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How many long branch orders occur in Chelicerata? Opposing effects of Palpigradi and Opilioacariformes on phylogenetic stability
Abstract
Excepting a handful of nodes, phylogenetic relationships between chelicerate orders remain poorly resolved, due to both the incidence of long branch attraction artifacts and the limited sampling of key lineages. It has recently been shown that increasing representation of basal nodes plays an outsized role in resolving the higher-level placement of long-branch chelicerate orders. Two lineages have been consistently undersampled in chelicerate phylogeny. First, sampling of the miniaturized order Palpigradi has been restricted to a fragmentary transcriptome of a single species. Second, sampling of Opilioacariformes, a rarely encountered and key group of Parasitiformes, has been restricted to a single exemplar. These two lineages exhibit dissimilar properties with respect to branch length; Opilioacariformes shows relatively low evolutionary rate compared to other Parasitiformes, whereas Palpigradi possibly acts as another long-branch order (an effect that may be conflated with the degree of missing data). To assess these properties and their effects on tree stability, we constructed a phylogenomic dataset of Chelicerata wherein both lineages were sampled with three terminals, increasing the representation of these taxa per locus. We examined the effect of subsampling phylogenomic matrices using (1) taxon occupancy, (2) evolutionary rate, and (3) a principal components-based approach. We further explored the impact of taxon deletion experiments that mitigate the effect of long branches. Here, we show that Palpigradi constitutes a fourth long-branch chelicerate order (together with Acariformes, Parasitiformes, and Pseudoscorpiones), which further destabilizes the chelicerate backbone topology. By contrast, the slow-evolving Opilioacariformes were consistently recovered within Parasitiformes, with certain subsampling practices recovering their placement as the sister group to the remaining Parasitiformes. Whereas the inclusion of Opilioacariformes always resulted in the non-monophyly of Acari with support, deletion of Opilioacariformes from datasets consistently incurred the monophyly of Acari except in matrices constructed on the basis of evolutionary rate. Our results strongly suggest that Acari is an artifact of long- branch attraction.
... However, mites are probably not a natural group. The majority of phylogenomic analyses have recovered mites as non-monophyletic [6][7][8][9][10][11], and the few occasions when mite monophyly has instead been recovered [10,12,13] can be readily attributed to taxonomic undersampling (overtly problematic for two studies [10,13]) and long-branch attraction [8,11,14]. A high proportion of the most taxonomically comprehensive phylogenomic analyses have recovered Acariformes as sister to a clade comprising the rest of Arachnida and Xiphosura [8,11]. ...
... However, mites are probably not a natural group. The majority of phylogenomic analyses have recovered mites as non-monophyletic [6][7][8][9][10][11], and the few occasions when mite monophyly has instead been recovered [10,12,13] can be readily attributed to taxonomic undersampling (overtly problematic for two studies [10,13]) and long-branch attraction [8,11,14]. A high proportion of the most taxonomically comprehensive phylogenomic analyses have recovered Acariformes as sister to a clade comprising the rest of Arachnida and Xiphosura [8,11]. ...
... The majority of phylogenomic analyses have recovered mites as non-monophyletic [6][7][8][9][10][11], and the few occasions when mite monophyly has instead been recovered [10,12,13] can be readily attributed to taxonomic undersampling (overtly problematic for two studies [10,13]) and long-branch attraction [8,11,14]. A high proportion of the most taxonomically comprehensive phylogenomic analyses have recovered Acariformes as sister to a clade comprising the rest of Arachnida and Xiphosura [8,11]. ...
In recent years, the case for the monophyly of mites or Acari (Parasitiformes + Acariformes) has looked increasingly weak. Much of the remaining doubt about the artificiality of this taxon stems from the importance long attributed to the gnathosoma, widely considered the most convincing morphological character supporting monophyly. The gnathosoma has long been interpreted as originating via the fusion together of the palpal coxae, which is thought to have contributed to the consolidation of the mouthparts into a compact feeding apparatus that articulates as a single unit. However, an investigation of the mouthparts of Acariformes, reported herein, revealed that fusion together of the palpal coxae is an uncommon state that convergently evolved in multiple acariform taxa rather than evolving only once, as a synapomorphy uniting Acariformes and Parasitiformes. Moreover, other defining features of the gnathosoma involve either very different modifications or structures that are not homologous between both main lineages of mites. Therefore, the gnathosoma is a bad character—poorly defined and based on a series of misinterpretations—that should not be treated as evidence for mite monophyly.
... With respect to phylogenetics, genome duplications are often useful arbiters for breaking polytomies, in that they serve as rare genomic changescomplex characters that exhibit low levels of homoplasy (Salichos and Rokas 2014; One Thousand Plant Transcriptomes Initiative 2019). Apropos, the discovery of the arachnopulmonate duplication lent itself as a rare genomic change to test the placement of Pseudoscorpiones, an unstable group of rapidly-evolving and small-bodied arachnids Ontano et al. 2022). The first developmental and genomic resources for pseudoscorpions revealed shared patterns of duplication with the remaining arachnopulmonates and placed them as the likely sister group of scorpions (Ontano et al. 2021), with downstream implications for the evolutionary origin of arachnopulmonate venoms (Santibáñez-López et al. 2018;Krämer et al. 2019). ...
... The first developmental and genomic resources for pseudoscorpions revealed shared patterns of duplication with the remaining arachnopulmonates and placed them as the likely sister group of scorpions (Ontano et al. 2021), with downstream implications for the evolutionary origin of arachnopulmonate venoms (Santibáñez-López et al. 2018;Krämer et al. 2019). Relationships of other parts of the chelicerate tree of life remain obscured by conflicting signal surrounding an ancient rapid radiation of apulmonate arachnid orders, but these are being sequentially illuminated by dedicated improvements in sampling of enigmatic and poorly studied taxa Ban et al. 2022;Ontano et al. 2022;Pepato et al. 2022). ...
... The diversity of spiders is rivaled by Acariformes, a diverse group of mites that includes numerous lineages of parasites and highly miniaturized taxa, and whose described diversity is almost certainly a poorly understood fraction of its extant biodiversity. The sister group of Acariformes is similarly not evident, with the monophyly of Acari (Acariformes + Parasitiformes) presently in question (Pepato et al. 2010;Ballesteros et al. 2022;Ban et al. 2022;Ontano et al. 2022). However, if Acari were monophyletic, the combined diversity of Acariformes and Parasitiformes would easily surpass that of spiders, both with regard to described number of species, as well as ecological and morphological diversity. ...
The proliferation of genomic resources for Chelicerata in the past ten 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 region of some orders, such as spiders and scorpions. 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.
... The monophyly of Arachnida is controversial, accepted by some arachnologists (Howard et al., 2020;Lozano-Fernandez et al., 2019;Shultz, 2007), yet rejected by others (reviewed by Sharma et al., 2021). Furthermore, the monophyly of subclass Acari is unresolved (reviewed by Dunlop & Alberti, 2007), even by multiple phylogenomic efforts, recovered by analyses using genome sequences (Lozano-Fernandez et al., 2019) or rejected by genome and transcriptome sequences Ontano et al., 2021Ontano et al., , 2022Regier et al., 2010;Richart et al., 2016;Sharma et al., 2014). ...
... The discrepancies for arachnid interordinal relationships inferred by morphological characters or molecular approaches are likely caused by incomplete lineage sorting , long-branch attraction of Pseudoscorpiones, Acariformes, Palpigradi and Parasitiformes (Arabi et al., 2012;Ontano et al., 2021Ontano et al., , 2022Pepato et al., 2010;Sharma et al., 2014), or the ancient rapid radiation of orders (Dunlop & Selden, 2009). Nevertheless, several interordinal relationships have been resolved: (1) Pseudoscorpiones is the sister group to Scorpiones by evidence from both morphological synapomorphies and genome architectures (Ontano et al., 2021), (2) sharing a genome duplication unites the Tetrapulmonata and Panscorpiones (sensu Ontano, et al., 2021), and (3) the monophyly of Acariformes and Parasitiformes was consistently recovered by genomic-scale analyses Xue et al., 2017). ...
... Although we recovered the monophyly of ten orders, their interordinal relationships are unstable, differing among datasets, partition strategies and algorithms (Fig. 1). However, in light of the latest evidence from phylogenomic studies Lozano-Fernandez et al., 2019;Ontano et al., 2021Ontano et al., , 2022Sharma et al., 2014) as well as our inferred topologies and mt gene arrangements, we propose a plausible arachnid tree of life (Fig. 3). All of our inferred topologies reject monophyly of Arachnida due to the unstable position of Xiphosura (Fig. 1). ...
Arachnida is an exceptionally diverse class in the Arthropoda, consisting of 20 orders and playing crucial roles in the terrestrial ecosystems. However, their interordinal relationships have been debated for over a century. Rearranged or highly rearranged mitochondrial genomes (mitogenomes) were consistently found in this class, but their various extent in different lineages and efficiency for resolving arachnid phylogenies are unclear. Here, we reconstructed phylogenetic trees using mitogenome sequences of 290 arachnid species to decipher interordinal relationships as well as diversification through time. Our results recovered monophyly of ten orders (i.e. Amblypygi, Araneae, Ixodida, Mesostigmata, Opiliones, Pseudoscorpiones, Ricinulei, Sarcop-tiformes, Scorpiones and Solifugae), while rejecting monophyly of the Trombidiformes due to the unstable position of the Eriophyoidea. The monophyly of Acari (subclass) was rejected, possibly due to the long-branch attraction of the Pseudoscorpi-ones. The monophyly of Arachnida was further rejected because the Xiphosura nested within arachnid orders with unstable positions. Mitogenomes that are highly rearranged in mites but less rearranged or conserved in the remaining lineages point to their exceptional diversification in mite orders; however, shared derived mitochondrial (mt) gene clusters were found within superfamilies rather than interorders, confusing phylogenetic signals in arachnid interordinal relationships. Molecular dating results show that arachnid orders have ancient origins, ranging from the Ordovician to the Carboniferous, yet have significantly diversified since the Cretaceous in orders Araneae, Mesostigmata, Sarcoptiformes, and Trombidiformes. By summarizing previously resolved key positions of some orders, we propose a plausible arachnid tree of life. Our results underline a more precise framework for interordinal phylogeny in the Arachnida and provide new insights into their ancient evolution.
