Tarantula phylogenomics: A robust phylogeny of deep theraphosid clades inferred from transcriptome data sheds light on the prickly issue of urticating setae evolution.

Mygalomorph spiders of the family Theraphosidae, known to the broader public as tarantulas, are among the most recognizable arachnids on earth due to their large size and widespread distribution. Their use of urticating setae is a notable adaptation that has evolved exclusively in certain New World theraphosids. Thus far, the evolutionary history of Theraphosidae remains poorly understood; theraphosid systematics still largely relies on morphological datasets, which suffer from high degrees of homoplasy, and traditional Sanger sequencing of preselected genes failed to provide strong support for supra-generic clades. In this study, we provide the first robust phylogenetic hypothesis of theraphosid evolution inferred from transcriptome data. A core ortholog approach was used to generate a phylogeny from 2460 orthologous genes across 25 theraphosid genera, representing all of the major theraphosid subfamilies, except Selenogyrinae. Our phylogeny recovers an unprecedented monophyletic group that comprises the vast majority of New World theraphosid subfamilies including Aviculariinae, Schismatothelinae and Theraphosinae. Concurrently, we provide additional evidence for the integrity of questionable subfamilies, such as Poecilotheriinae and Psalmopoeinae, and support the non-monophyly of Ischnocolinae. The deeper relationships between almost all subfamilies are confidently inferred. We also used our phylogeny in tandem with published morphological data to perform ancestral state analyses on urticating setae, and contextualize our reconstructions with emphasis on the complex evolutionary history of the trait.

Discovering the silk road: Nuclear and mitochondrial sequence data resolve the phylogenetic relationships among theraphosid spider subfamilies.

The mygalomorph spiders in the family Theraphosidae, also known as "tarantulas", are one of the most popular and diverse groups of arachnids, but their evolutionary history remains poorly understood because morphological analyses have only provided mostly controversial results, and a broad molecular perspective has been lacking until now. In this study we provide a preliminary molecular phylogenetic hypothesis of relationships among theraphosid subfamilies, based on 3.5 kbp of three nuclear and three mitochondrial markers, for 52 taxa representing 10 of the 11 commonly accepted subfamilies. Our analysis confirms the monophyly of the Theraphosidae and of most recognized theraphosid subfamilies, supports the validity of the Stromatopelminae and Poecilotheriinae, and indicates paraphyly of the Schismatothelinae. The placement of representatives of Schismatothelinae also indicates possible non-monophyly of Aviculariinae and supports the distinction of the previously contentious subfamily Psalmopoeinae. Major clades typically corresponded to taxa occurring in the same biogeographic region, with two of them each occurring in Africa, South America and Asia. Because relationships among these major clades were poorly supported, more extensive molecular data sets are required to test the hypothesis of independent colonization and multiple dispersal events among these continents.

On the Way to Speciation: Shedding Light on the Karstic Phylogeography of the Microendemic Cave Beetle Aphaenops cerberus in the Pyrenees.

The highly modified morphology and ecological features of cave-dwelling organisms are a strong obstacle to dispersion. Hence, they represent ideal models for the study of historical biogeography at both large and fine timescales. Here, we study the phylogeography of Aphaenops cerberus, an endemic hypogean ground beetle with a fragmented distribution in the French Northern Pyrenees. We extracted 75 exemplars of 17 populations of A. cerberus and sequenced one mitochondrial and one nuclear marker to assess the geographic structuration as well as the recent biogeographic history of this species. We used Bayesian Inference and Maximum Likelihood to reconstruct the relationships among most of the extant populations of this species across its distributional range. We inferred divergence time estimates using carabid substitution rates and reconstructed haplotype networks to investigate the recent biogeographic history of this lineage. We recover a strong geographic structuration of the populations across the mountain range. The strong impact of geology on the structure of the populations is evidenced although geological continuity does not systematically lead to continual gene flow. The origin of the species is dated from the Early Pleistocene and the dispersal predates the main Last Glacial Maximum. Our results indicate broad similitudes between islands and karsts, which make cave organisms an excellent model for the study of evolution mechanisms.

