A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements

Environmental specificity of karst cave habitats evidenced by diverse symbiotic bacteria in Opiliones

BACKGROUND

Karst caves serve as natural laboratories, providing organisms with extreme and constant conditions that promote isolation, resulting in a genetic relationship and living environment that is significantly different from those outside the cave. However, research on cave creatures, especially Opiliones, remains scarce, with most studies focused on water, soil, and cave sediments.

RESULTS

The structure of symbiotic bacteria in different caves were compared, revealing significant differences. Based on the alpha and beta diversity, symbiotic bacteria abundance and diversity in the cave were similar, but the structure of symbiotic bacteria differed inside and outside the cave. Microorganisms in the cave play an important role in material cycling and energy flow, particularly in the nitrogen cycle. Although microbial diversity varies inside and outside the cave, Opiliones in Beijing caves and Hainan Island exhibited a strong similarity, indicating that the two environments share commonalities.

CONCLUSIONS

The karst cave environment possesses high microbial diversity and there are noticeable differences among different caves. Different habitats lead to significant differences in the symbiotic bacteria in Opiliones inside and outside the cave, and cave microorganisms have made efforts to adapt to extreme environments. The similarity in symbiotic bacteria community structure suggests a potential similarity in host environments, providing an explanation for the appearance of Sinonychia martensi in caves in the north.

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.

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.

Neglected no longer: Phylogenomic resolution of higher-level relationships in Solifugae

Advanced sequencing technologies have expedited resolution of 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 have thus been 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 that Solifugae radiated by the Permian, and most families diverged prior to the Paleogene-Cretaceous extinction, likely 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.

A novel probe set for the phylogenomics and evolution of RTA spiders

Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders, and are not optimized for the retrolateral tibial apophysis (RTA) clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41 845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.

Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with the description of a new species from montane California

Hypochilus is a relictual lineage of Nearctic spiders distributed disjunctly across the United States in three montane regions (California, southern Rocky Mountains, southern Appalachia). Phylogenetic resolution of species relationships in Hypochilus has been challenging, and conserved morphology coupled with extreme genetic divergence has led to uncertain species limits in some complexes. Here, Hypochilus interspecies relationships have been reconstructed and cryptic speciation more critically evaluated using a combination of ultraconserved elements, mitochondrial CO1 by-catch, and morphology. Phylogenomic data strongly support the monophyly of regional clades and support a ((California, Appalachia), southern Rocky Mountains) topology. In Appalachia, five species are resolved as four lineages (H.thorelli Marx, 1888 and H.coylei Platnick, 1987 are clearly sister taxa), but the interrelationships of these four lineages remain unresolved. The Appalachian species H.pococki Platnick, 1987 is recovered as monophyletic but is highly genetically structured at the nuclear level. While algorithmic analyses of nuclear data indicate many species (e.g., all H.pococki populations as species), male morphology instead reveals striking stasis. Within the California clade, nuclear and mitochondrial lineages of H.petrunkevitchi Gertsch, 1958 correspond directly to drainage basins of the southern Sierra Nevada, with H.bernardino Catley, 1994 nested within H.petrunkevitchi and sister to the southernmost basin populations. Combining nuclear, mitochondrial, geographical, and morphological evidence a new species from the Tule River and Cedar Creek drainages is described, Hypochilusxomotesp. nov. We also emphasize the conservation issues that face several microendemic, habitat-specialized species in this remarkable genus.

Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data

The diversity of biological and ecological characteristics of organisms, and the underlying genetic patterns and processes of speciation, makes the development of universally applicable genetic species delimitation methods challenging. Many approaches, like those incorporating the multispecies coalescent, sometimes delimit populations and overestimate species numbers. This issue is exacerbated in taxa with inherently high population structure due to low dispersal ability, and in cryptic species resulting from nonecological speciation. These taxa present a conundrum when delimiting species: analyses rely heavily, if not entirely, on genetic data which over split species, while other lines of evidence lump. We showcase this conundrum in the harvester Theromaster brunneus, a low dispersal taxon with a wide geographic distribution and high potential for cryptic species. Integrating morphology, mitochondrial, and sub-genomic (double-digest RADSeq and ultraconserved elements) data, we find high discordance across analyses and data types in the number of inferred species, with further evidence that multispecies coalescent approaches over split. We demonstrate the power of a supervised machine learning approach in effectively delimiting cryptic species by creating a "custom" training data set derived from a well-studied lineage with similar biological characteristics as Theromaster. This novel approach uses known taxa with particular biological characteristics to inform unknown taxa with similar characteristics, using modern computational tools ideally suited for species delimitation. The approach also considers the natural history of organisms to make more biologically informed species delimitation decisions, and in principle is broadly applicable for taxa across the tree of life.

