Selection Across the Three-Dimensional Structure of Venom Proteins from North American Scolopendromorph Centipedes.

Gene duplication followed by nucleotide differentiation is one of the simplest mechanisms to develop new functions for genes. However, the evolutionary processes underlying the divergence of multigene families remain controversial. We used multigene families found within the diversity of toxic proteins in centipede venom to test two hypotheses related to venom evolution: the two-speed mode of venom evolution and the rapid accumulation of variation in exposed residues (RAVER) model. The two-speed mode of venom evolution proposes that different types of selection impact ancient and younger venomous lineages with negative selection being the predominant form in ancient lineages and positive selection being the dominant form in younger lineages. The RAVER hypothesis proposes that, instead of different types of selection acting on different ages of venomous lineages, the different types of selection will selectively contribute to amino acid variation based on whether the residue is exposed to the solvent where it can potentially interact directly with toxin targets. This hypothesis parallels the longstanding understanding of protein evolution that suggests that residues found within the structural or active regions of the protein will be under negative or purifying selection, and residues that do not form part of these areas will be more prone to positive selection. To test these two hypotheses, we compared the venom of 26 centipedes from the order Scolopendromorpha from six currently recognized species from across North America using both transcriptomics and proteomics. We first estimated their phylogenetic relationships and uncovered paraphyly among the genus Scolopendra and evidence for cryptic diversity among currently recognized species. Using our phylogeny, we then characterized the diverse venom components from across the identified clades using a combination of transcriptomics and proteomics. We conducted selection-based analyses in the context of predicted three-dimensional properties of the venom proteins and found support for both hypotheses. Consistent with the two-speed hypothesis, we found a prevalence of negative selection across all proteins. Consistent with the RAVER hypothesis, we found evidence of positive selection on solvent-exposed residues, with structural and less-exposed residues showing stronger signal for negative selection. Through the use of phylogenetics, transcriptomics, proteomics, and selection-based analyses, we were able to describe the evolution of venom from an ancient venomous lineage and support principles of protein evolution that directly relate to multigene family evolution.

Two complete mitochondrial genomes in Scolopendra and a comparative analysis of tRNA rearrangements in centipedes.

BACKGROUND: Centipedes are one of the oldest terrestrial arthropods belonging to the sub phylum Myriapoda. With the expansion of our understanding of the application of the two centipedes Scolopendra morsitans and Scolopendra hainanum, belonging to the order Scolopendromorpha, an exhaustive classification was required. Although consensus has been reached on the phylogeny of Chilopoda based on morphological traits, recent analyses based on molecular data exhibited differences in results. METHODS AND RESULTS: The mitochondrial genome sequences of S. morsitans and S. hainanum were obtained by next-generation sequencing. S. morsitans contains 13 PCGs, two rRNAs, 11 tRNAs, and one CR. whereas S. hainanum contains 12 PCGs, of which ATP8 remains unpredicted, two rRNAs, 14 tRNAs, and one CR. An obvious tRNA rearrangement was found in the genus Scolopendra. S. morsitans exhibited a loss of trnW, trnC, trnI, trnK, trnD, trnA, trnN, trnQ, trnF, trnT, trnS, trnL, and trnV, and a repeat of trnR and trnL. S. hainanum exhibited a loss of trnQ, trnC, trnW, trnI, trnD, trnQ, trnP, and trnV. Phylogenetic analyses of centipedes based on 12 PCGs supported the sister relationship between the orders Geophilomorpha and Lithobiomorpha and a close relationship between Scolopendra dehaani and S. hainanum. CONCLUSIONS: The new mitogenomes determined in this study provide new genomic resources for gene rearrangements and contribute to the understanding of the evolution of gene rearrangement in Chilopoda.

Inventory and DNA-barcode library of ground-dwelling predatory arthropods from Krokar virgin forest, Slovenia.

Background: At a time of immense human pressure on nature and the resulting global environmental changes, the inventory of biota - especially of undisturbed natural areas - is of unprecedented value as it provides a baseline for future research. Krokar, an example of such an undisturbed area, is the largest virgin forest remnant in Slovenia. It is located in the Dinaric Alps, which are believed to harbour the most diverse fauna of soil invertebrates in Europe. Nevertheless, the soil fauna of the Krokar virgin forest has not been thoroughly studied. Moreover, modern taxonomic approaches often rely on genetic information (e.g. DNA-barcodes), while extensive reference libraries from the Dinaric area are lacking. Our work, therefore, focused on addressing this lack of faunistic and genetic data from the Dinaric area. New information: A total of 2336 specimens belonging to 100 taxa (45 spiders, 30 centipedes, 25 ground-dwelling beetles) were collected and deposited to GBIF. DNA-barcodes of 124 specimens belonging to 73 species were successfully obtained and deposited in GenBank and BOLD databases.

An overview of the extant genera and subgenera of the order Scolopendromorpha (Chilopoda): a new identification key and updated diagnoses.

