable characters as missing data, noting that this strategy may favor trees where interval nodes are assigned impossible states, where the arrangement of taxa within subclades is unduly influenced by variation in distant parts of the tree, and/or where taxa that otherwise share most primary characters are grouped distantly. Approaches that avoid the first two problems have recently been proposed. Here, we propose an alternative approach which avoids all three problems. We focus on data matrices that use reductive coding of traits, that is, explicitly incorporate the innate hierarchy induced by inapplicability, and as such our approach extend to hierarchical characters, in general. In the spirit of maximum parsimony, the proposed criterion seeks the phylogenetic tree with the minimal changes across any tree branch, but where changes are defined in terms of dissimilarity metrics that weigh the affects of inapplicable characters. The approach can accommodate binary, multistate, ordered, unordered, and polymorphic characters. We give a polynomial-time algorithm, inspired by Fitch's algorithm, to score trees under a family of dissimilarity metrics, and prove its correctness. We show that the resulting optimality criteria is computationally hard, by reduction to the NP-hardness of the maximum parsimony optimality criteria. We demonstrate our approach using synthetic and empirical data sets and compare the results with other recently proposed methods for choosing optimal phylogenetic trees when the data includes hierarchical characters.
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Affiliation(s)
- Melanie J Hopkins
- Division of Paleontology (Invertebrates), American Museum of Natural History, New York, NY, USA
| | - Katherine St John
- Department of Computer Science, Hunter College, City University of New York, New York, NY, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer. Nat Commun 2021; 12:818. [PMID: 33547293 PMCID: PMC7864903 DOI: 10.1038/s41467-021-21093-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023] Open
Abstract
Venoms have evolved over a hundred times in animals. Venom toxins are thought to evolve mostly by recruitment of endogenous proteins with physiological functions. Here we report phylogenetic analyses of venom proteome-annotated venom gland transcriptome data, assisted by genomic analyses, to show that centipede venoms have recruited at least five gene families from bacterial and fungal donors, involving at least eight horizontal gene transfer events. These results establish centipedes as currently the only known animals with venoms used in predation and defence that contain multiple gene families derived from horizontal gene transfer. The results also provide the first evidence for the implication of horizontal gene transfer in the evolutionary origin of venom in an animal lineage. Three of the bacterial gene families encode virulence factors, suggesting that horizontal gene transfer can provide a fast track channel for the evolution of novelty by the exaptation of bacterial weapons into animal venoms.
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Fusco G, Minelli A. The Development of Arthropod Segmentation Across the Embryonic/Post-embryonic Divide – An Evolutionary Perspective. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.622482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In many arthropods, the appearance of new segments and their differentiation are not completed by the end of embryogenesis but continue, in different form and degree, well after hatching, in some cases up to the last post-embryonic molt. Focusing on the segmentation process currently described as post-embryonic segment addition (or, anamorphosis), we revise here the current knowledge and discuss it in an evolutionary framework which involves data from fossils, comparative morphology of extant taxa and gene expression. We advise that for a better understanding of the developmental changes underlying the evolution of arthropod segmentation, some key concepts should be applied in a critical way. These include the notion of the segment as a body block and the idea that hatching represents a well-defined divide, shared by all arthropods, between two contrasting developmental phases, embryonic vs. post-embryonic. This eventually reveals the complexity of the developmental processes occurring across hatching, which can evolve in different directions and with a different pace, creating the observed vagueness of the embryonic/post-embryonic divide.
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Hilken G, Rosenberg J, Edgecombe GD, Blüml V, Hammel JU, Hasenberg A, Sombke A. The tracheal system of scutigeromorph centipedes and the evolution of respiratory systems of myriapods. ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 60:101006. [PMID: 33246291 DOI: 10.1016/j.asd.2020.101006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/30/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
The tracheal system of scutigeromorph centipedes (Chilopoda) is special, as it consists of dorsally arranged unpaired spiracles. In this study, we investigate the tracheal systems of five different scutigeromorph species. They are strikingly similar to each other but depict unique characters compared to the tracheal systems of pleurostigmophoran centipedes, which has engendered an ongoing debate over a single versus independent origin of tracheal systems in Chilopoda. Up to now, only the respiratory system of Scutigera coleoptrata was investigated intensively using LM-, TEM-, and SEM-techniques. We supplement this with data for species from all three families of Scutigeromorpha. These reveal interspecific differences in atrial width and the shape and branching pattern of the tracheal tubules. Further, we investigated the tracheal system of Scutigera coleoptrata with three additional techniques: light sheet microscopy, microCT and synchrotron radiation based microCT analysis. This set of techniques allows a comparison between fresh versus fixed and dried material. The question of a unique vs. multiple origin of tracheal systems in centipedes and in Myriapoda as a whole is discussed with regard to their structural similarities and differences and the presence of hemocyanin as an oxygen carrier. We used morphological and molecular data and the fossil record to evaluate the alternative hypotheses.