Multiple transgressions of Wallace's Line explain diversity of flightless Trigonopterus weevils on Bali.

The fauna of Bali, situated immediately west of Wallace's Line, is supposedly of recent Javanese origin and characterized by low levels of endemicity. In flightless Trigonopterus weevils, however, we find 100% endemism for the eight species here reported for Bali. Phylogeographic analyses show extensive in situ differentiation, including a local radiation of five species. A comprehensive molecular phylogeny and ancestral area reconstruction of Indo-Malayan-Melanesian species reveals a complex colonization pattern, where the three Balinese lineages all arrived from the East, i.e. all of them transgressed Wallace's Line. Although East Java possesses a rich fauna of Trigonopterus, no exchange can be observed with Bali. We assert that the biogeographic picture of Bali has been dominated by the influx of mobile organisms from Java, but different relationships may be discovered when flightless invertebrates are studied. Our results highlight the importance of in-depth analyses of spatial patterns of biodiversity.

Integrative taxonomy on the fast track - towards more sustainability in biodiversity research.

BACKGROUND: A so called "taxonomic impediment" has been recognized as a major obstacle to biodiversity research for the past two decades. Numerous remedies were then proposed. However, neither significant progress in terms of formal species descriptions, nor a minimum standard for descriptions have been achieved so far. Here, we analyze the problems of traditional taxonomy which often produces keys and descriptions of limited practical value. We suggest that phylogenetics and phenetics had a subtle and so far unnoticed effect on taxonomy leading to inflated species descriptions. DISCUSSION: The term "turbo-taxonomy" was recently coined for an approach combining cox1 sequences, concise morphological descriptions by an expert taxonomist, and high-resolution digital imaging to streamline the formal description of larger numbers of new species. We propose a further development of this approach which, together with open access web-publication and automated pushing of content from journal into a wiki, may create the most efficient and sustainable way to conduct taxonomy in the future. On demand, highly concise descriptions can be gradually updated or modified in the fully versioned wiki-framework we use. This means that the visibility of additional data is not compromised, while the original species description -the first version- remains preserved in the wiki, and of course in the journal version. A DNA sequence database with an identification engine replaces an identification key, helps to avoid synonyms and has the potential to detect grossly incorrect generic placements. We demonstrate the functionality of a species-description pipeline by naming 101 new species of hyperdiverse New Guinea Trigonopterus weevils in the open-access journal ZooKeys. SUMMARY: Fast track taxonomy will not only increase speed, but also sustainability of global species inventories. It will be of great practical value to all the other disciplines that depend on a usable taxonomy and will change our perception of global biodiversity. While this approach is certainly not suitable for all taxa alike, it is the tool that will help to tackle many hyperdiverse groups and pave the road for more sustainable comparative studies, e.g. in community ecology, phylogeography and large scale biogeographic studies.

Transoceanic origin of microendemic and flightless New Caledonian weevils.

The origin of the astonishing New Caledonian biota continues to fuel a heated debate among advocates of a Gondwanan relict scenario and defenders of late oceanic dispersal. Here, we study the origin of New Caledonian Trigonopterus flightless weevils using a multimarker molecular phylogeny. We infer two independent clades of species found in the archipelago. Our dating estimates suggest a Late Miocene origin of both clades long after the re-emergence of New Caledonia about 37 Ma. The estimation of ancestral ranges supports an ancestral origin of the genus in a combined region encompassing Australia and New Guinea with subsequent colonizations of New Caledonia out of New Guinea in the mid-Miocene. The two New Caledonian lineages have had very different evolutionary trajectories. Colonizers belonging to a clade of foliage dwellers greatly diversified, whereas species inhabiting leaf-litter have been less successful.

