A new genus of scutigerid centipede from southern South America with the description of two new species and an updated molecular phylogeny of the myriapod order Scutigeromorpha (Myriapoda: Chilopoda)

Scutigeromorph centipedes are conspicuous, yet often ignored myriapods for which little work has been conducted in southern South America. After examining recent and museum collections from Chile and Argentina, two new species of generic uncertainty were identified. A new genus of scutigerid centipede, Edgethreua , is therefore described with two new species, E. chilensis from Central Chile (type species of the genus) and E. goloboffi from Argentinian Patagonia. The new genus is characterised by the presence of scattered setiform bristles with short paired spines and the absence of simple spinulae and spines on all stomatotergites, the presence of a single spine-bristle in the prefemur of the second maxilla, a patch of cuticular ridges and pores surrounding the sensilla of the proximal labral portion of the epipharynx, the morphology of the sensilla of the distal patch of the hypopharynx and the morphology of the female gonopods. A phylogenetic analysis of the new species using two nuclear ribosomal RNA genes (18S and 28S rRNA), two mitochondrial ribosomal RNA genes (12S and 16S rRNA) and the mitochondrial protein-encoding gene cytochrome c oxidase subunit I show that the new genus does not cluster with any other described genus of scutigeromorph represented in molecular phylogenies. The data indicate that the new genus is probably sister group to a clade including the genera Lassophora , Ballonema and the subfamily Thereuoneminae, although one analysis suggests a position as sister group to Scutigerinae. ZooBank: urn:lsid:zoobank.org:pub:A4D453F3-9031-4E21-84C7-87F16C07AD51.

Under the hood: Phylogenomics of hooded tick spiders (Arachnida, Ricinulei) uncovers discordance between morphology and molecules

Ricinulei or hooded tick-spiders are a cryptic and ancient group of arachnids. The order consists of around 100 highly endemic extant species restricted to the Afrotropics and the Neotropics along with 22 fossil species. Their antiquity and low vagility make them an excellent group with which to interrogate biogeographic questions. To date, only four molecular analyses have been conducted on the group and they failed to resolve the relationships of the main lineages and even recovering the non-monophyly of the three genera. These studies were limited to a few Sanger loci or phylogenomic analyses with at most seven ingroup samples. To increase phylogenetic resolution in this little-understood and poorly studied group, we present the most comprehensive phylogenomic study of Ricinulei to date leveraging the Arachnida ultra-conserved element probe set. With a data set of 473 loci across 96 ingroup samples, analyses resolved a monophyletic Neotropical clade consisting of four main lineages. Two of them correspond to the current genera Cryptocellus and Pseudocellus while topology testing revealed one lineage to likely be a phylogenetic reconstruction artefact. The fourth lineage, restricted to Northwestern, Andean South America, is consistent with the Cryptocellus magnus group, likely corresponding to the historical genus Heteroricinoides. Since we did not sample the type species for this old genus, we do not formally re-erect Heteroricinoides but our data suggest the need for a thorough morphological re-examination of Neotropical Ricinulei.

Global diversity of enterococci and description of 18 previously unknown species

Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common constituents of the human microbiome. They are also now leading causes of multidrug-resistant hospital-associated infection. The basis for host association of enterococcal species is unknown. To begin identifying traits that drive host association, we collected 886 enterococcal strains from widely diverse hosts, ecologies, and geographies. This identified 18 previously undescribed species expanding genus diversity by >25%. These species harbor diverse genes including toxins and systems for detoxification and resource acquisition. Enterococcus faecalis and E. faecium were isolated from diverse hosts highlighting their generalist properties. Most other species showed a more restricted distribution indicative of specialized host association. The expanded species diversity permitted the Enterococcus genus phylogeny to be viewed with unprecedented resolution, allowing features to be identified that distinguish its four deeply rooted clades, and the entry of genes associated with range expansion such as B-vitamin biosynthesis and flagellar motility to be mapped to the phylogeny. This work provides an unprecedentedly broad and deep view of the genus Enterococcus, including insights into its evolution, potential new threats to human health, and where substantial additional enterococcal diversity is likely to be found.

An Opiliones-specific ultraconserved element probe set with a near-complete family-level phylogeny

Sequence capture of ultraconserved elements (UCEs) has transformed molecular systematics across many taxa, with arachnids being no exception. The probe set available for Arachnida has been repeatedly used across multiple arachnid lineages and taxonomic levels, however more specific probe sets for spiders have demonstrated that more UCEs can be recovered with higher probe specificity. In this study, we develop an Opiliones-specific UCE probe set targeting 1915 UCEs using a combination of probes designed from genomes and transcriptomes, as well as the most useful probes from the Arachnida probe set. We demonstrate the effectiveness of this probe set across Opiliones with the most complete family-level phylogeny made to date, including representatives from 61 of 63 currently described families. We also test UCE recovery from historical specimens with degraded DNA, examine population-level data sets, and assess "backwards compatibility" with samples hybridized with the Arachnida probe set. The resulting phylogenies - which include specimens hybridized using both the Opiliones and Arachnida probe sets, historical specimens, and transcriptomes - are largely congruent with previous multi-locus and phylogenomic analyses. The probe set is also "backwards compatible", increasing the number of loci obtained in samples previously hybridized with the Arachnida probe set, and shows high utility down to shallow population-level divergences. This probe set has the potential to further transform Opiliones molecular systematics, resolving many long-standing taxonomic issues plaguing this lineage.

Rampant loss of universal metazoan genes revealed by a chromosome-level genome assembly of the parasitic Nematomorpha

Parasites may manipulate host behavior to increase the odds of transmission or to reach the proper environment to complete their life cycle.1,2 Members of the phylum Nematomorpha (known as horsehair worms, hairworms, or Gordian worms) are large endoparasites that affect the behavior of their arthropod hosts. In terrestrial hosts, they cause erratic movements toward bodies of water,3,4,5,6 where the adult worm emerges from the host to find mates for reproduction. We present a chromosome-level genome assembly for the freshwater Acutogordius australiensis and a draft assembly for one of the few known marine species, Nectonema munidae. The assemblies span 201 Mbp and 213 Mbp in length (N50: 38 Mbp and 716 Kbp), respectively, and reveal four chromosomes in Acutogordius, which are largely rearranged compared to the inferred ancestral condition in animals. Both nematomorph genomes have a relatively low number of genes (11,114 and 8,717, respectively) and lack a high proportion (∼30%) of universal single-copy metazoan orthologs (BUSCO genes7). We demonstrate that missing genes are not an artifact of the assembly process, with the majority of missing orthologs being shared by the two independent assemblies. Missing BUSCOs are enriched for Gene Ontology (GO) terms associated with the organization of cilia and cell projections in other animals. We show that most cilium-related genes conserved across eukaryotes have been lost in Nematomorpha, providing a molecular basis for the suspected absence of ciliary structures in these animals.