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Affiliation(s)
- Gero Hilken
- Central Animal Laboratory, University Clinic, University Duisburg-Essen, Hufelandstraße 55, 45122, Essen, Germany.
| | | | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, London, SW7 5BD, United Kingdom
| | - Valentin Blüml
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Jörg U Hammel
- X-ray Imaging with Synchrotron Radiation, Helmholz-Zentrum Geesthacht, Institute of Materials Research, Max-Planck-Straße 1, 21502, Geesthacht, Germany
| | - Anja Hasenberg
- Institute for Experimental Immunology and Imaging, University Clinic, University Duisburg-Essen, Universitätsstraße 2, 45141, Essen, Germany
| | - Andy Sombke
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
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Dermauw W, Van Leeuwen T, Feyereisen R. Diversity and evolution of the P450 family in arthropods. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 127:103490. [PMID: 33169702 DOI: 10.1016/j.ibmb.2020.103490] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 05/13/2023]
Abstract
The P450 family (CYP genes) of arthropods encodes diverse enzymes involved in the metabolism of foreign compounds and in essential endocrine or ecophysiological functions. The P450 sequences (CYPome) from 40 arthropod species were manually curated, including 31 complete CYPomes, and a maximum likelihood phylogeny of nearly 3000 sequences is presented. Arthropod CYPomes are assembled from members of six CYP clans of variable size, the CYP2, CYP3, CYP4 and mitochondrial clans, as well as the CYP20 and CYP16 clans that are not found in Neoptera. CYPome sizes vary from two dozen genes in some parasitic species to over 200 in species as diverse as collembolans or ticks. CYPomes are comprised of few CYP families with many genes and many CYP families with few genes, and this distribution is the result of dynamic birth and death processes. Lineage-specific expansions or blooms are found throughout the phylogeny and often result in genomic clusters that appear to form a reservoir of catalytic diversity maintained as heritable units. Among the many P450s with physiological functions, six CYP families are involved in ecdysteroid metabolism. However, five so-called Halloween genes are not universally represented and do not constitute the unique pathway of ecdysteroid biosynthesis. The diversity of arthropod CYPomes has only partially been uncovered to date and many P450s with physiological functions regulating the synthesis and degradation of endogenous signal molecules (including ecdysteroids) and semiochemicals (including pheromones and defense chemicals) remain to be discovered. Sequence diversity of arthropod P450s is extreme, and P450 sequences lacking the universally conserved Cys ligand to the heme have evolved several times. A better understanding of P450 evolution is needed to discern the relative contributions of stochastic processes and adaptive processes in shaping the size and diversity of CYPomes.
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Affiliation(s)
- Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - René Feyereisen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium; Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871, Frederiksberg C, Copenhagen, Denmark.
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Mongiardino Koch N, Thompson JR. A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data. Syst Biol 2020; 70:421-439. [PMID: 32882040 DOI: 10.1093/sysbio/syaa069] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 08/14/2020] [Accepted: 08/23/2020] [Indexed: 12/13/2022] Open
Abstract
Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.].
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Affiliation(s)
| | - Jeffrey R Thompson
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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Stojanović DZ, Vujić VD, Lučić LR, Tomić VT, Makarov SE, Mitić BM. Life after the mother's hug: Late post-embryonic development of Cryptops parisi (Chilopoda: Scolopendromorpha: Cryptopidae). ARTHROPOD STRUCTURE & DEVELOPMENT 2020; 57:100948. [PMID: 32416473 DOI: 10.1016/j.asd.2020.100948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Here we describe in detail the late post-embryonic development of the common European scolopendromorph centipede Cryptops parisi. Canonical variate analyses of two groups of external morphological characters, viz., cephalic capsule characters (head length, length of the anterior and posterior paramedian cephalic sutures) and coxopleuron surface characters (number of pores in the coxal pore-field, number of setae on the posterior coxopleuron edge, their number on the coxal pore-field, and their number posterior to the coxal pore-field) were conducted on a large sample of specimens collected from two localities in Serbia. Ten free-living stages are recognized: three pre-adult stages (adolescens I, II, and III) and seven adult stages (one maturus junior stage, four maturus, and two maturus senior stages). The fourth late post-embryonic stage is the first mature stage in both sexes. Sexual dimorphism in the aforementioned characters was not observed. Morphological variation of coxopleuron characters was more informative for the discrimination of developmental stages in Cryptops than the morphological variation of cephalic capsule characters.