Revision of the Australian species of the weevil genus Trigonopterus Fauvel.

The Australian species of the genus Trigonopterus Fauvel are revised. Eight previously recognized species are redescribed and 24 additional new species are described: Trigonopterus allaetus Riedel, sp. n., Trigonopterus athertonensis Riedel, sp. n., Trigonopterus australinasutus Riedel, sp. n., Trigonopterus australis Riedel, sp. n., Trigonopterus bisignatus Riedel, sp. n., Trigonopterus bisinuatus Riedel, sp. n., Trigonopterus boolbunensis Riedel, sp. n., Trigonopterus cooktownensis Riedel, sp. n., Trigonopterus daintreensis Riedel, sp. n., Trigonopterus deplanatus Riedel, sp. n., Trigonopterus finniganensis Riedel, sp. n., Trigonopterus fraterculus Riedel, sp. n., Trigonopterus garradungensis Riedel, sp. n., Trigonopterus hasenpuschi Riedel, sp. n., Trigonopterus hartleyensis Riedel, sp. n., Trigonopterus kurandensis Riedel, sp. n., Trigonopterus lewisensis Riedel, sp. n., Trigonopterus montanus Riedel, sp. n., Trigonopterus monteithi Riedel, sp. n., Trigonopterus mossmanensis Riedel, sp. n., Trigonopterus oberprieleri Riedel, sp. n., Trigonopterus robertsi Riedel, sp. n., Trigonopterus terraereginae Riedel, sp. n., Trigonopterus yorkensis Riedel, sp. n.. All new species are authored by the taxonomist-in-charge, Alexander Riedel. Lectotypes are designated for the following names: Idotasia aequalis Pascoe, Idotasia albidosparsa Lea, Idotasia evanida Pascoe, Idotasia laeta Lea, Idotasia rostralis Lea, Idotasia sculptirostris Lea, Idotasia squamosa Lea. A new combination of the name Idotasia striatipennis Lea is proposed: Trigonopterus striatipennis (Lea), comb. n.. A key to the species is provided. Australian Trigonopterus occur in coastal Queensland, narrowly crossing into New South Wales. The southern parts of the range are inhabited by species found on foliage. A rich fauna of 19 edaphic species inhabiting the leaf litter of tropical forests is reported for the first time from the Australian Wet Tropics.

Macroevolution of hyperdiverse flightless beetles reflects the complex geological history of the Sunda Arc.

The Sunda Arc forms an almost continuous chain of islands and thus a potential dispersal corridor between mainland Southeast Asia and Melanesia. However, the Sunda Islands have rather different geological histories, which might have had an important impact on actual dispersal routes and community assembly. Here, we reveal the biogeographical history of hyperdiverse and flightless Trigonopterus weevils. Different approaches to ancestral area reconstruction suggest a complex east to west range expansion. Out of New Guinea, Trigonopterus repeatedly reached the Moluccas and Sulawesi transgressing Lydekker's Line. Sulawesi repeatedly acted as colonization hub for different segments of the Sunda Arc. West Java, East Java and Bali are recognized as distinct biogeographic areas. The timing and diversification of species largely coincides with the geological chronology of island emergence. Colonization was not inhibited by traditional biogeographical boundaries such as Wallace's Line. Rather, colonization patterns support distance dependent dispersal and island age limiting dispersal.

Ninety-eight new species of Trigonopterus weevils from Sundaland and the Lesser Sunda Islands.

