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The Rediscovery of a Relict Unlocks the First Global Phylogeny of Whip Spiders (Amblypygi)
Abstract
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.
... Charinidae with Charontidae. Charinus now belongs to Charontidae, the most diverse family in the order, with around 150 species 10 . The two sequenced Charinus are narrow-range species endemic to ferruginous caves in the Serra dos Carajás 5 , an iron ore mining region, while H. longicornis is widely distributed in northern and central South America 16 . ...
... Thus, the monophyly of the family Phrynidae and the superfamily Phrynoidea were only recovered in the Bayesian inference from amino acids, in which we implement the CAT mixture model. In the phylogenomics of Amblypygi, all datasets (UCE matrices and their combination with Sanger loci) recovered the monophyly of Phrynidae and Phrynoidea with full support 10 . The success in retrieving these taxa only by the Bayesian CAT-GTR model may have been because site-heterogeneous mixture models better fit highly variable sequences and are less prone to systematic errors than classical empirical matrices [39][40][41][42] . ...
The complete mitochondrial genomes of the whip spiders Charinus carajas, C. ferreus, and Heterophrynus longicornis were sequenced, annotated, and compared with other mitogenomes of whip spiders and arachnids. The three new mitogenomes have the 37 genes usually observed in Metazoa: 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs), plus a non-coding control region (CR). Most PCGs presented an ATN start codon, except cox1 in both Charinus species, initiating with TTA. Most PCGs terminated with stop codons TAA or TAG, except nad5 of C. carajas and cox3 of H. longicornis, which presented an incomplete stop codon (T). The Ka/Ks ratios were less than one for all the PCGs, indicating these genes are under purifying selection. All the tRNAs, except for serine 1 (trnS1), had the typical cloverleaf-shaped secondary structure. All the phylogenetic analyses resolved Charinus carajas and C. ferreus as monophyletic groups. Nonetheless, we did not recover the monophyly of Heterophrynus longicornis. The phylogenies under partitioned models did not recover suprageneric taxonomic groups as clades, but the Bayesian inference under the CAT infinite mixture model recovered the family Phrynidae and the superfamily Phrynoidea as monophyletic groups.
... Given the provided information, our study aimed to investigate whether the degree of specialization and the presence of rhythmic elements influence the locomotor activity patterns of troglobitic and troglophilic (non-obligate, capable of establishing populations on the surface) amblypygid species belonging to the genus Charinus. Currently belonging to the family Charontidae (formerly the family Charinidae-junior synonym), this genus boasts a wide distribution, currently comprising 97 species (de Miranda et al., 2024;Miranda et al., 2021). In Brazil, nearly 45% of these species have been recorded (de Souza et al., 2024), with 22 of them identified in cave environments (Chapin & Hebets, 2016;Miranda et al., 2018Miranda et al., , 2021Weygoldt, 2000). ...
The lack of understanding regarding how endogenous and behavioral factors affect the biological rhythms of amblypygid arachnids in cave environments underscores a gap in chronobiologic knowledge for this group. This study investigates the influence of specialization on subterranean habitats and the presence of biological rhythms on the locomotor activity patterns of the troglobitic and troglophilic species of the genus Charinus. Specimens collected from carbonate caves in Brazil were subjected to experimental treatments of constant light (LL), constant darkness (DD), and light–dark cycles (LD). The results revealed variations in the distribution of main periods among species, without a uniform pattern. Although some specimens showed greater variability in activity patterns in the DD and LL treatments, no significant differences were observed between troglobites and troglophiles. The lack of a clear distinction in rhythms between the two groups suggests the dynamic nature of circadian rhythms in these populations, where individual variations in activity patterns indicate this behavioral diversity. Additionally, intraspecific competition for food resources, probably intensified by the oligotrophic conditions of the cave environments, may play an important role in shaping these patterns and differences in activity phases. The presence of infradian rhythms and weak circadian rhythms in some individuals underscores the importance of considering non‐photic zeitgebers for a deeper understanding of these rhythms in cave organisms.
... Within arthropods, the most comprehensive probe set was designed for Arachnida, a group spanning more than 500 million years of evolution (Starrett et al., 2017). However, despite this huge divergence, this probe set has proven to be very useful across all chelicerate groups and across a variety of phylogenetic levels (e.g., Hedin et al., 2020;Ballesteros et al., 2021;Boyer et al., 2022;de Miranda et al., 2024;Sato et al., 2024b). ...
Introduction
Since its introduction about a decade ago, target enrichment sequencing of ultraconserved elements (UCEs) has proven to be an invaluable tool for studies across evolutionary scales, and thus employed from population genetics, to historical biogeography as well as deep-time phylogenetics. Here, we present the first probe set targeting UCEs in crustaceans, specifically designed for decapods and tested beyond decapods in other malacostracan lineages.
Methods
Probes were designed using published genomes of nine decapod and one peracarid species, as well as raw Nanopore long reads of one additional brachyuran species. The final probe set consists of about 20,000 probes, targeting 1,384 unique UCE loci. We compiled a dataset across Malacostraca,as well as datasets of a deep-sea squat lobster genus, and an intertidal mangrove crab species, to test the probe set at different phylogenetic levels (i.e., class, order, genus, within species).
Results
Final mean UCE recovery from fresh samples across Malacostraca was 568 loci, with up to 847 and 658 loci recovered from decapod and non-decapod species, respectively. Final mean recovery from fresh samples in the genus- and within species-level datasets was 849 and 787 loci, respectively. Up to several hundreds of UCEs were recovered from historical museum specimens (10 to > 150 years old), that were included in all datasets. UCE-based phylogenies largely reflected the known relationships of the included taxa, and we were able to infer population differentiation based on >600 SNPs extracted from the species-level dataset.
Discussion
Our results showcase the versatility of this UCE probe set, yielding informative data from phylogenetic as well as population-genetic datasets. They demonstrate once more that UCEs are a promising technique for leveraging museum specimens for genomic studies, and overall highlight the probe set's potential for crustacean evolutionary studies.