The Coume Ouarnède System, a Hotspot of Subterranean Biodiversity in Pyrenees (France)

Located in Northern Pyrenees, in the Arbas massif, France, the system of the Coume Ouarnède, also known as Réseau Félix Trombe—Henne Morte, is the longest and the most complex cave system of France. The system, developed in massive Mesozoic limestone, has two distinct resurgences. Despite relatively limited sampling, its subterranean fauna is rich, composed of a number of local endemics, terrestrial as well as aquatic, including two remarkable relictual species, Arbasus caecus (Simon, 1911) and Tritomurus falcifer Cassagnau, 1958. With 38 stygobiotic and troglobiotic species recorded so far, the Coume Ouarnède system is the second richest subterranean hotspot in France and the first one in Pyrenees. This species richness is, however, expected to increase because several taxonomic groups, like Ostracoda, as well as important subterranean habitats, like MSS (“Milieu Souterrain Superficiel”), have not been considered so far in inventories. Similar levels of subterranean biodiversity are expected to occur in less-sampled karsts of central and western Pyrenees.

Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data

The infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3000 nominal species. This ancient group has a worldwide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel-web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here, we present a comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae. We employ 472 loci obtained through anchored hybrid enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We sampled nearly all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing insights to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). Three families Entypesidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY), and one subfamily Australothelinae (NEW SUBFAMILY) are newly proposed. Such a major rearrangement in classification, recognizing nine newly established family-level rank taxa, is the largest the group has seen in over three decades. [Biogeography; molecular clocks; phylogenomics; spider web foraging; taxonomy.].

A phylogenetic and taxonomic review of baviine jumping spiders (Araneae, Salticidae, Baviini)

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: Bavianessagyna, Indopadillabamilin, I.kodagura, I.nesinor, I.redunca, I.redynis, I.sabivia, I.vimedaba, Maripanthusdraconis (type species of Maripanthus), M.jubatus, M.reinholdae, Padillothoraxbadut, P.mulu, Piranthusapi, P.bakau, P.kohi, P.mandai, and Stagetillusirri, 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: Baviamaurerae (Freudenschuss & Seiter, 2016), Indopadillaannamita (Simon, 1903), I.kahariana (Prószyński & Deeleman-Reinhold, 2013), I.sonsorol (Berry, Beatty & Prószyński, 1997), I.suhartoi (Prószyński & Deeleman-Reinhold, 2013), Maripanthusmenghaiensis (Cao & Li, 2016), M.smedleyi (Reimoser, 1929), Nungiahatamensis (Thorell, 1881), N.modesta (Keyserling, 1883), N.papakula (Strand, 1911), N.xiaolonghaensis (Cao & Li, 2016), Padillothoraxcasteti (Simon, 1900), P.exilis (Cao & Li, 2016), P.flavopunctus (Kanesharatnam & Benjamin, 2018), Stagetillusbanda (Strand, 1911), all comb. nov. One combination is restored, Baviacapistrata (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.

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 & Derkarabetian, fam. nov., consisting of Lomanella Pocock, 1903, and a newly described genus Abaddon Derkarabetian & 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 & Giribet, gen. nov., with one species, T. fadriquei Derkarabetian, Prieto & 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

Historical biogeography of a neglected family of armoured harvestmen (Opiliones : Laniatores : Icaleptidae) with the first record and a new genus for tropical Mesoamerica

Among Opiliones (Arachnida), there are many taxa either with no familial assignment or erroneously located in their current family. This is the case of Ethobunus pilosus, formerly in Phalangodidae and before this work in Zalmoxidae. To assess the phylogenetic position of this taxon, we started with a revision of the male genitalia; followed by the inclusion of three molecular markers: nuclear 28S and 18S, and mitochondrial protein-encoding cytochrome c oxidase subunit I (COI) from E. pilosus in the previously published phylogenies of the Samooidea + Zalmoxoidea clade. The results revealed that E. pilosus is a derived lineage within the family Icaleptidae, thus it is transferred from Zalmoxidae, and the new name Trypophobica gen. nov. is proposed to accommodate it, with the new combination Trypophobica pilosa comb. nov. With its inclusion in Icaleptidae, and the description of Trypophobica llama sp. nov., the current diagnosis of the family needs updating, and further morphological characters should be considered as putative synapomorphies. In addition, the reconstruction of the ancestral ranges of Icaleptidae suggests a mid-Cretaceous origin c. 104 Ma in South America, with a subsequent colonisation to north Mesoamerica c. 80 Ma.