The genus Trigonopterus Fauvel, 1862 is highly diverse in Melanesia. Only one species, Trigonopterusamphoralis Marshall, 1925 was so far recorded West of Wallace's Line (Eastern Sumatra). Based on focused field-work the fauna from Sundaland (Sumatra, Java, Bali, Palawan) and the Lesser Sunda Islands (Lombok, Sumbawa, Flores) is here revised. We redescribe Trigonopterusamphoralis Marshall and describe an additional 98 new species: Trigonopterusacuminatus sp. n., Trigonopterusaeneomicans sp. n., Trigonopterusalaspurwensis sp. n., Trigonopterusallopatricus sp. n., Trigonopterusallotopus sp. n., Trigonopterusangulicollis sp. n., Trigonopterusargopurensis sp. n., Trigonopterusarjunensis sp. n., Trigonopterusasper sp. n., Trigonopterusattenboroughi sp. n., Trigonopterusbaliensis sp. n., Trigonopterusbatukarensis sp. n., Trigonopterusbawangensis sp. n., Trigonopterusbinodulus sp. n., Trigonopterusbornensis sp. n., Trigonopteruscahyoi sp. n., Trigonopteruscostipennis sp. n., Trigonopteruscuprescens sp. n., Trigonopteruscupreus sp. n., Trigonopterusdacrycarpi sp. n., Trigonopterusdelapan sp. n., Trigonopterusdentipes sp. n., Trigonopterusdiengensis sp. n., Trigonopterusdimorphus sp. n., Trigonopterusdisruptus sp. n., Trigonopterusdua sp. n., Trigonopterusduabelas sp. n., Trigonopterusechinatus sp. n., Trigonopterusempat sp. n., Trigonopterusenam sp. n., Trigonopterusfissitarsis sp. n., Trigonopterusflorensis sp. n., Trigonopterusfoveatus sp. n., Trigonopterusfulgidus sp. n., Trigonopterusgedensis sp. n., Trigonopterushalimunensis sp. n., Trigonopterushonjensis sp. n., Trigonopterusijensis sp. n., Trigonopterusjavensis sp. n., Trigonopteruskalimantanensis sp. n., Trigonopteruskintamanensis sp. n., Trigonopterusklatakanensis sp. n., Trigonopteruslampungensis sp. n., Trigonopteruslatipes sp. n., Trigonopteruslima sp. n., Trigonopteruslombokensis sp. n., Trigonopterusmerubetirensis sp. n., Trigonopterusmesehensis sp. n., Trigonopterusmicans sp. n., Trigonopterusmisellus sp. n., Trigonopteruspalawanensis sp. n., Trigonopteruspangandaranensis sp. n., Trigonopterusparaflorensis sp. n., Trigonopteruspararugosus sp. n., Trigonopterusparasumbawensis sp. n., Trigonopteruspauxillus sp. n., Trigonopteruspayungensis sp. n., Trigonopterusporcatus sp. n., Trigonopteruspseudoflorensis sp. n., Trigonopteruspseudosumbawensis sp. n., Trigonopteruspunctatoseriatus sp. n., Trigonopterusranakensis sp. n., Trigonopterusrelictus sp. n., Trigonopterusrinjaniensis sp. n., Trigonopterusroensis sp. n., Trigonopterusrugosostriatus sp. n., Trigonopterusrugosus sp. n., Trigonopterusrutengensis sp. n., Trigonopterussaltator sp. n., Trigonopterussantubongensis sp. n., Trigonopterussasak sp. n., Trigonopterussatu sp. n., Trigonopterusschulzi sp. n., Trigonopterussebelas sp. n., Trigonopterussembilan sp. n., Trigonopterussepuluh sp. n., Trigonopterusseriatus sp. n., Trigonopterusserratifemur sp. n., Trigonopterussetifer sp. n., Trigonopterussilvestris sp. n., Trigonopterussingkawangensis sp. n., Trigonopterussingularis sp. n., Trigonopterussinuatus sp. n., Trigonopterussqualidus sp. n., Trigonopterussumatrensis sp. n., Trigonopterussumbawensis sp. n., Trigonopterussundaicus sp. n., Trigonopterussuturalis sp. n., Trigonopterussyarbis sp. n., Trigonopterustelagensis sp. n., Trigonopterustepalensis sp. n., Trigonopterustiga sp. n., Trigonopterustrigonopterus sp. n., Trigonopterustujuh sp. n., Trigonopterusujungkulonensis sp. n., Trigonopterusvariolosus sp. n., Trigonopterusvulcanicus sp. n., Trigonopteruswallacei sp. n.. All new species are authored by the taxonomist-in-charge, Alexander Riedel. Most species belong to the litter fauna of primary wet evergreen forests. This habitat has become highly fragmented in the study area and many of its remnants harbor endemic species. Conservation measures should be intensified, especially in smaller and less famous sites to minimize the number of species threatened by extinction.