Using eDNA to find Micrognathozoa

Over the past decades the sampling of environmental DNA (eDNA) - encompassing the DNA of all organisms present in an environmental sample¹ - has emerged as a technique for biodiversity monitoring and discovery in a diversity of environments. Avoiding the physical collection and identification of biota, this approach is praised for its independence of taxonomic expertise and has changed the way biologists study biodiversity. However, a common result in eDNA studies is the finding of unexpected taxa which are often removed by conservative bioinformatic filters or disregarded, since the authors are uncertain about the result and rarely have the interest, time, skills, and/or resources to return to the field and confirm with actual specimens². Here, we report a case in which an eDNA discovery led to the physical localization of a member of the Micrognathozoa (Figure 1B) - a rare group of limnic micrometazoans, and the animal phylum to be discovered last³, which is the sister group to rotifers^4,5. To this day, Micrognathozoa still comprises only a single named species from Greenland and a few additional disparate places.

Raymond Gibson (1938-2023): in memoriam

N.

Expanding on our knowledge of ecdysozoan genomes, a contiguous assembly of the meiofaunal priapulan Tubiluchus corallicola

Genomic data for priapulans are limited to a single species, restricting broad comparative analyses, and thorough interrogation of questions spanning phylogenomics, ecdysozoan physiology, and development. To help fill this void, we present here a high-quality priapulan genome for the meiofaunal species Tubiluchus corallicola. Our assembly combines Nanopore and Illumina sequencing technologies, and makes use of a whole genome amplification, to generate enough DNA to sequence this small meiofaunal species. We generated a moderately contiguous assembly (2547 scaffolds), with a high level of completeness (Metazoan BUSCOs n = 954, single copy complete = 89.6%, duplicated = 3.9%, fragmented = 3.5%, missing = 3.0%). We then screened the genome for homologs of the Halloween genes, key genes implicated in the ecdysis (moulting) pathway of arthropods, recovering a putative homolog of shadow. The presence of a shadow orthologue in two priapulan genomes suggests that the Halloween genes may not have evolved in a stepwise manner in Panarthropoda, as previously thought, but may have a deeper origin at the base of Ecdysozoa.

An unexpected diversity of Cyphophthalmi (Arachnida: Opiliones) in Upper Cretaceous Burmese amber

Ten new Cyphophthalmi specimens (Arachnida: Opiliones) from the Upper Cretaceous (Lower Cenomanian) Burmese amber of northern Myanmar are described. Seven of these are placed in Stylocellidae, the predominant extant family found today in Southeast Asia. Sirocellus iunctus gen. et sp. nov. represents the first fossil with a combination of sironid and stylocellid characters, suggesting a still ongoing transition in some lineages during the Upper Cretaceous. Mesopsalis oblongus gen. et sp. nov. represents a second fossil with elongated ozophores, a character not known from modern species. Leptopsalis breyeri sp. nov. is the first Cretaceous cyphophthalmid assignable to an extant genus. The species Foveacorpus cretaceus gen. et sp. nov. and F. parvus gen. et sp. nov., which cannot be placed in an extant family, show morphological novelties for Cyphophthalmi such as numerous pits covering the whole body. The possible function of these pits is discussed. Three more adult males with unique adenostyles and two juveniles are not formally named but further indicate an already highly diverse cyphophthalmid fauna during the Cretaceous. The total number of named Burmese amber Cyphophthalmi species is raised from one to six, and the total fossil record for this suborder now stands at eight.

Sizing Up the Onychophoran Genome: Repeats, Introns, and Gene Family Expansion Contribute to Genome Gigantism in Epiperipatus broadwayi

Genome assemblies are growing at an exponential rate and have proved indispensable for studying evolution but the effort has been biased toward vertebrates and arthropods with a particular focus on insects. Onychophora or velvet worms are an ancient group of cryptic, soil dwelling worms noted for their unique mode of prey capture, biogeographic patterns, and diversity of reproductive strategies. They constitute a poorly understood phylum of exclusively terrestrial animals that is sister group to arthropods. Due to this phylogenetic position, they are crucial in understanding the origin of the largest phylum of animals. Despite their significance, there is a paucity of genomic resources for the phylum with only one highly fragmented and incomplete genome publicly available. Initial attempts at sequencing an onychophoran genome proved difficult due to its large genome size and high repeat content. However, leveraging recent advances in long-read sequencing technology, we present here the first annotated draft genome for the phylum. With a total size of 5.6Gb, the gigantism of the Epiperipatus broadwayi genome arises from having high repeat content, intron size inflation, and extensive gene family expansion. Additionally, we report a previously unknown diversity of onychophoran hemocyanins that suggests the diversification of copper-mediated oxygen carriers occurred independently in Onychophora after its split from Arthropoda, parallel to the independent diversification of hemocyanins in each of the main arthropod lineages.

Three new species of Nautilus Linnaeus, 1758 (Mollusca, Cephalopoda) from the Coral Sea and South Pacific

Nautiloids are a charismatic group of marine molluscs best known for their rich fossil record, but today they are restricted to a handful of species in the family Nautilidae from around the Coral Triangle. Recent genetic work has shown a disconnect between traditional species, originally defined on shell characters, but now with new findings from genetic structure of various Nautilus populations. Here, three new species of Nautilus from the Coral Sea and South Pacific region are formally named using observations of shell and soft anatomical data augmented by genetic information: N. samoaensissp. nov. (from American Samoa), N. vitiensissp. nov. (from Fiji), and N. vanuatuensissp. nov. (from Vanuatu). The formal naming of these three species is timely considering the new and recently published information on genetic structure, geographic occurrence, and new morphological characters, including color patterns of shell and soft part morphology of hood, and will aid in managing these possibly endangered animals. As recently proposed from genetic analyses, there is a strong geographic component affecting taxonomy, with the new species coming from larger island groups that are separated by at least 200 km of deep water (greater than 800 m) from other Nautilus populations and potential habitats. Nautilid shells implode at depths greater than 800 m and depth therefore acts as a biogeographical barrier separating these species. This isolation, coupled with the unique, endemic species in each locale, are important considerations for the conservation management of the extant Nautilus species and populations.