... Recently, following the discovery of a new species of Paracharon from Colombia, the first molecular phylogeny for the order was inferred (de Miranda et al., 2022). This phylogeny supports Paracharontidae as the sister group to Euamblypygi. ...
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.
The biota of cave habitats faces heightened conservation risks, due to geographic isolation and high levels of endemism. Molecular datasets, in tandem with ecological surveys, have the potential to precisely delimit the nature of cave endemism and identify conservation priorities for microendemic species. Here, we sequenced ultraconserved elements of Tegenaria within, and at the entrances of, 25 cave sites to test phylogenetic relationships, combined with an unsupervised machine learning approach for detecting species. Our analyses identified clear and well-supported genetic breaks in the dataset that accorded closely with morphologically diagnosable units. Through these analyses, we also detected some previously unidentified, potential cryptic morphospecies. We then performed conservation assessments for seven troglobitic Israeli species of this genus and determined five of these to be critically endangered.
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the interrelationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger-based markers with newly generated and publicly available genome-scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoi-dea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.
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.
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.
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.
Whole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7 Gb, N50 = 90.2 Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2 n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7 Gb, N50 = 109.7 Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD. Comparison of C. rotundicauda and T. tridentatus genomes from populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for improving our understanding of invertebrate WGD events on the evolutionary fates of genes and microRNAs, at both the individual and population level. We also provide improved genomic resources for horseshoe crabs, of applied value for breeding programs and conservation of this fascinating and unusual invertebrate lineage.
Lungfishes belong to lobe-fined fish (Sarcopterygii) that in the Devonian ‘conquered’ land and gave rise to all land vertebrates, including humans 1–3 . We determined the largest chromosome-quality animal genome, the Australian lungfish, Neoceratodus forsteri . Its vast size (~14x of human) is attributable mostly to huge intergenic regions and introns with high repeat content (≈90%) whose components resemble tetrapods more (mostly LINE elements) than ray-finned fish. The lungfish genome continues to expand (its TEs are still active) independently and by different mechanisms than enormous salamander genomes. Synteny to other vertebrate chromosomes of 17 fully assembled macrochromosomes is maintained just as its conserved ancient homology of all microchromosomes to the ancestral vertebrate karyotype. Phylogenomic analyses ascertained that lungfish occupy an evolutionary key-position as closest living relatives to tetrapods, underscoring their importance for understanding innovations associated with terrestrialization 4,5 . Preadaptations to living on land include gaining of limb-like expression of developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and duplication of genes associated with obligate air-breathing such as lung surfactants and the expansion of odorant receptor gene-families that detect airborne odours contribute to their tetrapod-like biology. These findings advance our understanding of this major transition during vertebrate evolution.
The systematics and taxonomy of the tropical Asian jumping spiders of the tribe Baviini is reviewed, with a molecular phylogenetic study (UCE sequence capture, traditional Sanger sequencing) guiding a reclassification of the group’s genera. The well-studied members of the group are placed into six genera: Bavia Simon, 1877, Indopadilla Caleb & Sankaran, 2019, Padillothorax Simon, 1901, Piranthus Thorell, 1895, Stagetillus Simon, 1885, and one new genus, Maripanthus Maddison, gen. nov. The identity of Padillothorax is clarified, and Bavirecta Kanesharatnam & Benjamin, 2018 synonymized with it. Hyctiota Strand, 1911 is synonymized with Stagetillus. The molecular phylogeny divides the baviines into three clades, the Piranthus clade with a long embolus (Piranthus, Maripanthus), the genus Padillothorax with a flat body and short embolus, and the Bavia clade with a higher body and (usually) short embolus (remaining genera). In general, morphological synapomorphies support or extend the molecularly delimited groups. Eighteen new species are described: Bavia nessagyna, Indopadilla bamilin, I. kodagura, I. nesinor, I. redunca, I. redynis, I. sabivia, I. vimedaba, Maripanthus draconis (type species of Maripanthus), M. jubatus, M. reinholdae, Padillothorax badut, P. mulu, Piranthus api, P. bakau, P. kohi, P. mandai, and Stagetillus irri, all sp. nov., with taxonomic authority W. Maddison. The distinctions between baviines and the astioid Nungia Żabka, 1985 are reviewed, leading to four species being moved into Nungia from Bavia and other genera. Fifteen new combinations are established: Bavia maurerae (Freudenschuss & Seiter, 2016), Indopadilla annamita (Simon, 1903), I. kahariana (Prószyński & Deeleman-Reinhold, 2013), I. sonsorol (Berry, Beatty & Prószyński, 1997), I. suhartoi (Prószyński & Deeleman-Reinhold, 2013), Maripanthus menghaiensis (Cao & Li, 2016), M. smedleyi (Reimoser, 1929), Nungia hatamensis (Thorell, 1881), N. modesta (Keyserling, 1883), N. papakula (Strand, 1911), N. xiaolonghaensis (Cao & Li, 2016), Padillothorax casteti (Simon, 1900), P. exilis (Cao & Li, 2016), P. flavopunctus (Kanesharatnam & Benjamin, 2018), Stagetillus banda (Strand, 1911), all comb. nov. One combination is restored, Bavia capistrata (C. L. Koch, 1846). Five of these new or restored combinations correct previous errors of placing species in genera that have superficially similar palps but extremely different body forms, in fact belonging in distantly related tribes, emphasizing that the general shape of male palps should be used with caution in determining relationships. A little-studied genus, Padillothorus Prószyński, 2018, is tentatively assigned to the Baviini. Ligdus Thorell, 1895 is assigned to the Ballini.