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Affiliation(s)
- Dalibor Z Stojanović
- University of Belgrade - Faculty of Biology, Institute of Zoology, Studentski Trg 16, 11000 Belgrade, Serbia.
| | - Vukica D Vujić
- University of Belgrade - Faculty of Biology, Institute of Zoology, Studentski Trg 16, 11000 Belgrade, Serbia.
| | - Luka R Lučić
- University of Belgrade - Faculty of Biology, Institute of Zoology, Studentski Trg 16, 11000 Belgrade, Serbia.
| | - Vladimir T Tomić
- University of Belgrade - Faculty of Biology, Institute of Zoology, Studentski Trg 16, 11000 Belgrade, Serbia.
| | - Slobodan E Makarov
- University of Belgrade - Faculty of Biology, Institute of Zoology, Studentski Trg 16, 11000 Belgrade, Serbia.
| | - Bojan M Mitić
- University of Belgrade - Faculty of Biology, Institute of Zoology, Studentski Trg 16, 11000 Belgrade, Serbia.
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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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Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves. BMC Evol Biol 2020; 20:50. [PMID: 32357841 PMCID: PMC7195748 DOI: 10.1186/s12862-020-01614-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice. RESULTS In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade. CONCLUSIONS The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exaptations existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.
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Hu C, Wang S, Huang B, Liu H, Xu L, Zhigang Hu, Liu Y. The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes. Zookeys 2020; 925:73-88. [PMID: 32390741 PMCID: PMC7197263 DOI: 10.3897/zookeys.925.47820] [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: 10/31/2019] [Accepted: 02/20/2020] [Indexed: 02/07/2023] Open
Abstract
Scolopendramutilans L. Koch, 1878 is an important Chinese animal with thousands of years of medicinal history. However, the genomic information of this species is limited, which hinders its further application. Here, the complete mitochondrial genome (mitogenome) of S.mutilans was sequenced and assembled by next-generation sequencing. The genome is 15,011 bp in length, consisting of 13 protein-coding genes (PCGs), 14 tRNA genes, and two rRNA genes. Most PCGs start with the ATN initiation codon, and all PCGs have the conventional stop codons TAA and TAG. The S.mutilans mitogenome revealed nine simple sequence repeats (SSRs), and an obviously lower GC content compared with other seven centipede mitogenomes previously sequenced. After analysis of homologous regions between the eight centipede mitogenomes, the S.mutilans mitogenome further showed clear genomic rearrangements. The phylogenetic analysis of eight centipedes using 13 conserved PCG genes was finally performed. The phylogenetic reconstructions showed Scutigeromorpha as a separate group, and Scolopendromorpha in a sister-group relationship with Lithobiomorpha and Geophilomorpha. Collectively, the S.mutilans mitogenome provided new genomic resources, which will improve its medicinal research and applications in the future.
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Affiliation(s)
| | | | | | | | | | - Zhigang Hu
- College of Pharmacy.,Hubei University of Chinese Medicine, No. 1 Huangjiahu West Road, Hongshan District, Wuhan, China
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Mason AJ, Margres MJ, Strickland JL, Rokyta DR, Sasa M, Parkinson CL. Trait differentiation and modular toxin expression in palm-pitvipers. BMC Genomics 2020; 21:147. [PMID: 32046632 PMCID: PMC7014597 DOI: 10.1186/s12864-020-6545-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
Background Modularity is the tendency for systems to organize into semi-independent units and can be a key to the evolution and diversification of complex biological systems. Snake venoms are highly variable modular systems that exhibit extreme diversification even across very short time scales. One well-studied venom phenotype dichotomy is a trade-off between neurotoxicity versus hemotoxicity that occurs through the high expression of a heterodimeric neurotoxic phospholipase A2 (PLA2) or snake venom metalloproteinases (SVMPs). We tested whether the variation in these venom phenotypes could occur via variation in regulatory sub-modules through comparative venom gland transcriptomics of representative Black-Speckled Palm-Pitvipers (Bothriechis nigroviridis) and Talamancan Palm-Pitvipers (B. nubestris). Results We assembled 1517 coding sequences, including 43 toxins for B. nigroviridis and 1787 coding sequences including 42 toxins for B. nubestris. The venom gland transcriptomes were extremely divergent between these two species with one B. nigroviridis exhibiting a primarily neurotoxic pattern of expression, both B. nubestris expressing primarily hemorrhagic toxins, and a second B. nigroviridis exhibiting a mixed expression phenotype. Weighted gene coexpression analyses identified six submodules of transcript expression variation, one of which was highly associated with SVMPs and a second which contained both subunits of the neurotoxic PLA2 complex. The sub-module association of these toxins suggest common regulatory pathways underlie the variation in their expression and is consistent with known patterns of inheritance of similar haplotypes in other species. We also find evidence that module associated toxin families show fewer gene duplications and transcript losses between species, but module association did not appear to affect sequence diversification. Conclusion Sub-modular regulation of expression likely contributes to the diversification of venom phenotypes within and among species and underscores the role of modularity in facilitating rapid evolution of complex traits.