Phylogenomics and biogeography of leptonetid spiders (Araneae:Leptonetidae)

Leptonetidae are rarely encountered spiders, usually associated with caves and mesic habitats, and are disjunctly distributed across the Holarctic. Data from ultraconserved elements (UCEs) were used in concatenated and coalescent-based analyses to estimate the phylogenetic history of the family. Our taxon sample included close outgroups, and 90% of described leptonetid genera, with denser sampling in North America and Mediterranean Europe. Two data matrices were assembled and analysed; the first ‘relaxed’ matrix includes the maximum number of loci and the second ‘strict’ matrix is limited to the same set of core orthologs but with flanking introns mostly removed. A molecular dating analysis incorporating fossil and geological calibration points was used to estimate divergence times, and dispersal–extinction–cladogenesis analysis (DEC) was used to infer ancestral distributions. Analysis of both data matrices using maximum likelihood and coalescent-based methods supports the monophyly of Archoleptonetinae and Leptonetinae. However, relationships among Archoleptonetinae, Leptonetinae, and Austrochiloidea are poorly supported and remain unresolved. Archoleptonetinae is elevated to family rank Archoleptonetidae (new rank) and Leptonetidae (new status) is restricted to include only members of the subfamily Leptonetinae; a taxonomic review with morphological diagnoses is provided for both families. Four well supported lineages within Leptonetidae (new status) are recovered: (1) the Calileptoneta group, (2) the Leptoneta group, (3) the Paraleptoneta group, and (4) the Protoleptoneta group. Most genera within Leptonetidae are monophyletic, although Barusia, Cataleptoneta, and Leptoneta include misplaced species and require taxonomic revision. The origin of Archoleptonetidae (new rank), Leptonetidae, and the four main lineages within Leptonetidae date to the Cretaceous. DEC analysis infers the Leptoneta and Paraleptoneta groups to have ancestral distributions restricted to Mediterranean Europe, whereas the Calileptoneta and Protoleptoneta groups include genera with ancestral distributions spanning eastern and western North America, Mediterranean Europe, and east Asia. Based on a combination of biology, estimated divergence times, and inferred ancestral distributions we hypothesise that Leptonetidae was once widespread across the Holarctic and their present distributions are largely the result of vicariance. Given the wide disjunctions between taxa, we broadly interpret the family as a Holarctic relict fauna and hypothesise that they were once part of the Boreotropical forest ecosystem.

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.

Sitticine jumping spiders: phylogeny, classification, and chromosomes (Araneae, Salticidae, Sitticini)

The systematics of sitticine jumping spiders is reviewed, with a focus on the Palearctic and Nearctic regions, in order to revise their generic classification, clarify the species of one region (Canada), and study their chromosomes. A genome-wide molecular phylogeny of 23 sitticine species, using more than 700 loci from the arachnid Ultra-Conserved Element (UCE) probeset, confirms the Neotropical origins of sitticines, whose basal divergence separates the new subtribeAillutticina (a group of five Neotropical genera) from the subtribe Sitticina (five genera of Eurasia and the Americas). The phylogeny shows that most Eurasian sitticines form a relatively recent and rapid radiation, which we unite into the genus Attulus Simon, 1868, consisting of the subgenera Sitticus Simon, 1901 (seven described species), Attulus (41 described species), and Sittilong Prószyński, 2017 (one species). Five species of Attulus occur natively in North America, presumably through dispersals back from the Eurasian radiation, but an additional three species were more recently introduced from Eurasia. Attuspalustris Peckham & Peckham, 1883 is considered to be a full synonym of Euophrysfloricola C. L. Koch, 1837 (not a distinct subspecies). Attussylvestris Emerton, 1891 is removed from synonymy and recognized as a senior synonym of Sitticusmagnus Chamberlin & Ivie, 1944. Thus, the five native Attulus in North America are Attulusfloricola, A.sylvestris, A.cutleri, A.striatus, and A.finschi. The other sitticines of Canada and the U.S.A. are placed in separate genera, all of which arose from a Neotropical radiation including Jollas Simon, 1901 and Tomis F.O.Pickard-Cambridge, 1901: (1) Attinella Banks, 1905 (A.dorsata, A.concolor, A.juniperi), (2) Tomis (T.welchi), and (3) Sittisax Prószyński, 2017 (S.ranieri). All Neotropical and Caribbean “Sitticus” are transferred to either Jollas (12 species total) or Tomis (14 species). Attinella (three species) and Tomis are both removed from synonymy with Sitticus; the synonymy of Sitticuscabellensis Prószyński, 1971 with Pseudattuluskratochvili Caporiacco, 1947 is restored; Pseudattulus Caporiacco, 1947 is synonymized with Tomis. Six generic names are newly synonymized with Attulus and one with Attinella. Two Neotropical species are described as new, Jollascupreussp. nov. and Tomismanabitasp. nov. Forty-six new combinations are established and three are restored. Three species synonymies are restored, one is new, and two are rejected. Across this diversity of species is a striking diversification of chromosome complements, with X-autosome fusions occurring at least four times to produce neo-Y sex chromosome systems (X₁X₂Y and X₁X₂X₃Y), some of which (Sittisaxranieri and S.saxicola) are sufficiently derived as to no longer preserve the simple traces of ancestral X material. The correlated distribution of neo-Y and a base autosome number of 28 suggests that neo-Y origins occurred preferentially in lineages with the presence of an extra pair of autosomes.