The whip spider (Amblypygi) genus Paraphrynus Moreno, 1940 is distributed from the southern U.S.A. to the Greater Antilles and northern South America. Mexico is the diversity hotspot of the genus where many morphologically similar species occur, often in close geographical proximity. The present contribution aimed to resolve the diversity and phylogenetic relationships within the aztecus group of species, which includes the type species, Paraphrynus mexicanus (Bilimek, 1867), resulting in the description of a new species from Mexico, Paraphrynus pseudomexicanus sp.n. This is the first study to integrate morphology, karyotype, and DNA for species delimitation in whip spiders. Karyotype data have not been previously used for the taxonomy of these arachnids. Sequence analysis included seven species of the aztecus group, two other species of Paraphrynus, and an outgroup species of the putative sister genus, Phrynus Lamarck, 1801. Two nuclear genes (18S rDNA and 28S rDNA) and three mitochondrial genes (12S rDNA, 16S rDNA, and Cytochrome c Oxidase Subunit I) were analyzed phylogenetically. Hypotheses of karyotype evolution of Paraphrynus are consistent with conclusions based on the morphological and molecular data. The ancestral karyotype of the aztecus group probably consisted of a relatively low number of bi-armed chromosomes. Diploid numbers decreased by cycles consisting of inversion and consequent centric fusion during the evolution of the clade comprising P. mexicanus and P. pseudomexicanus.
The tuatara (Sphenodon punctatus)—the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2—is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which—at approximately 5 Gb—is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
We implement two measures for quantifying genealogical concordance in phylogenomic datasets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of "decisive" gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org).
Aim
We explored the extent to which Gondwanan vicariance contributed to the circum‐Antarctic distribution of the mite harvestman family Pettalidae, a group of small, dispersal‐limited arachnids whose phylogeny has been poorly resolved, precluding rigorous biogeographic hypothesis testing.
Location
Continental landmasses of former temperate Gondwana (Chile, South Africa, Sri Lanka, Australia and New Zealand).
Taxon
Pettalidae, Opiliones.
Methods
We generated transcriptomes for a phylogeny of 16 pettalids, spanning 9 genera. Data were analysed using maximum likelihood, Bayesian inference and coalescence methods. The phylogenetic position of the Sri Lankan genus Pettalus was further explored using quartet likelihood mapping and changes in gene likelihood scores. We also estimated divergence times and looked for signatures of extinction across Antarctica and central Australia using previously published phylogenies with near‐complete species sampling constrained to match our transcriptomic results. Finally, we estimated ancestral ranges and inferred instances of vicariance.
Results
We recovered a well‐supported topology with a division between taxa from landmasses that made up East Gondwana, and a grade of taxa from West Gondwana. Pettalus was resolved either as the sister group of the Queensland‐endemic Austropurcellia, or as the sister group to a larger clade from East Gondwana, though favouring Pettalus + Austropurcellia. Divergence times for multiple vicariance events coincided with Gondwana's breakup. Speciation–extinction analysis found one diversification process for the family: an initial burst of cladogenesis that slowed down through time.
Main Conclusions
Given that the order of cladogenesis corresponds to the order in which Gondwana fragmented, and the concurrent timing of vicariance and rifting, Gondwanan breakup explains major biogeographic patterns in Pettalidae. Some divergences predate initial rifting, but there is no evidence of trans‐oceanic dispersal. The Sri Lanka–eastern Australia relationship makes sense in the light of large‐scale extinction across Antarctica and central Australia; however, we find no clear signatures of mass extinction.
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.
Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long‐standing debate in spider evolution – we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous–Paleogene (K–Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA‐clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA‐clade spiders.
Phylogenomic methods have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. Across arachnids, transcriptomic approaches may generate thousands of loci, and target‐capture methods, using the previously designed arachnid‐specific probe set, can target a maximum of about 1,000 loci. Here, we develop a specialized target‐capture probe set for spiders that contains over 2,000 ultraconserved elements (UCEs) and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. We designed the ‘spider‐specific’ probe set using three spider genomes (Loxosceles, Parasteatoda and Stegodyphus) and ensured that the newly designed probe set includes UCEs from the previously designed Arachnida probe set. The new ‘spider‐specific’ probes were used to sequence UCE loci in 51 specimens. The remaining samples included five spider genomes and taxa that were enriched using Arachnida probe set. The ‘spider‐specific’ probes were also used to gather loci from a total of 84 representative taxa across Araneae. On mapping these 84 taxa to the Arachnida probe set, we captured at most 710 UCE loci, while the spider‐specific probe set captured up to 1,547 UCE loci from the same taxon sample. Phylogenetic analyses using maximum likelihood and coalescent methods corroborate most nodes resolved by recent transcriptomic analyses, but not all (e.g. UCE data suggest monophyly of ‘symphytognathoids’). Our preferred hypothesis based on topology tests, suggests monophyly of the ‘symphytognathoids’ (the miniature orb weavers), which in previous studies has only been supported by a combination of morphological and behavioural characters.
Bayesian methods for molecular clock dating of species divergences have been greatly developed during the past decade. Advantages of the methods include the use of relaxed-clock models to describe evolutionary rate variation in the branches of a phylogenetic tree and the use of flexible fossil calibration densities to describe the uncertainty in node ages. The advent of next-generation sequencing technologies has led to a flood of genome-scale datasets for organisms belonging to all domains in the tree of life. Thus, a new era has begun where dating the tree of life using genome-scale data is now within reach. In this protocol, we explain how to use the computer program MCMCTree to perform Bayesian inference of divergence times using genome-scale datasets. We use a ten-species primate phylogeny, with a molecular alignment of over three million base pairs, as an exemplar on how to carry out the analysis. We pay particular attention to how to set up the analysis and the priors and how to diagnose the MCMC algorithm used to obtain the posterior estimates of divergence times and evolutionary rates.
After tumultuous revisions to the family-level systematics of Laniatores (the armored harvestmen), the basally branching family Phalangodidae presently bears a disjunct and irregular distribution, attributed to the fragmentation of Pangea. One of the curious lineages assigned to Phalangodidae is the monotypic Israeli genus Haasus, the only Laniatores species that occurs in Israel, and whose presence in the Levant has been inferred to result from biogeographic connectivity with Eurasia. Recent surveys of Israeli caves have also yielded a new troglobitic morphospecies of Haasus. Here, we describe this new species as Haasus naasane sp. nov. So as to test the biogeographic affinity of Haasus, we sequenced DNA from both species and RNA from Haasus naasane sp. nov., to assess their phylogenetic placement. Our results showed that the new species is clearly closely related to Haasus judaeus, but Haasus itself is unambiguously nested within the largely Afrotropical family Pyramidopidae. In addition, the Japanese ‘phalangodid’ Proscotolemon sauteri was recovered as nested within the Southeast Asian family Petrobunidae. Phylogenomic placement of Haasus naasane sp. nov. in a 1550-locus matrix indicates that Pyramidopidae has an unstable position in the tree of Laniatores, with alternative partitioning of the matrix recovering high nodal support for mutually exclusive tree topologies. Exploration of phylogenetic signal showed the cause of this instability to be a considerable conflict between partitions, suggesting that the basal phylogeny of Laniatores may not yet be stable to addition of taxa. We transfer Haasus to Pyramidopidae (new familial assignment). Additionally, we transfer Proscotolemon to the family Petrobunidae (new familial assignment). Future studies on basal Laniatores phylogeny should emphasise the investigation of small-bodied and obscure groups that superficially resemble Phalangodidae.