... The recovery of this pair as sister groups (forming Acari) is consistent with similar adaptations of mouthparts in the two groups but is controversial from the perspective of molecular data, with matrices emphasizing intensive sampling failing to recover Acari (8, 83,95). Notably, the addition of basally branching groups of these orders (e.g., Opilioacaridae, the putative sister group of Parasitiformes) to phylogenomic analyses tends to precipitate the breakup of Acari, suggesting that recovery of Acari in molecular data sets is an artifact of undersampling (96). ...
... Nodal support for the interrelationships of these biodiverse groups is generally modest in deeper parts of the tree, partly due to the limitations of Sanger data sets and the lack of genome-scale matrices informing acariform higher-level phylogeny. Parasitiformes is somewhat better resolved, with early Sanger-based efforts recovering strong support for the order and its four constituent lineages (Opilioacariformes, Mesostigmata, Holothyrida, and Ixodida), although the placement of the fast-evolving Mesostigmata within Parasitiformes was subsequently shown to be unstable (75,96). ...
Chelicerata constitutes an ancient, biodiverse, and ecologically significant group of Arthropoda. The study of chelicerate evolution has undergone a renaissance in the past decade, resulting in major changes to our understanding of the higher-level phylogeny and internal relationships of living orders. Included among these conceptual advances are the discoveries of multiple whole-genome duplication events in a subset of chelicerate orders, such as horseshoe crabs, spiders, and scorpions. As a result, longstanding hypotheses and textbook scenarios of chelicerate evolution, such as the monophyly of Arachnida and a single colonization of land by the common ancestor of arachnids, have come into contention. The retention of ancient, duplicated genes across this lineage also offers fertile ground for investigating the role of gene duplication in chelicerate macroevolution. This new frontier of investigation is paralleled by the timely establishment of the first gene editing protocols for arachnid models, facilitating a new generation of experimental approaches.
... As anticipated, several groups in our phylogeny reflected long root-to-tip distances, constituting lineages prone to LBA artifacts. The inclusion of Opilioacariformes, a slowly evolving group of Parasitiformes (Klompen et al. 2007;Pepato et al. 2010), was recently shown to break up the grouping of Acariformes and Parasitiformes, suggesting that Acari is a long-branch artifact (Ontano et al. 2021;Ontano et al. 2022). In this study, we sampled Opilioacariformes with two libraries, and concordantly, never obtained the monophyly of Acari, particularly when pursuing approaches best suited to mitigating LBA ( fig. 3) MBE (e.g., mouthparts; patterns of tagmosis) represent a case of morphological convergence in chelicerates. ...
... In tandem with such approaches, investigations of chelicerate phylogeny should emphasize the expansion of whole-genome data sets, with the aim of leveraging rare genomic changes, such as genome duplications, as potential arbiters of competing phylogenetic hypotheses (Schwager et al. 2017). This strategy has shown strong promise as a source of benchmarks for assessing performance of molecular data sets in the face of LBA, as well as for realigning interpretations of morphological data, toward reconciliation of chelicerate relationships (Ontano et al. 2021;Ontano et al. 2022). [Camacho et al. 2009]) against the D. melanogaster proteome for annotation using the best hit. ...
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, despite historical lack of support in molecular datasets. 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 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 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.
... Downloaded from https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syae021/7669116 by University of Wisconsin-Madison Libraries user on 15 July 2024 (Scorpiones), and pseudoscorpions (Pseudoscorpiones), a relationship supported by rare genomic changes (e.g., Ontano et al. 2021Ontano et al. , 2022Ballesteros et al. 2022). We therefore included 2 representatives of spiders, 1 vinegaroon, 3 short-tailed whip scorpions, and rooted the tree with 3 scorpions. ...
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 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, which bears upon the ancestral range reconstruction for the group. 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. The lack of reciprocal monophyly for Charontidae and Charinidae leads us to subsume them into one family, Charontidae, new synonymy.
... This recalcitrance can be attributed, in part, to an ancient origin and subsequent rapid diversification of the extant orders (Dunlop, 2010;Rota-Stabelli et al., 2013), producing short internodes. Likewise, several long-branch orders occur among the chelicerates (Acariformes, Parasitiformes, Pseudoscorpiones, and Palpigradi) demonstrating accelerated rates of evolution and yielding artifactual clustering of such lineages near the base of the tree (Ontano et al., 2022;Sharma et al., 2014a). Chelicerate phylogeny has also been hindered by consistent undersampling of key lineages (e.g., Opilioacariformes; Palpigradi). ...
Recent advances in higher-level invertebrate phylogeny have leveraged shared features of genomic architecture to resolve contentious nodes across the tree of life. Yet, the interordinal relationships within Chelicerata have remained recalcitrant given competing topologies in recent molecular analyses. As such, relationships between topologically unstable orders remain supported primarily by morphological cladistic analyses. Solifugae, one such unstable chelicerate order, has long been thought to be the sister group of Pseudoscorpiones, forming the clade Haplocnemata, on the basis of eight putative morphological synapomorphies. The discovery, however, of a shared whole genome duplication placing Pseudoscorpiones in Arachnopulmonata provides the opportunity for a simple litmus test evaluating the validity of Haplocnemata. Here, we present the first developmental transcriptome of a solifuge (Titanopuga salinarum) and survey copy numbers of the homeobox genes for evidence of systemic duplication. We find that over 70% of the identified homeobox genes in T. salinarum are retained in a single copy, while representatives of the arachnopulmonates retain orthologs of those genes as two or more copies. Our results refute the placement of Solifugae in Haplocnemata. Subsequent reevaluation of putative interordinal morphological synapomorphies among chelicerates reveals a high incidence of homoplasy, reversals, and inaccurate coding within Haplocnemata and other small clades, as well as Arachnida more broadly, suggesting existing morphological character matrices are insufficient to resolve chelicerate phylogeny.
... Ontano et al. 24 reasoned that applying this remedy to other fast-evolving orders may greatly stabilize chelicerate phylogeny, given that at least four orders exhibit a propensity for long branch attraction artifacts in Chelicerata. 26,42,52 This proposed remedy for long branch attraction is greatly potentiated by the availability of higher-level phylogenies for unstable groups, such as Acariformes 11 and Palpigradi. 2 However, representation of solifuges in phylogenomic works has historically been driven entirely by the availability of sequencegrade tissues, rather than by representation of phylogenetically significant exemplars, given that the internal phylogenetic structure of this order has never been fathomed. [25][26][27][28]53,54 It is possible that this oversight may have underlain their known predilection for topological instability in some phylogenomic datasets. ...
Advanced sequencing technologies have expedited resolving higher-level arthropod relationships. Yet, dark branches persist, principally among groups occurring in cryptic habitats. Among chelicerates, Solifugae (“camel spiders”) is the last order lacking a higher-level phylogeny and thus, historically characterized as “neglected [arachnid] cousins”. Though renowned for aggression, remarkable running speed, and xeric adaptation, inferring solifuge relationships has been hindered by inaccessibility of diagnostic morphological characters, whereas molecular investigations have been limited to one of 12 recognized families. Our phylogenomic dataset via capture of ultraconserved elements sampling all extant families recovered a well-resolved phylogeny, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. Divergence times using fossil calibrations inferred Solifugae radiated by the Permian, and most families diverged pre-Paleogene-Cretaceous extinction, largely driven by continental breakup. We establish Boreosolifugae new suborder uniting five Laurasian families, and Australosolifugae new suborder uniting seven Gondwanan families using morphological and biogeographic signal.
... Arachnida traditionally excluding Xiphosura) has once been deemed solid (Shultz, 2001;Coddington et al., 2004), most molecular studies do not recover it (Ballesteros et al., 2022;Ban et al., 2022), nor do they recover some of the classical groups within Arachnida . Monophyly and phylogenetic placement of several arachnid lineages continue to be ambiguous due to long branch attraction artifacts (Ontano et al., 2022). Additionally, a divide seems to persist between students of fossils and morphologies on the one hand and the proponents of genomics on the other, hampering a total evidence resolution of the problem. ...
This perspective identifies the grand challenges in arachnid science: 1. Grasp the arachnid species diversity. There is a need to accelerate taxonomic research to obtain a sense of arachnid species diversity, however, at the same time, taxonomy needs to increase its quality, rigor, and repeatability. 2. Standardize arachnid systematics research. A solid phylogenetic definition and morphological diagnosis of Arachnida and its composing subgroups, usually treated at the rank of order, are needed. Studies should aim to stabilize and standardize phylogenetic efforts at all levels of hierarchy, and systematists should adopt criteria for higher level ranks in arachnid classification. 3. Interpret arachnid trait evolution through omics approaches. Among the field’s grand challenges is to define the genetic diversity encoding for the diverse arachnid traits, including developmental, morphological and ecological characteristics, biomaterials such as silks, venoms, digestive fluids, or allergens and bioproducts that cause diseases. Comparative genomics, transcriptomics, and proteomics will provide the empirical basis for biotechnology to modify arachnid genomes to fit numerous applications. 4. Facilitate biotechnological applications of arachnid molecules and biomaterials. Among the grand field challenges is to define potential applications of arachnid bioproducts from therapeutics to industry. New natural and biodegradable products, e.g. from spider silks, should ease our burden on ecosystems. 5. Utilize arachnids as models in ecological and biogeographic research. Biodiversity inventory sampling and analytical techniques should be extended from spiders to other arachnid groups. Spiders and their webs could be used as environmental DNA samplers, measuring or monitoring ecosystems’ overall biodiversity. Arachnids are excellent models to address biogeographical questions at the global to local scales. 6. Disentangle evolutionary drivers of arachnid diversity. Among the field grand challenges is a more precise evaluation to what extent the emergence of arachnid phenotypes is shaped by classical selection processes, and under what conditions, if any, sexual conflict needs to be invoked. 7. Define effective conservation measures for arachnids in the light of global changes. Effective conservation measures in arachnology should integrate the data from phylogenetic diversity, physiology, ecology, biogeography, and global change biology.
