Arachnid Order Opiliones Research Articles

Sequence capture phylogenomics of historical ethanol-preserved museum specimens: Unlocking the rest of the vault.

Natural history collections play a crucial role in biodiversity research, and museum specimens are increasingly being incorporated into modern genetics-based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin-fixed squamates and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol-preserved museum specimens. Alongside sequencing of "fresh" specimens preserved in >95% ethanol and stored at -80°C, we used extraction techniques specifically designed for degraded DNA coupled with sequence capture protocols to sequence UCEs from historical museum specimens preserved in 70%-80% ethanol and stored at room temperature, the standard for such ethanol-preserved museum collections. Across 35 fresh and 15 historical museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from six to 495 loci. We successfully demonstrate the inclusion of historical ethanol-preserved museum specimens in modern sequence capture phylogenomic studies, show a high frequency of variant bases at the species and population levels, and from off-target reads successfully recover multiple loci traditionally sequenced in multilocus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol-preserved museum specimens held in collections worldwide.

When troglomorphism dupes taxonomists: morphology and molecules reveal the first pyramidopid harvestman (Arachnida, Opiliones, Pyramidopidae) from the New World

Cavernicolous species that exhibit a high degree of troglomorphism often provide some of the most intriguing evolutionary riddles. For such taxa, the correct systematic arrangement is difficult to determine and becomes problematic when based solely on highly convergent external morphological characters, leading to exaggerated support of spurious relationships. For the arachnid order Opiliones, examination of male genitalia morphology often aids in determining the family to which a particular taxon belongs. However, many taxa described prior to the 1990s lack detailed descriptions or drawings of this important character and, for highly-derived species, it is may still be necessary to seek support from additional sources of characters (e.g. molecular data) to accurately assess systematic placement. The enigmatic species Stygnomma pecki Goodnight & Goodnight, 1977 from a cave in Belize proved to be especially difficult to place based on morphological characters alone. Thus, using a previously published dataset for laniatorean harvestmen, we carried out a robust phylogenetic analysis aiming to determine the evolutionary relationship of this Neotropical troglomophic species. Informed by the results of the molecular phylogenetic analysis of 88 terminals representing Laniatores, we describe Jarmilana gen. nov. and provide a redescription of the type species Jarmilana pecki (Goodnight & Goodnight, 1977) comb. nov. Morphological evidence, including male genitalia morphology, supports the inclusion of J. pecki in the family Pyramidopidae. This represents the first record for the family Pyramidopidae in the New World, raising the question of whether this represents transoceanic dispersal or a relict of an ancient widespread tropical Gondwanan distribution.

Opiliones are no longer the same--on suprafamilial groups in harvestmen (Arthropoda: Arachnida).

A review of the names used in the arachnid order Opiliones above superfamily level is presented. Many historical branching patterns of Opiliones (for five terminals), of Laniatores (for six terminals), and of Cyphophthalmi (for six terminals) are extrapolated, compared and graphically displayed. For the first time a historical review is made of the circumscriptions of those names and comparisons are drawn to current usage. Critical clades are used as terminals and represented by the oldest valid generic name of each. Comments are made on the variant usage for 25 suprafamilial names from the literature. Cladistic definitions are provided for these names under relevant hypotheses of phylogeny. It is noted that virtually all important suprafamilial names in Opiliones changed concept over time, and the purpose of this project is to clarify the original usage compared to current, and to add historical perspective. Two options are considered for higher-level nomenclature in Opiliones: (1) a circumscriptional option, sticking to the original inclusion of the names; (2) an inertial option, where no name has priority, and follows recent use in the literature. As there is no priority for names not regulated by ICZN, option 2 prevails, because it entails massive momentum. The following new names are introduced as unranked taxa to define clades under different hypotheses of phylogeny: Tricospilata (= Triaenonychidae + Grassatores), Lomaniatores (Laniatores in the restricted sense used by Loman/Pocock), and Eulaniatores (Laniatores excluding the bizarre Synthetonychiidae). Some of the hypotheses implied by these names are conflicting and mutually exclusive, but the state of knowledge of harvestman taxonomy is quickly changing, and no hypothesis that clearly supersedes the others can be detected.

Chemosystematics in the Opiliones (Arachnida): a comment on the evolutionary history of alkylphenols and benzoquinones in the scent gland secretions of Laniatores.

Large prosomal scent glands constitute a major synapomorphic character of the arachnid order Opiliones. These glands produce a variety of chemicals very specific to opilionid taxa of different taxonomic levels, and thus represent a model system to investigate the evolutionary traits in exocrine secretion chemistry across a phylogenetically old group of animals. The chemically best-studied opilionid group is certainly Laniatores, and currently available chemical data allow first hypotheses linking the phylogeny of this group to the evolution of major chemical classes of secretion chemistry. Such hypotheses are essential to decide upon a best-fitting explanation of the distribution of scent-gland secretion compounds across extant laniatorean taxa, and hence represent a key toward a well-founded opilionid chemosystematics.

