Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates

Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider

Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.

Gene Function is a Driver of Activin Signaling Pathway Evolution Following Whole-Genome Duplication in Rainbow Trout (Oncorhynchus mykiss)

The genomes of plant and animal species are influenced by ancestral whole-genome duplication (WGD) events, which have profound impacts on the regulation and function of gene networks. To gain insight into the consequences of WGD events, we characterized the sequence conservation and expression patterns of ohnologs in the highly duplicated activin receptor signaling pathway in rainbow trout (RBT). The RBT activin receptor signaling pathway is defined by tissue-specific expression of inhibitors and ligands and broad expression of receptors and Co-Smad signaling molecules. Signaling pathway ligands exhibited shared expression, while inhibitors and Smad signaling molecules primarily express a single dominant ohnolog. Our findings suggest that gene function influences ohnolog evolution following duplication of the activin signaling pathway in RBT.

Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication

Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes can undergo subfunctionalization to partition ancestral functions and/or neofunctionalization to assume a new function. We previously found there had been a whole genome duplication (WGD) in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues originated by WGD versus smaller-scale events such as tandem duplications. Understanding this is a key to determining the contribution of the WGD to arachnopulmonate genome evolution. Here we characterized the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that most duplicated homeobox genes in spiders are consistent with an origin by WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE clusters, in all eight species. Consistently, we observed one copy of each cluster was degenerated in terms of gene content and organization while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalization between the duplicated NK genes in the spider Parasteatoda tepidariorum compared to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the relative contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.

Expression of posterior Hox genes and opisthosomal appendage development in a mygalomorph spider

Spiders represent an evolutionary successful group of chelicerate arthropods. The body of spiders is subdivided into two regions (tagmata). The anterior tagma, the prosoma, bears the head appendages and four pairs of walking legs. The segments of the posterior tagma, the opisthosoma, either lost their appendages during the course of evolution or their appendages were substantially modified to fulfill new tasks such as reproduction, gas exchange, and silk production. Previous work has shown that the homeotic Hox genes are involved in shaping the posterior appendages of spiders. In this paper, we investigate the expression of the posterior Hox genes in a tarantula that possesses some key differences of posterior appendages compared to true spiders, such as the lack of the anterior pair of spinnerets and a second set of book lungs instead of trachea. Based on the observed differences in posterior Hox gene expression in true spiders and tarantulas, we argue that subtle changes in the Hox gene expression of the Hox genes abdA and AbdB are possibly responsible for at least some of the morphological differences seen in true spiders versus tarantulas.

The Impact of Whole Genome Duplication on the Evolution of the Arachnids

The proliferation of genomic resources for Chelicerata in the past 10 years has revealed that the evolution of chelicerate genomes is more dynamic than previously thought, with multiple waves of ancient whole genome duplications affecting separate lineages. Such duplication events are fascinating from the perspective of evolutionary history because the burst of new gene copies associated with genome duplications facilitates the acquisition of new gene functions (neofunctionalization), which may in turn lead to morphological novelties and spur net diversification. While neofunctionalization has been invoked in several contexts with respect to the success and diversity of spiders, the overall impact of whole genome duplications on chelicerate evolution and development remains imperfectly understood. The purpose of this review is to examine critically the role of whole genome duplication on the diversification of the extant arachnid orders, as well as assess functional datasets for evidence of subfunctionalization or neofunctionalization in chelicerates. This examination focuses on functional data from two focal model taxa: the spider Parasteatoda tepidariorum, which exhibits evidence for an ancient duplication, and the harvestman Phalangium opilio, which exhibits an unduplicated genome. I show that there is no evidence that taxa with genome duplications are more successful than taxa with unduplicated genomes. I contend that evidence for sub- or neofunctionalization of duplicated developmental patterning genes in spiders is indirect or fragmentary at present, despite the appeal of this postulate for explaining the success of groups like spiders. Available expression data suggest that the condition of duplicated Hox modules may have played a role in promoting body plan disparity in the posterior tagma of some orders, such as spiders and scorpions, but functional data substantiating this postulate are critically missing. Spatiotemporal dynamics of duplicated transcription factors in spiders may represent cases of developmental system drift, rather than neofunctionalization. Developmental system drift may represent an important, but overlooked, null hypothesis for studies of paralogs in chelicerate developmental biology. To distinguish between subfunctionalization, neofunctionalization, and developmental system drift, concomitant establishment of comparative functional datasets from taxa exhibiting the genome duplication, as well as those that lack the paralogy, is sorely needed.