... 1 0 a propensity for long branch attraction artifacts in Chelicerata (Ballesteros and Sharma 2019;Ballesteros et al. 2019;Ontano et al. 2022). This proposed remedy for long branch attraction is greatly potentiated by the availability of higher-level phylogenies for unstable groups, such as Acariformes (Klimov et al. 2017) and Palpigradi ). ...
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 Bayesian 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.
... We applied a conservative calibration scheme for maximum bounds and the most phylogenetic-near-accurate groups as the minimum bounds (as suggested by Phillips, 2016). Given uncertainty regarding the identity of the sister group of Opiliones in phylogenomic datasets (Ballesteros et al., 2022Ontano et al., 2022Ontano et al., , 2021Sharma et al., 2014), we used the earliest known terrestrial chelicerate fossils from the early Silurian to constrain the maximum bounds of all calibration nodes at 437.5 Ma (Waddington et al., 2015). ...
Opiliones (harvestmen) have come to be regarded as an abundant source of model groups for study of historical biogeography, due to their ancient age, poor dispersal capability, and high fidelity to biogeographic terranes. One of the least understood harvestman groups is the Paleotropical Assamiidae, one of the more diverse families of Opiliones. Due to a labyrinthine taxonomy, poorly established generic and subfamilial boundaries, and the lack of taxonomic keys for the group, few efforts have been undertaken to decipher relationships within this arachnid lineage. Neither the monophyly of the family, nor its exact placement in the harvestman phylogeny, have been established. Here, we assessed the internal phylogeny of Assamiidae using a ten-locus Sanger dataset, sampling key lineages putatively ascribed to this family for five of the ten markers. Our analyses recovered Assamiidae as a monophyletic group, in a clade with the primarily Afrotropical Pyramidopidae and the southeast Asian Beloniscidae. Internal relationships of assamiids disfavored the systematic validity of subfamilies, with biogeography reflecting much better phylogenetic structure than the existing higher-level taxonomy. To assess whether the Asian assamiids came to occupy Indo-Pacific terranes via rafting on the Indian subcontinent, we performed divergence dating to infer the age of the family. Our results show that Indo-Pacific clades are ancient, originating well before the Cretaceous and therefore predate a vicariant mechanism commonly encountered for Paleotropical taxa.
... Specimens sequenced for this study were hand collected from field sites or contributed by form a clade with spiders, scorpions, and pseudoscorpions, a relationship supported by rare genomic changes (e.g., Ontano et al. 2021Ontano et al. , 2022Ballesteros et al. 2022). We therefore included two representatives of spiders, one vinegaroon, three Schizomida, and rooted the tree with three scorpions. ...
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.
Chromosome-level genome assemblies are powerful tools for identifying the presence of rare genomic changes that can overcome phylogenetically intractable problems. Chelicerata, the sister group to the remaining arthropods, harbors a soft polytomy at the base of an internal node named Euchelicerata, which is variably resolved across phylogenomic studies. As a result, seven orders, comprising horseshoe crabs and six apulmonate arachnid lineages, exhibit highly unstable placements from one study to the next, typically with maximal nodal support. Here, we analyzed recently released chromosome-level genomes of two of these orders, Opiliones (harvestmen) and Solifugae (camel spiders). We show that both Opiliones and Solifugae exhibit the plesiomorphic, unduplicated genome condition, as inferred from analysis of gene clusters, microRNAs, and macrosynteny. These results are congruent with phylogenomic studies that have refuted traditional morphological placements of Opiliones and Solifugae as close relatives of orders within Arachnopulmonata, a subset of six arachnid orders that are united by a shared whole genome duplication. Additionally, we examine irreversible chromosome fusion-with-mixing events as potential sources of phylogenetic data. We show that while fusion and mixing events are common in apulmonate arachnids, multiple mixing events support mutually exclusive unrooted tree topologies. These results suggest that fusion and mixing events have evolved convergently in the chelicerate tree of life, particularly for extant taxa with a small number of chromosomes, such as the solifuge. Overall, our findings demonstrate that broader sampling of chelicerate genomes and establishment of genomic resources for key missing orders are essential to unlocking the potential of rare genomic changes as phylogenetic data sources.
Background/Objectives: Arachnids are a megadiverse arthropod group. The present study investigated the chromosomes of pedipalpid tetrapulmonates (orders Amblypygi, Thelyphonida, Schizomida) and two arachnid orders of uncertain phylogenetic placement, Ricinulei and Solifugae, to reconstruct their karyotype evolution. Except for amblypygids, the cytogenetics of these arachnid orders was almost unknown prior to the present study. Methods: Chromosomes were investigated using methods of standard (Giemsa-stained preparations, banding techniques) and molecular cytogenetics (fluorescence in situ hybridization, comparative genomic hybridization). Results and Conclusions: New data for 38 species, combined with previously published data, suggest that ancestral arachnids possessed low to moderate 2n (22–40), monocentric chromosomes, one nucleolus organizer region (NOR), low levels of heterochromatin and recombinations, and no or homomorphic sex chromosomes. Karyotypes of Pedipalpi and Solifugae diversified via centric fusions, pericentric inversions, and changes in the pattern of NORs and, in solifuges, also through tandem fusions. Some solifuges display an enormous amount of constitutive heterochromatin and high NOR number. It is hypothesized that the common ancestor of amblypygids, thelyphonids, and spiders exhibited a homomorphic XY system, and that telomeric heterochromatin and NORs were involved in the evolution of amblypygid sex chromosomes. The new findings support the Cephalosomata clade (acariforms, palpigrades, and solifuges). Hypotheses concerning the origin of acariform holocentric chromosomes are presented. Unlike current phylogenetic hypotheses, the results suggest a sister relationship between Schizomida and a clade comprising other tetrapulmonates as well as a polyploidization in the common ancestor of the clade comprising Araneae, Amblypygi, and Thelyphonida.
Water flux across cells predominantly occurs through the pore formed by the aquaporin channels. Since water balance is one of the most important challenges to terrestrial animals, aquaporin evolution and diversity is known to play roles in animal terrestrialisation. Arachnids (Arthropoda: Chelicerata: Arachnida) are the second most diverse group and represent the pioneer land colonists in animals; however, there remains no thorough investigation on aquaporin evolution and diversity in this evolutionarily important lineage. Here we reported a phylogenetic study of aquaporin evolution and diversity using genomic data from 116 arachnid species covering almost all (15/16) extant orders. A previously unrecognised subfamily related to aquaporin-4 (i.e. Aqp4-like subfamily) via phylogenetic analysis was identified, suggesting certain underestimate of the arachnid aquaporin diversity in earlier studies probably due to limited taxonomic sampling. Further analysis indicates that this subfamily emerged deep within the life tree of arthropods. Gene tree of another Aqp4-like subfamily (PripL) shows an unexpected basal split between acariform mites (Acariformes) and other arachnids. A closer inspection demonstrated that the PripL evolved quickly and has been under differential selection pressure in acariform mites. Evidence is provided that the evolutionarily ancient Glp subfamily (i.e. aquaglyceroporin) is significantly expanded in terrestrial arachnids compared with their marine relatives. Finally, in spite of the phylogenetic diversity, there exists conservation of some exons in size, functional domain, and intron-insertion phase: an 81-bp and a 218-bp exon, respectively, in apq4-like and glp genes across Eumetazoa lineages including arachnids and human beings. Both exons encode the carboxyl-terminal NPA motif, implying the coding and splicing pressure during hundreds of million years of animal evolution. Hypotheses were tested to explore the possible link between these findings and arachnid terrestrialisation.
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, despite historical lack of support in molecular datasets. 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 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 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.
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.
Chelicerate arthropods exhibit dynamic genome evolution, with ancient whole-genome duplication (WGD) events affecting several orders. Yet, genomes remain unavailable for a number of poorly studied orders, such as Opiliones (daddy-long-legs), which has hindered comparative study. We assembled the first harvestman draft genome for the species Phalangium opilio , which bears elongate, prehensile appendages, made possible by numerous distal articles called tarsomeres. Here, we show that the genome of P. opilio exhibits a single Hox cluster and no evidence of WGD. To investigate the developmental genetic basis for the quintessential trait of this group—the elongate legs—we interrogated the function of the Hox genes Deformed ( Dfd ) and Sex combs reduced ( Scr ), and a homologue of Epidermal growth factor receptor ( Egfr ). Knockdown of Dfd incurred homeotic transformation of two pairs of legs into pedipalps, with dramatic shortening of leg segments in the longest leg pair, whereas homeosis in L3 is only achieved upon double Dfd + Scr knockdown. Knockdown of Egfr incurred shortened appendages and the loss of tarsomeres. The similarity of Egfr loss-of-function phenotypic spectra in insects and this arachnid suggest that repeated cooption of EGFR signalling underlies the independent gains of supernumerary tarsomeres across the arthropod tree of life.
Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale datasets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods, or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different datasets. Here, I calculate multiple gene properties for a range of phylogenomic datasets spanning animal, fungal and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared to alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties, and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.
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 (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.
Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.
Despite application of genome-scale datasets, the phylogenetic placement of scorpions within arachnids remains contentious between two different phylogenetic data classes. Paleontologists continue to recover scorpions in a basally branching position, partly owing to their morphological similarity to extinct marine orders like Eurypterida (sea scorpions). Phylogenomic datasets consistently recover scorpions in a derived position, as the sister group of Tetrapulmonata (a clade of arachnids that includes spiders). To adjudicate between these hypotheses using a rare genomic change (RGC), we leveraged the recent discovery of ancient paralogy in spiders and scorpions to assess phylogenetic placement. We identified homologs of four transcription factors required for appendage patterning (dachshund, homothorax, extradenticle, and optomotor blind) in arthropods that are known to be duplicated in spiders. Using genomic resources for a spider, a scorpion, and a harvestman, we conducted gene tree analyses and assayed expression patterns of scorpion gene duplicates. Here we show that scorpions, like spiders, retain two copies of all four transcription factors, whereas arachnid orders like mites and harvestmen bear a single copy. A survey of embryonic expression patterns of the scorpion paralogs closely matches those of their spider counterparts, with one paralog consistently retaining the putatively ancestral pattern found in the harvestman, as well as the mite, and/or other outgroups. These data comprise a rare genomic change in chelicerate phylogeny supporting the inference of a distal placement of scorpions. Beyond demonstrating the diagnostic power of developmental genetic data as a phylogenetic data class, a derived placement of scorpions within the arachnids, together with an array of stem-group Paleozoic scorpions that occupied marine habitats, effectively rules out a scenario of a single colonization of terrestrial habitat within Chelicerata, even in tree topologies contrived to recover the monophyly of Arachnida.
The miniaturized arachnid order Palpigradi has ambiguous phylogenetic affinities owing to its odd combination of plesiomorphic and derived morphological traits. This lineage has never been sampled in phylogenomic datasets because of the small body size and fragility of most species, a sampling gap of immediate concern to recent disputes over arachnid mono-phyly. To redress this gap, we sampled a population of the cave-inhabiting species Eukoenenia spelaea from Slovakia and inferred its placement in the phy-logeny of Chelicerata using dense phylogenomic matrices of up to 1450 loci, drawn from high-quality transcriptomic libraries and complete genomes. The complete matrix included exemplars of all extant orders of Chelicerata. Analyses of the complete matrix recovered palpigrades as the sister group of the long-branch order Parasitiformes (ticks) with high support. However, sequential deletion of long-branch taxa revealed that the position of palpi-grades is prone to topological instability. Phylogenomic subsampling approaches that maximized taxon or dataset completeness recovered palpi-grades as the sister group of camel spiders (Solifugae), with modest support. While this relationship is congruent with the location and architecture of the coxal glands, a long-forgotten character system that opens in the pedipalpal segments only in palpigrades and solifuges, we show that nodal support values in concatenated supermatrices can mask high levels of underlying topological conflict in the placement of the enigmatic Palpigradi.
Historically, morphological characters have been used to support the monophyly, composition, and phylogenetic relationships of scorpion families. Although recent phylogenomic analyses have recovered most of these traditional higher-level relationships as non-monophyletic, certain key taxa have yet to be sampled using a phylogenomic approach. Salient among these is the monotypic genus Caraboctonus Pocock, 1893, the type species of the family Caraboctonidae Kraepelin, 1905. Here, we examined the putative monophyly and phylogenetic placement of this family, sampling the library of C. keyserlingi Pocock, 1893 using high throughput transcriptomic sequencing. Our phylogenomic analyses recovered Caraboctonidae as polyphyletic due to the distant placement of the genera Caraboctonus and Hadrurus Thorell, 1876. Caraboctonus was stably recovered as the sister-group of the monotypic family Superstitioniidae Stahnke, 1940, whereas Hadrurus formed an unstable relationship with Uroctonus Thorell, 1876 and Belisarius Simon, 1879. Four-cluster likelihood mapping revealed that the instability inherent to the placement of Hadrurus, Uroctonus and Belisarius was attributable to significant gene tree conflict in the internodes corresponding to their divergences. To redress the polyphyly of Caraboctonidae, the following systematic actions have been taken: (1) the family Caraboctonidae has been delimited to consist of 23 species in the genera Caraboctonus and Hadruroides Pocock, 1893; (2) Caraboctonidae, previously included in the superfamily Iuroidea Thorell, 1876 or as incertae sedis, is transferred to the superfamily Caraboctonoidea (new rank); (3) the superfamily Hadruroidea (new rank) is established and the status of Hadrurinae Stahnke, 1973 is elevated to family (Hadruridae new status) including 9 species in the genera Hadrurus and Hoffmannihadrurus Fet & Soleglad, 2004 and (4) we treat Uroctonus and Belisarius as insertae sedis with respect to superfamilial placement. Our systematic actions engender the monophyly of both Iuroidea and Caraboctonidae. Future phylogenomic investigations should target similar taxon-poor and understudied lineages of potential phylogenetic significance, which are anticipated to reveal additional non-monophyletic groups.
Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa-or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.
We found support for clades that clarified key controversies in chelicerate phylogeny. Foremost among these is the alliance between mites and ticks, resulting in a grouping of arachnids with even more species than spiders. More broadly, our results suggest that the success of the arachnid order was most likely based on a single terrestrialisation event that happened after the last common ancestor of the horseshoe crabs diverged from the last common ancestor of Arachnida. Our analyses have also proposed some novel clades that need corroboration (such as a putative sister group relationship between Opiliones and Ricinulei, and an alliance between Pseudoscorpiones and Arachnopulmonata). We caution, however, that such lineages as Palpigradi and Opiliocarida remain unsampled. While further taxonomic sampling is needed to fully clarify the evolutionary history of chelicerates, consilience of genomic and morphological results marks a significant advance in our understanding of chelicerate evolution.
OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up of the resource coverage, sampling the genomic diversity of 1271 eukaryotes, 6013 prokaryotes and 6488 viruses. These include putative orthologs among 448 metazoan, 117 plant, 549 fungal, 148 protist, 5609 bacterial, and 404 archaeal genomes, picking up the best sequenced and annotated representatives for each species or operational taxonomic unit. OrthoDB relies on a concept of hierarchy of levels-of-orthology to enable more finely resolved gene orthologies for more closely related species. Since orthologs are the most likely candidates to retain functions of their ancestor gene, OrthoDB is aimed at narrowing down hypotheses about gene functions and enabling comparative evolutionary studies. Optional registered-user sessions allow on-line BUSCO assessments of gene set completeness and mapping of the uploaded data to OrthoDB to enable further interactive exploration of related annotations and generation of comparative charts. The accelerating expansion of genomics data continues to add valuable information, and OrthoDB strives to provide orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations and to compute evolutionary annotations. The data can be browsed online, downloaded or assessed via REST API or SPARQL RDF compatible with both UniProt and Ensembl.
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.
Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic datasets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code to make it more flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment datasets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi, and prokaryotes that greatly enhance resolution, and datasets are now also available for nematodes, protists, and plants. Here we present BUSCO v3 with example analyses that highlight the wide-ranging utility of BUSCO assessments, which extend beyond quality control of genomics datasets to applications in comparative genomics analyses, gene predictor training, metagenomics, and phylogenomics.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.
Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested datasets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
Opiliones are iconic arachnids with a Palaeozoic origin and a diversity that
reflects ancient biogeographic patterns dating back at least to the times of
Pangea. Owing to interest in harvestman diversity, evolution and biogeography,
their relationships have been thoroughly studied using morphology
and PCR-based Sanger approaches to infer their systematic relationships.
More recently, two studies utilized transcriptomics-based phylogenomics
to explore their basal relationships and diversification, but sampling was
limiting for understanding deep evolutionary patterns, as they lacked
good taxon representation at the family level. Here, we analysed a set of
the 14 existing transcriptomes with 40 additional ones generated for this
study, representing approximately 80% of the extant familial diversity in
Opiliones. Our phylogenetic analyses, including a set of data matrices
with different gene occupancy and evolutionary rates, and using a multitude
of methods correcting for a diversity of factors affecting phylogenomic data
matrices, provide a robust and stable Opiliones tree of life, where most families
and higher taxa are precisely placed. Our dating analyses using alternative
calibration points, methods and analytical parameters provide well-resolved
old divergences, consistent with ancient regionalization in Pangea in some
groups, and Pangean vicariance in others. The integration of state-of-the-art
molecular techniques and analyses, together with the broadest taxonomic
sampling to date presented in a phylogenomic study of harvestmen, provide
new insights into harvestmen interrelationships, as well as an overview of
the general biogeographic patterns of this ancient arthropod group.
MicroRNAs are small (~22 nucleotide) noncoding RNAs that repress translation and therefore regulate the production of proteins
from specific target mRNAs. microRNAs have been found to function in diverse aspects of gene regulation within animal development
and many other processes. Among invertebrates, both conserved and novel, lineage specific, microRNAs have been extensively
studied predominantly in holometabolous insects such as Drosophila melanogaster. However little is known about microRNA repertoires in other arthropod lineages such as the chelicerates. To understand the
evolution of microRNAs in this poorly sampled subphylum, we characterized the microRNA repertoire expressed during embryogenesis
of the common house spider Parasteatoda tepidariorum. We identified a total of 148 microRNAs in P. tepidariorum representing 66 families. Approximately half of these microRNA families are conserved in other metazoans, while the remainder
are specific to this spider. Of the 35 conserved microRNAs families 15 had at least two copies in the P. tepidariorum genome. A BLAST based approach revealed a similar pattern of duplication in other spiders and a scorpion, but not among other
chelicerates and arthropods, with the exception of a horseshoe crab. Among the duplicated microRNAs we found examples of lineage
specific tandem duplications, and the duplication of entire microRNA clusters in three spiders, a scorpion, and in a horseshoe
crab. Furthermore, we found that paralogs of many P. tepidariorum microRNA families exhibit arm switching, which suggests that duplication was often followed by sub- or neofunctionalization.