Microhabitat changes are thought to be among the main drivers of diversification. However, this
conclusion is mostly based on studies on vertebrates. Here, we investigate the influence of microhabitat on
diversification rates in pholcid spiders (Araneae, Pholcidae). Diversification analyses were conducted in the
framework of the largest molecular phylogeny of pholcid spiders to date based on three nuclear and three
mitochondrial loci from 600 species representing more than 85% of the currently described pholcid genera.
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.
Living fossils are survivors of previously more diverse lineages that originated millions of years ago and persisted with little morphological change. Therefore, living fossils are model organisms to study both long-term and ongoing adaptation and speciation processes. However, many aspects of living fossils evolution and their persistence in the modern world remain unclear. Here, we investigate three major aspects of the evolutionary history of living fossils: cryptic speciation, population genetics, and effective population sizes; using members of the genera Nautilus and Allonautilus as classic examples of true living fossils. For this, we analyzed genome-wide ddRAD-Seq data for all six currently recognized nautiloid species throughout their distribution range. Our analyses identified three major allopatric Nautilus clades: a South Pacific clade, subdivided into three subclades with no signs of admixture between them; a Coral Sea clade, consisting of two genetically distinct populations with significant admixture; and a widespread Indo-Pacific clade, devoid of significant genetic substructure. Within these major clades we detected five Nautilus groups, which likely correspond to five distinct species. With the exception of Nautilus macromphalus, all previously described species are at odds with genome-wide data, testifying to the prevalence of cryptic species among living fossils. Detailed FST analyses further revealed significant genome-wide and locus-specific signatures of selection between species and differentiated populations, which is demonstrated here for the first time in a living fossil. Finally, approximate Bayesian computation (ABC) simulations suggested large effective population sizes, which may explain the low levels of population differentiation commonly observed in living fossils. This article is protected by copyright. All rights reserved.
Background: Arachnids are a highly successful group of land-dwelling arthropods. They are major contributors to modern terrestrial ecosystems, and have a deep evolutionary history. Whip spiders (Arachnida, Amblypygi), are one of the smaller arachnid orders with ca. 190 living species. Here we restudy one of the oldest fossil representatives of the group, Graeophonus anglicus Pocock, 1911 from the Late Carboniferous (Duckmantian, ca. 315 Ma) British Middle Coal Measures of the West Midlands, UK. Using X-ray microtomography, our principal aim was to resolve details of the limbs and mouthparts which would allow us to test whether this fossil belongs in the extant, relict family Paracharontidae; represented today by a single, blind species Paracharon caecus Hansen, 1921.
Results: Tomography reveals several novel and significant character states for G. anglicus; most notably in the chelicerae, pedipalps and walking legs. These allowed it to be scored into a phylogenetic analysis together with
the recently described Paracharonopsis cambayensis Engel & Grimaldi, 2014 from the Eocene (ca. 52 Ma) Cambay amber, and Kronocharon prendinii Engel & Grimaldi, 2014 from Cretaceous (ca. 99 Ma) Burmese amber. We recovered relationships of the form ((Graeophonus (Paracharonopsis + Paracharon)) + (Charinus (Stygophrynus (Kronocharon (Charon (Musicodamon + Paraphrynus)))))). This tree largely reflects Peter Weygoldt’s 1996 classification with its basic split into Paleoamblypygi and Euamblypygi lineages; we were able to score several of his characters for the first time in fossils. Our analysis draws into question the monophyly of the family Charontidae.
Conclusions: Our data suggest that Graeophonus is a crown group amblypygid, and falls within a monophyletic Paleoamblypgi clade, but outside the family Paracharontidae (= Paracharonopsis + Paracharon). Our results also suggest a new placement for the Burmese amber genus Kronocharon, a node further down from its original position. Overall, we offer a broad phylogenetic framework for both the fossil and Recent whip spiders against which future discoveries can be tested.
Keywords: Amblypygi, Coal Measures, Amber, Fossil, Systematics, Pennsylvanian
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.
