Biology subjects

Sharma, P. P.

Publications and source records attributed to Sharma, P. P..

At least 19 recordsLinked to original sources

bioRxiv2026

Homoplastic evolution of proximal podomere patterning across Arthropoda

The jointed arthropod leg is often credited as a key innovation spurring the evolutionary success of the phylum. Across lineages, each territory of the appendage has served as the substrate for myriad adaptations and structural innovations. While much of the available data has supported a conserved suite of transcription factors responsible for the initiation and patterning of the arthropod appendage, recent works have begun to highlight instances of lineage-specific shifts in expression dynamics, particularly amongst the chelicerates, correlated both with the emergence of novel structures and developmental system drift in the specification of plesiomorphic structures. These works confound efforts to align or homologize the leg segments across arthropod lineages, an effort already challenged by ground plan differences in segment number between the subphyla. An even more unusual architecture of leg segments occurs in sea spiders (Pycnogonida), which alone among Arthropoda are considered by systematists to bear three coxae (proximal segments), in contrast to the single coxa of the remaining arthropods. Here, we examined proximal podomere patterning in the developing appendages of a sea spider and an arachnid. We find that a particular spatial arrangement of Lim1 and SoxNeuro characterizes the developing coxa and trochanter of the harvestman Phalangium opilio (Opiliones) throughout appendage formation, with RNAi depletions of Lim1 yielding deletions of coxa and trochanter. Comparison of expression patterns across taxa shows that Lim1 and SoxNeuro have a similar spatial arrangement in the harvestman and sea spider, but these suggest conflicting interpretations of leg segment homology. We show that this is attributable to homoplastic patterns of evolution in SoxNeuro across Arthropoda. Expanding our surveys of prominent PD axis-patterning transcription factors supports additional instances of homoplasy in the domains of Sp6-9 and Irx2. The pervasiveness of homoplasy in gene expression patterns demands measured skepticism of homology statements and careful comparisons of multiple patterning genes, toward achieving falsifiability in the homology of structures.

developmental biology↗

bioRxiv2026

Genomic expansion in the dark: A repeat-rich genome of a cave-dwelling remipede sheds light on the evolution of the hexapod sister group.

Remipedes are enigmatic blind, venomous crustaceans endemic to anchialine cave ecosystems (aphotic, hypoxic subterranean environments) and occupy a pivotal phylogenomic position within Pancrustacea as the sister group to Hexapoda. A high-quality genome assembly has long proven elusive for this taxon, due to accessibility challenges and the fragility of remipedes when removed from their habitat. Here we present a highly contiguous, chromosome-level genome assembly for the remipede Xibalbanus tulumensis (Xibalbanidae) spanning 8.05 Gb on 30 chromosome-scale scaffolds, placing it among the largest arthropod genomes reported to date. The protein-coding gene repertoire was highly conserved, with over 97% of arthropod orthologs recovered, and microRNA surveys showed a high level of completeness (94%) relative to pancrustacean genomes. Genome expansion appears to be driven primarily by proliferation of intronic and repetitive elements, which comprise ~71% of the genome. Comparative genomic analyses reveal extensive gene family turnover, with relatively few families showing lineage-specific expansions and contractions. Venom-associated gene families included the remipede-specific Xibalbins, while significant expansion and episodic positive selection affected other venom-associated gene families. Comparative analysis of macrosynteny revealed that the remipede genome retains the signature of ancient fusion-with-mixing events that unite Pancrustacea and Allotriocarida, with considerable similarity in the chromosome architecture of remipedes and basally branching insect orders. Our findings provide the first genomic framework for Remipedia and reveal a highly expanded, repeat-rich genome that retains deep phylogenetic signals in its architecture, despite being adapted to a highly unusual environment.

genomics↗

bioRxiv2026

Comparative genomics of the unusual arachnid order Solifugae spotlight the molecular and genetic basis for adaptations to arid habitats

