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Prashant P Sharma - One of the best experts on this subject based on the ideXlab platform.
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systemic paralogy and function of retinal determination network homologs in Arachnids
BMC Genomics, 2020Co-Authors: Guilherme Gainett, Jesus A Ballesteros, Charlotte R Kanzler, Jakob T Zehms, John M Zern, Shlomi Aharon, Efrat Gavishregev, Prashant P SharmaAbstract: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. 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. 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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how spiders make their eyes systemic paralogy and function of retinal determination network homologs in Arachnids
bioRxiv, 2020Co-Authors: Guilherme Gainett, Jesus A Ballesteros, Charlotte R Kanzler, Jakob T Zehms, John M Zern, Shlomi Aharon, Efrat Gavishregev, Prashant P SharmaAbstract: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, paralogy of Retinal Determination Gene Network (RDGN) homologs in spiders has convoluted functional inferences extrapolated from single-copy homologs in pancrustacean models. Here, we investigated a sister species pair of Israeli cave whip spiders (Arachnopulmonata, Amblypygi, Charinus) of which one species has reduced eyes. We generated the first embryonic transcriptomes for Amblypygi, and discovered that several RDGN homologs exhibit duplications. We show that paralogy 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 in a spider, 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. Our results support the conservation of at least one RDGN component across Arthropoda and establish a framework for investigating the role of gene duplications in Arachnid eye diversity.
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systemic paralogy and function of retinal determination network homologs in Arachnids
bioRxiv, 2020Co-Authors: Guilherme Gainett, Jesus A Ballesteros, Charlotte R Kanzler, Jakob T Zehms, John M Zern, Shlomi Aharon, Efrat Gavishregev, Prashant P SharmaAbstract: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, paralogy of Retinal Determination Gene Network (RDGN) homologs in spiders has convoluted functional inferences extrapolated from single-copy homologs in pancrustacean models. Here, we investigated a sister species pair of Israeli cave whip spiders (Arachnopulmonata, Amblypygi, Charinus) of which one species has reduced eyes. We generated the first embryonic transcriptomes for Amblypygi, and discovered that several RDGN homologs exhibit duplications. We show that paralogy 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 in a spider, 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. Our results support the conservation of at least one RDGN component across Arthropoda and establish a framework for investigating the role of gene duplications in Arachnid eye diversity.
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a critical appraisal of the placement of xiphosura chelicerata with account of known sources of phylogenetic error
Systematic Biology, 2019Co-Authors: Jesus A Ballesteros, Prashant P SharmaAbstract:Horseshoe 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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Homeobox gene duplication and divergence in Arachnids.
Molecular Biology and Evolution, 2018Co-Authors: Daniel J. Leite, Luis Baudouin-gonzalez, Sawa Iwasaki-yokozawa, Natascha Turetzek, Nikola-michael Prpic, Yasuko Akiyama, Jesus Lozano-fernandez, Prashant P SharmaAbstract:: 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 characterised 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 non-arachnopumonate Arachnids (Phalangium opilio, Neobisium carcinoides, Hesperochernes sp. and Ixodes scapularis). To assess divergence in the roles of homeobox ohnologs, we analysed 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 subfunctionlisation and neofunctionalisation 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 subfunctionlisation and neofunctionalisation, and paralleling the outcome of WGD in vertebrates.
Jason A. Dunlop - One of the best experts on this subject based on the ideXlab platform.
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Arachnids in Bitterfeld amber: A unique fauna of fossils from the heart of Europe or simply old friends?