A Paleozoic Stem Group to Mite Harvestmen Revealed through Integration of Phylogenetics and Development

Successfully placing fossils in phylogenies is integral to understanding the tree of life. Crown-group Paleozoic members of the arachnid order Opiliones are indicative of ancient origins and one of the earliest arthropod terrestrialization events [1, 2]. Opiliones epitomize morphological stasis, and all known fossils have been placed within the four extant suborders [3-5]. Here we report a Carboniferous harvestman species, Hastocularis argusgen. nov., sp. nov., reconstructed with microtomography (microCT). Phylogenetic analysis recovers this species, and the Devonian Eophalangium sheari, as members of an extinct harvestman clade. We establish the suborder Tetrophthalmi subordo nov., which bore four eyes, to accommodate H.argus and E.sheari, the latter previously considered to be a phalangid [6-9]. Furthermore, embryonic gene expression in the extant species Phalangium opilio demonstrates vestiges of lateral eye tubercles. These lateral eyes are lost in all crown-group Phalangida, but are observed in both our fossil and outgroup chelicerate orders. These data independently corroborate the diagnosis of two eye pairs in the fossil and demonstrate retention of eyes of separate evolutionary origins in modern harvestmen [10-12]. The discovery of Tetrophthalmi alters molecular divergence time estimates, supporting Carboniferous rather than Devonian diversification for extant suborders and directly impacting inferences of terrestrialization history and biogeography. Multidisciplinary approaches integrating fossil and neontological data increase confidence in phylogenies and elucidate evolutionary history.

Phylogenomic resolution of paleozoic divergences in harvestmen (Arachnida, Opiliones) via analysis of next-generation transcriptome data.

Next-generation sequencing technologies are rapidly transforming molecular systematic studies of non-model animal taxa. The arachnid order Opiliones (commonly known as “harvestmen”) includes more than 6,400 described species placed into four well-supported lineages (suborders). Fossil plus molecular clock evidence indicates that these lineages were diverging in the late Silurian to mid-Carboniferous, with some fossil harvestmen representing the earliest known land animals. Perhaps because of this ancient divergence, phylogenetic resolution of subordinal interrelationships within Opiliones has been difficult. We present the first phylogenomics analysis for harvestmen, derived from comparative RNA-Seq data for eight species representing all suborders. Over 30 gigabases of original Illumina short-read data were used in de novo assemblies, resulting in 50–80,000 transcripts per taxon. Transcripts were compared to published scorpion and tick genomics data, and a stringent filtering process was used to identify over 350 putatively single-copy, orthologous protein-coding genes shared among taxa. Phylogenetic analyses using various partitioning strategies, data coding schemes, and analytical methods overwhelmingly support the “classical” hypothesis of Opiliones relationships, including the higher-level clades Palpatores and Phalangida. Relaxed molecular clock analyses using multiple alternative fossil calibration strategies corroborate ancient divergences within Opiliones that are possibly deeper than the recorded fossil record indicates. The assembled data matrices, comprising genes that are conserved, highly expressed, and varying in length and phylogenetic informativeness, represent an important resource for future molecular systematic studies of Opiliones and other arachnid groups.

A synopsis of catalogs and checklists of harvestmen (Arachnida, Opiliones)

An annotated synopsis is presented of the publications which offer species checklists and catalogs of the arachnid orderOpiliones. Catalogs and checklists are included if they cover both (1) a suprafamilial group and (2) a country, continentalor zoogeographical region. Standardized information is given on the number of species treated and the taxonomic and geo-graphic scope. A total of 100 catalog works (7 of which are online only) are listed. They record from 4 to 6125 species,and they are classified into 3 categories: (1) manuals, which contain diagnoses and keys, (2) catalogs, which contain no-menclatural acts and synonymic literature headings and (3) checklists, which contain only a species list. Finally, a synopsisof key systematic works for each area in each zoogeographical region is given, and a species count is provided for all zogeographical regions of the world.

An exquisitely preserved harvestman (Arthropoda, Arachnida, Opiliones) from the Middle Jurassic of China

Sclerosomatids constitute the largest family of the arachnid order Opiliones, and one of the two families commonly found in the temperate regions of the northern Hemisphere. Harvestmen have a sparse fossil record in the Mesozoic, with only two species known from the Jurassic, one of them poorly preserved and none with precise phylogenetic placement. Here we report a new fossil, Mesobunus dunlopi sp. nov., from the Middle Jurassic (approx. 165 Mya) of Daohugou, Inner Mongolia, China. The new species is related to another genus of the same formation, but the preservation quality and details of the penis and pedipalps allow us to place them in the extant sclerosomatid subfamilies Gagrellinae or Leiobuninae. The first recognisable fossil in this subfamily highlights morphological stasis over ca. 165 Mya and the finding of this species along with lacustrine insects suggests a life mode similar to that of some modern sclerosomatids, and a possible connection between morphological and ecological stasis.