The evolutionary transition to terrestrial life required overcoming several physiological hurdles; however, such challenges were amplified in desert environments. While several xeric-adapted arachnids utilize permanent burrows or "sit-and-wait" foraging strategies as possible energy conservation adaptations in harsh habitats, camel spiders exhibit a counterintuitive, high-energy lifestyle. To investigate the molecular underpinnings distinguishing Solifugae within Chelicerata, we utilized a comparative genomics framework that incorporates a newly sequenced, previously unpublished solifuge genome. We identified lineage-specific expanded orthogroups and evaluated selective pressures acting upon paralogous sequences within our ingroup solifuge species. Additionally, we also focused on fatty acid-associated proteins and heat shock proteins to elucidate how Solifugae may have evolved such anomalous behaviors compared to their arachnid relatives. Our analyses revealed significant signatures of positive selection within key gene families across the solifuge lineage. Notably, paralogs within the cytochrome P450 and biotinidase families showed consistent evidence of selection across all three taxa, suggesting specialized metabolic or detoxification requirements. Furthermore, we identified candidate loci implicated in axonal guidance and lipid metabolism, and a specialized fatty acid enzyme repertoire. While subsequent research is required to determine whether some of the genomic signatures unveiled here are shared across a broader phylogenetic distribution within Solifugae, we establish a critical baseline for future functional validation.

evolutionary biology↗

bioRxiv2026

No silver bullet: Patterns of macrosynteny recapitulate systemic conflicts in the higher-level relationships of the arachnids

Rare genomic changes have long been sought by phylogeneticists for their potential to resolve obdurate nodes in the tree of life. Recently, patterns of macrosynteny have been proffered as a breakthrough for challenging relationships within invertebrates. One taxon that stands to benefit from the application of this approach is Chelicerata (the sister group to the rest of Arthropoda), whose radiation has long defied resolution, despite intensive investigations using morphological characters, molecular sequence data, and a combination thereof. Challenges to the resolution of chelicerate phylogeny include an ancient rapid radiation, the incidence of several fast-evolving lineages prone to long-branch attraction artifacts, and extinction of multiple ordinal level lineages that cannot be sampled for breaking long branches. At present, only a subset of nodes has been stably resolved. To break this impasse, we brought to bear multiple classes of phylogenetically informative rare genomic changes, including the sequencing of the first genomes for Ricinulei and Palpigradi. Here, we show that an ancient, shared whole genome duplication event is restricted to Arachnopulmonata (the most recent common ancestor of spiders and scorpions), disfavoring traditional placements of either Ricinulei or Palpigradi as close relatives of tetrapulmonates. Intriguingly, investigation of fusion-with-mixing events identified equal support for mutually exclusive placements for Acariformes, the least stable of the arachnid orders. Our results suggest that fusion-with-mixing, far from being a silver bullet, likely exhibits the same emergent property as all character systems, in that it is prone to homoplasy and conflicting signal stemming from ancient rapid radiations.

evolutionary biology↗

bioRxiv2026

Pax6 homologs are required for patterning both visual systems of the daddy-longlegs Phalangium opilio

The evolution of visual systems has compelled numerous investigations of developmental processes underlying eye patterning across Bilateria. It is well-established that homologs of the transcription factor Pax6 play a highly conserved role in eye fate specification and are at the top of the retinal determination gene network (RDGN) hierarchy. In insects, the two Pax6 homologs eyeless (ey) and twin of eyeless (toy) are required for the development of the two visual systems broadly found within the phylum (i.e., median and lateral eyes). Curiously, Pax6 homologs do not appear to maintain this function in well-studied chelicerate models, with emphasis on spiders, a lineage of arachnids with great diversity of eye form and acuity. It was recently proposed that the gene Pax2 (shaven; sv) may have subsumed the role of eye fate specification in chelicerates, a hypothesis predicated upon the observation that one of two spider Pax2 copies is strongly expressed in the developing lateral eyes during embryogenesis. However, no functional data are available for any Pax homologs across Chelicerata. We examined the incidence of Pax family genes across Chelicerata, as well as interrogated the expression and function of Pax2 and Pax6 homologs in the daddy-longlegs Phalangium opilio, an arachnid recently discovered to bear a highly plesiomorphic arrangement of visual systems. Here, we show that ey and toy are expressed early in the developing head lobes of P. opilio, whereas sv is not expressed until well after stages when downstream RDGN members (eyes absent and sine oculis) are already activated. Gene silencing of ey, toy, and sv individually had no discernible effect on eye development. By contrast, double knockdown of ey and toy resulted in an array of median eye defects, spanning loss of some cells of the eye to total loss of the median eyes. Gene expression assays also showed that depletion of the two Pax6 copies resulted in failure of the vestigial median and vestigial lateral eyes. These data are consistent with a conserved role for Pax6 homologs in patterning both visual systems and all three eye pairs in the daddy-longlegs. Our results comprise the first functional data for Pax6 genes in any chelicerate and suggest that heterochronic shifts in expression, rather than changes in function, underlie the atypical dynamics of Pax genes in derived arachnid groups such as spiders.