Pensoft Publishers, 2018Co-Authors: Jason A. Dunlop, Ulrich Kotthoff, Jörg U. Hammel, Jennifer Ahrens, Danilo HarmsAbstract:Bitterfeld amber, sometimes referred to as Saxon or Saxonian amber, is a potentially significant but poorly known source of arthropod data for the Palaeogene of northern Europe. An important aspect is a long-standing controversy about the age of this amber: namely whether it is equivalent to, and perhaps merely a southerly extension of, the better-known Baltic amber, or whether it is a unique and geological younger deposit sampling a different fauna. Here, we briefly review the Bitterfeld Arachnids with particular emphasis on how these data could be used to elucidate the age of this deposit. Five Arachnid orders have been recorded from Bitterfeld amber: spiders (Araneae), acariform mites (Acariformes), parasitiform mites (Parasitiformes), harvestmen (Opiliones) and pseudoscorpions (Pseudoscorpiones). This is a lower diversity than Baltic amber, where scorpions (Scorpiones) and camel spiders (Solifugae) have also been recorded. Spiders are the most comprehensively studied group, with more than 75 described species. Other groups such as pseudoscorpions and mites appear to be very diverse, but are virtually undescribed. Morphological overlap is apparent in the Arachnid fauna and 40 species are currently shared between Baltic and Bitterfeld amber whilst 50 species are unique to the Bitterfeld deposit. At the family level overlap is even higher, but in all groups Baltic amber appears more diverse than Bitterfeld. This overlap may be interpreted as evidence for temporal conspecifity of the Baltic and Bitterfeld ambers, albeit with the Bitterfeld and Baltic ambers possibly representing independent localities within a larger Eocene European amber area which also included the Rovno amber from the Ukraine. However, caution should be exercised because the taxonomic foundation for such assumptions is far from comprehensive, most of the material remains to be studied in detail using modern techniques of morphological reconstruction. There are further issues with date estimates because some Arachnid groups show extraordinary morphological stasis over time, even at species level, which may bias the analyses available. Here, we review the available knowledge on Bitterfeld Arachnids and discuss how a detailed assessment of this fauna, and other arthropod taxa, could be generated. Several natural history museums – including Hamburg and Berlin – as well as private collectors host major assemblages of Bitterfeld fossils which may help to clarify the debate about the age and provenance of the material, and the extent to which (morpho)-species were maintained both over geographical distances and potentially geological time
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The phylogeny of fossil whip spiders
'Springer Science and Business Media LLC', 2017Co-Authors: Russell J Garwood, Jason A. Dunlop, Brian J. Knecht, Thomas A. HegnaAbstract:Abstract Background Arachnids are a highly successful group of land-dwelling arthropods. They are major contributors to modern terrestrial ecosystems, and have a deep evolutionary history. Whip spiders (Arachnida, Amblypygi), are one of the smaller Arachnid orders with ca. 190 living species. Here we restudy one of the oldest fossil representatives of the group, Graeophonus anglicus Pocock, 1911 from the Late Carboniferous (Duckmantian, ca. 315 Ma) British Middle Coal Measures of the West Midlands, UK. Using X-ray microtomography, our principal aim was to resolve details of the limbs and mouthparts which would allow us to test whether this fossil belongs in the extant, relict family Paracharontidae; represented today by a single, blind species Paracharon caecus Hansen, 1921. Results Tomography reveals several novel and significant character states for G. anglicus; most notably in the chelicerae, pedipalps and walking legs. These allowed it to be scored into a phylogenetic analysis together with the recently described Paracharonopsis cambayensis Engel & Grimaldi, 2014 from the Eocene (ca. 52 Ma) Cambay amber, and Kronocharon prendinii Engel & Grimaldi, 2014 from Cretaceous (ca. 99 Ma) Burmese amber. We recovered relationships of the form ((Graeophonus (Paracharonopsis + Paracharon)) + (Charinus (Stygophrynus (Kronocharon (Charon (Musicodamon + Paraphrynus)))))). This tree largely reflects Peter Weygoldt’s 1996 classification with its basic split into Paleoamblypygi and Euamblypygi lineages; we were able to score several of his characters for the first time in fossils. Our analysis draws into question the monophyly of the family Charontidae. Conclusions Our data suggest that Graeophonus is a crown group amblypygid, and falls within a monophyletic Paleoamblypgi clade, but outside the family Paracharontidae (= Paracharonopsis + Paracharon). Our results also suggest a new placement for the Burmese amber genus Kronocharon, a node further down from its original position. Overall, we offer a broad phylogenetic framework for both the fossil and Recent whip spiders against which future discoveries can be tested
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A fossil whip-scorpion (Arachnida: Thelyphonida) from the Upper Carboniferous of the Carnic Alps (Friuli, NE Italy)
Rivista Italiana Di Paleontologia E Stratigrafia, 2016Co-Authors: Paul A. Selden, Jason A. Dunlop, Luca SimonettoAbstract:A new and well-preserved fossil whip scorpion (Arachnida: Uropygi: Thelyphonida) is described from the Late Carboniferous of the Carnic Alps, Friuli, Italy. It is referred to Parageralinura marsiglioi n. sp. The new specimen is the first Carboniferous Arachnid to be described from mainland Italy and is possibly the youngest Palaeozoic thelyphonid.