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Affiliation(s)
- Andrew J Mason
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Mark J Margres
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Jason L Strickland
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA
| | - Darin R Rokyta
- Department of Biological Sciences, Florida State University, Tallahassee, FL, 24105, USA
| | - Mahmood Sasa
- Instituto Clodomiro Picado, Facultad de Microbiologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Christopher L Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings St., Clemson, SC, 29634, USA. .,Department of Forestry, and Environmental Conservation, Clemson University, Clemson, SC, USA.
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39
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Noah KE, Hao J, Li L, Sun X, Foley B, Yang Q, Xia X. Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates. Evol Bioinform Online 2020; 16:1176934320903735. [PMID: 32076367 PMCID: PMC7003163 DOI: 10.1177/1176934320903735] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/02/2020] [Indexed: 01/04/2023] Open
Abstract
Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual gene. Such an approach has led to many robustly supported but contradictory phylogenies. A close examination shows that the supermatrix approach often suffers from two shortcomings. The first is that MSA is rarely checked for reliability and, as will be illustrated, can be poor. The second is that, to alleviate the problem of homoplasy at the third codon position of protein-coding genes due to convergent evolution of nucleotide frequencies, phylogeneticists may remove or degenerate the third codon position but may do it improperly and introduce new biases. We performed extensive reanalysis of one of such "big data" sets to highlight these two problems, and demonstrated the power and benefits of correcting or alleviating these problems. Our results support a new group with Xiphosura and Arachnopulmonata (Tetrapulmonata + Scorpiones) as sister taxa. This favors a new hypothesis in which the ancestor of Xiphosura and the extinct Eurypterida (sea scorpions, of which many later forms lived in brackish or freshwater) returned to the sea after the initial chelicerate invasion of land. Our phylogeny is supported even with the original data but processed with a new "principled" codon degeneration. We also show that removing the 1673 codon sites with both AGN and UCN codons (encoding serine) in our alignment can partially reconcile discrepancies between nucleotide-based and AA-based tree, partly because two sequences, one with AGN and the other with UCN, would be identical at the amino acid level but quite different at the nucleotide level.
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Affiliation(s)
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Luyan Li
- Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoyan Sun
- Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, China
| | - Brian Foley
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Qun Yang
- Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, China
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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40
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Gough HM, Allen JM, Toussaint EFA, Storer CG, Kawahara AY. Transcriptomics illuminate the phylogenetic backbone of tiger beetles. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz195] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Phylogenomics is progressing rapidly, allowing large strides forward into our understanding of the tree of life. In this study, we generated transcriptomes from ethanol-preserved specimens of 13 tiger beetle species (Coleoptera: Cicindelinae) and one Scaritinae outgroup. From these 14 transcriptomes and seven publicly available transcriptomes, we recovered an average of 2538 loci for phylogenetic analysis. We constructed an evolutionary tree of tiger beetles to examine deep-level relationships and examined the extent to which the composition of the dataset, missing data, gene tree inconsistency and codon position saturation impacted phylogenetic accuracy. Ethanol-preserved specimens yielded similar numbers of loci to specimens originally preserved in costly reagents, showcasing more flexibility in transcriptomics than anticipated. The number of loci and gene tree inconsistency had less impact on downstream results than third codon position saturation and missing data. Our results recovered tiger beetles as sister to Carabidae with strong support, confirming their taxonomic status as an independent family within Adephaga. Within tiger beetles, phylogenetic relationships were robust across all nodes. This new phylogenomic backbone represents a useful framework for future endeavours in tiger beetle systematics and serves as a starting point for the development of less costly target capture toolkits to expand the taxonomic breadth of the future tiger beetle tree of life.
