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Wanninger A. Hox, homology, and parsimony: An organismal perspective. Semin Cell Dev Biol 2024; 152-153:16-23. [PMID: 36670036 DOI: 10.1016/j.semcdb.2023.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/21/2022] [Accepted: 01/08/2023] [Indexed: 01/20/2023]
Abstract
Hox genes are important regulators in animal development. They often show a mosaic of conserved (e.g., longitudinal axis patterning) and lineage-specific novel functions (e.g., development of skeletal, sensory, or locomotory systems). Despite extensive research over the past decades, it remains controversial at which node in the animal tree of life the Hox cluster evolved. Its presence already in the last common metazoan ancestor has been proposed, although the genomes of both putative earliest extant metazoan offshoots, the ctenophores and the poriferans, are devoid of Hox sequences. The lack of Hox genes in the supposedly "simple"-built poriferans and their low number in cnidarians and the basally branching bilaterians, the xenacoelomorphs, seems to support the classical notion that the number of Hox genes is correlated with the degree of animal complexity. However, the 4-fold increase of the Hox cluster in xiphosurans, a basally branching chelicerate clade, as well as the situation in some teleost fishes that show a multitude of Hox genes compared to, e.g., human, demonstrates, that there is no per se direct correlation between organismal complexity and Hox number. Traditional approaches have tried to base homology on the morphological level on shared expression profiles of individual genes, but recent data have shown that, in particular with respect to Hox and other regulatory genes, complex gene-gene interactions rather than expression signatures of individual genes alone are responsible for shaping morphological traits during ontogeny. Accordingly, for sound homology assessments and reconstructions of character evolution on organ system level, additional independent datasets (e.g., morphological, developmental) need to be included in any such analyses. If supported by solid data, proposed structural homology should be regarded as valid and not be rejected solely on the grounds of non-parsimonious distribution of the character over a given phylogenetic topology.
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Affiliation(s)
- Andreas Wanninger
- University of Vienna, Department of Evolutionary Biology, Unit for Integrative Zoology, Djerassiplatz 1, 1030 Vienna, Austria.
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2
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Gainett G, Klementz BC, Setton EVW, Simian C, Iuri HA, Edgecombe GD, Peretti AV, Sharma PP. A plurality of morphological characters need not equate with phylogenetic accuracy: A rare genomic change refutes the placement of Solifugae and Pseudoscorpiones in Haplocnemata. Evol Dev 2023:e12467. [PMID: 38124251 DOI: 10.1111/ede.12467] [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: 08/30/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Recent advances in higher-level invertebrate phylogeny have leveraged shared features of genomic architecture to resolve contentious nodes across the tree of life. Yet, the interordinal relationships within Chelicerata have remained recalcitrant given competing topologies in recent molecular analyses. As such, relationships between topologically unstable orders remain supported primarily by morphological cladistic analyses. Solifugae, one such unstable chelicerate order, has long been thought to be the sister group of Pseudoscorpiones, forming the clade Haplocnemata, on the basis of eight putative morphological synapomorphies. The discovery, however, of a shared whole genome duplication placing Pseudoscorpiones in Arachnopulmonata provides the opportunity for a simple litmus test evaluating the validity of Haplocnemata. Here, we present the first developmental transcriptome of a solifuge (Titanopuga salinarum) and survey copy numbers of the homeobox genes for evidence of systemic duplication. We find that over 70% of the identified homeobox genes in T. salinarum are retained in a single copy, while representatives of the arachnopulmonates retain orthologs of those genes as two or more copies. Our results refute the placement of Solifugae in Haplocnemata. Subsequent reevaluation of putative interordinal morphological synapomorphies among chelicerates reveals a high incidence of homoplasy, reversals, and inaccurate coding within Haplocnemata and other small clades, as well as Arachnida more broadly, suggesting existing morphological character matrices are insufficient to resolve chelicerate phylogeny.
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Affiliation(s)
- Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin C Klementz
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Catalina Simian
- Departamento de Diversidad Biológica y Ecología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- Laboratorio de Biología Reproductiva y Evolución, Consejo Nacional de Investigaciones Científicas Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
| | - Hernán A Iuri
- División de Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina
| | - Gregory D Edgecombe
- Department of Earth Sciences, Division ES Invertebrates and Plants Palaeobiology, The Natural History Museum, London, UK
| | - Alfredo V Peretti
- Departamento de Diversidad Biológica y Ecología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- Laboratorio de Biología Reproductiva y Evolución, Consejo Nacional de Investigaciones Científicas Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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3
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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.
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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
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Cheatle Jarvela AM, Wexler JR. Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution. Dev Genes Evol 2023; 233:59-76. [PMID: 37982820 DOI: 10.1007/s00427-023-00712-y] [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: 06/16/2023] [Accepted: 11/05/2023] [Indexed: 11/21/2023]
Abstract
Current sequencing technology allows for the relatively affordable generation of highly contiguous genomes. Technological advances have made it possible for researchers to investigate the consequences of diverse sorts of genomic variants, such as gene gain and loss. With the extraordinary number of high-quality genomes now available, we take stock of how these genomic variants impact phenotypic evolution. We take care to point out that the identification of genomic variants of interest is only the first step in understanding their impact. Painstaking lab or fieldwork is still required to establish causal relationships between genomic variants and phenotypic evolution. We focus mostly on arthropod research, as this phylum has an impressive degree of phenotypic diversity and is also the subject of much evolutionary genetics research. This article is intended to both highlight recent advances in the field and also to be a primer for learning about evolutionary genetics and genomics.
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Affiliation(s)
- Alys M Cheatle Jarvela
- Department of Entomology, University of Maryland, College Park, MD, USA.
- HHMI Janelia Research Campus, Ashburn, VA, USA.
| | - Judith R Wexler
- Department of Ecology, Evolution, and Behavior, The Hebrew University in Jerusalem, Jerusalem, Israel.
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Janssen R, Pechmann M. Expression of posterior Hox genes and opisthosomal appendage development in a mygalomorph spider. Dev Genes Evol 2023; 233:107-121. [PMID: 37495828 PMCID: PMC10746769 DOI: 10.1007/s00427-023-00707-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023]
Abstract
Spiders represent an evolutionary successful group of chelicerate arthropods. The body of spiders is subdivided into two regions (tagmata). The anterior tagma, the prosoma, bears the head appendages and four pairs of walking legs. The segments of the posterior tagma, the opisthosoma, either lost their appendages during the course of evolution or their appendages were substantially modified to fulfill new tasks such as reproduction, gas exchange, and silk production. Previous work has shown that the homeotic Hox genes are involved in shaping the posterior appendages of spiders. In this paper, we investigate the expression of the posterior Hox genes in a tarantula that possesses some key differences of posterior appendages compared to true spiders, such as the lack of the anterior pair of spinnerets and a second set of book lungs instead of trachea. Based on the observed differences in posterior Hox gene expression in true spiders and tarantulas, we argue that subtle changes in the Hox gene expression of the Hox genes abdA and AbdB are possibly responsible for at least some of the morphological differences seen in true spiders versus tarantulas.
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Affiliation(s)
- Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden.
| | - Matthias Pechmann
- Institute for Zoology, Biocenter, University of Cologne, Zuelpicher Str. 47b, 50674, Cologne, Germany
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Sharma PP. The Impact of Whole Genome Duplication on the Evolution of the Arachnids. Integr Comp Biol 2023; 63:825-842. [PMID: 37263789 DOI: 10.1093/icb/icad050] [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: 03/01/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023] Open
Abstract
The proliferation of genomic resources for Chelicerata in the past 10 years has revealed that the evolution of chelicerate genomes is more dynamic than previously thought, with multiple waves of ancient whole genome duplications affecting separate lineages. Such duplication events are fascinating from the perspective of evolutionary history because the burst of new gene copies associated with genome duplications facilitates the acquisition of new gene functions (neofunctionalization), which may in turn lead to morphological novelties and spur net diversification. While neofunctionalization has been invoked in several contexts with respect to the success and diversity of spiders, the overall impact of whole genome duplications on chelicerate evolution and development remains imperfectly understood. The purpose of this review is to examine critically the role of whole genome duplication on the diversification of the extant arachnid orders, as well as assess functional datasets for evidence of subfunctionalization or neofunctionalization in chelicerates. This examination focuses on functional data from two focal model taxa: the spider Parasteatoda tepidariorum, which exhibits evidence for an ancient duplication, and the harvestman Phalangium opilio, which exhibits an unduplicated genome. I show that there is no evidence that taxa with genome duplications are more successful than taxa with unduplicated genomes. I contend that evidence for sub- or neofunctionalization of duplicated developmental patterning genes in spiders is indirect or fragmentary at present, despite the appeal of this postulate for explaining the success of groups like spiders. Available expression data suggest that the condition of duplicated Hox modules may have played a role in promoting body plan disparity in the posterior tagma of some orders, such as spiders and scorpions, but functional data substantiating this postulate are critically missing. Spatiotemporal dynamics of duplicated transcription factors in spiders may represent cases of developmental system drift, rather than neofunctionalization. Developmental system drift may represent an important, but overlooked, null hypothesis for studies of paralogs in chelicerate developmental biology. To distinguish between subfunctionalization, neofunctionalization, and developmental system drift, concomitant establishment of comparative functional datasets from taxa exhibiting the genome duplication, as well as those that lack the paralogy, is sorely needed.