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three dimensional reconstruction and the phylogeny of extinct chelicerate orders
PeerJ, 2014Co-Authors: Russell J Garwood, Jason A. DunlopAbstract:Arachnids are an important group of arthropods. They are: diverse and abundant; a major constituent of many terrestrial ecosystems; and possess a deep and extensive fossil record. In recent years a number of exceptionally preserved Arachnid fossils have been investigated using tomography and associated techniques, providing valuable insights into their morphology. Here we use X-ray microtomography to reconstruct members of two extinct Arachnid orders. In the Haptopoda, we demonstrate the presence of ‘clasp-knife’ chelicerae, and our novel redescription of a member of the Phalangiotarbida highlights leg details, but fails to resolve chelicerae in the group due to their small size. As a result of these reconstructions, tomographic studies of three-dimensionally preserved fossils now exist for three of the four extinct orders, and for fossil representatives of several extant ones. Such studies constitute a valuable source of high fidelity data for constructing phylogenies. To illustrate this, here we present a cladistic analysis of the chelicerates to accompany these reconstructions. This is based on a previously published matrix, expanded to include fossil taxa and relevant characters, and allows us to: cladistically place the extinct Arachnid orders; explicitly test some earlier hypotheses from the literature; and demonstrate that the addition of fossils to phylogenetic analyses can have broad implications. Phylogenies based on chelicerate morphology—in contrast to molecular studies—have achieved elements of consensus in recent years. Our work suggests that these results are not robust to the addition of novel characters or fossil taxa. Hypotheses surrounding chelicerate phylogeny remain in a state of flux.
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a trigonotarbid Arachnid from the pennsylvanian astrasado formation of the kinney brick quarry new mexico
Paleontological Contributions, 2014Co-Authors: Jason A. Dunlop, Paul A. Selden, Yinan Wang, Paula KrautzAbstract:Abstract. A new eophrynid trigonotarbid (Arachnida: Trigonotarbida: Eophrynidae) from the Pennsylvanian (Kasimovian) Astrasado Formation of the Kinney Brick Quarry, New Mexico is described. This fossil — the first Arachnid to be recorded from the Astrasado Formation — is preserved primarily as a dorsal opisthosoma. Pleophrynus hawesi sp. nov. diagnostically preserves evidence for three pairs of posterior opisthosomal spines rather than the two usually seen in other eophrynids. A comparison of opisthosomal tuberculation patterns among the best known eophrynid species is included. At ca. 304.0–306.5 Ma, our new taxon represents one of the youngest records of Eophrynidae, while the Kinney Brick Quarry is only the twelfth site in North America to yield trigonotarbid Arachnids; compared to more than 60 such localities in Europe.
Paul A. Selden - One of the best experts on this subject based on the ideXlab platform.