An old lineage of Cyphophthalmi (Opiliones) discovered on Mindanao highlights the need for biogeographical research in the Philippines

Abstract The arachnid order Opiliones, and the suborder Cyphophthalmi in particular, have recently been used to test biogeographical patterns in Southeast Asia due to their ancient age and extremely low vagility. Here we report the first Cyphophthalmi—two juveniles—known from Mindanao in the southern Philippine Archipelago, and we place them in a molecular phylogeny to test biogeographical hypotheses for their colonization of that island. Five molecular markers were sequenced from one specimen, three from the other, and these sequences were added to a previously completed phylogenetic analysis. The specimens were recovered as members of a clade found almost exclusively on Borneo. Their deep placement within this clade suggests a very old origin and colonization that perhaps involved the mysterious landmass now underlying Mindanao's Zamboanga Peninsula. This species prompts new questions about the abilities of Southeast Asian Cyphophthalmi (Stylocellidae) to disperse and colonize, and it emphasizes how muc...

A multilocus approach to harvestman (Arachnida: Opiliones) phylogeny with emphasis on biogeography and the systematics of Laniatores.

The internal phylogeny of the arachnid order Opiliones is investigated by including molecular data from five molecular markers for ca. 140 species totalling 43 families of Opiliones. The phylogenetic analyses consisted of a direct optimization (DO) approach using POY v. 4 and sophisticated tree search algorithms as well as a static alignment analysed under maximum likelihood. The four Opiliones suborders were well-supported clades, but subordinal relationships did not receive support in the DO analysis, with the exception of the monophyly of Palpatores (=Eupnoi + Dyspnoi). Maximum-likelihood analysis strongly supported the traditional relationship of Phalangida and Palpatores: (Cyphophthalmi ((Eupnoi + Dyspnoi) Laniatores)). Relationships within each suborder are well resolved and largely congruent between direct optimization and maximum-likelihood approaches. Age estimates for the main Opiliones lineages suggest a Carboniferous diversification of Cyphophthalmi, while its sister group, Phalangida, diversified in the Early Devonian. Diversification of all suborders predates the Triassic, and most major lineages predate the Cretaceous. The following taxonomic changes are proposed. Dyspnoi: Hesperonemastoma is transferred to Sabaconidae. Insidiatores: Sclerobunidae stat. nov. is erected as a family for Zuma acuta. © The Willi Hennig Society 2009.

Mitochondrial rRNA secondary structures and genome arrangements distinguish chelicerates: Comparisons with a harvestman (Arachnida: Opiliones: Phalangium opilio)

Arachnids are a highly diverse group of arthropods, and many of the mitochondrial genomes that have been sequenced from arachnids possess unusual features in their inferred gene structures and genome organization. The first complete sequence of a mitochondrial genome from the arachnid order Opiliones (harvestmen) is presented here. Secondary structures of the two mitochondrial ribosomal subunits of Phalangium opilio are inferred and compared to mitochondrial rRNA structures of a hexapod and a chelicerate. The large subunit rRNA of P. opilio is found to have more helices conserved than in other arthropods, while the small subunit rRNA shows a complexity similar to that of other arthropods. These comparisons suggest that a reduction in rRNA complexity occurred in Pancrustacea after the divergence of Pancrustacea and Chelicerata from a common ancestor. The gene arrangement of the mitochondrial genome of P. opilio is compared with the gene order of taxa from all seven other orders of arachnids for which representative mitochondrial genomes have been sequenced. Taxa from five of these seven orders possess gene arrangements identical to that of Limulus polyphemus, and P. opilio is found to have a similar arrangement. However, in P. opilio, some genes near the putative control region are rearranged, with the suite of genes encoding tRNA Gln, the control region, and tRNA Ile located downstream of the two ribosomal RNA genes, and upstream of where they are typically located in chelicerates. The genome encodes only 21 of the typical 22 mitochondrial tRNA genes and lacks the gene for tRNA Leu(CUN). The protein-coding genes in the mitochondrial genome of P. opilio show a significantly decreased use of codons recognized by tRNA Leu(CUN), likely due to selection to utilize the more specific tRNA Leu(UUR) anticodon. The gene arrangement and lack of a tRNA Leu(CUN) gene in P. opilio is most parsimoniously explained by the occurrence of at least two translocation events, one of which probably destroyed the function of the tRNA Leu(CUN) gene. Phylogenetic relationships among the major orders of arachnids are inferred, using all 13 mt protein-coding genes, and gene rearrangements are mapped onto the phylogeny. The phylogenetic analyses are unable to resolve the placement of P. opilio but are generally consistent with an early divergence of members of the Dromopoda (harvestmen, scorpions, and solifuges) from the Micruran arachnids (spiders, whip spiders, vinegaroons, ricinuleids, and mites). However, unlike some morphologically based phylogenetic analyses, the existence of a clade of Dromopoda is not supported. While data on genome arrangement and gene loss do not provide further information to help resolve relationships among the arachnid orders, they distinguish some groups of arachnids, distinguish chelicerates from other arthropods, and further clarify the ancestral gene order of this diverse group of arthropods.