High mitochondrial DNA sequence divergence in New Guinea Carabdytes stream beetles and the taxonomist's dilemma when other evidence is kind of subtle (and collecting localities are far far away).

Carabdytes upin tindigessp. n. is described from the Arfak Mountains Bird's Head Indonesian Papua. It is morphologically very similar to Carabdytes upin upin Balke et al. 1992 known from eastern Indonesian Papua eastward to the western limits of the Papuan Peninsula of Papua New Guinea. For 726 bp at the 3' end of the mitochondrial cox1 gene the subspecies differ by 8.1-9.2% uncorrected p-distance. However we also document considerable cox1 divergence within Carabdytes upin upin. We find few diagnostic positions in the nuclear genes argenine kinase as well as elongation factor 1 alpha that suggest there are indeed two isolated groups of Carabdytes but evidence in elongation factor 1 alpha is not unambiguous. We decided to highlight this phenomenon of ambiguous evidence for ongoing/just attained speciation by describing a subspecies. We argue that such cases are actually common once mitochondrial sequence data are routinely added to the taxonomist's toolkit and sometimes simply adding data from few nuclear genes will not suffice the solve taxonomic riddles. Here detailed population genetic investigations would be required - for which sufficient numbers of specimens from a sufficiently wide geographical sampling might be nearly impossible to acquire.

DNA barcoding for community ecology--how to tackle a hyperdiverse, mostly undescribed Melanesian fauna.

BACKGROUND: Trigonopterus weevils are widely distributed throughout Melanesia and hyperdiverse in New Guinea. They are a dominant feature in natural forests, with narrow altitudinal zonation. Their use in community ecology has been precluded by the "taxonomic impediment". METHODOLOGY/PRINCIPAL FINDINGS: We sampled >6,500 specimens from seven areas across New Guinea; 1,002 specimens assigned to 270 morphospecies were DNA sequenced. Objective clustering of a refined dataset (excluding nine cryptic species) at 3% threshold revealed 324 genetic clusters (DNA group count relative to number of morphospecies = 20.0% overestimation of species diversity, or 120.0% agreement) and 85.6% taxonomic accuracy (the proportion of DNA groups that "perfectly" agree with morphology-based species hypotheses). Agreement and accuracy were best at an 8% threshold. GMYC analysis revealed 328 entities (21.5% overestimation) with 227 perfect GMYC entities (84.1% taxonomic accuracy). Both methods outperform the parataxonomist (19% underestimation; 31.6% taxonomic accuracy). The number of species found in more than one sampling area was highest in the Eastern Highlands and Huon (Sørensen similarity index 0.07, 4 shared species); ⅓ of all areas had no species overlap. Success rates of DNA barcoding methods were lowest when species showed a pronounced geographical structure. In general, Trigonopterus show high α and ß-diversity across New Guinea. CONCLUSIONS/SIGNIFICANCE: DNA barcoding is an excellent tool for biodiversity surveys but success rates might drop when closer localities are included. Hyperdiverse Trigonopterus are a useful taxon for evaluating forest remnants in Melanesia, allowing finer-grained analyses than would be possible with vertebrate taxa commonly used to date. Our protocol should help establish other groups of hyperdiverse fauna as target taxa for community ecology. Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should help pave the road for the eventual formal naming of new species.