The extant genera and subgenera of the order Scolopendromorpha are critically reviewed and provided with updated diagnoses and a new identification key; the most recent revisions of scolopendromorph genera are concisely summarised. Rhoda Meinert, 1886 and Cryptops (Chromatanops) Verhoeff, 1906 are suggested to be a junior synonyms of Scolopendropsis Brandt, 1841 and Cryptops (Cryptops) Leach, 1814, respectively. The subgeneric status is formally fixed for Cryptops (Paracryptops) Pocock, 1891 and Cormocephalus (Campylostigmus) Ribaut, 1923; the taxonomic status of the former genus Kanparka Waldock Edgecombe, 2012 is discussed. As a result of synonymies, the number of scolopendromorph genera and subgenera is currently 37. The formal status of the former tribes Scolopendrini Leach, 1814, Asanadini Verhoeff, 1907 and Arrhabdotini Attems, 1930 is briefly discussed; the presence of the sexual dimorphism among the taxa of generic level is overviewed.

A synopsis of centipedes in Brazilian caves: hidden species diversity that needs conservation (Myriapoda, Chilopoda).

This study revises centipede fauna found in Brazilian caves, focusing on troglomorphic taxa and emphasizing conservation status. We present 563 centipede specimens from 274 caves across eleven Brazilian states. Of these, 22 records were derived from existing literature and 252 are newly collected. Specimens represent four orders, ten families, 18 genera, and 47 morphospecies. Together, the cave records represent 21 % of Brazil's centipede fauna. Scolopendromorpha was the most representative order (41 %), followed by Geophilomorpha (26 %), Scutigeromorpha (23 %), and Lithobiomorpha (10 %). Six species were found only in caves, with four considered troglobitic. The distribution of Cryptops iporangensis, the first Brazilian troglobitic centipede species to be discovered, was expanded to other three caves. Cryptops spelaeoraptor and Cryptops iporangensis are two troglobitic species considered Vulnerable and Endangered, respectively, according to the IUCN Red List. Main threats to Brazilian caves are mining, hydroelectric projects, water pollution, and unregulated tourism.

On the function of the ultimate legs of some Scolopendridae (Chilopoda, Scolopendromorpha).

The function of the variously shaped ultimate legs of Scolopendridae is briefly reviewed. Their function in Scolopendraheros Girard, 1853, Scolopendrasubspinipes Leach, 1815, Scolopendramorsitans (Linnaeus, 1758), Scolopendragalapagoensis Bollman, 1889, Scolopendrahainanum Kronmüller, 2012, Scolopendraspinosissima Kraepelin, 1903 Cormocephalusaurantiipes (Newport, 1844) and Ethmostigmustrigonopodus (Leach, 1817), in which they are least specialised has been investigated. Specimens were tapped with forceps on different parts of the trunk to simulate the attack of a predator. When tapped on the first third of the trunk (near the head), the centipedes attacked the forceps with their forcipules. When tapped on the last third or the ultimate legs, they adopted a warning position, raising the ultimate legs to display the ventral and medial prefemoral spines as well as the spined coxopleural processes. In some cases the centipedes attacked the forceps with the claws of the ultimate legs by chopping down on them after lifting the legs high into the warning position. When tapped in the mid part of the trunk, the centipedes curled sideways to reach the forceps with their forcipules and ultimate legs simultaneously. Scolopendragalapagoensis not only lifted the ultimate legs into the warning position but also the last 3-4 pairs of locomotory legs, presenting their distodorsal prefemoral spines. This resembles the warning posture of some spiders. In addition to their function in warning behaviour, defensive stabbing, ritualised meeting reactions and during courtship behaviour, the ultimate legs may in addition act as hooks and perhaps be involved in species recognition. No evidence was found that the ultimate legs are used to catch prey, nor of prey or predators being held between the prefemora.

Variation in venom yield and protein concentration of the centipedes Scolopendra polymorpha and Scolopendra subspinipes.

Venom generally comprises a complex mixture of compounds representing a non-trivial metabolic expense. Accordingly, natural selection should fine-tune the amount of venom carried within an animal's venom gland(s). The venom supply of scolopendromorph centipedes likely influences their venom use and has implications for the severity of human envenomations, yet we understand very little about their venom yields and the factors influencing them. We investigated how size, specifically body length, influenced volume yield and protein concentration of electrically extracted venom in Scolopendra polymorpha and Scolopendra subspinipes. We also examined additional potential influences on yield in S. polymorpha, including relative forcipule size, relative mass, geographic origin (Arizona vs. California), sex, time in captivity, and milking history. Volume yield was linearly related to body length, and S. subspinipes yielded a larger length-specific volume than S. polymorpha. Body length and protein concentration were uncorrelated. When considering multiple influences on volume yield in S. polymorpha, the most important factor was body length, but yield was also positively associated with relative forcipule length and relative body mass. S. polymorpha from California yielded a greater volume of venom with a higher protein concentration than conspecifics from Arizona, all else being equal. Previously milked animals yielded less venom with a lower protein concentration. For both species, approximately two-thirds of extractable venom was expressed in the first two pulses, with remaining pulses yielding declining amounts, but venom protein concentration did not vary across pulses. Further study is necessary to ascertain the ecological significance of the factors influencing venom yield and how availability may influence venom use.

The complete mitochondrial genome of Scolopocryptops sp. (Chilopoda: Scolopendromorpha: Scolopocryptopidae).

The first complete mitogenome sequence of Scolopendromorpha is reported herein. The mitochondrial genome of Scolopocryptops sp. (Scolopendromorpha: Scolopocryptopidae) is a circular molecule of 15,119 bp in length. The orientation and gene order of the Scolopocryptops mitogenome are identical to that of Limulus polyphemus, except that the position of trnL1 and trnL2 is interchanged. TrnS1 (AGN) lacks the dihydrouridine arm.