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Affiliation(s)
- Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Gainett G, Klementz BC, Blaszczyk PO, Bruce HS, Patel NH, Sharma PP. Dual Functions of labial Resolve the Hox Logic of Chelicerate Head Segments. Mol Biol Evol 2023; 40:7043718. [PMID: 36798978 PMCID: PMC10015621 DOI: 10.1093/molbev/msad037] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
Despite an abundance of gene expression surveys, comparatively little is known about Hox gene function in Chelicerata. Previous investigations of paralogs of labial (lab) and Deformed (Dfd) in a spider have shown that these play a role in tissue maintenance of the pedipalp segment (lab-1) and in patterning the first walking leg identity (Dfd-1), respectively. However, extrapolations of these data across chelicerates are hindered by the existence of duplicated Hox genes in arachnopulmonates (e.g., spiders and scorpions), which have resulted from an ancient whole genome duplication (WGD) event. Here, we investigated the function of the single-copy ortholog of lab in the harvestman Phalangium opilio, an exemplar of a lineage that was not subject to this WGD. Embryonic RNA interference against lab resulted in two classes of phenotypes: homeotic transformations of pedipalps to chelicerae, as well as reduction and fusion of the pedipalp and leg 1 segments. To test for combinatorial function, we performed a double knockdown of lab and Dfd, which resulted in a homeotic transformation of both pedipalps and the first walking legs into cheliceral identity, whereas the second walking leg is transformed into a pedipalpal identity. Taken together, these results elucidate a model for the Hox logic of head segments in Chelicerata. To substantiate the validity of this model, we performed expression surveys for lab and Dfd paralogs in scorpions and horseshoe crabs. We show that repetition of morphologically similar appendages is correlated with uniform expression levels of the Hox genes lab and Dfd, irrespective of the number of gene copies.
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Affiliation(s)
- Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI
| | - Benjamin C Klementz
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI
| | - Pola O Blaszczyk
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI
| | | | - Nipam H Patel
- Marine Biological Laboratory, Woods Hole, MA.,Organismal Biology & Anatomy, University of Chicago, Chicago, IL
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI
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8
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Hox genes in spiders: Their significance for development and evolution. Semin Cell Dev Biol 2022:S1084-9521(22)00355-X. [PMID: 36522242 DOI: 10.1016/j.semcdb.2022.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/13/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
Hox genes are known for their role in the specification of typical body plan features in animals. Evolutionary changes in Hox gene function are believed to be involved in the emergence of the diverse body plans we observe in animals today. Spiders share many body plan features with other arthropods, but also have numerous unique traits of their own. Studies of spider Hox genes have already provided insights into evolutionarily conserved and derived features of the spider body plan and their genetic basis. However, many aspects of Hox gene biology have been insufficiently studied in spiders so far. In this review, we highlight previous comparative studies of Hox genes in spiders and their significance for our understanding of the evolution of the spider body plan. We also identify aspects of Hox gene biology that need to be studied in greater detail. Many spider Hox genes have not been investigated beyond their mRNA expression patterns, and the role of Hox genes with apparently plesiomorphic or dual functions, like ftz and Hox3 is still unclear. Spiders have a duplicated Hox gene cluster, but possible sub- or neofunctionalisation of duplicates have not yet been studied systematically. Future research should therefore focus on these issues, in addition to the role of Polycomb and trithorax-mediated regulation, the identification of regulatory regions, cofactors or spider-specific target genes, and the significance of non-coding RNAs transcribed from within the Hox cluster and even from the antisense strand of particular Hox genes.
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9
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Gainett G, Crawford AR, Klementz BC, So C, Baker CM, Setton EVW, Sharma PP. Eggs to long-legs: embryonic staging of the harvestman Phalangium opilio (Opiliones), an emerging model arachnid. Front Zool 2022; 19:11. [PMID: 35246168 PMCID: PMC8896363 DOI: 10.1186/s12983-022-00454-z] [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: 11/02/2021] [Accepted: 02/09/2022] [Indexed: 11/18/2022] Open
Abstract
Background The comparative embryology of Chelicerata has greatly advanced in recent years with the integration of classical studies and genetics, prominently spearheaded by developmental genetic works in spiders. Nonetheless, the understanding of the evolution of development and polarization of embryological characters in Chelicerata is presently limited, as few non-spider species have been well studied. A promising focal species for chelicerate evo-devo is the daddy-long-legs (harvestman) Phalangium opilio, a member of the order Opiliones. Phalangium opilio, breeds prolifically and is easily accessible in many parts of the world, as well as tractable in a laboratory setting. Resources for this species include developmental transcriptomes, a draft genome, and protocols for RNA interference, but a modern staging system is critically missing for this emerging model system. Results We present a staging system of P. opilio embryogenesis that spans the most important morphogenetic events with respect to segment formation, appendage elongation and head development. Using time-lapse imaging, confocal microscopy, colorimetric in situ hybridization, and immunohistochemistry, we tracked the development of synchronous clutches from egg laying to adulthood. We describe key events in segmentation, myogenesis, neurogenesis, and germ cell formation. Conclusion Considering the phylogenetic position of Opiliones and the unduplicated condition of its genome (in contrast to groups like spiders and scorpions), this species is poised to serve as a linchpin for comparative studies in arthropod development and genome evolution. The staging system presented herein provides a valuable reference for P. opilio that we anticipate being useful to the arthropod evo-devo community, with the goal of revitalizing research in the comparative development of non-spider arachnids. Supplementary Information The online version contains supplementary material available at 10.1186/s12983-022-00454-z.
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Affiliation(s)
- Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, 438 Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA.
| | - Audrey R Crawford
- Department of Integrative Biology, University of Wisconsin-Madison, 438 Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Benjamin C Klementz
- Department of Integrative Biology, University of Wisconsin-Madison, 438 Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Calvin So
- Department of Integrative Biology, University of Wisconsin-Madison, 438 Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Caitlin M Baker
- Department of Integrative Biology, University of Wisconsin-Madison, 438 Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin-Madison, 438 Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, 438 Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA
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10
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Harper A, Baudouin Gonzalez L, Schönauer A, Janssen R, Seiter M, Holzem M, Arif S, McGregor AP, Sumner-Rooney L. Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates. G3 (BETHESDA, MD.) 2021; 11:jkab299. [PMID: 34849767 PMCID: PMC8664421 DOI: 10.1093/g3journal/jkab299] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 01/12/2023]
Abstract
Whole-genome duplications (WGDs) have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs, and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signaling pathway components and microRNAs are frequently retained as duplicates (so-called ohnologs) following WGD. These not only provide the best evidence for WGD, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate WGD, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt, and frizzled, across these and 12 existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, further supporting the ancestral arachnopulmonate WGD. We also found evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the six arachnopulmonate orders, with interorder variation in the retention of specific paralogs. We identified variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.
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Affiliation(s)
- Amber Harper
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Luis Baudouin Gonzalez
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Ralf Janssen
- Department of Earth Sciences, Uppsala University, Geocentrum, 752 36 Uppsala, Sweden
| | - Michael Seiter
- Department of Evolutionary Biology, Unit Integrative Zoology, University of Vienna, 1090 Vienna, Austria
| | - Michaela Holzem
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Division of Signalling and Functional Genomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 69120 Heidelberg, Germany
| | - Saad Arif
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
- Centre for Functional Genomics, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Lauren Sumner-Rooney
- Oxford University Museum of Natural History, University of Oxford, Oxford OX1 3PW, UK
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11
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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.
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Simone Y, van der Meijden A. Armed stem to stinger: a review of the ecological roles of scorpion weapons. J Venom Anim Toxins Incl Trop Dis 2021; 27:e20210002. [PMID: 34527038 PMCID: PMC8425188 DOI: 10.1590/1678-9199-jvatitd-2021-0002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/18/2021] [Indexed: 12/24/2022] Open
Abstract
Scorpions possess two systems of weapons: the pincers (chelae) and the stinger (telson). These are placed on anatomically and developmentally well separated parts of the body, that is, the oral appendages and at the end of the body axis. The otherwise conserved body plan of scorpions varies most in the shape and relative dimensions of these two weapon systems, both across species and in some cases between the sexes. We review the literature on the ecological function of these two weapon systems in each of three contexts of usage: (i) predation, (ii) defense and (iii) sexual contests. In the latter context, we will also discuss their usage in mating. We first provide a comparative background for each of these contexts of usage by giving examples of other weapon systems from across the animal kingdom. Then, we discuss the pertinent aspects of the anatomy of the weapon systems, particularly those aspects relevant to their functioning in their ecological roles. The literature on the functioning and ecological role of both the chelae and the telson is discussed in detail, again organized by context of usage. Particular emphasis is given on the differences in morphology or usage between species or higher taxonomic groups, or between genders, as such cases are most insightful to understand the roles of each of the two distinct weapon systems of the scorpions and their evolutionary interactions. We aimed to synthesize the literature while minimizing conjecture, but also to point out gaps in the literature and potential future research opportunities.