Our work shows that understanding the evolution of microRNAs in the chelicerates has great potential to provide insights into
the process of microRNA duplication and divergence and the evolution of animal development.
Metaseiulus occidentalis is an eyeless phytoseiid predatory mite employed for the biological control of agricultural pests including spider mites. Despite appearances, these predator and prey mites are separated by some 400 million years of evolution and radically different lifestyles. We present a 152 Mbp draft assembly of the M. occidentalis genome: larger than that of its favoured prey, Tetranychus urticae, but considerably smaller than those of many other chelicerates, enabling an extremely contiguous and complete assembly to be built - the best arachnid to date. Aided by transcriptome data, genome annotation catalogued 18,338 protein-coding genes and identified large numbers of Helitron transposable elements. Comparisons with other arthropods revealed a particularly dynamic and turbulent genomic evolutionary history. Its genes exhibit elevated molecular evolution, with strikingly high numbers of intron gains and losses, in stark contrast to the deer tick Ixodes scapularis. Uniquely amongst examined arthropods, this predatory mite's Hox genes are completely atomised, dispersed across the genome, and it encodes five copies of the normally single-copy RNA processing Dicer-2 gene. Examining gene families linked to characteristic biological traits of this tiny predator provides initial insights into processes of sex determination, development, immune defence, and how it detects, disables, and digests its prey. As the first reference genome for the Phytoseiidae, and for any species with the rare sex determination system of parahaploidy, the genome of the western orchard predatory mite improves genomic sampling of chelicerates and provides invaluable new resources for functional genomic analyses of this family of agriculturally important mites.
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.
Camel spiders (Arachnida: Solifugae) are one of the arachnid groups characterised by a prosomal dorsal shield composed of three distinct elements: the pro-, meso- and metapeltidium. These are associated respectively with prosomal appendages one to four, five, and six. What is less well known, although noted in the historical literature, is that the coxae of the 4th and 5th prosomal segments (i.e. walking legs 2 and 3) of camel spiders are also separated ventrally by a distinct membranous region, which is absent between the coxae of the other legs. We suggest that this essentially ventral division of the prosoma specifically between coxae 2 and 3 is homologous with the so-called sejugal furrow (the sejugal interval sensu van der Hammen). This division constitutes a fundamental part of the body plan in acariform mites (Arachnida: Acariformes). If homologous, this sejugal furrow could represent a further potential synapomorphy for (Solifugae + Acariformes); a relationship with increasing morphological and molecular support. Alternatively, outgroup comparison with sea spiders (Pycnogonida) and certain early Palaeozoic fossils could imply that the sejugal furrow defines an older tagma, derived from a more basal grade of organisation. In this scenario the (still) divided prosoma of acariform mites and camel spiders would be plesiomorphic. This interpretation challenges the textbook arachnid character of a peltidium (or 'carapace') covering an undivided prosoma.
Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology. We applied a phylogenomic assessment to resolve scorpion phylogeny, for the first time, to our knowledge, sampling extensive molecular sequence data from all superfamilies and examining basal relationships with up to 5025 genes. Analyses of supermatrices as well as species tree approaches converged upon a robust basal topology of scorpions that is entirely at odds with traditional systematics and controverts previous understanding of scorpion evolutionary history. All analyses unanimously support a single origin of katoikogenic development, a form of parental investment wherein embryos are nurtured by direct connections to the parent's digestive system. Based on the phylogeny obtained herein, we propose the following systematic emendations: Caraboctonidae is transferred to Chactoidea NEW SUPERFAMILIAL ASSIGNMENT: ; superfamily Bothriuroidea REVALIDATED: is resurrected and Bothriuridae transferred therein; and Chaerilida and Pseudochactida are synonymized with Buthida NEW PARVORDINAL SYNONYMIES: .
© 2015 The Author(s) Published by the Royal Society. All rights reserved.
In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption
of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary
model. Though partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search
algorithms due to the existence of phylogenetic (partial) terraces. Here we introduce the phylogenetic terrace aware (PTA)
data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces
and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial
speedup of up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML implementations, respectively. PTA is generally
applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic
inference software.
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast
programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus,
there is need for additional approaches that employ different search strategies to find ML trees and that are at the same
time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation
method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found
higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use
the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein
alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE
is freely available at http://www.cibiv.at/software/iqtree.
Palpigradi are a poorly understood group of delicate arachnids, often found in caves or other subterranean habitats. Concomitantly, they have been neglected from a phylogenetic point of view. Here we present the first molecular phylogeny of palpigrades based on specimens collected in different subterranean habitats, both endogean (soil) and hypogean (caves), from Australia, Africa, Europe, South America and North America. Analyses of two nuclear ribosomal genes and COI under an array of methods and homology schemes found monophyly of Palpigradi, Eukoeneniidae and a division of Eukoeneniidae into four main clades, three of which include samples from multiple continents. This supports either ancient vicariance or long-range dispersal, two alternatives we cannot distinguish with the data at hand. In addition, we show that our results are robust to homology scheme and analytical method, encouraging further use of the markers employed in this study to continue drawing a broader picture of palpigrade relationships.
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.
To tackle incongruence, the topological conflict between different gene trees, phylogenomic studies couple concatenation with practices such as rogue taxon removal or the use of slowly evolving genes. Phylogenomic analysis of 1,070 orthologues from 23 yeast genomes identified 1,070 distinct gene trees, which were all incongruent with the phylogeny inferred from concatenation. Incongruence severity increased for shorter internodes located deeper in the phylogeny. Notably, whereas most practices had little or negative impact on the yeast phylogeny, the use of genes or internodes with high average internode support significantly improved the robustness of inference. We obtained similar results in analyses of vertebrate and metazoan phylogenomic data sets. These results question the exclusive reliance on concatenation and associated practices, and argue that selecting genes with strong phylogenetic signals and demonstrating the absence of significant incongruence are essential for accurately reconstructing ancient divergences.
We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including
options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained
alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples
to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to
clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
Mites (Acari) have traditionally been treated as monophyletic, albeit composed of two major lineages: Acariformes and Parasitiformes. Yet recent studies based on morphology, molecular data, or combinations thereof, have increasingly drawn their monophyly into question. Furthermore, the usually basal (molecular) position of one or both mite lineages among the chelicerates is in conflict to their morphology, and to the widely accepted view that mites are close relatives of Ricinulei.
The phylogenetic position of the acariform mites is examined through employing SSU, partial LSU sequences, and morphology from 91 chelicerate extant terminals (forty Acariformes). In a static homology framework, molecular sequences were aligned using their secondary structure as guide, whereby regions of ambiguous alignment were discarded, and pre-aligned sequences analyzed under parsimony and different mixed models in a Bayesian inference. Parsimony and Bayesian analyses led to trees largely congruent concerning infra-ordinal, well-supported branches, but with low support for inter-ordinal relationships. An exception is Solifugae + Acariformes (P. P = 100%, J. = 0.91). In a dynamic homology framework, two analyses were run: a standard POY analysis and an analysis constrained by secondary structure. Both analyses led to largely congruent trees; supporting a (Palpigradi (Solifugae Acariformes)) clade and Ricinulei as sister group of Tetrapulmonata with the topology (Ricinulei (Amblypygi (Uropygi Araneae))). Combined analysis with two different morphological data matrices were run in order to evaluate the impact of constraining the analysis on the recovered topology when employing secondary structure as a guide for homology establishment. The constrained combined analysis yielded two topologies similar to the exclusively molecular analysis for both morphological matrices, except for the recovery of Pedipalpi instead of the (Uropygi Araneae) clade. The standard (direct optimization) POY analysis, however, led to the recovery of trees differing in the absence of the otherwise well-supported group Solifugae + Acariformes.
Previous studies combining ribosomal sequences and morphology often recovered topologies similar to purely morphological analyses of Chelicerata. The apparent stability of certain clades not recovered here, like Haplocnemata and Acari, is regarded as a byproduct of the way the molecular homology was previously established using the instrumentalist approach implemented in POY. Constraining the analysis by a priori homology assessment is defended here as a way of maintaining the severity of the test when adding new data to the analysis. Although the strength of the method advocated here is keeping phylogenetic information from regions usually discarded in an exclusively static homology framework; it still has the inconvenience of being uninformative on the effect of alignment ambiguity on resampling methods of clade support estimation. Finally, putative morphological apomorphies of Solifugae + Acariformes are the reduction of the proximal cheliceral podomere, medial abutting of the leg coxae, loss of sperm nuclear membrane, and presence of differentiated germinative and secretory regions in the testis delivering their products into a common lumen.