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A fossil whip-scorpion (Arachnida: Thelyphonida) from the Upper Carboniferous of the Carnic Alps (Friuli, NE Italy)
Rivista Italiana Di Paleontologia E Stratigrafia, 2016Co-Authors: Paul A. Selden, Jason A. Dunlop, Luca SimonettoAbstract:A new and well-preserved fossil whip scorpion (Arachnida: Uropygi: Thelyphonida) is described from the Late Carboniferous of the Carnic Alps, Friuli, Italy. It is referred to Parageralinura marsiglioi n. sp. The new specimen is the first Carboniferous Arachnid to be described from mainland Italy and is possibly the youngest Palaeozoic thelyphonid.
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an unusual euchelicerate linking horseshoe crabs and eurypterids from the lower devonian lochkovian of yunnan china
Zoologica Scripta, 2015Co-Authors: Paul A. Selden, James C. LamsdellAbstract:Two new specimens of the xiphosuran Kasibelinurus yueya Lamsdell, Xue & Selden, 2013 are described, from the same horizon and locality as the type. The new specimens are conspecific with the type, but show ventral morphology, which considerably alters interpretation of the species. It can no longer be referred to Kasibelinurus Pickett, 1993, and a new genus, Houia n. gen., is erected. Houia shows a unique combination of xiphosurid and chasmataspidid/eurypterid characteristics such as lack of opisthosomal pleura and possession of a large, ventral metastomal plate. Phylogenetic analysis of all the major chelicerate orders suggests that Houia branched from the main euchelicerate lineage prior to the divergence of the three constituent clades of the Dekatriata Lamsdell, 2013 (Eurypterida, Arachnida, Chasmataspidida). Together with bunodids and pseudoniscids, Houia provides evidence for basal dekatriatans persisting into the middle Palaeozoic alongside eurypterids and Arachnids and that the morphological diversity of these basal forms was greater than previously thought.
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a trigonotarbid Arachnid from the pennsylvanian astrasado formation of the kinney brick quarry new mexico
Paleontological Contributions, 2014Co-Authors: Jason A. Dunlop, Paul A. Selden, Yinan Wang, Paula KrautzAbstract:Abstract. A new eophrynid trigonotarbid (Arachnida: Trigonotarbida: Eophrynidae) from the Pennsylvanian (Kasimovian) Astrasado Formation of the Kinney Brick Quarry, New Mexico is described. This fossil — the first Arachnid to be recorded from the Astrasado Formation — is preserved primarily as a dorsal opisthosoma. Pleophrynus hawesi sp. nov. diagnostically preserves evidence for three pairs of posterior opisthosomal spines rather than the two usually seen in other eophrynids. A comparison of opisthosomal tuberculation patterns among the best known eophrynid species is included. At ca. 304.0–306.5 Ma, our new taxon represents one of the youngest records of Eophrynidae, while the Kinney Brick Quarry is only the twelfth site in North America to yield trigonotarbid Arachnids; compared to more than 60 such localities in Europe.
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a fossil Arachnid from slovakia the carboniferous trigonotarbid anthracomartus voelkelianus karsch 1882
Arachnology, 2013Co-Authors: Jason A. Dunlop, Paul A. SeldenAbstract:Summary A trigonotarbid Arachnid referable to Anthracomartus voelkelianus Karsch, 1882 is described from the Late Carboniferous (Moscovian) (= Westphalian C) of Jerusalemsberg near Dobsina in eastern Slovakia. This record is significant as both the first fossil Arachnid formally described from Slovakia and, whilst it does not come from a classic Coal Measures locality with a terrestrial palaeoenvironment, the sediments were deposited in a marine–deltaic environment typical for Arachnid fossils. An overview of the distribution of the 17 currently recognized species of Anthracomartidae is presented.
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a trigonotarbid Arachnid from the upper carboniferous of the san giorgio basin sardinia
Rivista Italiana Di Paleontologia E Stratigrafia, 2009Co-Authors: Paul A. Selden, Gian Luigi PillolaAbstract:A trigonotarbid Arachnid from the Upper Carboniferous (Westphalian D) of San Giorgio Basin, Sardinia, is described and referred to Anthracomartus voelkelianus Karsch, 1882, the type genus of the family Anthracomartidae. The occurrence extends the range of this Arachnid order outside of the major Euramerican coal basins and into the western Mediterranean region. This is the first pre-Miocene Arachnid from Italy to be described.