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Affiliation(s)
- Harlan M Gough
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Julie M Allen
- Department of Biology, University of Nevada, Reno, Reno, NV, USA
| | | | - Caroline G Storer
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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41
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Aria C, Zhao F, Zeng H, Guo J, Zhu M. Fossils from South China redefine the ancestral euarthropod body plan. BMC Evol Biol 2020; 20:4. [PMID: 31914921 PMCID: PMC6950928 DOI: 10.1186/s12862-019-1560-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/12/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Early Cambrian Lagerstätten from China have greatly enriched our perspective on the early evolution of animals, particularly arthropods. However, recent studies have shown that many of these early fossil arthropods were more derived than previously thought, casting uncertainty on the ancestral euarthropod body plan. In addition, evidence from fossilized neural tissues conflicts with external morphology, in particular regarding the homology of the frontalmost appendage. RESULTS Here we redescribe the multisegmented megacheirans Fortiforceps and Jianfengia and describe Sklerolibyon maomima gen. et sp. nov., which we place in Jianfengiidae, fam. nov. (in Megacheira, emended). We find that jianfengiids show high morphological diversity among megacheirans, both in trunk ornamentation and head anatomy, which encompasses from 2 to 4 post-frontal appendage pairs. These taxa are also characterized by elongate podomeres likely forming seven-segmented endopods, which were misinterpreted in their original descriptions. Plesiomorphic traits also clarify their connection with more ancestral taxa. The structure and position of the "great appendages" relative to likely sensory antero-medial protrusions, as well as the presence of optic peduncles and sclerites, point to an overall homology with the anterior head of radiodontans. This is confirmed by our Bayesian phylogeny, which places jianfengiids as the basalmost euarthropods, paraphyletic with other megacheirans, and in contiguity with isoxyids and radiodontans. CONCLUSIONS Sklerolibyon and other jianfengiids expand the disparity of megacheirans and suggest that the common euarthropod ancestor possessed a remarkable phenotypic variability associated with the externalized cephalon, as well as endopods that were already heptopodomerous, which differs from previous hypotheses and observations. These animals also demonstrate that the frontalmost pair of arthrodized appendage is homologous between radiodontans and megacheirans, refuting the claim that the radiodontan frontal appendages evolved into the euarthropod labrum, and questioning its protocerebral identity. This evidence based on external anatomy now constitutes a solid benchmark upon which we should address issues of homology, with the help of carefully examined palaeoneurological data.
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Affiliation(s)
- Cédric Aria
- State Key Laboratory of Palaeobiology and Stratigraphy & Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Fangchen Zhao
- State Key Laboratory of Palaeobiology and Stratigraphy & Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Han Zeng
- State Key Laboratory of Palaeobiology and Stratigraphy & Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Jin Guo
- Management Committee of the Chengjiang Fossil Site World Heritage, Chengjiang, 652599, China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy & Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China. .,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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42
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Maurer M, Hladik J, Iliffe TM, Stemme T. Histaminergic interneurons in the ventral nerve cord: assessment of their value for Euarthropod phylogeny. ZOOLOGICAL LETTERS 2019; 5:36. [PMID: 31890274 PMCID: PMC6929356 DOI: 10.1186/s40851-019-0151-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
Despite numerous approaches to the resolution of euarthropod phylogeny, mainly based on modern sequence information and traditional external morphology, the resulting hypotheses are often contradictory and leave many questions about euarthropod evolution unanswered. The comparison of developmental and structural aspects of the nervous system has shown to be a valuable contribution to the assessment of current phylogenetic hypotheses. One promising approach for the generation of new character sets is the morphology of transmitter systems and the discovery of individually identifiable neurons, which allow phylogenetic comparisons on the single cell level. In this context, the serotonin transmitter system has been investigated to a considerable degree. Studies to date have yielded important stimuli to our understanding of euarthropod relationships and the evolution of their nervous systems. However, data on other transmitter systems remain fragmented, and their value with respect to phylogenetic questions remains speculative. The biogenic amine histamine is a promising transmitter; a substantial amount of data has been reported in the literature and the homology of some histaminergic neurons has been suggested. Here, we present a comprehensive review of histaminergic neurons in the ventral nerve cord of Euarthropoda. Using immunocytochemical labeling of histamine combined with confocal laser-scanning microscopy, we investigated the transmitter system in phylogenetically relevant taxa, such as Zygentoma, Remipedia, Diplopoda, and Arachnida. By reconstructing ground patterns, we evaluated the significance of this specific character set for euarthropod phylogeny. With this approach, we identified a set of neurons, which can be considered homologous within the respective major taxon. In conclusion, the histaminergic system contains useful information for our understanding of euarthropod phylogeny, supporting the proposed clades Tetraconata and Mandibulata. Furthermore, this character set has considerable potential to help resolve relationships within the major clades at a deeper level of taxonomy, due to the considerable variability in neurite morphology.