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Affiliation(s)
- Yuri Simone
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Porto, Portugal
| | - Arie van der Meijden
- CIBIO Research Centre in Biodiversity and Genetic Resources, InBIO, Porto, Portugal
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13
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Hajirnis N, Mishra RK. Homeotic Genes: Clustering, Modularity, and Diversity. Front Cell Dev Biol 2021; 9:718308. [PMID: 34458272 PMCID: PMC8386295 DOI: 10.3389/fcell.2021.718308] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/22/2021] [Indexed: 11/13/2022] Open
Abstract
Hox genes code for transcription factors and are evolutionarily conserved. They regulate a plethora of downstream targets to define the anterior-posterior (AP) body axis of a developing bilaterian embryo. Early work suggested a possible role of clustering and ordering of Hox to regulate their expression in a spatially restricted manner along the AP axis. However, the recent availability of many genome assemblies for different organisms uncovered several examples that defy this constraint. With recent advancements in genomics, the current review discusses the arrangement of Hox in various organisms. Further, we revisit their discovery and regulation in Drosophila melanogaster. We also review their regulation in different arthropods and vertebrates, with a significant focus on Hox expression in the crustacean Parahyale hawaiensis. It is noteworthy that subtle changes in the levels of Hox gene expression can contribute to the development of novel features in an organism. We, therefore, delve into the distinct regulation of these genes during primary axis formation, segment identity, and extra-embryonic roles such as in the formation of hair follicles or misregulation leading to cancer. Toward the end of each section, we emphasize the possibilities of several experiments involving various organisms, owing to the advancements in the field of genomics and CRISPR-based genome engineering. Overall, we present a holistic view of the functioning of Hox in the animal world.
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Affiliation(s)
- Nikhil Hajirnis
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Rakesh K. Mishra
- CSIR – Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- AcSIR – Academy of Scientific and Innovative Research, Ghaziabad, India
- Tata Institute for Genetics and Society (TIGS), Bangalore, India
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14
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Gainett G, González VL, Ballesteros JA, Setton EVW, Baker CM, Barolo Gargiulo L, Santibáñez-López CE, Coddington JA, Sharma PP. The genome of a daddy-long-legs (Opiliones) illuminates the evolution of arachnid appendages. Proc Biol Sci 2021; 288:20211168. [PMID: 34344178 PMCID: PMC8334856 DOI: 10.1098/rspb.2021.1168] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/14/2021] [Indexed: 12/24/2022] Open
Abstract
Chelicerate arthropods exhibit dynamic genome evolution, with ancient whole-genome duplication (WGD) events affecting several orders. Yet, genomes remain unavailable for a number of poorly studied orders, such as Opiliones (daddy-long-legs), which has hindered comparative study. We assembled the first harvestman draft genome for the species Phalangium opilio, which bears elongate, prehensile appendages, made possible by numerous distal articles called tarsomeres. Here, we show that the genome of P. opilio exhibits a single Hox cluster and no evidence of WGD. To investigate the developmental genetic basis for the quintessential trait of this group-the elongate legs-we interrogated the function of the Hox genes Deformed (Dfd) and Sex combs reduced (Scr), and a homologue of Epidermal growth factor receptor (Egfr). Knockdown of Dfd incurred homeotic transformation of two pairs of legs into pedipalps, with dramatic shortening of leg segments in the longest leg pair, whereas homeosis in L3 is only achieved upon double Dfd + Scr knockdown. Knockdown of Egfr incurred shortened appendages and the loss of tarsomeres. The similarity of Egfr loss-of-function phenotypic spectra in insects and this arachnid suggest that repeated cooption of EGFR signalling underlies the independent gains of supernumerary tarsomeres across the arthropod tree of life.
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Affiliation(s)
- Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - Vanessa L. González
- Global Genome Initiative, Smithsonian Institution, National Museum of Natural History, 10th and Constitution, NW, Washington, DC 20560-0105, USA
| | - Jesús A. Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - Emily V. W. Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - Caitlin M. Baker
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | | | - Carlos E. Santibáñez-López
- Department of Biological and Environmental Sciences, Western Connecticut State University, 181 White St, Danbury, CT 06810, USA
| | - Jonathan A. Coddington
- Global Genome Initiative, Smithsonian Institution, National Museum of Natural History, 10th and Constitution, NW, Washington, DC 20560-0105, USA
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, 53706 WI, USA
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15
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Ontano AZ, Gainett G, Aharon S, Ballesteros JA, Benavides LR, Corbett KF, Gavish-Regev E, Harvey MS, Monsma S, Santibáñez-López CE, Setton EVW, Zehms JT, Zeh JA, Zeh DW, Sharma PP. Taxonomic Sampling and Rare Genomic Changes Overcome Long-Branch Attraction in the Phylogenetic Placement of Pseudoscorpions. Mol Biol Evol 2021; 38:2446-2467. [PMID: 33565584 PMCID: PMC8136511 DOI: 10.1093/molbev/msab038] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with long-branch attraction artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale data sets. Pseudoscorpion placement is particularly variable across data sets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount long-branch attraction, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.
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Affiliation(s)
- Andrew Z Ontano
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Shlomi Aharon
- National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ligia R Benavides
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kevin F Corbett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Efrat Gavish-Regev
- National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark S Harvey
- Collections & Research, Western Australian Museum, Welshpool, WA, Australia
| | | | | | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jakob T Zehms
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jeanne A Zeh
- Department of Biology and Program in Ecology, Evolution & Conservation Biology, University of Nevada, Reno, NV, USA
| | - David W Zeh
- Department of Biology and Program in Ecology, Evolution & Conservation Biology, University of Nevada, Reno, NV, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
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16
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Ballesteros JA, Setton EVW, Santibáñez-López CE, Arango CP, Brenneis G, Brix S, Corbett KF, Cano-Sánchez E, Dandouch M, Dilly GF, Eleaume MP, Gainett G, Gallut C, McAtee S, McIntyre L, Moran AL, Moran R, López-González PJ, Scholtz G, Williamson C, Woods HA, Zehms JT, Wheeler WC, Sharma PP. Phylogenomic Resolution of Sea Spider Diversification through Integration of Multiple Data Classes. Mol Biol Evol 2021; 38:686-701. [PMID: 32915961 PMCID: PMC7826184 DOI: 10.1093/molbev/msaa228] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.
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Affiliation(s)
- Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | | | - Claudia P Arango
- Queensland Museum, Biodiversity Program, Brisbane, QLD, Australia
| | - Georg Brenneis
- Zoologisches Institut und Museum, Cytologie und Evolutionsbiologie, Universität Greifswald, Greifswald, Germany
| | - Saskia Brix
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), c/o Biocenter Grindel (CeNak), Martin-Luther-King-Platz 3, Hamburg, Germany
| | - Kevin F Corbett
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Esperanza Cano-Sánchez
- Biodiversidad y Ecología Acuática, Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Merai Dandouch
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Geoffrey F Dilly
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Marc P Eleaume
- Départment Milieux et Peuplements Aquatiques, Muséum National d’Histoire Naturelle, Paris, France
| | - Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Cyril Gallut
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Concarneau, France
| | - Sean McAtee
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Lauren McIntyre
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Amy L Moran
- Department of Biology, University of Hawai’I at Mānoa, Honolulu, HI
| | - Randy Moran
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - Pablo J López-González
- Biodiversidad y Ecología Acuática, Departamento de Zoología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Gerhard Scholtz
- Institut für Biologie, Vergleichende Zoologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Clay Williamson
- Department of Biology, California State University-Channel Islands, Camarillo, CA
| | - H Arthur Woods
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Jakob T Zehms
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, NY
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI
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17
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Günther A, Monod L, Wirkner CS. Comparative morphology of scorpion metasomata: Muscles and cuticle. ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 60:101003. [PMID: 33444929 DOI: 10.1016/j.asd.2020.101003] [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: 04/15/2020] [Revised: 10/01/2020] [Accepted: 10/14/2020] [Indexed: 06/12/2023]
Abstract
Scorpions are among the most popular research objects within Arachnida and there is an impressive body of knowledge about their biology, distribution, morphology, etc. Although the poison sting has gained a lot of attention due to its potential lethal effects to humans, hitherto, there has been no comparative morphological study on the metasoma, the body part that delivers the poisonous injection. The metasoma always consists of five body segments terminated by a poison sting, but it presents significant morphological variations, both between sexes and between species. Its form ranges from long and thin to short and rather reduced to thick and dominant. In this study, we investigated species representing major scorpion clades and most of the known morphological disparity. Using high-resolution micro-computer-tomography and 3D-reconstruction, we present the first 3D visualizations of metasomal exo-skeletal elements in combination with their musculature. Despite of morphological varying metasomal forms, in all investigated species, a repeating pattern of muscles was found: four pairs of muscles in metasomal segment one to four and two pairs of muscles in metasomal segment five. However, the metasomal muscles are characterized by an antero-posterior change in their shapes and sizes and interspecific variation was also found in the extrinsic metasomal musculature, i.e. the muscles that link metasoma to mesosoma.