Re-evaluating and dating myriapod diversification with phylotranscriptomics under a regime of dense taxon sampling

Recent transcriptomic studies of myriapod phylogeny have been based on relatively small datasets with <40 myriapod terminals and variably supported or contradicted the traditional morphological groupings of Progoneata and Dignatha. Here we amassed a large dataset of 104 myriapod terminals, including multiple species for each of the four myriapod classes. Across the tree, most nodes are stable and well supported. Most analyses across a range of gene occupancy levels provide moderate to strong support for a deep split of Myriapoda into Symphyla + Pauropoda (=Edafopoda) and an uncontradicted grouping of Chilopoda + Diplopoda (=Pectinopoda nov.), as in other recent transcriptome-based analyses; no analysis recovers Progoneata or Dignatha as clades. As in all recent multi-locus and phylogenomic studies, chilopod interrelationships resolve with Craterostigmus excluded from Amalpighiata rather than uniting with other centipedes with maternal brood care in Phylactometria. Diplopod ordinal interrelationships are largely congruent with morphology-based classifications. Chilognathan clades that are not invariably advocated by morphologists include Glomerida + Glomeridesmida, such that the volvation-related characters of pill millipedes may be convergent, and Stemmiulida + Polydesmida more closely allied to Juliformia than to Callipodida + Chordeumatida. The latter relationship implies homoplasy in spinnerets and contradicts Nematophora. A time-tree with nodes calibrated by 25 myriapod and six outgroup fossil terminals recovers Cambrian-Ordovician divergences for the deepest splits in Myriapoda, Edafopoda and Pectinopoda, predating the terrestrial fossil record of myriapods as in other published chronograms, whereas age estimates within Chilopoda and Diplopoda overlap with or do not appreciably predate the calibration fossils. The grouping of Chilopoda and Diplopoda is recovered in all our analyses and is formalized as Pectinopoda nov., named for the shared presence of mandibular comb lamellae. New taxonomic proposals for Chilopoda based on uncontradicted clades are Tykhepoda nov. for the three blind families of Scolopendromorpha that share a "sieve-type" gizzard, and Taktikospina nov. for Scolopendromorpha to the exclusion of Mimopidae.

Too early for the ferry: The biogeographic history of the Assamiidae of southeast Asia (Chelicerata: Opiliones, Laniatores)

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.

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

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

Phylogenomic Analysis of Velvet Worms (Onychophora) Uncovers an Evolutionary Radiation in the Neotropics

Onychophora ("velvet worms") are charismatic soil invertebrates known for their status as a "living fossil," their phylogenetic affiliation to arthropods, and their distinctive biogeographic patterns. However, several aspects of their internal phylogenetic relationships remain unresolved, limiting our understanding of the group's evolutionary history, particularly with regard to changes in reproductive mode and dispersal ability. To address these gaps, we used RNA sequencing and phylogenomic analysis of transcriptomes to reconstruct the evolutionary relationships and infer divergence times within the phylum. We recovered a fully resolved and well-supported phylogeny for the circum-Antarctic family Peripatopsidae, which retains signals of Gondwanan vicariance and showcases the evolutionary lability of reproductive mode in the family. Within the Neotropical clade of Peripatidae, though, we found that amino acid-translated sequence data masked nearly all phylogenetic signal, resulting in highly unstable and poorly supported relationships. Analyses using nucleotide sequence data were able to resolve many more relationships, though we still saw discordant phylogenetic signal between genes, probably indicative of a rapid, mid-Cretaceous radiation in the group. Finally, we hypothesize that the unique reproductive mode of placentotrophic viviparity found in all Neotropical peripatids may have facilitated the multiple inferred instances of over-water dispersal and establishment on oceanic islands.

Museum Genomics

Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.

Insights into the genetic regulatory network underlying neurogenesis in the parthenogenetic marbled crayfish Procambarus virginalis

Nervous system development has been intensely studied in insects (especially Drosophila melanogaster), providing detailed insights into the genetic regulatory network governing the formation and maintenance of the neural stem cells (neuroblasts) and the differentiation of their progeny. Despite notable advances over the last two decades, neurogenesis in other arthropod groups remains by comparison less well understood, hampering finer resolution of evolutionary cell type transformations and changes in the genetic regulatory network in some branches of the arthropod tree of life. Although the neurogenic cellular machinery in malacostracan crustaceans is well described morphologically, its genetic molecular characterization is pending. To address this, we established an in situ hybridization protocol for the crayfish Procambarus virginalis and studied embryonic expression patterns of a suite of key genes, encompassing three SoxB group transcription factors, two achaete-scute homologs, a Snail family member, the differentiation determinants Prospero and Brain tumor, and the neuron marker Elav. We document cell type expression patterns with notable similarities to insects and branchiopod crustaceans, lending further support to the homology of hexapod-crustacean neuroblasts and their cell lineages. Remarkably, in the crayfish head region, cell emigration from the neuroectoderm coupled with gene expression data points to a neuroblast-independent initial phase of brain neurogenesis. Further, SoxB group expression patterns suggest an involvement of Dichaete in segmentation, in concordance with insects. Our target gene set is a promising starting point for further embryonic studies, as well as for the molecular genetic characterization of subregions and cell types in the neurogenic systems in the adult crayfish brain.

Converging on the orb: denser taxon sampling elucidates spider phylogeny and new analytical methods support repeated evolution of the orb web

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.