We present a phylogenetic analysis of spiders using a dataset of 932 spider species, representing 115 families (only the family Synaphridae is unrepresented), 700 known genera, and additional representatives of 26 unidentified or undescribed genera. Eleven genera of the orders Amblypygi, Palpigradi, Schizomida and Uropygi are included as outgroups. The dataset includes six markers from the mitochondrial (12S, 16S, COI) and nuclear (histone H3, 18S, 28S) genomes, and was analysed by multiple methods, including constrained analyses using a highly supported backbone tree from transcriptomic data. We recover most of the higher-level structure of the spider tree with good support, including Mesothelae, Opisthothelae, Mygalomorphae and Araneomorphae. Several of our analyses recover Hypochilidae and Filistatidae as sister groups, as suggested by previous transcriptomic analyses. The Synspermiata are robustly supported, and the families Trogloraptoridae and Caponiidae are found as sister to the Dysderoidea. Our results support the Lost Tracheae clade, including Pholcidae, Tetrablemmidae, Diguetidae, Plectreuridae and the family Pacullidae (restored status) separate from Tetrablemmidae. The Scytodoidea include Ochyroceratidae along with Sicariidae, Scytodidae, Drymusidae and Periegopidae; our results are inconclusive about the separation of these last two families. We did not recover monophyletic Austrochiloidea and Leptonetidae, but our data suggest that both groups are more closely related to the Cylindrical Gland Spigot clade rather than to Synspermiata. Palpimanoidea is not recovered by our analyses, but also not strongly contradicted. We find support for Entelegynae and Oecobioidea (Oecobiidae plus Hersiliidae), and ambiguous placement of cribellate orb-weavers, compatible with their non-monophyly. Nicodamoidea (Nicodamidae plus Megadictynidae) and Araneoidea composition and relationships are consistent with recent analyses. We did not obtain resolution for the titanoecoids (Titanoecidae and Phyxelididae), but the Retrolateral Tibial Apophysis clade is well supported. Penestomidae, and probably Homalonychidae, are part of Zodarioidea, although the latter family was set apart by recent transcriptomic analyses. Our data support a large group that we call the marronoid clade (including the families Amaurobiidae, Desidae, Dictynidae, Hahniidae, Stiphidiidae, Agelenidae and Toxopidae). The circumscription of most marronoid families is redefined here. Amaurobiidae include the Amaurobiinae and provisionally Macrobuninae. We transfer Malenellinae (Malenella, from Anyphaenidae), Chummidae (Chumma) (new syn.) and Tasmarubriinae (Tasmarubrius, Tasmabrochus and Teeatta, from Amphinectidae) to Macrobuninae. Cybaeidae are redefined to include Calymmaria, Cryphoeca, Ethobuella and Willisius (transferred from Hahniidae), and Blabomma and Yorima (transferred from Dictynidae). Cycloctenidae are redefined to include Orepukia (transferred from Agelenidae) and Pakeha and Paravoca (transferred from Amaurobiidae). Desidae are redefined to include five subfamilies: Amphinectinae, with Amphinecta, Mamoea, Maniho, Paramamoea and Rangitata (transferred from Amphinectidae); Ischaleinae, with Bakala and Manjala (transferred from Amaurobiidae) and Ischalea (transferred from Stiphidiidae); Metaltellinae, with Austmusia, Buyina, Calacadia, Cunnawarra, Jalkaraburra, Keera, Magua, Metaltella, Penaoola and Quemusia; Porteriinae (new rank), with Baiami, Cambridgea, Corasoides and Nanocambridgea (transferred from Stiphidiidae); and Desinae, with Desis, and provisionally Poaka (transferred from Amaurobiidae) and Barahna (transferred from Stiphidiidae). Argyroneta is transferred from Cybaeidae to Dictynidae. Cicurina is transferred from Dictynidae to Hahniidae. The genera Neoramia (from Agelenidae) and Aorangia, Marplesia and Neolana (from Amphinectidae) are transferred to Stiphidiidae. The family Toxopidae (restored status) includes two subfamilies: Myroinae, with Gasparia, Gohia, Hulua, Neomyro, Myro, Ommatauxesis and Otagoa (transferred from Desidae); and Toxopinae, with Midgee and Jamara, formerly Midgeeinae, new syn. (transferred from Amaurobiidae) and Hapona, Laestrygones, Lamina, Toxops and Toxopsoides (transferred from Desidae). We obtain a monophyletic Oval Calamistrum clade and Dionycha; Sparassidae, however, are not dionychans, but probably the sister group of those two clades. The composition of the Oval Calamistrum clade is confirmed (including Zoropsidae, Udubidae, Ctenidae, Oxyopidae, Senoculidae, Pisauridae, Trechaleidae, Lycosidae, Psechridae and Thomisidae), affirming previous findings on the uncertain relationships of the “ctenids” Ancylometes and Cupiennius, although a core group of Ctenidae are well supported. Our data were ambiguous as to the monophyly of Oxyopidae. In Dionycha, we found a first split of core Prodidomidae, excluding the Australian Molycriinae, which fall distantly from core prodidomids, among gnaphosoids. The rest of the dionychans form two main groups, Dionycha part A and part B. The former includes much of the Oblique Median Tapetum clade (Trochanteriidae, Gnaphosidae, Gallieniellidae, Phrurolithidae, Trachelidae, Gnaphosidae, Ammoxenidae, Lamponidae and the Molycriinae), and also Anyphaenidae and Clubionidae. Orthobula is transferred from Phrurolithidae to Trachelidae. Our data did not allow for complete resolution for the gnaphosoid families. Dionycha part B includes the families Salticidae, Eutichuridae, Miturgidae, Philodromidae, Viridasiidae, Selenopidae, Corinnidae and Xenoctenidae (new fam., including Xenoctenus, Paravulsor and Odo, transferred from Miturgidae, as well as Incasoctenus from Ctenidae). We confirm the inclusion of Zora (formerly Zoridae) within Miturgidae.
Opiliones are iconic arachnids with a Paleozoic origin and a diversity that reflects ancient biogeographical patterns dating back at least to the times of Pangea. Due to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to systematics. 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 analyze a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing ca. 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 are precisely placed. Our dating analyses also 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 a general overview of the general biogeographic patterns of this ancient arthropod group.
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite this applied importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have confounded these attempts. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved genomic regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion, and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales, even down to the level of species differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery, and conservation of these diverse arthropods.
A relict is a species that remains from a group largely extinct. It can be identifi ed according both to a phylogenetic analysis and to a fossil record of extinction. Conserving a relict species will amount to conserve the unique representative of a particular phylogenetic group and its combination of potentially original characters , thus lots of phylogenetic diversity. However, the focus on these original characters , often seen as archaic or primitive, commonly brought erroneous ideas. Actually, relict species are not necessarily old within their group and they can show as much genetic diversity as any species. A phylogenetic relict species can be geographically or climatically restricted or not. Empirical studies have often shown that relicts are at particular risks of extinction. The term relict should not be used for putting a misleading emphasis on remnant or isolated populations. In conclusion, relict species are extreme cases of phylogenetic diversity, often endangered and with high symbolic value, of important value for conservation.