Shahan Derkarabetian - One of the best experts on this subject based on the ideXlab platform.
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phylogenomic analysis and revised classification of atypoid mygalomorph spiders araneae mygalomorphae with notes on Arachnid ultraconserved element loci
PeerJ, 2019Co-Authors: Marshal Hedin, Shahan Derkarabetian, Adan Alfaro, Martin J Ramirez, Jason E BondAbstract:The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa (Mecicobothrium and Hexurella) key to understanding familial monophyly, divergence times, and patterns of entrance web evolution. We show that the conserved regions of the Arachnid UCE probe set target exons, such that it should be possible to combine UCE and transcriptome datasets in Arachnids. We also show that different UCE probes sometimes target the same protein, and under the matching parameters used here show that UCE alignments sometimes include non-orthologs. Using multiple curated phylogenomic matrices we recover a monophyletic Atypoidea, and reveal that the family Mecicobothriidae comprises four separate and divergent lineages. Fossil-calibrated divergence time analyses suggest ancient Triassic (or older) origins for several relictual atypoid lineages, with late Cretaceous/early Tertiary divergences within some genera indicating a high potential for cryptic species diversity. The ancestral entrance web construct for atypoids, and all mygalomorphs, is reconstructed as a funnel-and-sheet web.
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high phylogenetic utility of an ultraconserved element probe set designed for Arachnida
Molecular Ecology Resources, 2017Co-Authors: James Starrett, Shahan Derkarabetian, Marshal Hedin, Robert W Bryson, John E Mccormack, Brant C FairclothAbstract:Arachnida is an ancient, diverse and ecologically important animal group that contains a number of species of interest for medical, agricultural and engineering applications. Despite their importance, many aspects of the Arachnid tree of life remain unresolved, hindering comparative approaches to Arachnid biology. Biologists have made considerable efforts to resolve the Arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic toolkit for Arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the Arachnid tree of life. We used recently developed capture probes designed from conserved regions of available Arachnid genomes to enrich a sample of loci from 32 diverse Arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved Arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales and suggesting that these loci will be useful for species-level differences. This probe set will open the door to phylogenomic and population genomic studies across the Arachnid tree of life, enabling systematics, species delimitation, species discovery and conservation of these diverse arthropods.
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comparative performance of double digest rad sequencing across divergent Arachnid lineages
Molecular Ecology Resources, 2017Co-Authors: Mercedes Burns, James Starrett, Shahan Derkarabetian, Casey H Richart, Allan Cabrero, Marshal HedinAbstract:Next-generation sequencing technologies now allow researchers of non-model systems to perform genome-based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease (RE) selection in double-digest restriction-site-associated DNA sequencing (ddRADseq) by generating reduced representation genome-wide data using four different RE combinations. Our expectation was that RE selections targeting longer, more complex restriction sites would recover fewer loci than RE with shorter, less complex sites. We sequenced a diverse sample of non-model Arachnids, including five congeneric pairs of harvestmen (Opiliones) and four pairs of spiders (Araneae). Sample pairs consisted of either conspecifics or closely related congeneric taxa, and in total 26 sample pair analyses were tested. Sequence demultiplexing, read clustering and variant calling were performed in the pyRAD program. The 6-base pair cutter EcoRI combined with methylated site-specific 4-base pair cutter MspI produced, on average, the greatest numbers of intra-individual loci and shared loci per sample pair. As expected, the number of shared loci recovered for a sample pair covaried with the degree of genetic divergence, estimated with cytochrome oxidase I sequences, although this relationship was non-linear. Our comparative results will prove useful in guiding protocol selection for ddRADseq experiments on many Arachnid taxa where reference genomes, even from closely related species, are unavailable.