Investigating Sources of Conflict in Deep Phylogenomics of Vetigastropod Snails

Phylogenetic analyses may suffer from multiple sources of error leading to conflict between genes and methods of inference. The evolutionary history of the mollusc clade Vetigastropoda makes them susceptible to these conflicts, their higher level phylogeny remaining largely unresolved. Originating over 350 Ma, vetigastropods were the dominant marine snails in the Paleozoic. Multiple extinction events and new radiations have resulted in both very long and very short branches and a large extant diversity of over 4000 species. This is the perfect setting of a hard phylogenetic question in which sources of conflict can be explored. We present 41 new transcriptomes across the diversity of vetigastropods (62 terminals total), and provide the first genomic-scale phylogeny for the group. We find that deep divergences differ from previous studies in which long branch attraction was likely pervasive. Robust results leading to changes in taxonomy include the paraphyly of the order Lepetellida and the family Tegulidae. Tectinae subfam. nov. is designated for the clade comprising Tectus, Cittarium, and Rochia. For two early divergences, topologies disagreed between concatenated analyses using site heterogeneous models versus concatenated partitioned analyses and summary coalescent methods. We investigated rate and composition heterogeneity among genes, as well as missing data by locus and by taxon, none of which had an impact on the inferred topologies. We also found no evidence for ancient introgression throughout the phylogeny. We further tested whether uninformative genes and over-partitioning were responsible for this discordance by evaluating the phylogenetic signal of individual genes using likelihood mapping, and by analyzing the most informative genes with a full multispecies coalescent (MSC) model. We find that most genes are not informative at the two conflicting nodes, but neither this nor gene-wise partitioning are the cause of discordant results. New method implementations that simultaneously integrate amino acid profile mixture models and the MSC might be necessary to resolve these and other recalcitrant nodes in the Tree of Life. [Fissurellidae; Haliotidae; likelihood mapping; multispecies coalescent; phylogenetic signal; phylogenomic conflict; site heterogeneity; Trochoidea.]

Martensopsalis, a new genus of Neopilionidae from New Caledonia (Opiliones: Eupnoi)

New Caledonia has an endemic opiliofauna with two named species of Triaenonychidae, 17 Troglosironidae and eight Zalmoxidae. The recent finding of Neopilionidae on Grande Terre was thus surprising, and required the formal description of a new genus, which we undertake here. Martensopsalis gen. nov. is characterized by a small unsclerotized body with a unique palp with a pointed basal apophysis on the ventral side of the femur and with a distal apophysis on the prolateral side of the patella. The distinct external morphology, simple penis and unique phylogenetic position justify the erection of the new genus with Martensopsalis dogny spec. nov. as its type species. In addition to the type locality we report several other localities of putative congeneric, yet undescribed species.

An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods

Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for species in the family Antarctophilinidae. We also reevaluated the fossil record associated with this taxon to provide further insights into the origin of the group. Novel approaches to identify distinctive genetic lineages, including unsupervised machine learning variational autoencoder plots, were used to establish species hypothesis frameworks. In this sense, three undescribed species and a complex of cryptic species were identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further observed that the shallow waters around the Scotia Arc and on the continental shelf in the Weddell Sea present high endemism and diversity. In contrast, likely due to the glacial pressure during the Cenozoic, a deep-sea group with fewer species emerged expanding over great areas in the South-Atlantic Antarctic Ridge. Our study agrees on how diachronic paleoclimatic and current environmental factors shaped Antarctic communities both at the shallow and deep-sea levels, promoting Antarctica as the center of origin for numerous taxa such as gastropod mollusks.

Interrogating Genomic-Scale Data to Resolve Recalcitrant Nodes in the Spider Tree of Life

Genome-scale data sets are converging on robust, stable phylogenetic hypotheses for many lineages; however, some nodes have shown disagreement across classes of data. We use spiders (Araneae) as a system to identify the causes of incongruence in phylogenetic signal between three classes of data: exons (as in phylotranscriptomics), noncoding regions (included in ultraconserved elements [UCE] analyses), and a combination of both (as in UCE analyses). Gene orthologs, coded as amino acids and nucleotides (with and without third codon positions), were generated by querying published transcriptomes for UCEs, recovering 1,931 UCE loci (codingUCEs). We expected that congeners represented in the codingUCE and UCEs data would form clades in the presence of phylogenetic signal. Noncoding regions derived from UCE sequences were recovered to test the stability of relationships. Phylogenetic relationships resulting from all analyses were largely congruent. All nucleotide data sets from transcriptomes, UCEs, or a combination of both recovered similar topologies in contrast with results from transcriptomes analyzed as amino acids. Most relationships inferred from low-occupancy data sets, containing several hundreds of loci, were congruent across Araneae, as opposed to high occupancy data matrices with fewer loci, which showed more variation. Furthermore, we found that low-occupancy data sets analyzed as nucleotides (as is typical of UCE data sets) can result in more congruent relationships than high occupancy data sets analyzed as amino acids (as in phylotranscriptomics). Thus, omitting data, through amino acid translation or via retention of only high occupancy loci, may have a deleterious effect in phylogenetic reconstruction.

The Phylogeny and Evolution of the Flashiest of the Armored Harvestmen (Arachnida: Opiliones)

Gonyleptoidea, largely restricted to the Neotropics, constitutes the most diverse superfamily of Opiliones and includes the largest and flashiest representatives of this arachnid order. However, the relationships among its main lineages (families and subfamilies) and the timing of their origin are not sufficiently understood to explain how this tropical clade has been able to colonize the temperate zone. Here, we used transcriptomics and divergence time dating to investigate the phylogeny of Gonyleptoidea. Our results support the monophyly of Gonyleptoidea and all of its families with more than one species represented. Resolution within Gonyleptidae s.s. is achieved for many clades, but some subfamilies are not monophyletic (Gonyleptinae, Mitobatinae, and Pachylinae), requiring taxonomic revision. Our data show evidence for one colonization of today's temperate zone early in the history of Gonyleptidae, during the Paleogene, at a time when the Neotropical area extended poleward into regions now considered temperate. This provides a possible mechanism for the colonization of the extratropics by a tropical group following the Paleocene-Eocene Thermal Maximum, explaining how latitudinal diversity gradients can be established. Taxonomic acts: Ampycidae Kury 2003 is newly ranked as family; Neosadocus Mello-Leitão is transferred to Progonyleptoidellinae (new subfamilial assignment). [Arachnids; biogeography; phylogenomics; transcriptomics.].