developmental biology↗

bioRxiv2025

Developmental system drift in the patterning of the arthropod tarsus

The current understanding of proximodistal axis patterning in arthropod legs is grounded in insect models. The paradigm for appendage evolution in this phylum is that the gene regulatory network responsible for leg subdivision and patterning is broadly conserved. Recent surveys of these genes have suggested that chelicerate exemplars exhibit divergent appendage patterning dynamics, though functional data remain limited. One salient mismatch in expression occurs in homologs of the homeobox gene clawless. In insects, clawless is expressed in the distalmost leg territory, specifying the claw-bearing pretarsus. In the harvestman, Phalangium opilio, clawless occupies a broad tarsal domain early in development, localizing later to the metatarsus-tarsus boundary, suggestive of a tarsal patterning function. Here, we tested the function of harvestman clawless using RNAi. Unlike insects, we show that clawless knockdown results in disrupted tarsal growth and patterning of its proximal segmental boundary, with no effect on the claw. Truncation of the tarsus is associated with defective tarsomere formation. We additionally surveyed clawless homologs in exemplars of chelicerate diversity, which suggests that the tarsal-patterning function for clawless was likely present in the chelicerate common ancestor. These results, alongside available expression data, suggest panarthropod appendage patterning exhibits numerous cases of developmental system drift.

evolutionary biology↗

bioRxiv2024

The genome of a sea spider corroborates a shared Hox cluster motif in arthropods with reduced posterior tagma

BackgroundChelicerate evolution is contentiously debated, with recent studies challenging traditional phylogenetic hypotheses and scenarios of major evolutionary events, like terrestrialization. Sea spiders (Pycnogonida) represent the uncontested marine sister group of all other chelicerates, featuring a - likely plesiomorphic - indirect development mode. Accordingly, pycnogonids hold the potential to provide crucial insight into early chelicerate genome evolution and ancestral principles of chelicerate body patterning. Leveraging this potential, however, has hitherto been hampered by the lack of high-quality genomic resources for pycnogonids. ResultsWe employed long-read sequencing and proximity ligation data to assemble the first near chromosome-level sea spider genome for Pycnogonum litorale, complemented by developmental transcriptomes and a high-fidelity Iso-Seq dataset. The assembly has a size of 471Mb in 57 pseudochromosomes, a repeat content of 61.05%, 15,497 predicted protein-coding genes, and is highly complete (95.8% BUSCO Arthropoda score, 95.7% of conserved microRNA families present). We identified a single, intact Hox gene cluster that lacks abdominal-A/Hox9, suggesting the loss of this Hox gene. ConclusionsOur high-quality genomic and transcriptomic resources establish P. litorale as a key research organism for modern studies on chelicerate genome evolution, development, and phylogeny. The presence of a single Hox cluster in the P. litorale genome further strengthens the inference that no whole-genome duplication occurred at the base of the chelicerate tree. The lack of abdA suggests that the combination of abdA loss and posterior tagmata reduction is a common theme in arthropod evolution, as it is shared with other, distantly related arthropod taxa with a vestigial opisthosoma/abdomen.

