A dated molecular phylogeny of mite harvestmen (Arachnida: Opiliones: Cyphophthalmi) elucidates ancient diversification dynamics in the Australian Wet Tropics

Reassessing the phylogeny of Cyphophthalmi with phylogenomics: A UCE-based phylogeny of mite harvesters (Opiliones)

Cyphophthalmi (the mite harvesters) are a group of Opiliones with broad interest due to their species being classic examples of short-range endemics and displaying model biogeographical patterns for poor dispersers. Cyphophthalmi phylogeny has received attention using morphology, Sanger-based sequencing data, or transcriptomics. Here we turn to a new type of data, ultraconserved elements (UCEs) and provide a first phylogeny for the entire suborder Cyphophthalmi using such data and including representatives from 36 of the 46 currently recognized genera. Phylogenetic analysis of four occupancy matrices (50%, 75%, 90% and 95%), for a total of 840, 567, 129, and 23 loci, respectively, yielded a well resolved phylogeny with monophyly of Pettalidae, Parasironidae, Stylocellidae and Troglosironidae. However, Neogoveidae appeared paraphyletic with respect to Ogoveidae in all datasets and to Troglosironidae in some, and the traditional Sironidae, which was monophyletic, now appeared paraphyletic with respect to the recently erected family Parasironidae. Our phylogenomic results using UCE data resolve the position of several problematic genera (e.g., Pettalus) and add support to other parts of the tree that received low support in Sanger-based phylogenies. Our work also stresses the possibility to add museum samples to phylogenies although methods for optimizing DNA yield from such small-bodied specimens need further improvement. Finally, this backbone phylogeny demonstrates the feasibility of an all-species phylogeny using UCEs for Cyphophthalmi, and by extension, for all Opiliones.

Machine learning approaches delimit cryptic taxa in a previously intractable species complex

Cryptic species are not diagnosable via morphological criteria, but can be detected through analysis of DNA sequences. A number of methods have been developed for identifying species based on genetic data; however, these methods are prone to over-splitting taxa with extreme population structure, such as dispersal-limited organisms. Machine learning methodologies have the potential to overcome this challenge. Here, we apply such approaches, using a large dataset generated through hybrid target enrichment of ultraconserved elements (UCEs). Our study taxon is the Aoraki denticulata species complex, a lineage of extremely low-dispersal arachnids endemic to the South Island of Aotearoa New Zealand. This group of mite harvesters has been the subject of previous species delimitation studies using smaller datasets generated through Sanger sequencing and analytical approaches that rely on multispecies coalescent models and barcoding gap discovery. Those analyses yielded a number of putative cryptic species that seems unrealistic and extreme, based on what we know about species' geographic ranges and genetic diversity in non-cryptic mite harvesters. We find that machine learning approaches, on the other hand, identify cryptic species with geographic ranges that are similar to those seen in other morphologically diagnosable mite harvesters in Aotearoa New Zealand's South Island. We performed both unsupervised and supervised machine learning analyses, the latter with training data drawn either from animals broadly (vagile and non-vagile) or from a custom training dataset from dispersal-limited harvesters. We conclude that applying machine learning approaches to the analysis of UCE-derived genetic data is an effective method for delimiting species in complexes of low-vagility cryptic species, and that the incorporation of training data from biologically relevant analogues can be critically informative.

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.

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.

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.

First phylogenetic assessment and taxonomic synopsis of the open-holed trapdoor spider genus Namea (Mygalomorphae: Anamidae): a highly diverse mygalomorph lineage from Australia’s tropical eastern rainforests