Phylogenomic re-evaluation of Triaenonychoidea (Opiliones : Laniatores), and systematics of Triaenonychidae, including new families, genera and species

The Opiliones superfamily Triaenonychoidea currently includes two families, the monogeneric New Zealand–endemic Synthetonychiidae Forster, 1954 and Triaenonychidae Sørensen, 1886, a diverse family distributed mostly throughout the temperate Gondwanan terranes, with ~110 genera and ~500 species and subspecies currently described. Traditionally, Triaenonychidae has been divided into subfamilies diagnosed by very few morphological characters largely derived from the troublesome ‘Roewerian system’ of morphology, and classifications based on this system led to many complications. Recent research within Triaenonychoidea using morphology and traditional multilocus data has shown multiple deeply divergent lineages, non-monophyly of Triaenonychidae, and non-monophyly of subfamilies, necessitating a revision based on phylogenomic data. We used sequence capture of ultraconserved elements across 164 samples to create a 50% taxon occupancy matrix with 704 loci. Using phylogenomic and morphological examinations, we explored family-level relationships within Triaenonychoidea, including describing two new families: (1) Lomanellidae Mendes &amp; Derkarabetian, fam. nov., consisting of Lomanella Pocock, 1903, and a newly described genus Abaddon Derkarabetian &amp; Baker, gen. nov. with one species, A. despoliator Derkarabetian, sp. nov.; and (2) the elevation to family of Buemarinoidae Karaman, 2019, consisting of Buemarinoa Roewer, 1956, Fumontana Shear, 1977, Flavonuncia Lawrence, 1959, and a newly described genus Turonychus Derkarabetian, Prieto &amp; Giribet, gen. nov., with one species, T. fadriquei Derkarabetian, Prieto &amp; Giribet, sp. nov. With our dataset we also explored phylogenomic relationships within Triaenonychidae with an extensive taxon set including samples representing ~80% of the genus-level diversity. Based on our results we (1) discuss systematics of this family including the historical use of subfamilies, (2) reassess morphology in the context of our phylogeny, (3) hypothesise placement for all unsampled genera, (4) highlight lineages most in need of taxonomic revision, and (5) provide an updated species-level checklist. Aside from describing new taxa, our study provides the phylogenomic context necessary for future evolutionary and systematic research across this diverse lineage. ZooBank Registration: urn:lsid:zoobank.org:pub:81683834-98AB-43AA-B25A-C28C6A404F41

A revised phylogeny of the New Caledonian endemic genus Troglosiro (Opiliones : Cyphophthalmi : Troglosironidae) with the description of four new species

The Cyphophthalmi genus Troglosiro (the only genus of the family Troglosironidae) is endemic to New Caledonia, representing one of the oldest lineages of this emerged part of Zealandia. Its species are short-range endemics, many known from single localities. Here we examined the phylogenetic relationships of Troglosironidae using standard Sanger-sequenced markers (nuclear 18S rRNA, 28S rRNA, and mitochondrial 16S rRNA and cytochrome c oxidase subunit I) and a combination of phylogenetic methods, including parsimony under Direct Optimization and maximum likelihood with static homology. We also applied a diversity of species delimitation methods, including distance-based, topology-based and unsupervised machine learning to evaluate previous species designations. Finally, we used a combination of genetic and morphological information to describe four new species – T. dogny sp. nov., T. pin sp. nov., T. pseudojuberthiei sp. nov. and T. sharmai sp. nov. – and discuss them in the broader context of the phylogeny and biogeographic history of the family. A key to the species of Troglosiro is also provided. urn:lsid:zoobank.org:pub:93541314-8309-468C-BB77-B34C3A81137E

A molecular phylogeny of the circum-Antarctic Opiliones family Neopilionidae

The Opiliones family Neopilionidae is restricted to the terranes of the former temperate Gondwana: South America, Africa, Australia, New Caledonia and New Zealand. Despite decades of morphological study of this unique fauna, it has been difficult reconciling the classic species of the group (some described over a century ago) with recent cladistic morphological work and previous molecular work. Here we attempted to investigate the pattern and timing of diversification of Neopilionidae by sampling across the distribution range of the family and sequencing three markers commonly used in Sanger-based approaches (18S rRNA, 28S rRNA and cytochrome-c oxidase subunit I). We recovered a well-supported and stable clade including Ballarra (an Australian ballarrine) and the Enantiobuninae from South America, Australia, New Caledonia and New Zealand, but excluding Vibone (a ballarrine from South Africa). We further found a division between West and East Gondwana, with the South American Thrasychirus/Thrasychiroides always being sister group to an Australian–Zealandian (i.e. Australia + New Zealand + New Caledonia) clade. Resolution of the Australian–Zealandian taxa was analysis-dependent, but some analyses found Martensopsalis, from New Caledonia, as the sister group to an Australian–New Zealand clade. Likewise, the species from New Zealand formed a clade in some analyses, but Mangatangi often came out as a separate lineage from the remaining species. However, the Australian taxa never constituted a monophyletic group, with Ballarra always segregating from the remaining Australian species, which in turn constituted 1–3 clades, depending on the analysis. Our results identify several generic inconsistencies, including the possibility of Thrasychiroides nested within Thrasychirus, Forsteropsalis being paraphyletic with respect to Pantopsalis, and multiple lineages of Megalopsalis in Australia. In addition, the New Zealand Megalopsalis need generic reassignment: Megalopsalis triascuta will require its own genus and M. turneri is here transferred to Forsteropsalis, as Forsteropsalis turneri (Marples, 1944), comb. nov.

The Wynberg Cave System, the most important site for cave fauna in South Africa at risk

The Wynberg Cave System, located on the Cape Peninsula, represents one of the most significant sites of cave fauna in southern Africa. However, the continuous increase in cave visitation is severely impacting the system as evidenced by graffiti, the trampling and destruction of cave habitats and even a reduction in the sizes of bat colonies. In October 2019, the Wynberg Cave System was visited by a group of scientist, who discovered unregistered troglomorphic species. This, subsequently increased the number of troglobites occurring in the system to 19, which likely means that this system has the potential to become the first hotspot of subterranean biodiversity in Africa. Protecting the Wynberg Cave System is therefore of great importance. Here, we propose short and long-term strategies that include educating local communities on the importance of conserving caves and installing gated entrances.