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.

A demonstration of unsupervised machine learning in species delimitation

One major challenge to delimiting species with genetic data is successfully differentiating population structure from species-level divergence, an issue exacerbated in taxa inhabiting naturally fragmented habitats. Many fields of science are now using machine learning, and in evolutionary biology supervised machine learning has recently been used to infer species boundaries. These supervised methods require training data with associated labels. Conversely, unsupervised machine learning (UML) uses inherent data structure and does not require user-specified training labels, potentially providing more objectivity in species delimitation. In the context of integrative taxonomy, we demonstrate the utility of three UML approaches (random forests, variational autoencoders, t-distributed stochastic neighbor embedding) for species delimitation in an arachnid taxon with high population genetic structure (Opiliones, Laniatores, Metanonychus). We find that UML approaches successfully cluster samples according to species-level divergences and not high levels of population structure, while model-based validation methods severely over-split putative species. UML offers intuitive data visualization in two-dimensional space, the ability to accommodate various data types, and has potential in many areas of systematic and evolutionary biology. We argue that machine learning methods are ideally suited for species delimitation and may perform well in many natural systems and across taxa with diverse biological characteristics.

Evolution of a sensory cluster on the legs of Opiliones (Arachnida) informs multi-level phylogenetic relationships

Phylogenetic relationships in Opiliones (Arachnida) at the suborder level have greatly stabilized in recent years, largely due to advances in molecular systematics. Nonetheless, identifying morphological characters in the context of well-resolved phylogenies is essential for testing new systematic hypotheses and establishing diagnostic markers. Here, we investigate with SEM a promising character system across Opiliones: the sensilla on the distalmost article of legs I and II. We identified four discrete characters and scored species of nearly all families of Laniatores (28 families, 44 species), three Dyspnoi, two Eupnoi and two Cyphophthalmi. Using a phylogenetic backbone compiled from recent and ongoing phylogenomic studies, we trace the evolution of these sensilla using ancestral state reconstruction. We discover a widespread occurrence of three sensilla (a pair of sensilla basiconica and one hooded sensillum) on the anterior legs of all families of Laniatores studied, and that comparable structures occur in the other suborders of Opiliones. Our analysis shows that this sensory field provides diagnostic information at different levels of phylogenetic relationships. We discuss the implications of the widespread occurrence of these sensilla in Opiliones, which have recently been hypothesized as hygro-/thermoreceptors and their putative homology with tarsal organs in Arachnida.

Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci

The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa (Mecicobothrium and Hexurella) key to understanding familial monophyly, divergence times, and patterns of entrance web evolution. We show that the conserved regions of the arachnid UCE probe set target exons, such that it should be possible to combine UCE and transcriptome datasets in arachnids. We also show that different UCE probes sometimes target the same protein, and under the matching parameters used here show that UCE alignments sometimes include non-orthologs. Using multiple curated phylogenomic matrices we recover a monophyletic Atypoidea, and reveal that the family Mecicobothriidae comprises four separate and divergent lineages. Fossil-calibrated divergence time analyses suggest ancient Triassic (or older) origins for several relictual atypoid lineages, with late Cretaceous/early Tertiary divergences within some genera indicating a high potential for cryptic species diversity. The ancestral entrance web construct for atypoids, and all mygalomorphs, is reconstructed as a funnel-and-sheet web.