Two new cave-dwelling harvestmen from Western Australia (Arachnida: Opiliones: Assamiidae and "Phalangodidae")

Two new species of laniatorid harvestmen have been collected in the biologically significant caves of the Cape Range Peninsula, Western Australia. Dampetnls isolatus sp. novo (Assamiidae) has reduced eyes but is otherwise not especially adapted for a subterranean life; it has been collected in several Cape Range caves. Glennhuntia glennhunti gen. et sp. novo (Phalangodidae) is a minute, highly evolved troglobite known only from Camerons Cave. Both species are likely rainforest relics. Some notes are provided on the Australian fauna of the harvestman Infraorder Grassatores. Hunt (1991) noted that fewer than 200 species of the arachnid order Opiliones (harvestmen, phalangids) had been described from Australia, a number he estimated to be no more than 20% of the total fauna. Indeed, Hunt himself was the first and last productive resident harvestman specialist in Australia, who had personally described a substantial portion of those species. His untimely demise put an end to a succession of fine papers on the systematics of several Australian taxa, most notably the Triaenonychidae, Neopilionidae and Megalopsalididae. While taking notice of the richness of the Australian fauna of the laniatorid infraorder Grassatores, Hunt published little on them. Four families of the infraorder, Assamiidae, Podoctidae, Zalmoxidae and Phalangodidae have been recorded from Australia. Four zalmoxid species, all in the genus Zalmoxis Sorensen, are known from Queensland, New South Wales, and the Kimberley Plateau of northern Western Australia. Austribal­ onius Roewer, with a single named species, is the only podoctid genus. The Assamiidae of Australia are dealt with in the remarks below under the description of the new species, and likewise the phalangodids under the description of Glennhuntia glennhunti. Specimens are deposited in the Western Australian Museum (WAM), Perth, and I thank Mark Harvey for making them available to me for study. Comments from two anonymous reviewers materially improved the manuscript. Glenn Hunt (1944-1999), whom I knew only through correspondence, had produced a series of outstanding systematic papers on Australian opilionids, working on a fauna that was almost unknown (compared to its potential richness) at the time he began. He recognized the two species described below as new and determined the assamiid as a species of Dampetrus Karsch. I'm honoured to be able to dedicate this brief paper to his memory

Phylogeny of the Arachnid Order Opiliones (Arthropoda) Inferred from a Combined Approach of Complete 18S and Partial 28S Ribosomal DNA Sequences and Morphology

The phylogenetic relationships among the main evolutionary lines of the arachnid order Opiliones were investigated by means of molecular (complete 18S rDNA and the D3 region of the 28S rDNA genes) and morphological data sets. Equally and differentially weighted parsimony analyses of independent and combined data sets provide evidence for the monophyly of the Opiliones. In all the analyses, the internal relationships of the group coincide in the monophyly of the following main groups: Cyphophthalmi, Eupnoi Palpatores, Dyspnoi Palpatores, and Laniatores. The Cyphophthalmi are monophyletic and sister to a clade that includes all the remaining opilionid taxa (=Phalangida). Within the Phalangida the most supported hypothesis suggests that Palpatores are paraphyletic, as follows: (Eupnoi (Dyspnoi+Laniatores)), but the alternative hypothesis (Laniatores (Eupnoi+Dyspnoi)) is more parsimonious in some molecular data analyses. Relationships within the four main clades are also addressed. Evolution of some morphological characters is discussed, and plesiomorphic states of these characters are evaluated using molecular data outgroup polarization. Finally, Martens' hypothesis of opilionid evolution is assessed in relation to our results.

Scanning Electron Microscopy of the Palp Sense Organs of the Harvestman Leiobunum townsendi (Arachnida: Opiliones)

Scanning Electron Microscopy of the Palp Sense Organs of the Harvestman Leiobunum townsendi (Arachnida: Opiliones)