A polyvalent and universal tool for genomic studies in gastropod molluscs (Heterobranchia)

Molluscs are the second most diverse animal phylum and heterobranch gastropods present ~ 44,000 species. These comprise fascinating creatures with huge morphological and ecological disparity. Such great diversity comes with even larger phylogenetic uncertainty and many taxa have been largely neglected in molecular assessments. Genomic tools have provided resolution to deep cladogenic events but generating large numbers of transcriptomes/genomes is expensive and usually requires fresh material. Here we leverage a target enrichment approach to design and synthesize a probe set based on available genomes and transcriptomes across Heterobranchia. Our probe set contains 57,606 70mer baits and targets a total of 2,259 ultra-conserved elements (UCEs). Post-sequencing capture efficiency was tested against 31 marine heterobranchs from major groups, including Acochlidia, Acteonoidea, Aplysiida, Cephalaspidea, Pleurobranchida, Pteropoda, Runcinida, Sacoglossa, and Umbraculida. The combined Trinity and Velvet assemblies recovered up to 2,211 UCEs in Tectipleura, up to 1,978 in Nudipleura, and up to 1,927 in Acteonoidea, the latter two being the most distantly related taxa to our core study group. Total alignment length was 525,599 bp and contained 52% informative sites and 21% missing data. Maximum-likelihood and Bayesian inference approaches recovered the monophyly of all orders tested as well as the larger clades Nudipleura, Panpulmonata, and Euopisthobranchia. The successful enrichment of diversely preserved material and DNA concentrations demonstrate the polyvalent nature of UCEs, and the universality of the probe set designed. We believe this probe set will enable multiple, interesting lines of research, that will benefit from an inexpensive and largely informative tool that will, additionally, benefit from the access to museum collections to gather genomic data.

Phylogeny and Biogeography of Spinicaudata (Crustacea: Branchiopoda)

Spinicaudata (spiny clam shrimp) is a taxon of Branchiopoda occurring since the Devonian and today it occurs nearly globally in temporary water bodies. We present the most species-rich phylogenetic analyses of this taxon based on four molecular loci: COI, 16S rRNA, EF1α and 28S rRNA. Our results support previous findings that Cyzicidae sensu lato is paraphyletic. To render Cyzicidae monophyletic we establish a fourth extant spinicaudatan family to accommodate Eocyzicus. Within Cyzicidae, none of the genera Cyzicus, Caenestheria or Caenestheriella are monophyletic, and the morphological characters used to define these genera (condyle length and rostrum shape) are not associated with well-delimited clades within Cyzicidae. There is insufficient resolution to elucidate the relationships within Leptestheriidae. However, there is sufficient evidence to show that the leptestheriid genera Eoleptestheria and Leptestheria are non-monophyletic, and there is no support for the genus Leptestheriella. Molecular clock analyses suggest that the wide geographic distribution of many spinicaudatan taxa across multiple continents is largely based on vicariance associated with the break-up of Pangea and Gondwana. Trans-oceanic dispersal has occurred in some taxa (e.g., Eulimnadia and within Leptestheriidae) but has been relatively rare. Our results highlight the need to revise the taxonomy of Cyzicidae and Leptestheriidae and provide evidence that the global spinicaudatan diversity may be underestimated due to the presence of numerous cryptic species. We establish Eocyzicidae fam. nov. to accommodate the genus Eocyzicus. Consequently, Cyzicidae comprises only two genera -Cyzicus and Ozestheria. Ozestheria occurs also in Africa and Asia and Ozestheria pilosa new comb. is assigned to this genus.

Monophyly, Taxon Sampling, and the Nature of Ranks in the Classification of Orb-Weaving Spiders (Araneae: Araneoidea)

We address some of the taxonomic and classification changes proposed by Kuntner et al. (2019) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to recircumscribe araneids and to rank the subfamily Nephilinae as a family is fundamentally flawed as it renders the family Araneidae paraphyletic. We discuss the importance of monophyly, outgroup selection, and taxon sampling, the subjectivity of ranks, and the implications of the age of origin criterion to assign categorical ranks in biological classifications. We explore the outcome of applying the approach of Kuntner et al. (2019) to the classification of spiders with emphasis on the ecribellate orb-weavers (Araneoidea) using a recently published dated phylogeny. We discuss the implications of including the putative sister group of Nephilinae (the sexually dimorphic genus Paraplectanoides) and the putative sister group of Araneidae (the miniature, monomorphic family Theridiosomatidae). We propose continuation of the phylogenetic classification put forth by Dimitrov et al. (2017), and we formally rank Nephilinae and Phonognathinae as subfamilies of Araneidae. Our classification better reflects the understanding of the phylogenetic placement and evolutionary history of nephilines and phonognathines while maintaining the diagnosability of Nephilinae. It also fulfills the fundamental requirement that taxa must be monophyletic, and thus avoids the paraphyly of Araneidae implied by Kuntner et al. (2019).

A congruent topology for deep gastropod relationships

Gastropod molluscs are among the most diverse and abundant animals in the oceans, and are successful colonizers of terrestrial and freshwater environments. Past phylogenetic efforts to resolve gastropod relationships resulted in a range of conflicting hypotheses. Here, we use phylogenomics to address deep relationships between the five major gastropod lineages—Caenogastropoda, Heterobranchia, Neritimorpha, Patellogastropoda and Vetigastropoda—and provide one congruent and well-supported topology. We substantially expand taxon sampling for outgroups and for previously underrepresented gastropod lineages, presenting new transcriptomes for neritimorphs and patellogastropods. We conduct analyses under maximum-likelihood, Bayesian inference and a coalescent-based approach, accounting for the most pervasive sources of systematic errors in large datasets: compositional heterogeneity, site heterogeneity, heterotachy, variation in evolutionary rates among genes, matrix completeness, outgroup choice and gene tree conflict. We find that vetigastropods and patellogastropods are sister taxa, and that neritimorphs are the sister group to caenogastropods and heterobranchs. We name these two major unranked clades Psilogastropoda and Angiogastropoda, respectively. We additionally provide the first genomic-scale data for internal relationships of neritimorphs and patellogastropods. Our results highlight the need for reinterpreting the evolution of morphological and developmental characters in gastropods, especially for inferring their ancestral states.

Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life

Bivalvia has been the subject of extensive recent phylogenetic work to attempt resolving either the backbone of the bivalve tree using transcriptomic data, or the tips using morpho-anatomical data and up to five genetic markers. Yet the first approach lacked decisive taxon sampling and the second failed to resolve many interfamilial relationships, especially within the diverse clade Imparidentia. Here we combine dense taxon sampling with 108 deep-sequenced Illumina-based transcriptomes to provide resolution in nodes that required additional study. We designed specific data matrices to address the poorly resolved relationships within Imparidentia. Our results support the overall backbone of the bivalve tree, the monophyly of Bivalvia and all its main nodes, although the monophyly of Protobranchia remains less clear. Likewise, the inter-relationships of the six main bivalve clades were fully supported. Within Imparidentia, resolution increases when analysing Imparidentia-specific matrices. Lucinidae, Thyasiridae and Gastrochaenida represent three early branches. Gastrochaenida is sister group to all remaining imparidentians, which divide into six orders. Neoheterodontei is always fully supported, and consists of Sphaeriida, Myida and Venerida, with the latter now also containing Mactroidea, Ungulinoidea and Chamidae, a family particularly difficult to place in earlier work. Overall, our study, by using densely sampled transcriptomes, provides the best-resolved bivalve phylogeny to date.

Convergent evolution of sexually dimorphic glands in an amphi-Pacific harvestman family

Sexually dimorphic traits are widespread in animals, and include sex-specific weapons, ornamentation and, although less noticed, glands and associated structures. In arachnids, certain lineages of the order Opiliones exhibit diverse forms of dimorphism in the armature and length of appendages (common in Laniatores), as well as in the presence of sexually dimorphic glands (mostly investigated in Cyphophthalmi), positing harvestmen as promising models to study sexual dimorphism. Whereas the evolution and ecological significance of armature have been the focus of recent attention, sexually dimorphic glands remain understudied in groups other than Cyphophthalmi, despite being widespread in Opiliones. We therefore selected the amphi-Pacific family Zalmoxidae as an ideal taxon to investigate the evolutionary dynamics of this trait. We first describe four new species of Palaeotropical Zalmoxis, including a species with sexually dimorphic glands, and describe the morphology of zalmoxid species with sexually dimorphic glands using scanning electron microscopy. Using a previously assembled six-locus dataset supplemented with new terminals, and applying stochastic character mapping, we infer that sexually dimorphic glands evolved once in the Neotropics and at least four times in the Palaeotropic zalmoxids, revealing the evolutionary lability of this trait.

Corrigendum to: Phylogeny, evolution and systematic revision of the mite harvestman family Neogoveidae (Opiliones Cyphophthalmi)

Mite harvestmen of the family Neogoveidae have a tropical trans-Atlantic distribution with representatives in equatorial West Africa and the Neotropics, specifically in the south-east region of the USA and in northern South America, being conspicuously absent from Central America. We provide a comprehensive molecular phylogeny of the family including representatives of all genera but the monotypic Tucanogovea Karaman, 2013, and new information on the type species described by Jochen Martens in 1969 that were unavailable for molecular study until now: Brasiliogovea microphaga, Metagovea oviformis and ‘? Gen. enigmaticus'. Additionally, we revisit the somatic and male genitalic morphology of representatives of all genera by means of scanning electron microscopy and confocal laser scanning microscopy, and describe the new genera Leggogovia Benavides & Giribet, gen. nov., Microgovia Benavides, Hormiga & Giribet, gen. nov., Waiwaigovia Benavides, Hormiga & Giribet, gen. nov. and 13 new species: Brasiliogovea aphantostylus Benavides, Hormiga & Giribet, sp. nov., Brasiliogovea microstylus Benavides, Hormiga & Giribet, sp. nov., Brasiliogovea yacambuensis Benavides, Hormiga & Giribet, sp. nov., Metagovea matapi Benavides, Hormiga & Giribet, sp. nov., Metagovea planada Benavides, Hormiga & Giribet, sp. nov., Microgovia chenepau Benavides, Hormiga & Giribet, sp. nov., Neogovea branstetteri Benavides, Hormiga & Giribet, sp. nov., Neogovea enigmatica Martens, sp. nov., Neogovea matawai Benavides, Hormiga & Giribet, sp. nov., Parogovia montealensis Benavides & Giribet, sp. nov., Parogovia prietoi Benavides & Giribet, sp. nov., Parogovia putnami Benavides & Giribet, sp. nov. and Waiwaigovia schultzi Benavides, Hormiga & Giribet, sp. nov. Phylogenetic analyses based on maximum likelihood, parsimony and Bayesian inference support the monophyly of Neogoveidae and a sister group relationship of Neogoveidae + Ogoveidae with Troglosironidae (a clade named Sternophthalmi). Relationships among neogoveid genera are largely congruent between methods as follows: ((Leggogovia gen. nov., Metasiro), (Parogovia, ((Canga, Microgovia gen. nov.), ((Brasiliogovea, Neogovea), (Huitaca, (Waiwaigovia gen. nov., Metagovea)))))). In light of our results, the following taxonomic changes are proposed: Metagovea oviformis Martens, 1969 is transferred to Microgovia, gen. nov.; Parogovia pabsgarnoni Legg, 1990 is transferred to Leggogovia, gen. nov.; ‘? Gen. enigmaticus Martens, 1969' is an invalid name according to the ICZN; the corresponding taxon is redescribed and formally named as Neogovea enigmatica Martens, sp. nov.

Corrigendum to: Convergent evolution of sexually dimorphic glands in an amphi-Pacific harvestman family

Sexually dimorphic traits are widespread in animals, and include sex-specific weapons, ornamentation and, although less noticed, glands and associated structures. In arachnids, certain lineages of the order Opiliones exhibit diverse forms of dimorphism in the armature and length of appendages (common in Laniatores), as well as in the presence of sexually dimorphic glands (mostly investigated in Cyphophthalmi), positing harvestmen as promising models to study sexual dimorphism. Whereas the evolution and ecological significance of armature have been the focus of recent attention, sexually dimorphic glands remain understudied in groups other than Cyphophthalmi, despite being widespread in Opiliones. We therefore selected the amphi-Pacific family Zalmoxidae as an ideal taxon to investigate the evolutionary dynamics of this trait. We first describe four new species of Palaeotropical Zalmoxis, including a species with sexually dimorphic glands, and describe the morphology of zalmoxid species with sexually dimorphic glands using scanning electron microscopy. Using a previously assembled six-locus dataset supplemented with new terminals, and applying stochastic character mapping, we infer that sexually dimorphic glands evolved once in the Neotropics and at least four times in the Palaeotropic zalmoxids, revealing the evolutionary lability of this trait.