Gonzalo Giribet - One of the best experts on this subject based on the ideXlab platform.
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current views on chelicerate phylogeny a tribute to peter weygoldt
Zoologischer Anzeiger, 2018Co-Authors: Gonzalo GiribetAbstract:Abstract Peter Weygoldt pioneered studies of Arachnid phylogeny by providing the first synapomorphy scheme to underpin inter-ordinal relationships. Since this seminal work, Arachnid relationships have been evaluated using morphological characters of extant and fossil taxa as well as multiple generations of molecular sequence data. While nearly all datasets agree on the monophyly of Tetrapulmonata, and modern analyses of molecules and novel morphological and genomic data support Arachnopulmonata (a sister group relationship of Scorpiones to Tetrapulmonata), the relationships of the apulmonate Arachnid orders remain largely unresolved. Three threads may allow us to resolve the recalcitrant phylogeny of Arachnids: the careful evaluation of large amounts of molecular data; novel techniques grounded in comparative morphology and evolutionary developmental biology, which add improved homology statements and explain the transition between character states; and new fossil discoveries, which continue to incorporate relevant novel data to the discussion of the relationships among the Arachnid orders.
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first global molecular phylogeny and biogeographical analysis of two Arachnid orders schizomida and uropygi supports a tropical pangean origin and mid cretaceous diversification
Journal of Biogeography, 2017Co-Authors: Ronald M Clouse, Mark S. Harvey, Gonzalo Giribet, Michael G Branstetter, Perry Archival C Buenavente, Louise Crowley, Jesse E Czekanskimoir, David M General, Daniel JaniesAbstract:Aim We sought to illuminate the history of the Arachnid orders Schizomida and Uropygi, neither of which have previously been subjected to global molecular phylogenetic and biogeographical analyses. Location Specimens used in this study were collected in all major tropical and subtropical areas where they are presently found, including the Americas, Africa, Australia and the Indo-Pacific region. Methods From field-collected specimens, we sequenced two nuclear and two mitochondrial markers, combined these with publicly available data, and conducted multi-gene phylogenetic analyses on 240 Schizomida, 24 Uropygi and 12 other Arachnid outgroups. Schizomid specimens included one specimen from the small family Protoschizomidae; other schizomid specimens were in Hubbardiidae, subfamily Hubbardiinae, which holds 289 of the order's 305 named species. We inferred ancestral areas using the Dispersal-Extinction-Cladogenesis model of range evolution, and we used fossil calibrations to estimate divergence times. Results We recovered monophyletic Schizomida and Uropygi as each other's sister group, forming the clade Thelyphonida, and terminals from the New World were usually positioned as the earliest diverging lineages. The ancestral area for schizomids reconstructed unambiguously to the region comprised of Mexico, Southern California and Florida (the xeric New World subtropics). Optimal trees suggested a single colonization of the Indo-Pacific in both orders, although this did not receive bootstrap support. Molecular dating gave an Upper Carboniferous origin for each order, and a mid-Cretaceous expansion of Schizomida, including the origin and initial diversification of those in the Indo-Pacific. Main conclusions Ancestral area reconstructions, molecular dating and fossil evidence all support an Upper Carboniferous, tropical Pangean origin for Thelyphonida, Schizomida and perhaps Uropygi. Much of this region became unsuitable habitat for these Arachnids during the breakup of Pangea, but they persisted in the area that is now Meso- and South America. From there they then expanded to the Indo-Pacific, where schizomids today display an idiosyncratic combination of microendemism and long-range dispersal.