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Affiliation(s)
- Alice Günther
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Germany.
| | - Lionel Monod
- Secteur Invertébrés, Muséum d'histoire Naturelle, Route de Malagnou 1, 1208, Genève, Switzerland
| | - Christian S Wirkner
- Allgemeine & Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Germany
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18
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Gainett G, Ballesteros JA, Kanzler CR, Zehms JT, Zern JM, Aharon S, Gavish-Regev E, Sharma PP. Systemic paralogy and function of retinal determination network homologs in arachnids. BMC Genomics 2020; 21:811. [PMID: 33225889 PMCID: PMC7681978 DOI: 10.1186/s12864-020-07149-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/13/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Arachnids are important components of cave ecosystems and display many examples of troglomorphisms, such as blindness, depigmentation, and elongate appendages. Little is known about how the eyes of arachnids are specified genetically, let alone the mechanisms for eye reduction and loss in troglomorphic arachnids. Additionally, duplication of Retinal Determination Gene Network (RDGN) homologs in spiders has convoluted functional inferences extrapolated from single-copy homologs in pancrustacean models. RESULTS We investigated a sister species pair of Israeli cave whip spiders, Charinus ioanniticus and C. israelensis (Arachnopulmonata, Amblypygi), of which one species has reduced eyes. We generated embryonic transcriptomes for both Amblypygi species, and discovered that several RDGN homologs exhibit duplications. We show that duplication of RDGN homologs is systemic across arachnopulmonates (arachnid orders that bear book lungs), rather than being a spider-specific phenomenon. A differential gene expression (DGE) analysis comparing the expression of RDGN genes in field-collected embryos of both species identified candidate RDGN genes involved in the formation and reduction of eyes in whip spiders. To ground bioinformatic inference of expression patterns with functional experiments, we interrogated the function of three candidate RDGN genes identified from DGE using RNAi in the spider Parasteatoda tepidariorum. We provide functional evidence that one of these paralogs, sine oculis/Six1 A (soA), is necessary for the development of all arachnid eye types. CONCLUSIONS Our work establishes a foundation to investigate the genetics of troglomorphic adaptations in cave arachnids, and links differential gene expression to an arthropod eye phenotype for the first time outside of Pancrustacea. Our results support the conservation of at least one RDGN component across Arthropoda and provide a framework for identifying the role of gene duplications in generating arachnid eye diversity.
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Affiliation(s)
- Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Charlotte R Kanzler
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jakob T Zehms
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John M Zern
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Shlomi Aharon
- National Natural History Collections, The Hebrew University of Jerusalem , Jerusalem, 9190401, Israel
| | - Efrat Gavish-Regev
- National Natural History Collections, The Hebrew University of Jerusalem , Jerusalem, 9190401, Israel
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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19
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Greenhalgh R, Dermauw W, Glas JJ, Rombauts S, Wybouw N, Thomas J, Alba JM, Pritham EJ, Legarrea S, Feyereisen R, Van de Peer Y, Van Leeuwen T, Clark RM, Kant MR. Genome streamlining in a minute herbivore that manipulates its host plant. eLife 2020; 9:56689. [PMID: 33095158 PMCID: PMC7738191 DOI: 10.7554/elife.56689] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host's natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite's minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species' highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size.
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Affiliation(s)
- Robert Greenhalgh
- School of Biological Sciences, University of Utah, Salt Lake City, United States
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Joris J Glas
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Nicky Wybouw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jainy Thomas
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Juan M Alba
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Ellen J Pritham
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Saioa Legarrea
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - René Feyereisen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Richard M Clark
- School of Biological Sciences, University of Utah, Salt Lake City, United States.,Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, United States
| | - Merijn R Kant
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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20
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Gainett G, Sharma PP. Genomic resources and toolkits for developmental study of whip spiders (Amblypygi) provide insights into arachnid genome evolution and antenniform leg patterning. EvoDevo 2020; 11:18. [PMID: 32874529 PMCID: PMC7455915 DOI: 10.1186/s13227-020-00163-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/11/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The resurgence of interest in the comparative developmental study of chelicerates has led to important insights, such as the discovery of a genome duplication shared by spiders and scorpions, inferred to have occurred in the most recent common ancestor of Arachnopulmonata (a clade comprising the five arachnid orders that bear book lungs). Nonetheless, several arachnid groups remain understudied in the context of development and genomics, such as the order Amblypygi (whip spiders). The phylogenetic position of Amblypygi in Arachnopulmonata posits them as an interesting group to test the incidence of the proposed genome duplication in the common ancestor of Arachnopulmonata, as well as the degree of retention of duplicates over 450 Myr. Moreover, whip spiders have their first pair of walking legs elongated and modified into sensory appendages (a convergence with the antennae of mandibulates), but the genetic patterning of these antenniform legs has never been investigated. RESULTS We established genomic resources and protocols for cultivation of embryos and gene expression assays by in situ hybridization to study the development of the whip spider Phrynus marginemaculatus. Using embryonic transcriptomes from three species of Amblypygi, we show that the ancestral whip spider exhibited duplications of all ten Hox genes. We deploy these resources to show that paralogs of the leg gap genes dachshund and homothorax retain arachnopulmonate-specific expression patterns in P. marginemaculatus. We characterize the expression of leg gap genes Distal-less, dachshund-1/2 and homothorax-1/2 in the embryonic antenniform leg and other appendages, and provide evidence that allometry, and by extension the antenniform leg fate, is specified early in embryogenesis. CONCLUSION This study is the first step in establishing P. marginemaculatus as a chelicerate model for modern evolutionary developmental study, and provides the first resources sampling whip spiders for comparative genomics. Our results suggest that Amblypygi share a genome duplication with spiders and scorpions, and set up a framework to study the genetic specification of antenniform legs. Future efforts to study whip spider development must emphasize the development of tools for functional experiments in P. marginemaculatus.
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Affiliation(s)
- Guilherme Gainett
- 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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21
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Leite DJ, Baudouin-Gonzalez L, Iwasaki-Yokozawa S, Lozano-Fernandez J, Turetzek N, Akiyama-Oda Y, Prpic NM, Pisani D, Oda H, Sharma PP, McGregor AP. Homeobox Gene Duplication and Divergence in Arachnids. Mol Biol Evol 2020; 35:2240-2253. [PMID: 29924328 PMCID: PMC6107062 DOI: 10.1093/molbev/msy125] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Homeobox genes are key toolkit genes that regulate the development of metazoans and changes in their regulation and copy number have contributed to the evolution of phenotypic diversity. We recently identified a whole genome duplication (WGD) event that occurred in an ancestor of spiders and scorpions (Arachnopulmonata), and that many homeobox genes, including two Hox clusters, appear to have been retained in arachnopulmonates. To better understand the consequences of this ancient WGD and the evolution of arachnid homeobox genes, we have characterized and compared the homeobox repertoires in a range of arachnids. We found that many families and clusters of these genes are duplicated in all studied arachnopulmonates (Parasteatoda tepidariorum, Pholcus phalangioides, Centruroides sculpturatus, and Mesobuthus martensii) compared with nonarachnopulmonate arachnids (Phalangium opilio, Neobisium carcinoides, Hesperochernes sp., and Ixodes scapularis). To assess divergence in the roles of homeobox ohnologs, we analyzed the expression of P. tepidariorum homeobox genes during embryogenesis and found pervasive changes in the level and timing of their expression. Furthermore, we compared the spatial expression of a subset of P. tepidariorum ohnologs with their single copy orthologs in P. opilio embryos. We found evidence for likely subfunctionlization and neofunctionalization of these genes in the spider. Overall our results show a high level of retention of homeobox genes in spiders and scorpions post-WGD, which is likely to have made a major contribution to their developmental evolution and diversification through pervasive subfunctionlization and neofunctionalization, and paralleling the outcomes of WGD in vertebrates.
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Affiliation(s)
- Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Luís Baudouin-Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | | | - Jesus Lozano-Fernandez
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Natascha Turetzek
- Department of Cellular Neurobiology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University, Göttingen, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, Takatsuki, Osaka, Japan.,Microbiology and Infection Control, Osaka Medical College, Takatsuki, Osaka, Japan
| | - Nikola-Michael Prpic
- Department of Cellular Neurobiology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University, Göttingen, Germany
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, United Kingdom
| | - Hiroki Oda
- JT Biohistory Research Hall, Takatsuki, Osaka, Japan.,Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
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22
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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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23
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Nolan ED, Santibáñez-López CE, Sharma PP. Developmental gene expression as a phylogenetic data class: support for the monophyly of Arachnopulmonata. Dev Genes Evol 2020; 230:137-153. [PMID: 31927629 DOI: 10.1007/s00427-019-00644-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/10/2019] [Indexed: 01/01/2023]
Abstract
Despite application of genome-scale datasets, the phylogenetic placement of scorpions within arachnids remains contentious between two different phylogenetic data classes. Paleontologists continue to recover scorpions in a basally branching position, partly owing to their morphological similarity to extinct marine orders like Eurypterida (sea scorpions). Phylogenomic datasets consistently recover scorpions in a derived position, as the sister group of Tetrapulmonata (a clade of arachnids that includes spiders). To adjudicate between these hypotheses using a rare genomic change (RGC), we leveraged the recent discovery of ancient paralogy in spiders and scorpions to assess phylogenetic placement. We identified homologs of four transcription factors required for appendage patterning (dachshund, homothorax, extradenticle, and optomotor blind) in arthropods that are known to be duplicated in spiders. Using genomic resources for a spider, a scorpion, and a harvestman, we conducted gene tree analyses and assayed expression patterns of scorpion gene duplicates. Here we show that scorpions, like spiders, retain two copies of all four transcription factors, whereas arachnid orders like mites and harvestmen bear a single copy. A survey of embryonic expression patterns of the scorpion paralogs closely matches those of their spider counterparts, with one paralog consistently retaining the putatively ancestral pattern found in the harvestman, as well as the mite, and/or other outgroups. These data comprise a rare genomic change in chelicerate phylogeny supporting the inference of a distal placement of scorpions. Beyond demonstrating the diagnostic power of developmental genetic data as a phylogenetic data class, a derived placement of scorpions within the arachnids, together with an array of stem-group Paleozoic scorpions that occupied marine habitats, effectively rules out a scenario of a single colonization of terrestrial habitat within Chelicerata, even in tree topologies contrived to recover the monophyly of Arachnida.