The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed. The discovery that terrestrial insects (Hexapoda) are more closely related to aquatic Crustacea than to the terrestrial centipedes and millipedes (Myriapoda) was an early, if exceptional, success. More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions. Here we present strongly supported results from likelihood, Bayesian and parsimony analyses of over 41 kilobases of aligned DNA sequence from 62 single-copy nuclear protein-coding genes from 75 arthropod species. These species represent every major arthropod lineage, plus five species of tardigrades and onychophorans as outgroups. Our results strongly support Pancrustacea (Hexapoda plus Crustacea) but also strongly favour the traditional morphology-based Mandibulata (Myriapoda plus Pancrustacea) over the molecule-based Paradoxopoda (Myriapoda plus Chelicerata). In addition to Hexapoda, Pancrustacea includes three major extant lineages of 'crustaceans', each spanning a significant range of morphological disparity. These are Oligostraca (ostracods, mystacocarids, branchiurans and pentastomids), Vericrustacea (malacostracans, thecostracans, copepods and branchiopods) and Xenocarida (cephalocarids and remipedes). Finally, within Pancrustacea we identify Xenocarida as the long-sought sister group to the Hexapoda, a result confirming that 'crustaceans' are not monophyletic. These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships.
Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized.
Availability: trimAl has been written in C++, it is portable to all platforms. trimAl is freely available for download (http://trimal.cgenomics.org) and can be used online through the Phylemon web server (http://phylemon2.bioinfo.cipf.es/). Supplementary Material is available at http://trimal.cgenomics.org/publications.
Contact: tgabaldon@crg.es
The phylogeny of the extant chelicerate orders is examined in the light of morphological and molecular evidence. Representatives from each of the chelicerate 'orders' and mandibulate and onychophoran outgroups are examined. Molecular (small and large ribosomal subunit DNA) and morphological information is combined in a total evidence regime to determine the most consistent picture of extant chelicerate relationships for these data. Multiple phylogenetic analyses are performed with variable analysis parameters yielding largely consistent results. A normalized incongruence length metric is used to assay the relative merit of the multiple analyses. The combined analysis with lowest character incongruence yields the scheme of relationships (Pycnogonida+ (Xiphosura+((Opiliones+((Solifugae+Pseudoscorpiones)+Scorpiones))+((Ricinulei+Acari)+(Palpigradi+ ((Thelyphonida+Schizomida=Uropygi)+(Amblypygi+ Araneae))))))). This result is fairly robust to variation in analysis parameters, with the placement of solifugids and the status of the pedipalps responsible for most disagreement.
Pedipalpi Latreille, 1810 is a poorly studied clade of arachnids comprising the whip spiders (Amblypygi Thorell, 1883), short‐tailed whip scorpions (Schizomida Petrunkevitch, 1945) and whip scorpions (Thelyphonida Cambridge, 1872). It has recently been shown that whip spiders coat their exoskeleton with a solid cement layer (cerotegument) that forms elaborate microstructures and turns the cuticle into a super‐hydrophobic state. The amblypygid cerotegument provides taxonomic information due to its fine structural diversity, but its presence and variation in the sister groups was unknown. The present contribution reports the structure of the cuticle in species of Palpigradi, Thelyphonida, and Schizomida to determine if they possess an epicuticular secretion coat. Scanning electron microscopy revealed that only species of Thelyphonida possess such secretions. Unlike in the Amblypygi, this layer does not usually form microstructures and is less rigidly attached to the underlying cuticle. A species of Typopeltis Pocock, 1894, which exhibited globular structures analogous to the amblypygid cerotegument, was the exception. Glandular structures associated with cement secretions in Amblypygi and Thelyphonida were considered homologous due to similar structure. Solid epicuticular secretion coats were absent from Schizomida, which is interpreted as a secondary loss despite the presence of slit‐like glandular openings that appear to produce such epicuticular secretions. The micro‐whip scorpion order Palpigradi Thorell, 1900 exhibited markedly different cuticular surface structures and lacked solid epicuticular secretions, consistent with the hypothesis that this order is not closely related to Pedipalpi. These results enhance knowledge of the small, enigmatic orders of Arachnida.
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The majority of extant arachnids are terrestrial, but other chelicerates are generally aquatic, including horseshoe crabs, sea spiders, and the extinct eurypterids. It is necessary to determine whether arachnids are exclusively descended from a single common ancestor (monophyly), because only that relationship is compatible with one land colonisation in chelicerate evolutionary history. Some studies have cast doubt on arachnid monophyly and recast the origins of their terrestrialization. These include some phyloge-nomic analyses placing horseshoe crabs within Arachnida, and from aquatic Palaeozoic stem-group scorpions. Here, we evaluate the possibility of arachnid monophyly by considering morphology, fossils and molecules holistically. We argue arachnid monophyly obviates the need to posit reacquisition/ retention of aquatic characters such as gnathobasic feeding and book gills without trabeculae from terrestrial ancestors in horseshoe crabs, and that the scorpion total-group contains few aquatic taxa. We built a matrix composed of 200 slowly-evolving genes and re-analysed two published molecular data-sets. We retrieved arachnid monophyly where other studies did not-highlighting the difficulty of resolving chelicerate relationships from current molecular data. As such, we consider arachnid mono-phyly the best-supported hypothesis. Finally, we inferred that arachnids terrestrialized during the CambrianeOrdovician using the slow-evolving molecular matrix, in agreement with recent analyses.
The Neartic family Vaejovidae (Scorpiones: Chactoidea) has long been treated as a diverse and systematically cohesive group of scorpions, but its monophyly and relationship to other scorpion families have historically been questioned. Morphological data have supported its monophyly and a variety of phylogenetic placements within the superfamily Chactoidea. Recent phylogenomic analyses have instead recovered vaejovids as polyphyletic (albeit with minimal taxonomic sampling) and Chactoidea as paraphyletic. Here, we reexamined the monophyly and phylogenetic placement of the family Vaejovidae, sampling 17 new vaejovid libraries using high throughput transcriptomic sequencing. Our phylogenomic analyses revealed a previous misplacement of Smeringurus mesaensis. Regardless, we recovered Vaejovidae as diphyletic due to the placement of the enigmatic genus Uroctonus. The remaining vaejovids formed a clade that was strongly supported as the sister group of the superfamily Scorpionoidea, a placement insensitive to matrix completeness or concatenation vs. species tree approaches to inferring the tree topology. Chactoidea was invariably recovered as a paraphyletic group due to the nested placement of Scorpionoidea. As first steps to resolving the paraphyly of Chactoidea, we take the following systematic actions: (1) we establish the superfamily Superstitionoidea (new superfamily) to accommodate Superstitioniidae; (2) we restore Vaejovoidea (status revalidated) as a valid superfamily that excludes Uroctonus; and (3) we treat the families Caraboctonidae, Troglotayosicidae, and the subfamily Uroctoninae as incertae sedis with respect to superfamilial placement. Our systematic actions thus establish the monophyly of the presently redefined Chactoidea and Vaejovoidea.
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 reevaluated the placement of Xiphosura among chelicerates using the most complete phylogenetic dataset 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 incomplete lineage sorting. 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.
Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, reject a single origin of the orb web (the "ancient orb-web hypothesis") and suggest that orb webs evolved multiple times since the late Triassic-Jurassic. We find no significant association between the loss of foraging webs and increases in diversification rates, suggesting that other factors (e.g., habitat heterogeneity or biotic interactions) potentially played a key role in spider diversification. Finally, we report notable genomic differences in the main spider lineages: while araneoids (ecribellate orb-weavers and their allies) reveal an enrichment in genes related to behavior and sensory reception, the retrolateral tibial apophysis (RTA) clade-the most diverse araneomorph spider lineage-shows enrichment in genes related to immune responses and polyphenic determination. This study, one of the largest invertebrate phylogenomic analyses to date, highlights the usefulness of transcriptomic data not only to build a robust backbone for the Spider Tree of Life, but also to address the genetic basis of diversification in the spider evolutionary chronicle.
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________________________________Eriophyoid, or four-legged mites, represent a large and ancient radiation of exclusively phytophagous organisms known from the Triassic (230 Mya). Hypothesizing phylogenetic relatedness of Eriophyoidea among mites is a major challenge due to the absence of unambiguous morphological synapomorphies, resulting in ten published hypotheses placing eriophyoids in various places in the acariform tree of life. Here we test the evolutionary relationships of eriophyoids using six genes and a representative taxonomic sampling of acariform mites. The total evidence analysis places eriophyoids as the sister group of the deep soil-dwelling, vermiform family Nematalycidae (Endeostigmata). This arrangement was supported by the rDNA and CO1 partitions. In contrast, the nuclear protein partition (genes EF1-α, SRP54, HSP70) suggests that Eriophyoidea is sister to a lineage including Tydeidae, Ereynetidae, and Eupodidae (Eupodina: Trombidiformes). On both of these alternative topologies, eriophyoids appear as a long branch, probably involving the loss of basal diversity in early evolution. We analyze this result by using phylogenetically explicit hypothesis testing, investigating the phylogenetic signal from individual genes and rDNA stem and loop regions, and removing long branches and rogue taxa. Regardless of the two alternative placements, (i) the cheliceral morphology of eriophyoids, one of the traits deemed phylogenetically important, was likely derived directly from the plesiomorphic acariform chelicerae rather than from the modified chelicerae of some trombidiform lineages with a reduced fixed digit; and (ii) two potential synapomorphies of Eriophyoidea+Raphignathina (Trombidiformes) related to the reduction of genital papillae and to the terminal position of PS segment can be dismissed as result of convergent evolution. Our analyses substantially narrow the remaining available hypotheses on eriophyoid relationships and provide insights on the early evolution of acariform mites.
Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum likelihood (ML) frameworks, their formidable computational time and memory usage severely limits their use in large phylogenomic analyses. Here we propose a posterior mean site frequency (PMSF) method as a rapid and efficient approximation to full empirical profile mixture models for ML analysis. The PMSF approach assigns a conditional mean amino acid frequency profile to each site calculated based on a mixture model fitted to the data using a preliminary guide tree. These PMSF profiles can then be used for in-depth tree-searching in place of the full mixture model. Compared with widely used empirical mixture models with
k
classes, our implementation of PMSF in IQ-TREE (http://www.iqtree.org) speeds up the computation by approximately
k
/1.5-fold and requires a small fraction of the RAM. Furthermore, this speedup allows, for the first time, full nonparametric bootstrap analyses to be conducted under complex site-heterogeneous models on large concatenated data matrices. Our simulations and empirical data analyses demonstrate that PMSF can effectively ameliorate long-branch attraction artefacts. In some empirical and simulation settings PMSF provided more accurate estimates of phylogenies than the mixture models from which they derive.
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Current sequencing technologies are making available unprecedented amounts of genetic data for a large variety of species
including non-model organisms. Although many phylogenomic surveys spend considerable time finding orthologs from the wealth
of sequence data, these results do not transcend the original study and after being processed for specific phylogenetic purposes
these orthologs do not become stable orthology hypotheses. We describe a procedure to detect and document the phylogenetic
distribution of orthologs allowing researchers to use this information to guide selection of loci best suited to test specific evolutionary questions. At the core of this pipeline is a new phylogenetic orthology method
that is neither affected by the position of the root nor requires explicit assignment of outgroups. We discuss the properties
of this new orthology assessment method and exemplify its utility for phylogenomics using a small insects dataset. Additionally
we exemplify the pipeline to identify and document stable orthologs for the group of orb-weaving spiders (Araneoidea) using
RNAseq data.The scripts used in this study, along with sample files and additional documentation, are available at https://github.com/ballesterus/UPhO.
Genomics has revolutionised biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50.
We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. We implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO.
Software implemented in Python and datasets available for download from http://busco.ezlab.org.
Evgeny.Zdobnov@unige.ch.
© The Author (2015). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
The monophyly of Ecdysozoa, which comprise molting phyla, has received strong support from several lines of evidence. However, the internal relationships of Ecdysozoa are still contended. We generated expressed sequence tags from a priapulid (penis worm), a kinorhynch (mud dragon), a tardigrade (water bear) and five chelicerate taxa by 454 transcriptome sequencing. A multigene alignment was assembled from 63 taxa, which comprised after matrix optimization 24,249 amino acid positions with high data density (2.6% gaps, 19.1% missing data). Phylogenetic analyses employing various models support the monophyly of Ecdysozoa. A clade combining Priapulida and Kinorhyncha (i.e. Scalidophora) was recovered as the earliest branch among Ecdysozoa. We conclude that Cycloneuralia, a taxon erected to combine Priapulida, Kinorhyncha and Nematoda (and others), are paraphyletic. Rather Arthropoda (including Onychophora) are allied with Nematoda and Tardigrada. Within Arthropoda, we found strong support for most clades, including monophyletic Mandibulata and Pancrustacea. The phylogeny within the Euchelicerata remained largely unresolved. There is conflicting evidence on the position of tardigrades: While Bayesian and maximum likelihood analyses of only slowly evolving genes recovered Tardigrada as a sister group to Arthropoda, analyses of the full data set, and of subsets containing genes evolving at fast and intermediate rates identified a clade of Tardigrada and Nematoda. Notably, the latter topology is also supported by the analyses of indel patterns.
Chelicerata represents one of the oldest groups of arthropods, with a fossil record extending to the Cambrian, and is sister to the remaining extant arthropods, the mandibulates. Attempts to resolve the internal phylogeny of chelicerates have achieved little consensus, due to marked discord in both morphological and molecular hypotheses of chelicerate phylogeny. The monophyly of Arachnida, the terrestrial chelicerates, is generally accepted, but has garnered little support from molecular data, which have been limited either in breadth of taxonomic sampling or depth of sequencing. To address the internal phylogeny of this group, we employed a phylogenomic approach, generating transcriptomic data for 17 species in combination with existing data, including two complete genomes. We analyzed multiple datasets containing up to 1,235,912 sites across 3,644 loci, using alternative approaches to optimization of matrix composition. Here we show that phylogenetic signal for the monophyly of Arachnida is restricted to the 500 slowest-evolving genes in the dataset. Accelerated evolutionary rates in the orders Acariformes, Pseudoscorpiones, and Parasitiformes potentially engender long-branch attraction artifacts, yielding non-monophyly of Arachnida with increasing support upon incrementing the number of concatenated genes. Mutually exclusive hypotheses are supported by locus groups of variable evolutionary rate, revealing significant conflicts in phylogenetic signal. Analyses of gene-tree discordance indicate marked incongruence in relationships among chelicerate orders, whereas derived relationships are demonstrably robust. Consistently recovered and supported relationships include the monophyly of Chelicerata, Euchelicerata, Tetrapulmonata, and all orders represented by multiple terminals. Relationships supported by subsets of slow-evolving genes include Ricinulei + Solifugae; a clade comprised of Ricinulei, Opiliones, and Solifugae; and a clade comprised of Tetrapulmonata, Scorpiones, and Pseudoscorpiones. We demonstrate that outgroup selection without regard for branch length distribution exacerbates long branch attraction artifacts and does not mitigate gene-tree discordance, regardless of high gene representation for outgroups that are model organisms. Arachnopulmonata (new name) is proposed for the clade comprising Scorpiones + Tetrapulmonata (previously named Pulmonata).
Progress in sequencing technology allows researchers to assemble ever-larger supermatrices for phylogenomic inference. However, current phylogenomic studies often rest on patchy data sets, with some having 80% missing (or ambiguous) data or more. Though early simulations had suggested that missing data per se do not harm phylogenetic inference when using sufficiently large data sets, Lemmon et al. (Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM. 2009. The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference. Syst Biol. 58:130-145.) have recently cast doubt on this consensus in a study based on the introduction of parsimony-uninformative incomplete characters. In this work, we empirically reassess the issue of missing data in phylogenomics while exploring possible interactions with the model of sequence evolution. First, we note that parsimony-uninformative incomplete characters are actually informative in a probabilistic framework. A reanalysis of Lemmon's data set with this in mind gives a very different interpretation of their results and shows that some of their conclusions may be unfounded. Second, we investigate the effect of the progressive introduction of missing data in a complete supermatrix (126 genes × 39 species) capable of resolving animal relationships. These analyses demonstrate that missing data perturb phylogenetic inference slightly beyond the expected decrease in resolving power. In particular, they exacerbate systematic errors by reducing the number of species effectively available for the detection of multiple substitutions. Consequently, large sparse supermatrices are more sensitive to phylogenetic artifacts than smaller but less incomplete data sets, which argue for experimental designs aimed at collecting a modest number (∼50) of highly covered genes. Our results further confirm that including incomplete yet short-branch taxa (i.e., slowly evolving species or close outgroups) can help to eschew artifacts, as predicted by simulations. Finally, it appears that selecting an adequate model of sequence evolution (e.g., the site-heterogeneous CAT model instead of the site-homogeneous WAG model) is more beneficial to phylogenetic accuracy than reducing the level of missing data.