The tropical and subtropical rainforests of Australia’s eastern mesic zone have given rise to a complex and highly diverse biota. Numerous old endemic, niche-conserved groups persist in the montane rainforests south of Cooktown, where concepts of serial allopatric speciation resulting from the formation of xeric interzones have largely driven our biogeographic understanding of the region. Among invertebrate taxa, studies on less vagile arachnid lineages now complement extensive research on vertebrate taxa, and phylogenetic studies on mygalomorph spiders in particular are revealing significant insights about the biogeographic history of the Australian continent since the Eocene. One mygalomorph lineage entirely endemic to Australia’s tropical and subtropical eastern rainforests is the open-holed trapdoor spider genus Namea Raven, 1984 (family Anamidae). We explore, for the first time, the phylogenetic diversity and systematics of this group of spiders, with the aims of understanding patterns of rainforest diversity in Namea, of exploring the relative roles of lineage overlap versus in situ speciation in driving predicted high levels of congeneric sympatry, and of broadly reconciling morphology with evolutionary history. Original and legacy sequences were obtained for three mtDNA and four nuDNA markers from 151 specimens, including 82 specimens of Namea. We recovered a monophyletic genus Namea sister to the genus Teyl Main, 1975, and monophyletic species clades corresponding to 30 morphospecies OTUs, including 22 OTUs nested within three main species-complex lineages. Remarkable levels of sympatry for a single genus of mygalomorph spiders were revealed in rainforest habitats, with upland subtropical rainforests in south-eastern Queensland often home to multiple (up to six) congeners of usually disparate phylogenetic affinity living in direct sympatry or close parapatry, likely the result of simultaneous allopatric speciation in already co-occurring lineages, and more recent dispersal in a minority of taxa. In situ speciation, in contrast, appears to have played a relatively minor role in generating sympatric diversity within rainforest ‘islands’. At the population level, changes in the shape and spination of the male first leg relative to evolutionary history reveal subtle but consistent interspecific morphological shifts in the context of otherwise intraspecific variation, and understanding this morphological variance provides a useful framework for future taxonomic monography. Based on the phylogenetic results, we further provide a detailed taxonomic synopsis of the genus Namea, formally diagnosing three main species-complexes (the brisbanensis-complex, the dahmsi-complex and the jimna-complex), re-illustrating males of all 15 described species, and providing images of live spiders and burrows where available. In doing so, we reveal a huge undescribed diversity of Namea species from tropical and subtropical rainforest habitats, and an old endemic fauna that is beginning to shed light on more complex patterns of rainforest biogeography.

Six Impossible Things before Breakfast: Assumptions, Models, and Belief in Molecular Dating

Confidence in molecular dating analyses has grown with the increasing sophistication of the methods. Some problematic cases where molecular dates disagreed with paleontological estimates appear to have been resolved with a growing agreement between molecules and fossils. But we cannot relax just yet. The growing analytical sophistication of many molecular dating methods relies on an increasingly large number of assumptions about evolutionary history and processes. Many of these assumptions are based on statistical tractability rather than being informed by improved understanding of molecular evolution, yet changing the assumptions can influence molecular dates. How can we tell if the answers we get are driven more by the assumptions we make than by the molecular data being analyzed?

The anatomy of an unstable node: a Levantine relict precipitates phylogenomic dissolution of higher-level relationships of the armoured harvestmen (Arachnida: Opiliones: Laniatores)

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.

Evolutionary biogeography of Australian jumping spider genera (Araneae : Salticidae)

Phylogenetic relationships and estimated dates of origin, plus distributional, ecological and morphological data for salticid genera were used to examine a series of hypotheses related to the evolution of the Australian salticid fauna. Though independent, the time patterns of evolution of genera in Australia and South America were similar, while that for Northern Hemisphere taxa differed. In each case the production of new genera occurred during the warmer parts of the mid Tertiary but not during cooler and drier times. Asian elements entered Australia as early as 31 million years ago, long before the collision of the Australasian and Asian continental plates. Endemic and derivatives of Asian genera were similarly distributed across Australian biomes. However, arriving taxa were more successful when conditions matched their mesic origins (tropical), but less so when different (temperate). While endemic genera often extended their ranges into drier environments by increasing the number of species, recent arrivals did so by extending the range of individual species. Maximum Parsimony analyses of a range of presumed adaptive, morphological and ecological characters showed these did not reflect genus-level processes; however, the analysis did show all endemic genera had mesic origins.