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Affiliation(s)
- Erik D Nolan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Developmental Biology, Washington University of St. Louis, St. Louis, MO, 63110, USA
| | - Carlos E Santibáñez-López
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Biology, Eastern Connecticut State University, 83 Windham Street, Willimantic, CT, 06266, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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24
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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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25
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Vaschetto LM, Ortiz N. The Role of Sequence Duplication in Transcriptional Regulation and Genome Evolution. Curr Genomics 2019; 20:405-408. [PMID: 32476997 PMCID: PMC7235390 DOI: 10.2174/1389202920666190320140721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 12/26/2022] Open
Abstract
Sequence duplication is nowadays recognized as an important mechanism that underlies the evolution of eukaryote genomes, being indeed one of the most powerful strategies for the generation of adaptive diversity by modulating transcriptional activity. The evolutionary novelties simultaneously associated with sequence duplication and differential gene expression can be collectively referred to as duplication-mediated transcriptional regulation. In the last years, evidence has emerged supporting the idea that sequence duplication and functionalization represent important evolutionary strategies acting at the genome level, and both coding and non-coding sequences have been found to be targets of such events. Moreover, it has been proposed that deleterious effects of sequence duplication might be potentially silenced by endogenous cell machinery (i.e., RNA interference, epigenetic repressive marks, etc). Along these lines, our aim is to highlight the role of sequence duplication on transcriptional activity and the importance of both in genome evolution.
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Affiliation(s)
- Luis M Vaschetto
- Instituto de Diversidad y Ecología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEA, CONICET), Av. Vélez Sarsfield 299, X5000JJC Córdoba, Argentina.,Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, (FCEFyN, UNC), Av. Vélez Sarsfield 299, X5000JJC Córdoba, Argentina
| | - Natalia Ortiz
- Instituto de Diversidad y Ecología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEA, CONICET), Av. Vélez Sarsfield 299, X5000JJC Córdoba, Argentina.,Cátedra de Genética de Poblaciones y Evolución, Facultad de Ciencias Exactas, Físicas y Naturales, UNC, Córdoba, Argentina
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26
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March LE, Smaby RM, Setton EVW, Sharma PP. The evolution of selector gene function: Expression dynamics and regulatory interactions of tiptop/teashirt across Arthropoda. Evol Dev 2018; 20:219-232. [PMID: 30221814 DOI: 10.1111/ede.12270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The transcription factors spineless (ss) and tiptop/teashirt (tio/tsh) have been shown to be selectors of distal appendage identity in an insect, but it is unknown how they regulate one another. Here, we examined the regulatory relationships between these two determinants in the milkweed bug Oncopeltus faciatus, using maternal RNA interference (RNAi). We show that Ofas-ss RNAi embryos bear distally transformed antennal buds with heterogeneous Ofas-tio/tsh expression domains comparable to wild type legs. In the reciprocal experiment, Ofas-tio/tsh RNAi embryos bear distally transformed walking limb buds with ectopic expression of Ofas-ss in the distal leg primordia. These data suggest that Ofas-ss is required for the maintenance of Ofas-tio/tsh expression in the distal antenna, whereas Ofas-tio/tsh represses Ofas-ss in the leg primordia. To assess whether expression boundaries of tio/tsh are associated with the trunk region more generally, we surveyed the expression of one myriapod and two chelicerate tio/tsh homologs. Our expression survey suggests that tio/tsh could play a role in specifying distal appendage identity across Arthropoda, but Hox regulation of tio/tsh homologs has been evolutionarily labile.
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Affiliation(s)
- Logan E March
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Rachel M Smaby
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin
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27
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Di Z, Edgecombe GD, Sharma PP. Homeosis in a scorpion supports a telopodal origin of pectines and components of the book lungs. BMC Evol Biol 2018; 18:73. [PMID: 29783957 PMCID: PMC5963125 DOI: 10.1186/s12862-018-1188-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/03/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The morphological and functional evolution of appendages has played a key role in the diversification of arthropods. While the ancestral arthropod appendage is held to be polyramous, terrestriality is associated with the reduction or loss of appendage rami, which may obscure the homology of different appendage derivatives. Proxies for appendage homology have included surveys of cross-reactive antibodies for wing markers like Nubbin/PDM, which have suggested that the abdominal appendages of arachnids (e.g., book lungs, tracheal tubules) are derived from ancestral gills (epipods). RESULTS Here, we discovered a rare case of inferred homeosis in a scorpion in which the bilobed genital opercula and the pectines are transformed to walking legs, and an abnormal sternite shows a book lung close to an everted structure comparable to the morphology of some Palaeozoic scorpion fossils. CONCLUSIONS The observed morphology is consistent with abnormal expression of homeotic genes during embryonic development. The phenotype of this abnormal specimen suggests that the genital opercula, the pectines, and parts of the book lung may be derived from the telopodite of abdominal appendages rather than from epipods. This interpretation contradicts the "ancestral gill" hypothesis but reconciles features of the Palaeozoic scorpion fossil record with the embryology of modern scorpions.
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Affiliation(s)
- Zhiyong Di
- Key Laboratory of Invertebrate Systematics and Application, College of Life Sciences, Hebei University, Baoding, 071002, Hebei, China
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, 352 Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA.
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28
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Cooption of an appendage-patterning gene cassette in the head segmentation of arachnids. Proc Natl Acad Sci U S A 2018; 115:E3491-E3500. [PMID: 29581309 DOI: 10.1073/pnas.1720193115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The jointed appendages of arthropods have facilitated the spectacular diversity and success of this phylum. Key to the regulation of appendage outgrowth is the Krüppel-like factor (KLF)/specificity protein (Sp) family of zinc finger transcription factors. In the fruit fly, Drosophila melanogaster, the Sp6-9 homolog is activated by Wnt-1/wingless (wg) and establishes ventral appendage (leg) fate. Subsequently, Sp6-9 maintains expression of the axial patterning gene Distal-less (Dll), which promotes limb outgrowth. Intriguingly, in spiders, Dll has been reported to have a derived role as a segmentation gap gene, but the evolutionary origin and regulation of this function are not understood because functional investigations of the appendage-patterning regulatory network are restricted to insects. We tested the evolutionary conservation of the ancestral appendage-patterning network of arthropods with a functional approach in the spider. RNAi-mediated knockdown of the spider Sp6-9 ortholog resulted in diminution or loss of Dll expression and truncation of appendages, as well as loss of the two body segments specified by the early Dll function. In reciprocal experiments, Dll is shown not to be required for Sp6-9 expression. Knockdown of arrow (Wnt-1 coreceptor) disrupted segmentation and appendage development but did not affect the early Sp6-9 expression domain. Ectopic appendages generated in the spider "abdomen" by knockdown of the Hox gene Antennapedia-1 (Antp-1) expressed Sp6-9 comparably to wild-type walking legs. Our results support (i) the evolutionary conservation of an appendage-patterning regulatory network that includes canonical Wnt signaling, Sp6-9, and Dll and (ii) the cooption of the Sp6-9/Dll regulatory cassette in arachnid head segmentation.
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29
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Sharma PP. Chelicerates and the Conquest of Land: A View of Arachnid Origins Through an Evo-Devo Spyglass. Integr Comp Biol 2018; 57:510-522. [PMID: 28957520 DOI: 10.1093/icb/icx078] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The internal phylogeny of Chelicerata and the attendant evolutionary scenario of arachnid terrestrialization have a long and contentious history. Previous studies of developmental gene expression data have suggested that respiratory systems of spiders, crustaceans, and insects are all serially homologous structures derived from the epipods (outer appendage rami) of the arthropod ancestor, corresponding to an ancestral gill. A separate body of evidence has suggested that the respiratory systems of arachnids are modified, inverted telopods (inner rami, or legs). Here I review these dissonant homology statements and compare the developmental genetic basis for respiratory system development in insects and arachnids. I show that the respiratory primordia of arachnids are not positionally homologous to those of insects. I further demonstrate that candidate genes critical to tracheal fate specification in Drosophila melanogaster are expressed very differently in arachnid exemplars. Taken together, these data suggest that mechanisms of respiratory system development are not derived from homologous structures or mechanisms in insects and arachnids, and that different terrestrial arthropod lineages have solved the challenge of aerial respiration using different developmental mechanisms.