ZusamrnenfassungIm letzten Jahrzehnt sind eine Reihe von Klassifikationen der Chelicerata veröffentlicht worden, die nicht auf Synapomorphien gründen. Das Ziel der vorliegenden Untersuchung ist ein cladistisches System und eine plausible Vorstellung von der Entfaltung der Chelicerata.Zum Grundbauplan der Chelicerata gehört ein ungeteiltes Prosoma mit sechs extremitätentragenden Segmenten sowie ein Opisthosoma aus 12 Segmenten und dem Tergaldorn eines reduzierten 13. Segmentes.Es gibt keinen Hinweis darauf, daß die Scorpiones ein Tergit reduziert haben; ihre 12 Tergite entsprechen den ursprünglichen 12 Opisthosomasegmenten. Jedoch werden die ventralen Teile der Anlage des zweiten Opisthosomasegmentes sekundär unterteilt. Diese Unterteilung und die daraus entstehenden Kämme mit ihren Ganglien und Blutgefäßen stellen eine Synapomorphie der Scorpiones dar.Ein Schlüsselereignis in der Evolution der Chelicerata ist die Entwicklung der räuberischen Lebensweise. Sie hat zur Verkürzung der ursprünglichen ventralen Nahrungsrinne geführt. Die Extremitäten des ersten Opisthosomasegmentes (Chilaria, Metastoma) übernehmen zunächst die hintere Begrenzung der Nahrungsrinne bzw. des daraus entstehenden Mundvorraumes.Zahlreiche mohologische, ultrastrukturelle, entwicklungsgeschichtliche und ethologische Merkmale werden darauxin untersucht, ob sie Synapomorphien zur Begründung eines cladistischen Systems liefem. Neben den klassischen morphologischen Merkmalen ergaben besonders die Feinstruktur der Spermatozoen und der Lichtsinnesorgane überzeugende Synapomorphien. Das Ergebnis dieser Unter-suchungen ist das Cladogramm (I) (S. 179/180) und die ihm zugrunde liegenden Synapomorphien (Tab., S. 178/179). Die wichtigsten Folgerungen sind:1. Die Chelicerata sind ein monophyletisches Taxon; ihre Schwestergruppe sind die Olenellida.2. Die Aglaspida sind die plesiomorphe Schwestergruppe aller übrigen Chelicerata (Euchelicerata).3. Innerhalb dieser sind die Xiphosurida die plesiomorphe Schwestergruppe aller übrigen Chelicerata (Metastomata).4. Diese spalten sich früh in die Eurypterida und Arachnida. Die Arachnida sind also eine mono-phyletische Gruppe, und wahrscheinlich ist schon ihre Stammform zum Landleben übergegangen.5. Innerhalb der Arachnida sind die Ctenophora oder Pectinifera (einzige Ordnung: Scorpiones) die Schwestergruppe aller übrigen (epectinaten) Arachniden (Lipoctena).6. Innerhalb der Lipoctena sind die Uropygi, Amblypygi, Araneae (Megoperculata) die Schwestergruppe der übrigen Ordnungen, die als Apulrnonata zusammengefaßt werden.7. Die Pantopoda werden als Chelicerata aufgefaßt, doch 1äßt sich zur Zeit nicht entscheiden, ob sie als die Schwestergruppe aller anderen Chelicerata angesehen werden müssen oder als die Schwestergruppe der Euchelicerata.SummaryStudies on the morphology, taxonomy and phylogeny of the Chelicerata. Part I and IIThe aim of the present investigation is to present a cladistic classification of the Chelicerata based on synapomorphies and to develop plausible ideas on the evolution of the Chelicerata.The basic body pattern (Grundbauplan, that is, the most plesiomorphous condition of the chelicerate body) comprises an undivided prosoma containing six limb-bearing segments and an opisthosoma consisting of 12 segments and terminating in a tergal spine of a reduced 13th segment (usually erroneously termed telson).There is no indication of a reduced first tergite in scorpions; their 12 tergites correspond to the original 12 opisthosomal segments. However, the ventral parts of the second opisthosomal segment have been divided secondarily thereby giving rise to the combs or pectines with their ganglia and blood vessels. This division of the ventral arts of the second oisthosomal segment and the pectines and their associated structures are considered synapomorphous characters of the Scorpiones.One of the key events of chelicerate evolution was the acuisition of a predatory mode of life. This has lead to the reduction and disappearance of the ventral Sood roove. The appendages of the first opisthosomal segment (Chilaria, Metastoma) became transformed to form the posterior border of the food groove or preoral cavity.Numerous morphological, ultrastructural, embryological, and ethological characters have been investigated with respect to the question whether they offer synapomorphies which can be used to construct a cladistic classification. The fine structure of spermatozoa and light sense organs proved to be especially interesting and rewarding in this respect. The most important results, represented in Cladogram (I) (fig. 1) and Tab. (p. 178–179), are:1. The Chelicerata constitute a monophyletic taxon; their sister grou are the Olenellida.2. The Aglaspida are the lesiomorphous sister group of the other Clelicerata (Euchelicerata).3. Within these, the Xiphosurida are the plesiomorphous sister group of the remaining chelicerates (Metastomata).4. These have subsequently split into the Eurypterida and Arachnida. The Arachnida, therefore, are a monophletic taxon, and their stem species started invasion of land and terrestrial life.5. Within the Arachnida, the Ctenophora or Pectinifera (only order: Scorpiones) are the sister group of all other (epectinate) arachnids (Lipostena).6. Within these, the Uropygi, Amblypygi, Araneae (Megoperculata) constitute the sister group of the remaining orders which are uniteed as the Apulmonata.7. These early split into the Palpiradi and the Holotracheata, and these again into the Haplocnemata (= Pseudoscorpiones and Solifugae) and the Cryptoperculata (= Opiliones, Ricinulei, Acari).8. The Acari are considered a monophyletic taxon because all attempts to indicate a closer relationship of parts of the Acari with other arachnids have not been convincing so far.9. The classification of the Apulmonata and their further subdivisions are problematical because supposed synapomorphies become increasingly less convincing. However, as long as no other synapomorphies are shown which make a different classification more probable, we consider the present classification the most plausible one.10. Pantopoda (Pycnogonida) are considered to be chelicerates. They have probably separated from the main stem very early and should be considered either the sister group of all other Chelicerata or of the Euchelicerata.11. The last part of the paper presents a short outline of the possible routes of evolution of the Chelicerata. It could be shown that the first evolutionary steps or changes lead to increasingly more efficient predators and finally to the emergence of a terrestrial line (Arachnida). At least part of the adaptive radiation of the Arachnida most likely was the result of several splittings giving rise to forms which acquired different niches by means of different body sizes.
Abstract— This paper reports results from a cladistic analysis of the 11 Recent arachnid orders. The polarities of 64 newly discovered and traditional characters were determined through outgroup comparisons that included Eurypterida, Xiphosura, Trilobita and Crustacea. A branch-and-bound algorithm was used to discover a single tree (consistency index 0–59). The relationships suggested by this analysis differ substantially from previous interpretations of arachnid phylogeny, and a new taxonomic system is introduced to accommodate these results. This analysis suggests that Arachnida is monophyletic and composed of two principal lineages, Micrura and Dromopoda. Possible synapomorphies of Micrura include a pygidmm, tntosternum, six principal lateral eyes, poorly sclerotized postgenital appendages, coxal gland orifices near leg 1, an array of micxotubules associated with the spermatozoan nucleus, and absence of coxal endites on the walking legs. The micruran orders appear to have the following relationships: (Palpigradi (Araneae (Amblypygi (I helyphonida, Schizomida)))) (Ricinulei, Acari). Possible synapomorphies of Dromopoda include transverse carapaeal furrows, greatly reduced prosomal sternum, prosomal endosternite with two segmental components, stomotheca, bicondylar femoropatellar and patellotibial joints and extensor muscles. The dromopodan orders appear to have the following relationships: Opiliones (Scorpioncs (Pscudo-scorpiones, Solifugae)).
Morphological evidence for resolving relationships among arachnid orders was surveyed and assembled in a matrix comprising 59 euchelicerate genera (41 extant, 18 fossil) and 202 binary and unordered multistate characters. Parsimony analysis of extant genera recovered a monophyletic Arachnida with the topology (Palpigradi (Acaromorpha (Tetrapulmonata (Haplocnemata, Stomothecata nom. nov.)))), with Acaromorpha containing Ricinulei and Acari, Tetrapulmonata containing Araneae and Pedipalpi (Amblypygi, Uropygi), Haplocnemata (Pseudoscorpiones, Solifugae) and Stomothecata (Scorpiones, Opiliones). However, nodal support and results from exploratory implied weights analysis indicated that relationships among the five clades were effectively unresolved. Analysis of extant and fossil genera recovered a clade, Pantetrapulmonata nom nov., with the topology (Trigonotarbida (Araneae (Haptopoda (Pedipalpi)))). Arachnida was recovered as monophyletic with the internal relationships (Stomothecata (Palpigradi, Acaromorpha (Haplocnemata, Pantetrapulmonata))). Nodal support and exploratory implied weights indicated that relationships among these five clades were effectively unresolved. Thus, some interordinal relationships were strongly and/or consistently supported by morphology, but arachnid phylogeny is unresolved at its deepest levels. Alternative hypotheses proposed in the recent literature were evaluated by constraining analyses to recover hypothesized clades, an exercise that often resulted in the collapse of otherwise well-supported clades. These results suggest that attempts to resolve specific nodes based on individual characters, lists of similarities, evolutionary scenarios, etc., are problematic, as they ignore broader impacts on homoplasy and analytical effects on non-target nodes. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 150, 221–265.
The history of long-branch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBA-artifacts include excluding long-branch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LBA such as likelihood, the Aguinaldo et al. approach, sampling more taxa to break up long branches and sampling more characters especially of another kind, and the pros and cons of these are discussed. Methods suggested to detect LBA are numerous and include methodological disconcordance, RASA, separate partition analyses, parametric simulation, random outgroup sequences, long-branch extraction, split decomposition and spectral analysis. Less than 10 years ago it was doubted if LBA occurred in real datasets. Today, examples are numerous in the literature and it is argued that the development of methods to deal with the problem is warranted. A 16 kbp dataset of placental mammals and a morphological and molecular combined dataset of gall waSPS are used to illustrate the particularly common problem of LBA of problematic ingroup taxa to outgroups. The preferred methods of separate partition analysis, methodological disconcordance, and long branch extraction are used to demonstrate detection methods. It is argued that since outgroup taxa almost always represent long branches and are as such a hazard towards misplacing long branched ingroup taxa, phylogenetic analyses should always be run with and without the outgroups included. This will detect whether only the outgroup roots the ingroup or if it simultaneously alters the ingroup topology, in which case previous studies have shown that the latter is most often the worse. Apart from that LBA to outgroups is the major and most common problem; scanning the literature also detected the ill advised comfort of high support values from thousands of characters, but very few taxa, in the age of genomics. Taxon sampling is crucial for an accurate phylogenetic estimate and trust cannot be put on whole mitochondrial or chloroplast genome studies with only a few taxa, despite their high support values. The placental mammal example demonstrates that parsimony analysis will be prone to LBA by the attraction of the tenrec to the distant marsupial outgroups. In addition, the murid rodents, creating the classic “the guinea-pig is not a rodent” hypothesis in 1996, are also shown to be attracted to the outgroup by nuclear genes, although including the morphological evidence for rodents and Glires overcomes the artifact. The gall wasp example illustrates that Bayesian analyses with a partition-specific GTR + Γ + I model give a conflicting resolution of clades, with a posterior probability of 1.0 when comparing ingroup alone versus outgroup rooted topologies, and this is due to long-branch attraction to the outgroup.
© The Willi Hennig Society 2005.
For some simple three- and four-species cases involving a character with two states, it is determined under what conditions
several methods of phylogenetic inference will fail to converge to the true phylogeny as more and more data are accumulated.
The methods are the Camin-Sokal parsimony method, the compatibility method, and Farris's unrooted Wagner tree parsimony method.
In all cases the conditions for this failure (which is the failure to be statistically consistent) are essentially that parallel
changes exceed informative, nonparallel changes. It is possible for these methods to be inconsistent even when change is improbable
a priori, provided that evolutionary rates in different lineages are sufficiently unequal. It is by extension of this approach
that we may provide a sound methodology for evaluating methods of phylogenetic inference.