evolutionary biology↗

bioRxiv2024

A chromosome-level genome of the giant vinegaroon Mastigoproctus giganteus exhibits the signature of pre-Silurian whole genome duplication

Within the arachnids, chromosome-level genome assemblies have greatly accelerated the understanding of gene family evolution and developmental genomics in key groups, such as spiders (Araneae), mites and ticks (Acariformes and Parasitiformes). Among other poorly studied arachnid orders that lack genome assemblies altogether are the clade Pedipalpi, which is comprised of three orders that form the sister group of spiders, which diverged over 400 Mya. We close this gap by generating the first chromosome-level assembly from a single specimen of the vinegaroon Mastigoproctus giganteus (Uropygi). We show that this highly complete genome retains plesiomorphic conditions for many gene families that have undergone lineage-specific derivations within the more diverse spiders. Consistent with the phylogenetic position of Uropygi, macrosynteny in the M. giganteus genome substantiates the signature of an ancient whole genome duplication.

genomics↗

bioRxiv2024

A novel expression domain of extradenticle underlies the evolutionary developmental origin of the chelicerate patella

Neofunctionalization of duplicated gene copies is thought to be an important process underlying the origin of evolutionary novelty and provides an elegant mechanism for the origin of new phenotypic traits. One putative case where a new gene copy has been linked to a novel morphological trait is the origin of the arachnid patella, a taxonomically restricted leg segment. In spiders, the origin of this segment has been linked to the origin of the paralog dachshund-2, suggesting that a new gene facilitated the expression of a new trait. However, various arachnid groups that possess patellae do not have a copy of dachshund-2, disfavoring the direct link between gene origin and trait origin. We investigated the developmental genetic basis for patellar patterning in the harvestman Phalangium opilio, which lacks dachshund-2. Here, we show that the harvestman patella is established by a novel expression domain of the transcription factor extradenticle. Leveraging this definition of patellar identity, we surveyed targeted groups across chelicerate phylogeny to assess when this trait evolved. We show that a patellar homolog is present in Pycnogonida (sea spiders) and various arachnid orders, suggesting a single origin of the patella in the ancestor of Chelicerata. A potential loss of the patella is observed in Ixodida. Our results suggest that the modification of an ancient gene, rather than the neofunctionalization of a new gene copy, underlies the origin of the patella. Broadly, this work underscores the value of comparative data and broad taxonomic sampling when testing hypotheses in evolutionary developmental biology.

evolutionary biology↗

bioRxiv2023

Machine learning approaches to assess microendemicity and conservation risk in cave-dwelling arachnofauna

The biota of cave habitats faces heightened conservation risks, due to geographic isolation and high levels of endemism. Molecular datasets, in tandem with ecological surveys, have the potential to delimit precisely the nature of cave endemism and identify conservation priorities for microendemic species. Here, we sequenced ultraconserved elements of Tegenaria within, and at the entrances of, 25 cave sites to test phylogenetic relationships, combined with an unsupervised machine learning approach to delimit species. Our data identified clear species limits, as well as the incidence of previously unidentified, potential cryptic species. We employed the R package canaper and Categorical Analysis of Neo- and Paleo-Endemism (CANAPE) to generate conservation metrics that are informative for future policy, in tandem with conservation assessments for the troglobitic Israeli species of this genus.

evolutionary biology↗

bioRxiv2023

A taxon-restricted duplicate of Iroquois3 is required for patterning the spider waist