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Affiliation(s)
- Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 352 Birge Hall, 430 Lincoln Drive, Madison, WI 53706, USA
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30
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31
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Mattos VF, Carvalho LS, Carvalho MA, Schneider MC. Insights into the origin of the high variability of multivalent-meiotic associations in holocentric chromosomes of Tityus (Archaeotityus) scorpions. PLoS One 2018; 13:e0192070. [PMID: 29466400 PMCID: PMC5821447 DOI: 10.1371/journal.pone.0192070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/16/2018] [Indexed: 12/21/2022] Open
Abstract
Scorpions represent an intriguing group of animals characterized by a high incidence of heterozygous chromosomal rearrangements. In this work, we examined six species of Tityus (Archaeotityus) from Brazilian fauna with a particular focus on elucidating the rearrangements responsible for the intraspecific variability of diploid number and the presence of long chromosomal chains in meiosis. To access any interpopulation diversity, we also studied individuals from four species representing distinct localities. Most species demonstrated intraspecific polymorphism in diploid number (2n = 19 and 2n = 20 in T. clathratus, T. mattogrossensis, and T. pusillus, 2n = 16, 2n = 17 and 2n = 18 in T. paraguayensis, and 2n = 16 and 2n = 24 in T. silvestris) and multi-chromosomal associations during meiosis I, which differed even among individuals with the same chromosome number. In some species, the heterozygous rearrangements were not fixed, resulting such as in Tityus clathatrus, in 11 different chromosomal configurations recognized within a same population. Based on meiotic chromosome behaviour, we suggested that independent rearrangements (fusion/fission and reciprocal translocations), occurring in different combinations, originated the multi-chromosomal chains. To evaluate the effects of these chromosome chains on meiotic segregation, we applied the chi-square test in metaphase II cells. The non-significant occurrence of aneuploid nuclei indicated that non-disjunction was negligible in specimens bearing heterozygous rearrangements. Finally, based on our analysis of many chromosome characteristics, e.g., holocentricity, achiasmate meiosis, endopolyploidy, ability to segregate heterosynaptic or unsynapsed chromosomes, (TTAGG)n sequence located in terminal regions of rearranged chromosomes, we suggest that the maintenance of multi-chromosomal associations may be evolutionarily advantageous for these species.
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Affiliation(s)
- Viviane Fagundes Mattos
- Universidade Estadual Paulista “Júlio de Mesquita Filho”, UNESP, Departamento de Biologia, Rio Claro, São Paulo, Brazil
| | | | - Marcos André Carvalho
- Universidade Federal de Mato Grosso, UFMT, Departamento de Biologia e Zoologia, Cuiabá, Mato Grosso, Brazil
| | - Marielle Cristina Schneider
- Universidade Federal de São Paulo, UNIFESP, Departamento de Ecologia e Biologia Evolutiva, Diadema, São Paulo, Brazil
- * E-mail:
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32
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Garb JE, Sharma PP, Ayoub NA. Recent progress and prospects for advancing arachnid genomics. CURRENT OPINION IN INSECT SCIENCE 2018; 25:51-57. [PMID: 29602362 PMCID: PMC6658092 DOI: 10.1016/j.cois.2017.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/10/2017] [Indexed: 06/08/2023]
Abstract
Arachnids exhibit tremendous species richness and adaptations of biomedical, industrial, and agricultural importance. Yet genomic resources for arachnids are limited, with the first few spider and scorpion genomes becoming accessible in the last four years. We review key insights from these genome projects, and recommend additional genomes for sequencing, emphasizing taxa of greatest value to the scientific community. We suggest greater sampling of spiders whose genomes are understudied but hold important protein recipes for silk and venom production. We further recommend arachnid genomes to address significant evolutionary topics, including the phenotypic impact of genome duplications. A barrier to high-quality arachnid genomes are assemblies based solely on short-read data, which may be overcome by long-range sequencing and other emerging methods.
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Affiliation(s)
- Jessica E Garb
- Department of Biological Sciences, 198 Riverside Street, Olsen Hall 414, University of Massachusetts Lowell, Lowell, MA 01854, USA.
| | - Prashant P Sharma
- Department of Integrative Biology, 352 Birge Hall, 430 Lincoln Drive, University of Wisconsin-Madison, WI 53706, USA
| | - Nadia A Ayoub
- Department of Biology, 204 West Washington Street, Howe Hall, Washington and Lee University, Lexington, VA 24450, USA
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33
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017. [PMID: 28756775 DOI: 10.1186/s12915-017-0399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. RESULTS We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. CONCLUSIONS Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
- Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
- Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017; 15:62. [PMID: 28756775 PMCID: PMC5535294 DOI: 10.1186/s12915-017-0399-x] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022] Open
Abstract
Background The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. Results We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Conclusions Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0399-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.,Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark.,Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan. .,Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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35
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Dunlop JA, Lamsdell JC. Segmentation and tagmosis in Chelicerata. ARTHROPOD STRUCTURE & DEVELOPMENT 2017; 46:395-418. [PMID: 27240897 DOI: 10.1016/j.asd.2016.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 05/16/2023]
Abstract
Patterns of segmentation and tagmosis are reviewed for Chelicerata. Depending on the outgroup, chelicerate origins are either among taxa with an anterior tagma of six somites, or taxa in which the appendages of somite I became increasingly raptorial. All Chelicerata have appendage I as a chelate or clasp-knife chelicera. The basic trend has obviously been to consolidate food-gathering and walking limbs as a prosoma and respiratory appendages on the opisthosoma. However, the boundary of the prosoma is debatable in that some taxa have functionally incorporated somite VII and/or its appendages into the prosoma. Euchelicerata can be defined on having plate-like opisthosomal appendages, further modified within Arachnida. Total somite counts for Chelicerata range from a maximum of nineteen in groups like Scorpiones and the extinct Eurypterida down to seven in modern Pycnogonida. Mites may also show reduced somite counts, but reconstructing segmentation in these animals remains challenging. Several innovations relating to tagmosis or the appendages borne on particular somites are summarised here as putative apomorphies of individual higher taxa. We also present our observations within the concept of pseudotagma, whereby the true tagmata - the prosoma and opisthosoma - can be defined on a fundamental change in the limb series while pseudotagmata, such as the cephalosoma/proterosoma, are expressed as divisions in sclerites covering the body without an accompanying change in the appendages.
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Affiliation(s)
- Jason A Dunlop
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstrasse 43, D-10115 Berlin, Germany.
| | - James C Lamsdell
- American Museum of Natural History, Division of Paleontology, Central Park West at 79th St, New York, NY 10024, USA.
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36
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Sharma PP, Oberski JT, Santiago MA, Kriebel R, Lipps SM, Buenavente PAC, Diesmos AC, Janda M, Boyer SL, Clouse RM, Wheeler WC. There is no evidence that Podoctidae carry eggs of their own species: Reply to Machado and Wolff (2017). Mol Phylogenet Evol 2017; 129:349-353. [PMID: 28433248 DOI: 10.1016/j.ympev.2017.03.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/28/2017] [Indexed: 11/25/2022]
Abstract
In our recent publication (Sharma et al., 2017), we tested the hypothesis that eggs attached to the legs of male Podoctidae (Opiliones, Laniatores) constituted a case of paternal care, using molecular sequence data in tandem with multiple sequence alignments to test the prediction that sequences of the eggs and the adults that carried them would indicate conspecific identity. We discovered that the sequences of the eggs belonged to spiders, and thus rejected the paternal care hypothesis for these species. Machado and Wolff (2017) recently critiqued our work, which they regarded as a non-critical interpretation and over-reliance on molecular sequence data, and defended the traditional argument that the eggs attached to podoctids are in fact harvestman eggs. Here we show that additional molecular sequence data also refute the identity of the eggs as conspecific harvestman eggs, using molecular cloning techniques to rule out contamination. We show that individual gene trees consistently and reliably place the egg and adult sequences in disparate parts of the tree topology. Phylogenetic methods consistently place all egg sequences within the order Araneae (spiders). We submit that evidence for the paternal care hypothesis based on behavioral, morphological, and natural history approaches is either absent or insufficient for concluding that the eggs of podoctids are conspecific.
