1
|
Santibáñez-López CE, Ojanguren-Affilastro AA, Graham MR, Sharma PP. Congruence between ultraconserved element-based matrices and phylotranscriptomic datasets in the scorpion Tree of Life. Cladistics 2023; 39:533-547. [PMID: 37401727 DOI: 10.1111/cla.12551] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2023] [Indexed: 07/05/2023] Open
Abstract
Scorpions are ancient and historically renowned for their potent venom. Traditionally, the systematics of this group of arthropods was supported by morphological characters, until recent phylogenomic analyses (using RNAseq data) revealed most of the higher-level taxa to be non-monophyletic. While these phylogenomic hypotheses are stable for almost all lineages, some nodes have been hard to resolve due to minimal taxonomic sampling (e.g. family Chactidae). In the same line, it has been shown that some nodes in the Arachnid Tree of Life show disagreement between hypotheses generated using transcritptomes and other genomic sources such as the ultraconserved elements (UCEs). Here, we compared the phylogenetic signal of transcriptomes vs. UCEs by retrieving UCEs from new and previously published scorpion transcriptomes and genomes, and reconstructed phylogenies using both datasets independently. We reexamined the monophyly and phylogenetic placement of Chactidae, sampling an additional chactid species using both datasets. Our results showed that both sets of genome-scale datasets recovered highly similar topologies, with Chactidae rendered paraphyletic owing to the placement of Nullibrotheas allenii. As a first step toward redressing the systematics of Chactidae, we establish the family Anuroctonidae (new family) to accommodate the genus Anuroctonus.
Collapse
Affiliation(s)
| | | | - Matthew R Graham
- Department of Biology, Eastern Connecticut State University, Willimantic, CT, 06226, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| |
Collapse
|
2
|
Nystrom GS, Ellsworth SA, Ward MJ, Rokyta DR. Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus). J Mol Evol 2023; 91:935-962. [PMID: 38091038 DOI: 10.1007/s00239-023-10148-7] [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: 06/19/2023] [Accepted: 11/12/2023] [Indexed: 12/21/2023]
Abstract
Venoms are primarily believed to evolve under strong diversifying selection resulting from persistent coevolution between predator and prey. Recent research has challenged this hypothesis, proposing that venoms from younger venomous lineages (e.g., snakes and cone snails) are governed predominantly by diversifying selection, while venoms from older venomous lineages (e.g., centipedes, scorpions, and spiders) are under stronger purifying selection. However, most research in older lineages has tested selection at more diverse phylogenetic scales. Although these tests are important for evaluating broad macroevolutionary trends underlying venom evolution, they are less equipped to detect species-level evolutionary trends, which likely have large impacts on venom variation seen at more diverse phylogenetic scales. To test for selection among closely related species from an older venomous lineage, we generated high-throughput venom-gland transcriptomes and venom proteomes for four populations of Giant Desert Hairy Scorpions (Hadrurus), including three Hadrurus arizonensis populations and one Hadrurus spadix population. We detected significant episodic and pervasive diversifying selection across a highly abundant toxin family that likely has a major role in venom function ([Formula: see text]KTxs), providing a contrast to the stronger purifying selection identified from other studies on scorpion venoms. Conversely, we detected weak episodic diversifying and/or stronger purifying selection in four toxin families (non-disulfide bridged peptides, phospholipase A2s, scorpine-like antimicrobial peptides, and serine proteases), most of which were less abundant and likely have ancillary functional roles. Finally, although we detected several major toxin families at disproportionate transcriptomic and/or proteomic abundances, we did not identify significant sex-based variation in Hadrurus venoms.
Collapse
Affiliation(s)
- Gunnar S Nystrom
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA
| | - Schyler A Ellsworth
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA
| | - Micaiah J Ward
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, 319 Stadium Dr., Tallahassee, FL, 32306-4295, USA.
| |
Collapse
|
3
|
The Enzymatic Core of Scorpion Venoms. Toxins (Basel) 2022; 14:toxins14040248. [PMID: 35448857 PMCID: PMC9030722 DOI: 10.3390/toxins14040248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/16/2022] [Accepted: 03/26/2022] [Indexed: 12/11/2022] Open
Abstract
Enzymes are an integral part of animal venoms. Unlike snakes, in which enzymes play a primary role in envenomation, in scorpions, their function appears to be ancillary in most species. Due to this, studies on the diversity of scorpion venom components have focused primarily on the peptides responsible for envenomation (toxins) and a few others (e.g., antimicrobials), while enzymes have been overlooked. In this work, a comprehensive study on enzyme diversity in scorpion venoms was performed by transcriptomic and proteomic techniques. Enzymes of 63 different EC types were found, belonging to 330 orthogroups. Of them, 24 ECs conform the scorpion venom enzymatic core, since they were determined to be present in all the studied scorpion species. Transferases and lyases are reported for the first time. Novel enzymes, which can play different roles in the venom, including direct toxicity, as venom spreading factors, activators of venom components, venom preservatives, or in prey pre-digestion, were described and annotated. The expression profile for transcripts coding for venom enzymes was analyzed, and shown to be similar among the studied species, while being significantly different from their expression pattern outside the telson.