The chelicerate body plan is distinguished from other arthropod groups by its division of segments into two tagmata: the anterior prosoma ("cephalothorax") and the posterior opisthosoma ("abdomen"). Little is understood about the genetic mechanisms that establish the prosomal-opisthosomal (PO) boundary. To discover these mechanisms, we created high-quality genomic resources for the large-bodied spider Aphonopelma hentzi. We sequenced specific territories along the antero-posterior axis of developing embryos and applied differential gene expression analyses to identify putative regulators of regional identity. After bioinformatic screening for candidate genes that were consistently highly expressed in the posterior segments, we validated the function of highly ranked candidates in the tractable spider model Parasteatoda tepidariorum. Here, we show that an arthropod homolog of the Iroquois complex of homeobox genes is required for proper formation of the boundary between arachnid tagmata. The function of this homolog had not been previously characterized, because it was lost in the common ancestor of Pancrustacea, precluding its investigation in well-studied insect model organisms. Knockdown of the spider copy of this gene, which we designate as waist-less, in P. tepidariorum resulted in embryos with defects in the PO boundary, incurring discontinuous spider germ bands. We show that waist-less is required for proper specification of dorso-ventral identity in the segments that span the prosoma-opisthosoma boundary, which in adult spiders corresponds to the narrowed pedicel. Our results suggest the requirement of an ancient, taxon-restricted paralog for the establishment of the tagmatic boundary that defines Chelicerata.

evolutionary biology↗

bioRxiv2022

Dual functions of labial resolve the Hox logic of chelicerate head segments

Despite an abundance of gene expression surveys, comparatively little is known about Hox gene function in Chelicerata, with emphasis on the Hox logic of the anterior prosomal segments, which bear the mouthparts. Previous investigations of individual paralogs of labial (lab) and Deformed (Dfd) in the spider Parasteatoda tepidariorum have shown that these play a role in tissue maintenance of the pedipalpal segment (labial-1) and in patterning the first walking leg identity (Deformed-1), respectively. However, broader extrapolations of these data points across chelicerates are hindered by the existence of duplicated copies of Hox genes in arachnopulmonates (e.g., spiders and scorpions), which have resulted from an ancient whole genome duplication event. Here, we investigated the function of single-copy orthologs of lab in the harvestman Phalangium opilio, an exemplar of a lineage that was not subject of this whole genome duplication. Embryonic RNAi against lab resulted in homeotic transformations of pedipalps to chelicerae, as well as reduction and fusion of the pedipalpal segment with adjacent segments. To test for combinatorial function, we performed double knockdown of lab and Dfd, which results in homeotic transformation of both pedipalps and 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 additionally performed expression surveys for duplicated copies of lab and Dfd in scorpions and horseshoe crabs, toward understanding the genetic basis of a heteronomous prosoma. 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.

developmental biology↗

bioRxiv2022

Neglected no longer: Phylogenomic resolution of higher-level relationships in Solifugae

Considerable progress has been achieved in resolving higher-level relationships of Arthropoda in the past two decades, largely precipitated by advances in sequencing technology. Yet, dark branches persist in the arthropod tree of life, principally among groups that are difficult to collect, occur in cryptic habitats, or are characterized by minute body size. Among chelicerates, the mesodiverse order Solifugae (commonly called camel spiders or sun spiders) is one of the last orders of Arachnida that lacks a higher-level phylogeny altogether and has long been characterized as one of the "neglected cousins", a lineage of arachnid orders that are comparatively poorly studied with respect to evolutionary relationships. Though renowned for their aggression, remarkable running speed, and adaptation to arid habitats, inferring solifuge relationships has been hindered by inaccessibility of diagnostic characters in most ontogenetic stages for morphological datasets, whereas molecular investigations to date have been limited to one of the 12 recognized families. In this study we generated a phylogenomic dataset via capture of ultraconserved elements (UCEs) and sampled all extant families. We recovered a well-resolved phylogeny of solifuge families, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. To provide a temporal context to solifuge diversification, we estimated molecular divergence times using fossil calibrations within a least-squares framework. Solifugae were inferred to have radiated by the Permian, with divergences of most families dating to the post Paleogene-Cretaceous extinction. These results accord with a diversification history largely driven by vicariance as a result of continental breakup.

evolutionary biology↗

bioRxiv2022

The rediscovery of a relict unlocks the first global phylogeny of whip spiders (Amblypygi)

Asymmetrical rates of cladogenesis and extinction abound in the Tree of Life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or "living fossils" when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi ("whip spiders"), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous "whips"). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits, but is survived by a single living species, Paracharon caecus Hansen, 1921, that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report several individuals of a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of "dark taxa", and especially phylogenetic relicts in tropical and subtropical habitats.