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Affiliation(s)
- Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA.
| | - Jill T Oberski
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Marc A Santiago
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, USA
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Savana M Lipps
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA; Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Perry A C Buenavente
- Zoology Division, National Museum of the Philippines, Padre Burgos Avenue, Ermita 1000, Manila, Philippines
| | - Arvin C Diesmos
- Zoology Division, National Museum of the Philippines, Padre Burgos Avenue, Ermita 1000, Manila, Philippines
| | - Milan Janda
- Laboratorio Nacional de Análisis y Síntesis Ecológica, ENES, UNAM, Antigua Carretera a Pátzcuaro, 8701 Morelia, Mexico; Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic
| | - Sarah L Boyer
- Biology Department, Macalester College, 1600 Grand Avenue, St. Paul, MN 55105, USA
| | - Ronald M Clouse
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, USA
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, USA
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37
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Leite DJ, Ninova M, Hilbrant M, Arif S, Griffiths-Jones S, Ronshaugen M, McGregor AP. Pervasive microRNA Duplication in Chelicerates: Insights from the Embryonic microRNA Repertoire of the Spider Parasteatoda tepidariorum. Genome Biol Evol 2016; 8:2133-44. [PMID: 27324919 PMCID: PMC4987109 DOI: 10.1093/gbe/evw143] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs are small (∼22 nt) noncoding RNAs that repress translation and therefore regulate the production of proteins from specific target mRNAs. microRNAs have been found to function in diverse aspects of gene regulation within animal development and many other processes. Among invertebrates, both conserved and novel, lineage specific, microRNAs have been extensively studied predominantly in holometabolous insects such as Drosophila melanogaster However little is known about microRNA repertoires in other arthropod lineages such as the chelicerates. To understand the evolution of microRNAs in this poorly sampled subphylum, we characterized the microRNA repertoire expressed during embryogenesis of the common house spider Parasteatoda tepidariorum We identified a total of 148 microRNAs in P. tepidariorum representing 66 families. Approximately half of these microRNA families are conserved in other metazoans, while the remainder are specific to this spider. Of the 35 conserved microRNAs families 15 had at least two copies in the P. tepidariorum genome. A BLAST-based approach revealed a similar pattern of duplication in other spiders and a scorpion, but not among other chelicerates and arthropods, with the exception of a horseshoe crab. Among the duplicated microRNAs we found examples of lineage-specific tandem duplications, and the duplication of entire microRNA clusters in three spiders, a scorpion, and in a horseshoe crab. Furthermore, we found that paralogs of many P. tepidariorum microRNA families exhibit arm switching, which suggests that duplication was often followed by sub- or neofunctionalization. Our work shows that understanding the evolution of microRNAs in the chelicerates has great potential to provide insights into the process of microRNA duplication and divergence and the evolution of animal development.
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Affiliation(s)
- Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | - Maria Ninova
- Faculty of Life Sciences, University of Manchester, United Kingdom
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | - Saad Arif
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | | | | | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
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38
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Sharma PP, Santiago MA, González-Santillán E, Monod L, Wheeler WC. Evidence of duplicated Hox genes in the most recent common ancestor of extant scorpions. Evol Dev 2016; 17:347-55. [PMID: 26492826 DOI: 10.1111/ede.12166] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Scorpions (order Scorpiones) are unusual among arthropods, both for the extreme heteronomy of their bauplan and for the high gene family turnover exhibited in their genomes. These phenomena appear to be correlated, as two scorpion species have been shown to possess nearly twice the number of Hox genes present in most arthropods. Segmentally offset anterior expression boundaries of a subset of Hox paralogs have been shown to correspond to transitions in segmental identities in the scorpion posterior tagmata, suggesting that posterior heteronomy in scorpions may have been achieved by neofunctionalization of Hox paralogs. However, both the first scorpion genome sequenced and the developmental genetic data are based on exemplars of Buthidae, one of 19 families of scorpions. It is therefore not known whether Hox paralogy is limited to Buthidae or widespread among scorpions. We surveyed 24 high throughput transcriptomes and the single whole genome available for scorpions, in order to test the prediction that Hox gene duplications are common to the order. We used gene tree parsimony to infer whether the paralogy was consistent with a duplication event in the scorpion common ancestor. Here we show that duplicated Hox genes in non-buthid scorpions occur in six of the ten Hox classes. Gene tree topologies and parsimony-based reconciliation of the gene trees are consistent with a duplication event in the most recent common ancestor of scorpions. These results suggest that a Hox paralogy, and by extension the model of posterior patterning established in a buthid, can be extended to non-Buthidae scorpions.
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Affiliation(s)
- Prashant P Sharma
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA.,Department of Zoology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Marc A Santiago
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Edmundo González-Santillán
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigaciones y de Estudios Avanzados del Instituto Politecnico Nacional, and Laboratorio de Aracnología, Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacán, C.P. 04510, México D.F., México
| | - Lionel Monod
- Département des Arthropodes et d'Entomologie I, Muséum d'histoire naturelle de la Ville de Genève, Route de Malagnou 1, CH-1208 Genève, Suisse
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
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Pace RM, Grbić M, Nagy LM. Composition and genomic organization of arthropod Hox clusters. EvoDevo 2016; 7:11. [PMID: 27168931 PMCID: PMC4862073 DOI: 10.1186/s13227-016-0048-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/20/2016] [Indexed: 12/18/2022] Open
Abstract
Background The ancestral arthropod is believed to have had a clustered arrangement of ten Hox genes. Within arthropods, Hox gene mutations result in transformation of segment identities. Despite the fact that variation in segment number/character was common in the diversification of arthropods, few examples of Hox gene gains/losses have been correlated with morphological evolution. Furthermore, a full appreciation of the variation in the genomic arrangement of Hox genes in extant arthropods has not been recognized, as genome sequences from each major arthropod clade have not been reported until recently. Initial genomic analysis of the chelicerate Tetranychusurticae suggested that loss of Hox genes and Hox gene clustering might be more common than previously assumed. To further characterize the genomic evolution of arthropod Hox genes, we compared the genomic arrangement and general characteristics of Hox genes from representative taxa from each arthropod subphylum. Results In agreement with others, we find arthropods generally contain ten Hox genes arranged in a common orientation in the genome, with an increasing number of sampled species missing either Hox3 or abdominal-A orthologs. The genomic clustering of Hox genes in species we surveyed varies significantly, ranging from 0.3 to 13.6 Mb. In all species sampled, arthropod Hox genes are dispersed in the genome relative to the vertebrate Mus musculus. Differences in Hox cluster size arise from variation in the number of intervening genes, intergenic spacing, and the size of introns and UTRs. In the arthropods surveyed, Hox gene duplications are rare and four microRNAs are, in general, conserved in similar genomic positions relative to the Hox genes. Conclusions The tightly clustered Hox complexes found in the vertebrates are not evident within arthropods, and differential patterns of Hox gene dispersion are found throughout the arthropods. The comparative genomic data continue to support an ancestral arthropod Hox cluster of ten genes with a shared orientation, with four Hox gene-associated miRNAs, although the degree of dispersion between genes in an ancestral cluster remains uncertain. Hox3 and abdominal-A orthologs have been lost in multiple, independent lineages, and current data support a model in which inversions of the Abdominal-B locus that result in the loss of abdominal-A correlate with reduced trunk segmentation. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0048-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryan M Pace
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA ; Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Miodrag Grbić
- Department of Biology, University of Western Ontario, London, ON N6A 5B7 Canada ; Universidad de la Rioja, 26006 Logroño, Spain
| | - Lisa M Nagy
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
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40
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Sharma PP, Tarazona OA, Lopez DH, Schwager EE, Cohn MJ, Wheeler WC, Extavour CG. A conserved genetic mechanism specifies deutocerebral appendage identity in insects and arachnids. Proc Biol Sci 2016; 282:20150698. [PMID: 25948691 DOI: 10.1098/rspb.2015.0698] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The segmental architecture of the arthropod head is one of the most controversial topics in the evolutionary developmental biology of arthropods. The deutocerebral (second) segment of the head is putatively homologous across Arthropoda, as inferred from the segmental distribution of the tripartite brain and the absence of Hox gene expression of this anterior-most, appendage-bearing segment. While this homology statement implies a putative common mechanism for differentiation of deutocerebral appendages across arthropods, experimental data for deutocerebral appendage fate specification are limited to winged insects. Mandibulates (hexapods, crustaceans and myriapods) bear a characteristic pair of antennae on the deutocerebral segment, whereas chelicerates (e.g. spiders, scorpions, harvestmen) bear the eponymous chelicerae. In such hexapods as the fruit fly, Drosophila melanogaster, and the cricket, Gryllus bimaculatus, cephalic appendages are differentiated from the thoracic appendages (legs) by the activity of the appendage patterning gene homothorax (hth). Here we show that embryonic RNA interference against hth in the harvestman Phalangium opilio results in homeonotic chelicera-to-leg transformations, and also in some cases pedipalp-to-leg transformations. In more strongly affected embryos, adjacent appendages undergo fusion and/or truncation, and legs display proximal defects, suggesting conservation of additional functions of hth in patterning the antero-posterior and proximo-distal appendage axes. Expression signal of anterior Hox genes labial, proboscipedia and Deformed is diminished, but not absent, in hth RNAi embryos, consistent with results previously obtained with the insect G. bimaculatus. Our results substantiate a deep homology across arthropods of the mechanism whereby cephalic appendages are differentiated from locomotory appendages.