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Affiliation(s)
- Maite Maurer
- Institute of Neurobiology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Janina Hladik
- Institute of Neurobiology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Thomas M. Iliffe
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77553 USA
| | - Torben Stemme
- Institute of Neurobiology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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43
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Jenner RA, von Reumont BM, Campbell LI, Undheim EAB. Parallel Evolution of Complex Centipede Venoms Revealed by Comparative Proteotranscriptomic Analyses. Mol Biol Evol 2019; 36:2748-2763. [PMID: 31396628 PMCID: PMC6878950 DOI: 10.1093/molbev/msz181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Centipedes are among the most ancient groups of venomous predatory arthropods. Extant species belong to five orders, but our understanding of the composition and evolution of centipede venoms is based almost exclusively on one order, Scolopendromorpha. To gain a broader and less biased understanding we performed a comparative proteotranscriptomic analysis of centipede venoms from all five orders, including the first venom profiles for the orders Lithobiomorpha, Craterostigmomorpha, and Geophilomorpha. Our results reveal an astonishing structural diversity of venom components, with 93 phylogenetically distinct protein and peptide families. Proteomically-annotated gene trees of these putative toxin families show that centipede venom composition is highly dynamic across macroevolutionary timescales, with numerous gene duplications as well as functional recruitments and losses of toxin gene families. Strikingly, not a single family is found in the venoms of representatives of all five orders, with 67 families being unique for single orders. Ancestral state reconstructions reveal that centipede venom originated as a simple cocktail comprising just four toxin families, with very little compositional evolution happening during the approximately 50 My before the living orders had diverged. Venom complexity then increased in parallel within the orders, with scolopendromorphs evolving particularly complex venoms. Our results show that even venoms composed of toxins evolving under the strong constraint of negative selection can have striking evolutionary plasticity on the compositional level. We show that the functional recruitments and losses of toxin families that shape centipede venom arsenals are not concentrated early in their evolutionary history, but happen frequently throughout.
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Affiliation(s)
- Ronald A Jenner
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Bjoern M von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Institute for Insect Biotechnology, Justus-Liebig University Giessen, Giessen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Animal Venomics, Giessen, Germany
| | - Lahcen I Campbell
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, United Kingdom
| | - Eivind A B Undheim
- Centre for Advanced Imaging, University of Queensland, St Lucia, Australia
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
- Centre for Ecology and Evolutionary Synthesis, Department of Bioscience, University of Oslo, Oslo, Norway
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44
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Miller SW, Movsesyan A, Zhang S, Fernández R, Posakony JW. Evolutionary emergence of Hairless as a novel component of the Notch signaling pathway. eLife 2019; 8:48115. [PMID: 31545167 PMCID: PMC6777938 DOI: 10.7554/elife.48115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/23/2019] [Indexed: 11/30/2022] Open
Abstract
Suppressor of Hairless [Su(H)], the transcription factor at the end of the Notch pathway in Drosophila, utilizes the Hairless protein to recruit two co-repressors, Groucho (Gro) and C-terminal Binding Protein (CtBP), indirectly. Hairless is present only in the Pancrustacea, raising the question of how Su(H) in other protostomes gains repressive function. We show that Su(H) from a wide array of arthropods, molluscs, and annelids includes motifs that directly bind Gro and CtBP; thus, direct co-repressor recruitment is ancestral in the protostomes. How did Hairless come to replace this ancestral paradigm? Our discovery of a protein (S-CAP) in Myriapods and Chelicerates that contains a motif similar to the Su(H)-binding domain in Hairless has revealed a likely evolutionary connection between Hairless and Metastasis-associated (MTA) protein, a component of the NuRD complex. Sequence comparison and widely conserved microsynteny suggest that S-CAP and Hairless arose from a tandem duplication of an ancestral MTA gene.