Navigation is an ideal behavioral model for the study of sensory system integration and the neural substrates associated with complex behavior. For this broader purpose, however, it may be profitable to develop new model systems that are both tractable and sufficiently complex to ensure that information derived from a single sensory modality and path integration are inadequate to locate a goal. Here, we discuss some recent discoveries related to navigation by amblypygids, nocturnal arachnids that inhabit the tropics and sub-tropics. Nocturnal displacement experiments under the cover of a tropical rainforest reveal that these animals possess navigational abilities that are reminiscent, albeit on a smaller spatial scale, of true-navigating vertebrates. Specialized legs, called antenniform legs, which possess hundreds of olfactory and tactile sensory hairs, and vision appear to be involved. These animals also have enormous mushroom bodies, higher-order brain regions that, in insects, integrate contextual cues and may be involved in spatial memory. In amblypygids, the complexity of a nocturnal rainforest may impose navigational challenges that favor the integration of information derived from multimodal cues. Moreover, the movement of these animals is easily studied in the laboratory and putative neural integration sites of sensory information can be manipulated. Thus, amblypygids could serve as a model system for the discovery of neural substrates associated with a unique and potentially sophisticated navigational capability. The diversity of habitats in which amblypygids are found also offers an opportunity for comparative studies of sensory integration and ecological selection pressures on navigation mechanisms.
Background:
Next-generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole-genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, owing to the variation in gene expression levels and alternative splicing.
Findings:
We developed a k-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted k-mers in the input reads. Unlike WGS read correctors, which use a global threshold to determine trusted k-mers, Rcorrector computes a local threshold at every position in a read.
Conclusions:
Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from https://github.com/mourisl/Rcorrector/.
Phylogenies provide a useful way to understand the evolutionary history of genetic samples, and data sets with more than a thousand taxa are becoming increasingly common, notably with viruses (e.g. HIV). Dating ancestral events is one of the first, essential goals with such data. However, current sophisticated probabilistic approaches struggle to handle data sets of this size. Here we present very fast dating algorithms, based on a Gaussian model closely related to the Langley-Fitch molecular-clock model. We show that this model is robust to uncorrelated violations of the molecular clock. Our algorithms apply to serial data, where the tips of the tree have been sampled through times. They estimate the substitution rate and the dates of all ancestral nodes. When the input tree is unrooted, they can provide an estimate for the root position, thus representing a new, practical alternative to the standard rooting methods (e.g. mid-point). Our algorithms exploit the tree (recursive) structure of the problem at hand, and the close relationships between least-squares and linear algebra. We distinguish between an unconstrained setting and the case where the temporal precedence constraint (i.e. an ancestral node must be older that its daughter nodes) is accounted for. With rooted trees, the former is solved using linear algebra in linear computing time (i.e. proportional to the number of taxa), while the resolution of the latter, constrained setting, is based on an active-set method that runs in nearly linear time. With unrooted trees the computing time becomes (nearly) quadratic (i.e. proportional to the square of the number of taxa). In all cases very large input trees (>10,000 taxa) can easily be processed and transformed into time-scaled trees. We compare these algorithms to standard methods (root-to-tip, r8s version of Langley-Fitch method, and BEAST). Using simulated data, we show that their estimation accuracy is similar to that of the most sophisticated methods, while their computing time is much faster. We apply these algorithms on a large data set comprising 1,195 strains of Influenza virus from the pdm09 H1N1 Human pandemic. Again the results show that these algorithms provide a very fast alternative with results similar to those of other computer programs. These algorithms are implemented in the LSD software (Least-Squares Dating), which can be downloaded from http://www.atgc-montpellier.fr/LSD/, along with all our data sets and detailed results. An Online Appendix, providing additional algorithm descriptions, tables and figures can be found in the Dryad data repository*.
The African whip spider, Damon variegatus, exhibits a broad, discontinuous distribution from the Congo, through western Tanzania and Zimbabwe, to South Africa and Namibia. Variation in size, number of antenniform leg segments, and colouration, taken together with a discontinuous distribution, suggest that allopatric populations of D. variegatus may be reproductively isolated, and more than one species may be involved. Furthermore, many morphological characters of D. variegatus appear to be plesiomorphic if compared to closely related species, suggesting that D. variegatus might be paraphyletic, regardless of whether it is a single panmictic species or a group of partly or entirely reproductively isolated populations. This contribution attempts to determine whether D. variegatus is monophyletic and comprises more than one species, by investigating three sources of evidence: behaviour, morphology and DNA. Mating behaviour is observed and mate-recognition trials conducted between males and females from several populations of D. variegatus and related species of Damon. The morphology of spermatophores obtained during these matings is studied and a matrix of somatic and genitalic characters produced. These morphological data are analysed separately and in combination with DNA sequences from loci of three genes in the nuclear genome (18S rDNA, 28S rDNA and Histone H3) and three genes in the mitochondrial genome (12S rDNA, 16S rDNA and Cytochrome Oxidase I). Neither the comparative behavioural evidence gathered nor the spermatophore morphology conclusively suggest that D. variegatus comprises more than one species. However, the molecular data, analysed separately and in combination with the morphological data, reveal that D. variegatus is monophyletic and that the population of D. variegatus to the west of the Kalahari sand system (Namibia and southern Angola) is specifically distinct from those to the east. This new species is described as Damon sylviae, the diagnosis of D. variegatus s. str. is revised, and a key to the species of the D. variegatus group is provided.
Burmese amber is a significant source of fossils that documents the mid-Cretaceous biota. This deposit was formed around 99 Ma on the Burma Terrane, which broke away from Gondwana and later collided with Asia, although the timing is disputed. Palpimanoidea is a dispersal-limited group that was a dominant element of the Mesozoic spider fauna, and has an extensive fossil record, particularly from Burmese amber. Using morphological and molecular data, evolutionary relationships of living and fossil Palpimanoidea are examined. Divergence dating with fossils as terminal tips, followed by ancestral range estimations, shows timing of diversification is contemporaneous with continental break-up and that widespread ancestral ranges divide into lineages that inherit different Pangean fragments, consistent with vicariance. Our results suggest that the Burmese amber fauna has ties to Gondwana due to a historical connection in the Early Cretaceous, and that the Burma Terrane facilitated biotic exchange by transporting lineages from Gondwana into the Holarctic in the Cretaceous.