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Affiliation(s)
- Prashant P Sharma
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Oscar A Tarazona
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Davys H Lopez
- Department of Biology, University of Florida, Gainesville, FL 32611, USA Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Martin J Cohn
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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41
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Kenny NJ, Chan KW, Nong W, Qu Z, Maeso I, Yip HY, Chan TF, Kwan HS, Holland PWH, Chu KH, Hui JHL. Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs. Heredity (Edinb) 2016; 116:190-9. [PMID: 26419336 PMCID: PMC4806888 DOI: 10.1038/hdy.2015.89] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 08/17/2015] [Accepted: 08/18/2015] [Indexed: 01/03/2023] Open
Abstract
Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs-Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.
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Affiliation(s)
- N J Kenny
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - K W Chan
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - W Nong
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - Z Qu
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - I Maeso
- Centro Andaluz de Biología del
Desarrollo (CABD), Consejo Superior de Investigaciones
Científicas/Universidad Pablo de Olavide, Sevilla,
Spain
| | - H Y Yip
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - T F Chan
- School of Life Sciences, Center of
Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - H S Kwan
- School of Life Sciences, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - P W H Holland
- Department of Zoology, University of
Oxford, Oxford, UK
| | - K H Chu
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, The Chinese University of Hong Kong,
Shatin, Hong Kong
| | - J H L Hui
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
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Santibáñez-López CE, Possani LD. Overview of the Knottin scorpion toxin-like peptides in scorpion venoms: Insights on their classification and evolution. Toxicon 2015; 107:317-26. [PMID: 26187850 DOI: 10.1016/j.toxicon.2015.06.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/21/2015] [Accepted: 06/23/2015] [Indexed: 12/29/2022]
Abstract
Scorpion venoms include several compounds with different pharmacological activities. Within these compounds, toxins affecting ion channels are among the most studied. They are all peptides that have been classified based on their 3D structure, chain size and function. Usually, they show a spatial arrangement characterized by the presence of a cysteine-stabilized alpha beta motif; most of them affect Na(+) and K(+) ion-channels. These features have been revised in several occasions before, but a complete phylogenetic analysis of the disulfide containing peptides is not been done. In the present contribution, two databases (Pfam and InterPro) including more than 800 toxins from different scorpions were analyzed. Pfam database included toxins from several organisms other than scorpions such as insects and plants, while InterPro included only scorpion toxins. Our results suggest that Na(+) toxins have evolved independently from those of K(+) toxins no matter the length of the peptidic chains. These preliminary results suggest that current classification needs a more detailed revision, in order to have better characterized toxin families, so the new peptides obtained from transcriptomic analyses would be properly classified.
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Affiliation(s)
- Carlos E Santibáñez-López
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Apartado Postal 510-3, Cuernavaca Morelos 62210, Mexico.
| | - Lourival D Possani
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Apartado Postal 510-3, Cuernavaca Morelos 62210, Mexico
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43
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Farley RD. Book lung development in the embryo, postembryo and first instar of the cobweb spider, Parasteatoda tepidariorum C. L Koch, 1841 (Araneomorphae, Theridiidae). ARTHROPOD STRUCTURE & DEVELOPMENT 2015; 44:355-377. [PMID: 25936921 DOI: 10.1016/j.asd.2015.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/27/2015] [Accepted: 04/22/2015] [Indexed: 06/04/2023]
Abstract
Light and electron microscopy were used to compare spider book lung development with earlier studies of the development of horseshoe crab book gills and scorpion book lungs. Histological studies at the beginning of the 20th century provided evidence that spider and scorpion book lungs begin with outgrowth of a few primary lamellae (respiratory furrows, saccules) from the posterior surface of opisthosomal limb buds, reminiscent of the formation of book gills in the horseshoe crab. In spider embryos, light micrographs herein also show small primary lamellae formed at the posterior surface of opisthosomal limb buds. Later, more prominent primary lamellae extend into each book lung sinus from the inner wall of the book lung operculum formed from the limb bud. It appears most primary lamellae continue developing and become part of later book lungs, but there is variation in the rate and sequence of development. Electron micrographs show the process of air channel formation from parallel rows of precursor cells: mode I (cord hollowing), release of secretory vesicles into the extracellular space and mode II (cell hollowing), alignment and fusion of intracellular vesicles. Cell death (cavitation) is much less common but occurs in some places. Results herein support the early 20th century hypotheses that 1) book lungs are derived from book gills and 2) book lungs are an early step in the evolution of spider tracheae.
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Affiliation(s)
- Roger D Farley
- Department of Biology, University of California, Riverside, CA 92521, USA.
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44
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Di Z, Yu Y, Wu Y, Hao P, He Y, Zhao H, Li Y, Zhao G, Li X, Li W, Cao Z. Genome-wide analysis of homeobox genes from Mesobuthus martensii reveals Hox gene duplication in scorpions. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 61:25-33. [PMID: 25910680 DOI: 10.1016/j.ibmb.2015.04.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 04/10/2015] [Accepted: 04/12/2015] [Indexed: 06/04/2023]
Abstract
Homeobox genes belong to a large gene group, which encodes the famous DNA-binding homeodomain that plays a key role in development and cellular differentiation during embryogenesis in animals. Here, one hundred forty-nine homeobox genes were identified from the Asian scorpion, Mesobuthus martensii (Chelicerata: Arachnida: Scorpiones: Buthidae) based on our newly assembled genome sequence with approximately 248 × coverage. The identified homeobox genes were categorized into eight classes including 82 families: 67 ANTP class genes, 33 PRD genes, 11 LIM genes, five POU genes, six SINE genes, 14 TALE genes, five CUT genes, two ZF genes and six unclassified genes. Transcriptome data confirmed that more than half of the genes were expressed in adults. The homeobox gene diversity of the eight classes is similar to the previously analyzed Mandibulata arthropods. Interestingly, it is hypothesized that the scorpion M. martensii may have two Hox clusters. The first complete genome-wide analysis of homeobox genes in Chelicerata not only reveals the repertoire of scorpion, arachnid and chelicerate homeobox genes, but also shows some insights into the evolution of arthropod homeobox genes.
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Affiliation(s)
- Zhiyong Di
- College of Life Sciences, Wuhan University, Wuhan, China; College of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yao Yu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yingliang Wu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Pei Hao
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yawen He
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Huabin Zhao
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yixue Li
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xuan Li
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Wenxin Li
- College of Life Sciences, Wuhan University, Wuhan, China.
| | - Zhijian Cao
- College of Life Sciences, Wuhan University, Wuhan, China.
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45
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Sharma PP, Fernández R, Esposito LA, González-Santillán E, Monod L. Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal. Proc Biol Sci 2015; 282:20142953. [PMID: 25716788 PMCID: PMC4375871 DOI: 10.1098/rspb.2014.2953] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/26/2015] [Indexed: 01/22/2023] Open
Abstract
Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology. We applied a phylogenomic assessment to resolve scorpion phylogeny, for the first time, to our knowledge, sampling extensive molecular sequence data from all superfamilies and examining basal relationships with up to 5025 genes. Analyses of supermatrices as well as species tree approaches converged upon a robust basal topology of scorpions that is entirely at odds with traditional systematics and controverts previous understanding of scorpion evolutionary history. All analyses unanimously support a single origin of katoikogenic development, a form of parental investment wherein embryos are nurtured by direct connections to the parent's digestive system. Based on the phylogeny obtained herein, we propose the following systematic emendations: Caraboctonidae is transferred to Chactoidea new superfamilial assignment: ; superfamily Bothriuroidea revalidated: is resurrected and Bothriuridae transferred therein; and Chaerilida and Pseudochactida are synonymized with Buthida new parvordinal synonymies: .
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Affiliation(s)
- Prashant P Sharma
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Rosa Fernández
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Lauren A Esposito
- Essig Museum of Entomology, University of California at Berkeley, 130 Mulford Hall, Berkeley, CA 94720, USA
| | - Edmundo González-Santillán
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigaciones y de Estudios Avanzados del Instituto Politecnico Nacional, and Laboratorio de Aracnología, Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, Coyoacán, C.P. 04510, México DF, México
| | - Lionel Monod
- Département des Arthropodes et d'Entomologie I, Muséum d'Histoire Naturelle de la Ville de Genève, Route de Malagnou 1, Genève 1208, Switzerland
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Abstract
Opiliones are one of the largest arachnid orders, with more than 6,500 species in 50 families. Many of these families have been erected or reorganized in the last few years since the publication of The Biology of Opiliones. Recent years have also seen an explosion in phylogenetic work on Opiliones, as well as in studies using Opiliones as test cases to address biogeographic and evolutionary questions more broadly. Accelerated activity in the study of Opiliones evolution has been facilitated by the discovery of several key fossils, including the oldest known Opiliones fossil, which represents a new, extinct suborder. Study of the group's biology has also benefited from rapid accrual of genomic resources, particularly with respect to transcriptomes and functional genetic tools. The rapid emergence and utility of Phalangium opilio as a model for evolutionary developmental biology of arthropods serve as demonstrative evidence of a new area of study in Opiliones biology, made possible through transcriptomic data.
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Affiliation(s)
- Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138;
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47
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Sharma PP, Kaluziak ST, Pérez-Porro AR, González VL, Hormiga G, Wheeler WC, Giribet G. Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal. Mol Biol Evol 2014; 31:2963-84. [DOI: 10.1093/molbev/msu235] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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