Molecular phylogeny and biogeography of the temperate Gondwanan family Triaenonychidae (Opiliones : Laniatores) reveals pre-Gondwanan regionalisation, common vicariance, and rare dispersal

Triaenonychidae Sørensen in L. Koch, 1886 is a large family of Opiliones with ~480 described species broadly distributed across temperate forests in the Southern Hemisphere. However, it remains poorly understood taxonomically, as no comprehensive phylogenetic work has ever been undertaken. In this study we capitalise on samples largely collected by us during the last two decades and use Sanger DNA-sequencing techniques to produce a large phylogenetic tree with 300 triaenonychid terminals representing nearly 50% of triaenonychid genera and including representatives from all the major geographic areas from which they are known. Phylogenetic analyses using maximum likelihood and Bayesian inference methods recover the family as diphyletic, placing Lomanella Pocock, 1903 as the sister group to the New Zealand endemic family Synthetonychiidae Forster, 1954. With the exception of the Laurasian representatives of the family, all landmasses contain non-monophyletic assemblages of taxa. To determine whether this non-monophyly was the result of Gondwanan vicariance, ancient cladogenesis due to habitat regionalisation, or more recent over-water dispersal, we inferred divergence times. We found that most divergence times between landmasses predate Gondwanan breakup, though there has been at least one instance of transoceanic dispersal – to New Caledonia. In all, we identify multiple places in the phylogeny where taxonomic revision is needed, and transfer Lomanella outside of Triaenonychidae in order to maintain monophyly of the family.

Genetic differentiation in mountain-dwelling clam shrimp, Paralimnadia (Crustacea : Branchiopoda : Spinicaudata), in eastern Australia

The majority of Australian Spinicaudata Linder, 1945 inhabit the (semi)arid deserts of Australia’s lowlands. However, several closely related species of Paralimnadia Sars, 1896 inhabit small temporary habitats throughout the Great Dividing Range in eastern Australia. By combining analyses of mitochondrial cytochrome c oxidase subunit I (COI) with double-digest restriction-site associated DNA (ddRAD) data, we studied the species diversity and genetic diversity of this group of mountain-dwelling branchiopods. Levels of genetic differentiation in COI are relatively low between putative species (mostly between 1.5 and 6.7%), complicating COI-based species delimitation. Depending on the applied threshold, three to six species are inferred in the studied area, with most putative species being geographically restricted. Particularly notable are the high levels of population differentiation indicated by ddRAD analyses between nearby populations within putative species. This suggests that gene flow is limited, even between populations separated only by a few kilometres. This may lead to fast population differentiation, which in turn might drive speciation. Our data suggest that the species diversity of Paralimnadia in the Great Dividing Range is much higher than currently appreciated.

Predicting the Impact of Describing New Species on Phylogenetic Patterns

Although our inventory of Earth’s biodiversity remains incomplete, we still require analyses using the Tree of Life to understand evolutionary and ecological patterns. Because incomplete sampling may bias our inferences, we must evaluate how future additions of newly discovered species might impact analyses performed today. We describe an approach that uses taxonomic history and phylogenetic trees to characterize the impact of past species discoveries on phylogenetic knowledge using patterns of branch-length variation, tree shape, and phylogenetic diversity. This provides a framework for assessing the relative completeness of taxonomic knowledge of lineages within a phylogeny. To demonstrate this approach, we use recent large phylogenies for amphibians, reptiles, flowering plants, and invertebrates. Well-known clades exhibit a decline in the mean and range of branch lengths that are added each year as new species are described. With increased taxonomic knowledge over time, deep lineages of well-known clades become known such that most recently described new species are added close to the tips of the tree, reflecting changing tree shape over the course of taxonomic history. The same analyses reveal other clades to be candidates for future discoveries that could dramatically impact our phylogenetic knowledge. Our work reveals that species are often added non-randomly to the phylogeny over multiyear time-scales in a predictable pattern of taxonomic maturation. Our results suggest that we can make informed predictions about how new species will be added across the phylogeny of a given clade, thus providing a framework for accommodating unsampled undescribed species in evolutionary analyses.

Differential gene expression during substrate probing in larvae of the Caribbean coral Porites astreoides

The transition from larva to adult is a critical step in the life history strategy of most marine animals. However, the genetic basis of this life history change remains poorly understood in many taxa, including most coral species. Recent evidence suggests that coral planula larvae undergo significant changes at the physiological and molecular levels throughout the development. To investigate this, we characterized differential gene expression (DGE) during the transition from planula to adult polyp in the abundant Caribbean reef-building coral Porites astreoides, that is from nonprobing to actively substrate-probing larva, a stage required for colony initiation. This period is crucial for the coral, because it demonstrates preparedness to locate appropriate substrata for settlement based on vital environmental cues. Through RNA-Seq, we identified 860 differentially expressed holobiont genes between probing and nonprobing larvae (p ≤ .01), the majority of which were upregulated in probing larvae. Surprisingly, differentially expressed genes of endosymbiotic dinoflagellate origin greatly outnumbered coral genes, compared with a nearly 1:1 ratio of coral-to-dinoflagellate gene representation in the holobiont transcriptome. This unanticipated result suggests that dinoflagellate endosymbionts may play a significant role in the transition from nonprobing to probing behaviour in dinoflagellate-rich larvae. Putative holobiont genes were largely involved in protein and nucleotide binding, metabolism and transport. Genes were also linked to environmental sensing and response and integral signalling pathways. Our results thus provide detailed insight into molecular changes prior to larval settlement and highlight the complex physiological and biochemical changes that occur in early transition stages from pelagic to benthic stages in corals, and perhaps more importantly, in their endosymbionts.