A homology guide for Pacific salmon genus Oncorhynchus resolves patterns of ohnolog retention, resolution and local adaptation following the salmonid-specific whole-genome duplication event

Salmonid fishes have emerged as a tractable model to study whole-genome duplications (WGDs) as this group has undergone four rounds of WGDs. While most of the salmonid genome has returned to a diploid state, a significant proportion of genes are maintained as duplicates and are referred to as ohnologs. The fact that much of the modern salmonid gene repertoire is comprised of ohnologs, while other genes have returned to their singleton state creates complications for genetic studies by obscuring homology relationships. The difficulty this creates is particularly prominent in Pacific salmonids belonging to genus Oncorhynchus who are the focus of intense genetics-based conservation and management efforts owing to the important ecological and cultural roles these fish play. To address this gap, we generated a homology guide for six species of Oncorhynchus with available genomes and used this guide to describe patterns of ohnolog retention and resolution. Overall, we find that ohnologs comprise approximately half of each species modern gene repertoires, which are functionally enriched for genes involved in DNA binding, while the less numerous singleton genes are heavily enriched in dosage-sensitive processes such as mitochondrial metabolism. Additionally, by reanalyzing published expression data from locally adapted strains of O. mykiss, we show that numerous ohnologs exhibit adaptive expression profiles; however, ohnologs are not more likely to display adaptive signatures than either paralogs or singletons. Finally, we demonstrate the utility of our homology guide by investigating the evolutionary relationship among genes highlighted as playing a role in salmonid life-history traits or gene editing targets.

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. Previous investigations of paralogs of labial (lab) and Deformed (Dfd) in a spider have shown that these play a role in tissue maintenance of the pedipalp segment (lab-1) and in patterning the first walking leg identity (Dfd-1), respectively. However, extrapolations of these data across chelicerates are hindered by the existence of duplicated Hox genes in arachnopulmonates (e.g., spiders and scorpions), which have resulted from an ancient whole genome duplication (WGD) event. Here, we investigated the function of the single-copy ortholog of lab in the harvestman Phalangium opilio, an exemplar of a lineage that was not subject to this WGD. Embryonic RNA interference against lab resulted in two classes of phenotypes: homeotic transformations of pedipalps to chelicerae, as well as reduction and fusion of the pedipalp and leg 1 segments. To test for combinatorial function, we performed a double knockdown of lab and Dfd, which resulted in a homeotic transformation of both pedipalps and the first walking legs into cheliceral identity, whereas the second walking leg is transformed into a pedipalpal identity. Taken together, these results elucidate a model for the Hox logic of head segments in Chelicerata. To substantiate the validity of this model, we performed expression surveys for lab and Dfd paralogs in scorpions and horseshoe crabs. We show that repetition of morphologically similar appendages is correlated with uniform expression levels of the Hox genes lab and Dfd, irrespective of the number of gene copies.

Hox genes in spiders: Their significance for development and evolution

Hox genes are known for their role in the specification of typical body plan features in animals. Evolutionary changes in Hox gene function are believed to be involved in the emergence of the diverse body plans we observe in animals today. Spiders share many body plan features with other arthropods, but also have numerous unique traits of their own. Studies of spider Hox genes have already provided insights into evolutionarily conserved and derived features of the spider body plan and their genetic basis. However, many aspects of Hox gene biology have been insufficiently studied in spiders so far. In this review, we highlight previous comparative studies of Hox genes in spiders and their significance for our understanding of the evolution of the spider body plan. We also identify aspects of Hox gene biology that need to be studied in greater detail. Many spider Hox genes have not been investigated beyond their mRNA expression patterns, and the role of Hox genes with apparently plesiomorphic or dual functions, like ftz and Hox3 is still unclear. Spiders have a duplicated Hox gene cluster, but possible sub- or neofunctionalisation of duplicates have not yet been studied systematically. Future research should therefore focus on these issues, in addition to the role of Polycomb and trithorax-mediated regulation, the identification of regulatory regions, cofactors or spider-specific target genes, and the significance of non-coding RNAs transcribed from within the Hox cluster and even from the antisense strand of particular Hox genes.

The organizing role of Wnt signaling pathway during arthropod posterior growth

Wnt signaling pathways are recognized for having major roles in tissue patterning and cell proliferation. In the last years, remarkable progress has been made in elucidating the molecular and cellular mechanisms that underlie sequential segmentation and axial elongation in various arthropods, and the canonical Wnt pathway has emerged as an essential factor in these processes. Here we review, with a comparative perspective, the current evidence concerning the participation of this pathway during posterior growth, its degree of conservation among the different subphyla within Arthropoda and its relationship with the rest of the gene regulatory network involved. Furthermore, we discuss how this signaling pathway could regulate segmentation to establish this repetitive pattern and, at the same time, probably modulate different cellular processes precisely coupled to axial elongation. Based on the information collected, we suggest that this pathway plays an organizing role in the formation of the body segments through the regulation of the dynamic expression of segmentation genes, via controlling the caudal gene, at the posterior region of the embryo/larva, that is necessary for the correct sequential formation of body segments in most arthropods and possibly in their common segmented ancestor. On the other hand, there is insufficient evidence to link this pathway to axial elongation by controlling its main cellular processes, such as convergent extension and cell proliferation. However, conclusions are premature until more studies incorporating diverse arthropods are carried out.

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. Although conflicting hypotheses prevail in morphological and molecular data sets alike, the monophyly of Arachnida is nearly universally accepted, despite historical lack of support in molecular data sets. Some phylotranscriptomic analyses have recovered arachnid monophyly, but these did not sample all living orders, whereas analyses including all orders have failed to recover Arachnida. To understand this conflict, we assembled a data set 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 alternative algorithmic approaches to species tree inference. Investigation of sources of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the impact 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 merostomates appeared 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.

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.