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Affiliation(s)
- Steven W Miller
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States
| | - Artem Movsesyan
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States
| | - Sui Zhang
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States
| | - Rosa Fernández
- Bioinformatics and Genomics Unit, Center for Genomic Regulation, Barcelona, Spain
| | - James W Posakony
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States
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Dömel JS, Macher TH, Dietz L, Duncan S, Mayer C, Rozenberg A, Wolcott K, Leese F, Melzer RR. Combining morphological and genomic evidence to resolve species diversity and study speciation processes of the Pallenopsis patagonica (Pycnogonida) species complex. Front Zool 2019; 16:36. [PMID: 31516540 PMCID: PMC6728986 DOI: 10.1186/s12983-019-0316-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/06/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pallenopsis patagonica (Hoek, 1881) is a morphologically and genetically variable sea spider species whose taxonomic classification is challenging. Currently, it is considered as a species complex including several genetic lineages, many of which have not been formally described as species. Members of this species complex occur on the Patagonian and Antarctic continental shelves as well as around sub-Antarctic islands. These habitats have been strongly influenced by historical large-scale glaciations and previous studies suggested that communities were limited to very few refugia during glacial maxima. Therefore, allopatric speciation in these independent refugia is regarded as a common mechanism leading to high biodiversity of marine benthic taxa in the high-latitude Southern Hemisphere. However, other mechanisms such as ecological speciation have rarely been considered or tested. Therefore, we conducted an integrative morphological and genetic study on the P. patagonica species complex to i) resolve species diversity using a target hybrid enrichment approach to obtain multiple genomic markers, ii) find morphological characters and analyze morphometric measurements to distinguish species, and iii) investigate the speciation processes that led to multiple lineages within the species complex. RESULTS Phylogenomic results support most of the previously reported lineages within the P. patagonica species complex and morphological data show that several lineages are distinct species with diagnostic characters. Two lineages are proposed as new species, P. aulaeturcarum sp. nov. Dömel & Melzer, 2019 and P. obstaculumsuperavit sp. nov. Dömel, 2019, respectively. However, not all lineages could be distinguished morphologically and thus likely represent cryptic species that can only be identified with genetic tools. Further, morphometric data of 135 measurements showed a high amount of variability within and between species without clear support of adaptive divergence in sympatry. CONCLUSIONS We generated an unprecedented molecular data set for members of the P. patagonica sea spider species complex with a target hybrid enrichment approach, which we combined with extensive morphological and morphometric analyses to investigate the taxonomy, phylogeny and biogeography of this group. The extensive data set enabled us to delineate species boundaries, on the basis of which we formally described two new species. No consistent evidence for positive selection was found, rendering speciation in allopatric glacial refugia as the most likely model of speciation.
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Affiliation(s)
- Jana S. Dömel
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitaetsstr. 5, 45141 Essen, Germany
| | - Till-Hendrik Macher
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitaetsstr. 5, 45141 Essen, Germany
| | - Lars Dietz
- Zoological Research Museum Alexander Koenig, Statistical Phylogenetics and Phylogenomics, Adenauerallee 160, 53113 Bonn, Germany
| | - Sabrina Duncan
- Bavarian State Collection of Zoology – SNSB, Muenchhausenstr. 21, 81247 Munich, Germany
| | - Christoph Mayer
- Zoological Research Museum Alexander Koenig, Statistical Phylogenetics and Phylogenomics, Adenauerallee 160, 53113 Bonn, Germany
| | - Andrey Rozenberg
- Faculty of Biology, Technion – Israel Institute of Technology, 3200003 Haifa, Israel
| | - Katherine Wolcott
- Bavarian State Collection of Zoology – SNSB, Muenchhausenstr. 21, 81247 Munich, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitaetsstr. 5, 45141 Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitaetsstr. 2, 45141 Essen, Germany
| | - Roland R. Melzer
- Bavarian State Collection of Zoology – SNSB, Muenchhausenstr. 21, 81247 Munich, Germany
- Department Biologie II, LMU Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
- GeoBioCenter, LMU Munich, Richard-Wagner-Str. 10, 80333 Munich, Germany
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46
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Altenhoff AM, Levy J, Zarowiecki M, Tomiczek B, Warwick Vesztrocy A, Dalquen DA, Müller S, Telford MJ, Glover NM, Dylus D, Dessimoz C. OMA standalone: orthology inference among public and custom genomes and transcriptomes. Genome Res 2019; 29:1152-1163. [PMID: 31235654 PMCID: PMC6633268 DOI: 10.1101/gr.243212.118] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 05/24/2019] [Indexed: 11/24/2022]
Abstract
Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs—corresponding genes across multiple species—but this is far from trivial. The Orthologous MAtrix (OMA) database is a leading resource for identifying orthologs among publicly available, complete genomes. Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a cluster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. Another key feature of OMA standalone is that users can combine their own data with existing public data by exporting genomes and precomputed alignments from the OMA database, which currently contains over 2100 complete genomes. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of Lophotrochozoa, a challenging clade within the protostomes. We also discuss other potential applications of OMA standalone, including identifying gene families having undergone duplications/losses in specific clades, and identifying potential drug targets in nonmodel organisms. OMA standalone is available under the permissive open source Mozilla Public License Version 2.0.