Collapse
|
4
|
OUP accepted manuscript. Syst Biol 2022; 71:1281-1289. [DOI: 10.1093/sysbio/syac021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/01/2022] [Accepted: 03/05/2022] [Indexed: 11/14/2022] Open
|
5
|
Coelho GR, da Silva DL, Beraldo-Neto E, Vigerelli H, de Oliveira LA, Sciani JM, Pimenta DC. Neglected Venomous Animals and Toxins: Underrated Biotechnological Tools in Drug Development. Toxins (Basel) 2021; 13:toxins13120851. [PMID: 34941689 PMCID: PMC8708286 DOI: 10.3390/toxins13120851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022] Open
Abstract
Among the vast repertoire of animal toxins and venoms selected by nature and evolution, mankind opted to devote its scientific attention—during the last century—to a restricted group of animals, leaving a myriad of toxic creatures aside. There are several underlying and justifiable reasons for this, which include dealing with the public health problems caused by envenoming by such animals. However, these studies became saturated and gave rise to a whole group of animals that become neglected regarding their venoms and secretions. This repertoire of unexplored toxins and venoms bears biotechnological potential, including the development of new technologies, therapeutic agents and diagnostic tools and must, therefore, be assessed. In this review, we will approach such topics through an interconnected historical and scientific perspective that will bring up the major discoveries and innovations in toxinology, achieved by researchers from the Butantan Institute and others, and describe some of the major research outcomes from the study of these neglected animals.
Collapse
Affiliation(s)
- Guilherme Rabelo Coelho
- Laboratório de Bioquímica, Instituto Butantan, São Paulo 05503-900, Brazil; (G.R.C.); (D.L.d.S.); (E.B.-N.)
| | - Daiane Laise da Silva
- Laboratório de Bioquímica, Instituto Butantan, São Paulo 05503-900, Brazil; (G.R.C.); (D.L.d.S.); (E.B.-N.)
| | - Emidio Beraldo-Neto
- Laboratório de Bioquímica, Instituto Butantan, São Paulo 05503-900, Brazil; (G.R.C.); (D.L.d.S.); (E.B.-N.)
| | - Hugo Vigerelli
- Laboratório de Genética, Instituto Butantan, São Paulo 05503-900, Brazil;
| | - Laudiceia Alves de Oliveira
- Laboratório de Moléstias Infecciosas—Faculdade de Medicina de Botucatu, São Paulo State University (UNESP), São Paulo 01049-010, Brazil;
| | - Juliana Mozer Sciani
- Laboratório Multidisciplinar em Pesquisa, Universidade São Francisco, Bragança Paulista 12916-900, Brazil;
| | - Daniel Carvalho Pimenta
- Laboratório de Bioquímica, Instituto Butantan, São Paulo 05503-900, Brazil; (G.R.C.); (D.L.d.S.); (E.B.-N.)
- Correspondence:
| |
Collapse
|
6
|
What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata. DIVERSITY 2021. [DOI: 10.3390/d13110568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.
Collapse
|
7
|
Prendini L, Ehrenthal VL, Loria SF. Systematics of the Relictual Asian Scorpion Family Pseudochactidae Gromov, 1998, with a Review of Cavernicolous, Troglobitic, and Troglomorphic Scorpions. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2021. [DOI: 10.1206/0003-0090.453.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Lorenzo Prendini
- Scorpion Systematics Research Group, Division of Invertebrate Zoology, American Museum of Natural History
| | - Valentin L. Ehrenthal
- Section of Arachmology & Myriapodology, Center for Taxonomy and Morphology, Zoological Museum, Leibnitz Institute for the Analysis of Biodiversity Change; Department of Biology, University of Hamburg, Germany
| | - Stephanie F. Loria
- Scorpion Systematics Research Group, Division of Invertebrate Zoology; Richard Gilder Graduate School, American Museum of Natural History
| |
Collapse
|
8
|
Introduction to the Toxins Special Issue on Identification and Functional Characterization of Novel Venom Components. Toxins (Basel) 2020; 12:toxins12050336. [PMID: 32443716 PMCID: PMC7290916 DOI: 10.3390/toxins12050336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/13/2020] [Indexed: 11/16/2022] Open
Abstract
Throughout most of the 20th century, the toxinological literature consisted largely of pharmacological and functional characterizations of crude venoms and venom constituents, often constituents that could not be identified unambiguously [...].
Collapse
|