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unnoticed in the tropics phylogenomic resolution of the poorly known Arachnid order ricinulei Arachnida
Royal Society Open Science, 2015Co-Authors: Rosa Fernandez, Gonzalo GiribetAbstract:Ricinulei are among the most obscure and cryptic Arachnid orders, constituting a micro-diverse group with extreme endemism. The 76 extant species described to date are grouped in three genera: Ricinoides, from tropical Western and Central Africa, and the two Neotropical genera Cryptocellus and Pseudocellus. Until now, a single molecular phylogeny of Ricinulei has been published, recovering the African Ricinoides as the sister group of the American Pseudocellus and providing evidence for the diversification of the order pre-dating the fragmentation of Gondwana. Here, we present, to our knowledge, the first phylogenomic study of this neglected Arachnid order based on data from five transcriptomes obtained from the five major mitochondrial lineages of Ricinulei. Our results, based on up to more than 2000 genes, strongly support a clade containing Pseudocellus and Cryptocellus, constituting the American group of Ricinulei, with the African Ricinoides nesting outside. Our dating of the diversification of the African and American clades using a 76 gene data matrix with 90% gene occupancy indicates that this Arachnid lineage was distributed in the South American, North American and African plates of Gondwana and that its diversification is concordant with a biogeographic scenario (both for pattern and tempo) of Gondwanan vicariance.
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Evolution of the chelicera: a dachshund domain is retained in the deutocerebral appendage of Opiliones (Arthropoda, Chelicerata)
Evolution & development, 2012Co-Authors: Prashant P Sharma, Evelyn E. Schwager, Cassandra G. Extavour, Gonzalo GiribetAbstract:The proximo-distal axis of the arthropod leg is patterned by mutually antagonistic developmental expression domains of the genes extradenticle, homothorax, dachshund, and Distal-less. In the deutocerebral appendages (the antennae) of insects and crustaceans, the expression domain of dachshund is frequently either absent or, if present, is not required to pattern medial segments. By contrast, the dachshund domain is entirely absent in the deutocerebral appendages of spiders, the chelicerae. It is unknown whether absence of dachshund expression in the spider chelicera is associated with the two-segmented morphology of this appendage, or whether all chelicerates lack the dachshund domain in their chelicerae. We investigated gene expression in the harvestman Phalangium opilio, which bears the plesiomorphic three-segmented chelicera observed in "primitive" chelicerate orders. Consistent with patterns reported in spiders, in the harvestman chelicera homothorax, extradenticle, and Distal-less have broadly overlapping developmental domains, in contrast with mutually exclusive domains in the legs and pedipalps. However, unlike in spiders, the harvestman chelicera bears a distinct expression domain of dachshund in the proximal segment, the podomere that is putatively lost in derived Arachnids. These data suggest that a tripartite proximo-distal domain structure is ancestral to all arthropod appendages, including deutocerebral appendages. As a corollary, these data also provide an intriguing putative genetic mechanism for the diversity of Arachnid chelicerae: loss of developmental domains along the proximo-distal axis.
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first molecular phylogeny of the major clades of pseudoscorpiones arthropoda chelicerata
Molecular Phylogenetics and Evolution, 2008Co-Authors: Jerome Murienne, Mark S. Harvey, Gonzalo GiribetAbstract:The phylogenetic relationships of the major lineages of the Arachnid order Pseudoscorpiones are investigated for the first time using molecular sequence data from two nuclear ribosomal genes and one mitochondrial protein-encoding gene. The data were analyzed using a dynamic homology approach with the new program POY v.4 under parsimony as the optimality criterion. The data show monophyly of Pseudoscorpiones as well as many of its superfamilies (Feaelloidea, Chthonioidea, Cheiridioidea and Sternophoroidea), but not for Neobisiodea or Garypoidea. Cheliferoidea was not monophyletic either due to the position of Neochelanops, which grouped with some garypoids. In all the analyses, Feaelloidea constituted the sister group to all other pseudoscorpions; Chthonioidea is the sister group to the remaining families, which constitute the group Iocheirata sensu Harvey—a clade including pseudoscorpions with venom glands within the pedipalpal fingers. This phylogenetic pattern suggests that venom glands evolved just once within this order of Arachnids.