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Affiliation(s)
- Adrian M Altenhoff
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computer Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Jeremy Levy
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London WC1E 6BT, United Kingdom.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Magdalena Zarowiecki
- Genomics England, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Bartłomiej Tomiczek
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom.,Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland
| | - Alex Warwick Vesztrocy
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Daniel A Dalquen
- Department of Computer Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Steven Müller
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom
| | - Natasha M Glover
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - David Dylus
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christophe Dessimoz
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, United Kingdom.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Department of Computer Science, University College London, London WC1E 6BT, United Kingdom
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Vasilikopoulos A, Balke M, Beutel RG, Donath A, Podsiadlowski L, Pflug JM, Waterhouse RM, Meusemann K, Peters RS, Escalona HE, Mayer C, Liu S, Hendrich L, Alarie Y, Bilton DT, Jia F, Zhou X, Maddison DR, Niehuis O, Misof B. Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error. Mol Phylogenet Evol 2019; 135:270-285. [DOI: 10.1016/j.ympev.2019.02.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023]
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A. Schileyko A, N. Solovyeva E. On the taxonomic position of the enigmatic genus Tonkinodentus Schileyko, 1992 (Chilopoda, Scolopendromorpha): the first molecular data. Zookeys 2019; 840:133-155. [PMID: 31065230 PMCID: PMC6482132 DOI: 10.3897/zookeys.840.33635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 03/29/2019] [Indexed: 11/12/2022] Open
Abstract
The taxonomic position of the monotypic Vietnamese genus Tonkinodentus Schileyko, 1992 (for T.lestes Schileyko, 1992) has been considered in the light of the first obtained molecular data. Both molecular (28S rRNA) and morphological data support the position of this extraordinary eye-less genus within the family Scolopendridae Leach, 1814, a sighted clade, and thus suggests the polyphyly of blind scolopendromorphs. The species diagnosis has been amended and color images of T.lestes provided for the first time.
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Affiliation(s)
- Arkady A. Schileyko
- Zoological Museum of the Moscow Lomonosov State University, Bolshaya Nikitskaja Str. 6, Moscow, 103009, RussiaZoological Museum of Moscow Lomonosov State UniversityMoscowRussia
| | - Evgeniya N. Solovyeva
- Zoological Museum of the Moscow Lomonosov State University, Bolshaya Nikitskaja Str. 6, Moscow, 103009, RussiaZoological Museum of Moscow Lomonosov State UniversityMoscowRussia
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50
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Ballesteros JA, Sharma PP. A Critical Appraisal of the Placement of Xiphosura (Chelicerata) with Account of Known Sources of Phylogenetic Error. Syst Biol 2019; 68:896-917. [DOI: 10.1093/sysbio/syz011] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 12/20/2018] [Accepted: 02/10/2019] [Indexed: 11/13/2022] Open
Abstract
AbstractHorseshoe crabs (Xiphosura) are traditionally regarded as sister group to the clade of terrestrial chelicerates (Arachnida). This hypothesis has been challenged by recent phylogenomic analyses, but the non-monophyly of Arachnida has consistently been disregarded as artifactual. We re-evaluated the placement of Xiphosura among chelicerates using the most complete phylogenetic data set to date, expanding outgroup sampling, and including data from whole genome sequencing projects. In spite of uncertainty in the placement of some arachnid clades, all analyses show Xiphosura consistently nested within Arachnida as the sister group to Ricinulei (hooded tick spiders). It is apparent that the radiation of arachnids is an old one and occurred over a brief period of time, resulting in several consecutive short internodes, and thus is a potential case for the confounding effects of incomplete lineage sorting (ILS). We simulated coalescent gene trees to explore the effects of increasing levels of ILS on the placement of horseshoe crabs. In addition, common sources of systematic error were evaluated, as well as the effects of fast-evolving partitions and the dynamics of problematic long branch orders. Our results indicated that the placement of horseshoe crabs cannot be explained by missing data, compositional biases, saturation, or ILS. Interrogation of the phylogenetic signal showed that the majority of loci favor the derived placement of Xiphosura over a monophyletic Arachnida. Our analyses support the inference that horseshoe crabs represent a group of aquatic arachnids, comparable to aquatic mites, breaking a long-standing paradigm in chelicerate evolution and altering previous interpretations of the ancestral transition to the terrestrial habitat. Future studies testing chelicerate relationships should approach the task with a sampling strategy where the monophyly of Arachnida is not held as the premise.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
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