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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.
Sharma, Prashant (Ed.)
Pettalidae is a family of mite harvestmen that inhabits the former circum-Antarctic Gondwanan terranes, including southern South America, South Africa, Madagascar, Sri Lanka, Australia and New Zealand. Australia is home to two pettalid genera, Austropurcellia, in northern New South Wales and Queensland, and Karripurcellia, in Western Australia, until now showing a large distributional gap between these two parts of the Australian continent. Here we report specimens of a new pettalid from South Australia, Archaeopurcellia eureka, gen. et sp. nov., closing this distributional gap of Australian pettalids. Phylogenetic analyses using traditional Sanger markers as well as ultra-conserved elements (UCEs) reveal that the new genus is related to the Chilean Chileogovea, instead of any of the other East Gondwanan genera. This relationship of an Australian species to a South American clade can be explained by the Antarctic land bridge between these two terranes, a connection that was maintained with Australia until 45 Ma. The UCE dataset also shows the promise of using museum specimens to resolve relationships within Pettalidae and Cyphophthalmi. ZooBank: urn:lsid:zoobank.org:pub:9B57A054-30D8-4412-99A2-6191CBD3BD7E
null (Ed.)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-C28C6A404F41more » « less
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.
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 subtribe Aillutticina (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. Attus palustris Peckham & Peckham, 1883 is considered to be a full synonym of Euophrys floricola C. L. Koch, 1837 (not a distinct subspecies). Attus sylvestris Emerton, 1891 is removed from synonymy and recognized as a senior synonym of Sitticus magnus Chamberlin & Ivie, 1944. Thus, the five native Attulus in North America are Attulus floricola , 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 Sitticus cabellensis Prószyński, 1971 with Pseudattulus kratochvili 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, Jollas cupreus sp. nov. and Tomis manabita sp. 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 (X 1 X 2 Y and X 1 X 2 X 3 Y), some of which ( Sittisax ranieri 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.more » « less
Abstract The common ancestor of spiders likely used silk to line burrows or make simple webs, with specialized spinning organs and aerial webs originating with the evolution of the megadiverse “true spiders” (Araneomorphae). The base of the araneomorph tree also concentrates the greatest number of changes in respiratory structures, a character system whose evolution is still poorly understood, and that might be related to the evolution of silk glands. Emphasizing a dense sampling of multiple araneomorph lineages where tracheal systems likely originated, we gathered genomic-scale data and reconstructed a phylogeny of true spiders. This robust phylogenomic framework was used to conduct maximum likelihood and Bayesian character evolution analyses for respiratory systems, silk glands, and aerial webs, based on a combination of original and published data. Our results indicate that in true spiders, posterior book lungs were transformed into morphologically similar tracheal systems six times independently, after the evolution of novel silk gland systems and the origin of aerial webs. From these comparative data we put forth a novel hypothesis that early-diverging web building spiders were faced with new energetic demands for spinning, which prompted the evolution of similar tracheal systems via convergence; we also propose tests of predictions derived from this hypothesis.more » « less
null (Ed.)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.more » « less
We explore the biogeographic history of the Gondwanan lineage Triaenonychidae, a dispersal‐limited arachnid taxon that underwent a recent taxonomic revision based on phylogenomic data. We explicitly test hypotheses related to a biogeographical pattern of ‘common vicariance, rare dispersal’, predicted for dispersal‐limited taxa.
Continental landmasses of former temperate Gondwanan terranes (southern South America, southern Africa, Madagascar, Australia, New Zealand, and New Caledonia).
Triaenonychidae, Opiliones, Arachnida.
Utilizing a recently published phylogenomic data set based on ultra‐conserved elements, we conduct Bayesian divergence dating analyses, ancestral area estimation in a likelihood model testing framework, and analyses of macroevolutionary dynamics. Results are correlated with geological history and palaeoclimate reconstructions to infer biogeographic history and distribution.
We find that divergence dates of ancestral Triaenonychidae pre‐date continental breakup of Gondwana and could be attributed to palaeoclimatic differentiation across Gondwana. There is evidence for two separate expansion routes that span eastern and western Gondwana corresponding to northern warmer climate and southern cooler climate lineages. Many divergences across intercontinental lineages coincide with the timing of continental fragmentation, supporting vicariance as a dominant force. However, some lineages are supported as obvious examples of rare long‐distance dispersal. Biogeographic results support the predicted pattern of common vicariance and rare dispersal for these dispersal‐limited organisms.
Vicariance due to continental fragmentation was important in the early diversification of Triaenonychidae. Their unique combination and degrees of dispersal ability and microhabitat preference resulted in complex phylogenetic patterns of geographic distribution not typically seen in other animal taxa. Examining biogeographic patterns across recent studies of arachnid taxa with varying dispersal ability, it is clear that biological characteristics play an important role in the relative importance of dispersal and vicariance (dispersal–vicariance continuum) for any given taxon and can be useful in forming testable a priori hypotheses.