Scorpions constitute a charismatic lineage of arthropods and comprise more than 2500 described species. Found throughout various tropical and temperate habitats, these predatory arachnids have a long evolutionary history, with a fossil record that began in the Silurian. While all scorpions are venomous, the asymmetrically diverse family Buthidae harbors nearly half the diversity of extant scorpions, and all but one of the 58 species that are medically significant to humans. However, the lack of a densely sampled scorpion phylogeny has hindered broader inferences of the diversification dynamics of scorpion toxins. To redress this gap, we assembled a phylogenomic data set of 100 scorpion venom gland transcriptomes and genomes, emphasizing the sampling of highly toxic buthid genera. To infer divergence times of venom gene families, we applied a phylogenomic node dating approach for the species tree in tandem with phylostratigraphic bracketing to estimate the minimum ages of mammal-specific toxins. Our analyses establish a robustly supported phylogeny of scorpions, particularly with regard to relationships between medically significant taxa. Analysis of venom gene families shows that mammal-active sodium channel toxins (NaTx) have independently evolved in five lineages within Buthidae. Temporal windows of mammal-targeting toxin origins are correlated with the basal diversification of major scorpion mammal predators such as shrews, bats, and rodents. These results suggest an evolutionary model of relatively recent diversification of buthid NaTx homologs in response to the diversification of scorpion predators.
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.
en Ricinulei (hooded tick spiders or tick beetles), considered one of the smaller arachnid orders, is an ancient clade whose affinities are still debated. With three recognized genera, short-range endemism, and strict fidelity to the landmasses that have seen them evolve for hundreds of millions of years, the group has emerged as a novel system to understand deep biogeographic processes. Here we undertake a combined approach using phylotranscriptomics and deep Sanger sequencing of 133 ricinuleid specimens to better understand their relationships, divergence times, and species ranges by using a series of species delimitation analyses. Our results support the monophyly of the three recognized genera, Ricinoides in Africa, Pseudocellus in North America, and Cryptocellus in Mesoamerica and South America. Ricinoides is further divided into two or three deep clades corresponding to different ancestral forest refugia, and the sampled Cryptocellus segregate into a Mesoamerican and a South American clade, but a new species from Tobago is the sister group to the Mesoamerican clade in the transcriptomic analysis and not part of the South American clade. Despite not being known from adults, but given the fact that this is the only Ricinulei species from the Lesser Antilles and its pivotal phylogenetic position, the species is here formalized as Cryptocellus tobagoensis Giribet & Benavides sp. nov. Finally, species delimitation methods generally do well recognizing morphospecies, but they are unable to distinguish among some of them, suggesting the need for re-study of some of these species complexes and perhaps synonymy.
Resumen
es El orden Ricinulei (garrapatas encapuchadas), considerado uno de los órdenes de arácnidos con menor diversidad, es un linaje antiguo cuyas afinidades evolutivas aún se debaten. Con tres géneros reconocidos, endemismo muy localizado y una estricta fidelidad a las masas continentales que les ha visto evolucionar por cientos de millones de años, el grupo ha surgido como un sistema para estudiar procesos biogeográficos muy antiguos. Aquí presentamos un enfoque combinado filotranscriptómica y secuenciación masiva de Sanger de 133 especímenes de ricinúlidos para comprender mejor sus relaciones, tiempo de divergencia y rangos de especies mediante el uso de una serie de análisis de delimitación de especies. Nuestros resultados apoyan la monofilia de los tres géneros reconocidos, Ricinoides en África, Pseudocellus en América del Norte y Cryptocellus en Mesoamérica y América del Sur. Ricinoides se divide en dos o tres clados correspondientes a diferentes refugios forestales ancestrales, y nuestra muestra de Cryptocellus se segrega en un clado mesoamericano y uno sudamericano; una nueva especie de Tobago es el grupo hermano del clado mesoamericano en el análisis transcriptómico y no forma parte del clado sudamericano. A pesar de no tener individuos adultos, pero dado que esta es la única especie de Ricinulei de las Antillas Menores y además con una posición filogenética interesante, la especie se formaliza aquí como Cryptocellus tobagoensis Giribet & Benavides sp. nov. Finalmente, los métodos de delimitación de especies generalmente reconocen bien las morfoespecies, pero no pueden distinguir entre algunas de ellas, lo que sugiere la necesidad de volver a estudiar algunos de estos complejos de especies y sus sinonimias.
The present contribution addresses the phylogeny and biogeography of the pantropical whip spider family Charinidae Quintero, 1986, the most species-rich in the arachnid order Amblypygi Thorell, 1883, based on morphology and multilocus DNA sequences, analysed simultaneously using parsimony, maximum likelihood and Bayesian inference. The morphological matrix comprises 138 characters, scored for four outgroup taxa and 103 ingroup terminals representing all genera and 64% of the species of Charinidae. The multilocus dataset comprises sequences from two nuclear and three mitochondrial gene loci for four outgroup taxa and 48 ingroup representing 30 (23%) taxa of Charinidae. Charinidae are monophyletic, with Weygoldtia Miranda et al., 2018 sister to a monophyletic group comprising Charinus Simon, 1892 and Sarax Simon, 1892, neither of which are reciprocally monophyletic. Charinidae diverged from other amblypygid families in the Late Carboniferous, c. 318 Mya, on the supercontinent Pangaea. Weygoldtia diverged from the common ancestor of Charinus and Sarax during the Late Permian, c. 257 Mya, when changes in climate reduced tropical forests. The divergence of Charinus and Sarax coincides with the fragmentation of Pangaea, c. 216 Mya. Sarax colonized South-East Asia via Australia. The charinid fauna of New Caledonia originated before the Oligocene, when the island separated from Australia, c. 80 Mya.