genomics↗

bioRxiv2021

Comprehensive species sampling and sophisticated algorithmic approaches refute the monophyly of Arachnida

Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. While conflicting hypotheses prevail in morphological and molecular datasets alike, the monophyly of Arachnida is nearly universally accepted. Though a small number of phylotranscriptomic analyses have recovered arachnid monophyly, these did not sample all living chelicerate orders. We generated a dataset of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternatives algorithmic approaches to species tree inference. Investigation of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the effect of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.

evolutionary biology↗

bioRxiv2021

The genome of a daddy-long-legs (Opiliones) illuminates the evolution of arachnid appendages and chelicerate genome architecture

Chelicerates exhibit dynamic evolution of genome architecture, with multiple whole genome duplication events affecting groups like spiders, scorpions, and horseshoe crabs. Yet, genomes remain unavailable for several chelicerate orders, such as Opiliones (harvestmen), which has hindered comparative genomics and developmental genetics across arachnids. We assembled a draft genome of the daddy-long-legs Phalangium opilio, which revealed no signal of whole genome duplication. To test the hypothesis that single-copy Hox genes of the harvestman exhibit broader functions than subfunctionalized spider paralogs, we performed RNA interference against Deformed in P. opilio. Knockdown of Deformed incurred homeotic transformation of the two anterior pairs of walking legs into pedipalpal identity; by comparison, knockdown of the spatially restricted paralog Deformed-A in the spider affects only the first walking leg. To investigate the genetic basis for leg elongation and tarsomere patterning, we identified and interrogated the function of an Epidermal growth factor receptor (Egfr) homolog. Knockdown of Egfr incurred shortened appendages and the loss of distal leg structures. The overlapping phenotypic spectra of Egfr knockdown experiments in the harvestman and multiple insect models are striking because tarsomeres have evolved independently in these groups. Our results suggest a conserved role for Egfr in patterning distal leg structures across arthropods, as well as cooption of EGFR signaling in tarsomere patterning in both insects and arachnids. The establishment of genomic resources for P. opilio, together with functional investigations of appendage fate specification and distal patterning mechanisms, are key steps in understanding how daddy-long-legs make their long legs.

developmental biology↗

bioRxiv2020

Taxonomic sampling and rare genomic changes overcome long-branch attraction in the phylogenetic placement of pseudoscorpions

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 LBA 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 datasets. Pseudoscorpion placement is particularly variable across datasets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount LBA, 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, as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.

evolutionary biology↗

bioRxiv2020

Phylogenomics of scorpions reveal a co-diversification of scorpion mammalian predators and mammal-specific sodium channel toxins

Scorpions constitute a charismatic lineage of arthropods and comprise more than 2,500 described species. Found throughout various tropical and temperate habitats, these predatory arachnids have a long evolutionary history, with a fossil record that began in the Silurian. While all scorpions are venomous, the asymmetrically diverse family Buthidae harbors nearly half the diversity of extant scorpions, and all but one of the 58 species that are medically significant to humans. Many aspects of scorpion evolutionary history are unclear, such as the relationships of the most toxic genera and their constituent venom peptides. Furthermore, the diversification age of toxins that act specifically on mammalian ion channels have never been inferred. To redress these gaps, we assembled a large-scale phylogenomic dataset of 100 scorpion venom transcriptomes and/or genomes, emphasizing the sampling of highly toxic buthid genera. To infer divergence times of venom gene families, we applied a phylogenomic node dating approach for the species tree in tandem with phylostratigraphic bracketing to estimate minimum ages of mammal-specific toxins. Our analyses establish a robustly supported phylogeny of scorpions, particularly with regard to relationships between medically significant taxa. Analysis of venom gene families shows that mammal-specific sodium channel toxins have independently evolved in five lineages within Buthidae. The temporal windows of mammal-specific toxin origins are contiguous with the basal diversification of major scorpion mammal predators such as carnivores, shrews, bats and rodents. These results suggest an evolutionary arms race model comprised of co-diversification of mammalian predators and NaTx homologs in buthid venom.

evolutionary biology↗