Whip spiders (Amblypygi) reside in structurally complex habitats and are nocturnally active yet display notable navigational abilities. From the theory that uncertainty in sensory inputs should promote multisensory representations to guide behavior, we hypothesized that their navigation is supported by a multisensory and perhaps configural representation of navigational inputs, an ability documented in a few insects and never reported in arachnids. We trained Phrynus marginemaculatus to recognize a home shelter characterized by both discriminative olfactory and tactile stimuli. In tests, subjects readily discriminated between shelters based on the paired stimuli. However, subjects failed to recognize the shelter in tests with either of the component stimuli alone. This result is consistent with the hypothesis that the terminal phase of their navigational behavior, shelter recognition, can be supported by the integration of multisensory stimuli as an enduring, configural representation. We hypothesize that multisensory learning occurs in the whip spiders’ extraordinarily large mushroom bodies, which may functionally resemble the hippocampus of vertebrates.
High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long‐standing hypotheses. Likewise, the evolution of spider webs—perhaps their most emblematic attribute—is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze and evaluate the relationships among these lineages using a variety of orthology assessment methods, occupancy thresholds, tree inference methods and support metrics. Our analyses include families not previously sampled in transcriptomic analyses, such as Symphytognathidae, the only araneoid family absent in such prior works. We find support for the major established spider lineages, including Mygalomorphae, Araneomorphae, Synspermiata, Palpimanoidea, Araneoidea and the Retrolateral Tibial Apophysis Clade, as well as the uloborids, deinopids, oecobiids and hersiliids Grade. Resulting trees are evaluated using bootstrapping, Shimodaira–Hasegawa approximate likelihood ratio test, local posterior probabilities and concordance factors. Using structured Markov models to assess the evolution of spider webs while accounting for hierarchically nested traits, we find multiple convergent occurrences of the orb web across the spider tree‐of‐life. Overall, we provide the most comprehensive spider tree‐of‐life to date using transcriptomic data and use new methods to explore controversial issues of web evolution, including the origins and multiple losses of the orb web.
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.
The modestly diverse order Amblypygi Thorell, 1883 includes five families, of which Charinidae Quintero, 1986 is the most diverse and with the widest geographical distribution. The family currently comprises three genera, Catageus Thorell, 1889, Charinus Simon, 1892 and Sarax Simon, 1892, the first known by one species from a single locality in Myanmar, the second with currently 74 species globally distributed, and the last with 17 species present in Southeast Asia and India. In this paper we describe and illustrate a new genus to accommodate the species Sarax davidovi Fage, 1946 based on unique characters. Weygoldtia gen. nov. (Laos, Vietnam and Cambodia) is supported by two synapomorphies: the presence of a straight crest anterior to the lateral eyes and the longitudinal orientation of the rod sensilla on tarsus of leg I. The new genus can be distinguished from Charinus and Sarax by the number of trichobothria on distitibia IV and the presence of one or two setae on the base of the cleaning organ on pedipalp tarsus. The enigmatic species Catageus pusillus Thorell, 1889 (the single species in the genus) is here synonymized with Stygophrynus cavernicola (Thorell, 1889) (family Charontidae Simon, 1892) and a neotype is designated. As Stygophrynus cavernicola is the type species of the genus, the synonymization of the two species results in the synonymy of the genera. Following the principle of priority, Catageus is maintained and all eight species of Stygophrynus Kraepelin, 1895 now have the following new combination: Catageus berkeleyi (Gravely, 1915), comb. nov., C. brevispina (Weygoldt, 2002), comb. nov., C. cavernicola, comb.nov., C. cerberus (Simon, 1901), comb. nov., C. dammermani (Roewer, 1928), comb. nov., C. longispina (Gravely, 1915), comb. nov., C. moultoni (Gravely, 1915), comb. nov., C. orientalis (Seiter and Wolf, 2017), comb. nov. and C. sunda (Rahmadi and Harvey, 2008), comb. nov.
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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.
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.
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion, and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales, and suggesting that these loci will be useful for species-level differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery, and conservation of these diverse arthropods. This article is protected by copyright. All rights reserved.
The history of life is replete with apparent order. Much of this order may reflect the deterministic causes conventionally invoked, but we cannot be sure until we measure and subtract the order that arises in simple random systems. Consequently, we have constructed a random model that builds evolutionary trees by allowing lineages to branch and become extinct at equal probabilities. We proceed by dividing our simulated tree into clades and by comparing their sizes and shapes with the patterns exhibited by “real” clades as recorded by fossils.
We regard the similarity of real and random clades as the outstanding result of this comparison. In both real and random systems, extinct clades arising after an “ecological barrel” had been filled have their maximum diversity at the midpoint of their duration; clades arising during the initial “filling” reach an earlier climax during this preequilibrial period of rapid diversification. However, some potential differences also emerge. Clades still living are much larger than extinct clades. We may attribute this to the morphological superiority of survivors, but we can also simulate it in a model that chooses the originators of clades at random. Real clades undergo greater fluctuations in diversity than do random clades, but the effect is not marked.
Cavernicolous species that exhibit a high degree of troglomorphism often provide some of the most intriguing evolutionary riddles. For such taxa, the correct systematic arrangement is difficult to determine and becomes problematic when based solely on highly convergent external morphological characters, leading to exaggerated support of spurious relationships. For the arachnid order Opiliones, examination of male genitalia morphology often aids in determining the family to which a particular taxon belongs. However, many taxa described prior to the 1990s lack detailed descriptions or drawings of this important character and, for highly-derived species, it is may still be necessary to seek support from additional sources of characters (e.g. molecular data) to accurately assess systematic placement. The enigmatic species Stygnomma pecki Goodnight & Goodnight, 1977 from a cave in Belize proved to be especially difficult to place based on morphological characters alone. Thus, using a previously published dataset for laniatorean harvestmen, we carried out a robust phylogenetic analysis aiming to determine the evolutionary relationship of this Neotropical troglomophic species. Informed by the results of the molecular phylogenetic analysis of 88 terminals representing Laniatores, we describe Jarmilana gen. nov. and provide a redescription of the type species Jarmilana pecki (Goodnight & Goodnight, 1977) comb. nov. Morphological evidence, including male genitalia morphology, supports the inclusion of J. pecki in the family Pyramidopidae. This represents the first record for the family Pyramidopidae in the New World, raising the question of whether this represents transoceanic dispersal or a relict of an ancient widespread tropical Gondwanan distribution.