02384nas a2200253 4500008004100000020001400041245014700055210006900202260001500271300000800286490000700294520156900301653001501870653001801885653001601903653001601919100001601935700002101951700002801972700002302000700002402023700002102047856006202068 2023 eng d a1759-665300aSizing Up the Onychophoran Genome: Repeats, Introns, and Gene Family Expansion Contribute to Genome Gigantism in Epiperipatus broadwayi0 aSizing Up the Onychophoran Genome Repeats Introns and Gene Famil c15/02/2023 a1-60 v153 a

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.

10ahemocyanin10aPanarthropoda10aPeripatidae10avelvet worm1 aSato, Shoyo1 aCunha, Tauana, J1 ade Medeiros, Bruno, A S1 aKhost, Danielle, E1 aSackton, Timothy, B1 aGiribet, Gonzalo uhttps://academic.oup.com/gbe/article/15/3/evad021/703970402336nas a2200253 4500008004100000022001400041245010900055210006900164260001500233300001600248490000700264520155700271653001701828653001401845653001301859653001601872653001601888653001501904100002201919700003001941700003001971700002102001856006002022 2021 eng d a1537-171900aPhylogenomic Analysis of Velvet Worms (Onychophora) Uncovers an Evolutionary Radiation in the Neotropics0 aPhylogenomic Analysis of Velvet Worms Onychophora Uncovers an Ev c24/08/2021 a5391 - 54040 v383 a

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.

10abiogeography10adispersal10aGondwana10aOnychophora10asystematics10avicariance1 aBaker, Caitlin, M1 aBuckman-Young, Rebecca, S1 aCosta, Cristiano, Sampaio1 aGiribet, Gonzalo uhttps://academic.oup.com/mbe/article/38/12/5391/635704801937nas a2200217 4500008004100000022002500041245017200066210006900238260001500307300000900322490000800331520117100339653002001510653001501530653001501545653003301560653001301593100003001606700002101636856006201657 2021 eng d a1077-8306, 1744-741000aPanamanian velvet worms in the genus Epiperipatus, with notes on their taxonomy and distribution and the description of a new species (Onychophora, Peripatidae)0 aPanamanian velvet worms in the genus iEpiperipatusi with notes o c25/05/2021 a1-120 v1403 a

Among the least studied clade of velvet worms (Onychophora) is a clade of Neotropical Peripatidae (=Neopatida). Neopatida has been traditionally divided into an Andicoles group and a Caraïbes group, which now correspond to Oroperipatus and the remaining genera, respectively. Panama is located in a unique position bridging the faunas of both clades and of two large continents, both of which host an important diversity of velvet worms, yet taxonomic study of the Panamanian onychophorans has been largely neglected. In this study we critically evaluate the onychophoran diversity of Panama, redescribe a species from the former Canal Zone and describe a new species from the Pacific side, close to Costa Rica, as Epiperipatus bernali sp. nov., with a unique combination of characters visible under the SEM. We further discuss the existence of multiple lineages of Onychophora in Panama, both from the Andicoles and Caraïbes groups, and within the latter, with connections to different lineages, both from South and Central America.

 

10aCentral America10amorphology10aNeotropics10aScanning electron microscopy10aTaxonomy1 aCosta, Cristiano, Sampaio1 aGiribet, Gonzalo uhttps://onlinelibrary.wiley.com/doi/abs/10.1111/ivb.1233601693nas a2200241 4500008004100000022002500041245009200066210006900158260001500227300001000242490000700252520092200259653002001181653003101201653003001232100002901262700002101291700002201312700002201334700002101356700002601377856004801403 2020 eng d a1768-1448, 1314-261500aThe Wynberg Cave System, the most important site for cave fauna in South Africa at risk0 aWynberg Cave System the most important site for cave fauna in So c16/11/2020 a73-810 v363 a

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.

10aCave protection10aInvertebrates conservation10aSubterranean biodiversity1 aFerreira, Rodrigo, Lopes1 aGiribet, Gonzalo1 aPreez, Gerhard, D1 aVentouras, Oresti1 aJanion, Charlene1 aSilva, Marconi, Souza uhttps://subtbiol.pensoft.net/article/60162/00389nas a2200133 4500008004100000022002200041245001500063210001500078260004600093300001200139100002100151700002700172856005600199 2020 eng d a978-0-691-19706-700aArthropoda0 aArthropoda aPrinceton, NJbPrinceton University Press a231-2571 aGiribet, Gonzalo1 aEdgecombe, Gregory, D. uhttps://princetonup.degruyter.com/view/title/57537802543nam a2200145 4500008004100000022002200041245003400063210003000097260004600127300000800173520211200181100002102293700002702314856005602341 2020 eng d a978-0-691-19706-700aThe Invertebrate Tree of Life0 aInvertebrate Tree of Life aPrinceton, NJbPrinceton University Press a6083 a

The most up-to-date book on invertebrates, providing a new framework for understanding their place in the tree of life

In The Invertebrate Tree of Life, Gonzalo Giribet and Gregory Edgecombe, leading authorities on invertebrate biology and paleontology, utilize phylogenetics to trace the evolution of animals from their origins in the Proterozoic to today. Phylogenetic relationships between and within the major animal groups are based on the latest molecular analyses, which are increasingly genomic in scale and draw on the soundest methods of tree reconstruction.

Giribet and Edgecombe evaluate the evolution of animal organ systems, exploring how current debates about phylogenetic relationships affect the ways in which aspects of invertebrate nervous systems, reproductive biology, and other key features are inferred to have developed. The authors review the systematics, natural history, anatomy, development, and fossil records of all major animal groups, employing seminal historical works and cutting-edge research in evolutionary developmental biology, genomics, and advanced imaging techniques. Overall, they provide a synthetic treatment of all animal phyla and discuss their relationships via an integrative approach to invertebrate systematics, anatomy, paleontology, and genomics.

With numerous detailed illustrations and phylogenetic trees, The Invertebrate Tree of Life is a must-have reference for biologists and anyone interested in invertebrates, and will be an ideal text for courses in invertebrate biology.

Published on 03/03/2020

1 aGiribet, Gonzalo1 aEdgecombe, Gregory, D. uhttps://princetonup.degruyter.com/view/title/57537802424nas a2200277 4500008004100000022001400041245010600055210006900161260001500230300000900245520153800254653001701792653002801809653002501837653001701862653001501879653001401894653001401908653001601922653001801938653001601956100003001972700002102002700002802023856009502051 2020 eng d a0024-408200aMorphological and molecular phylogeny of Epiperipatus (Onychophora: Peripatidae): a combined approach0 aMorphological and molecular phylogeny of Epiperipatus Onychophor c07/11/2020 a1-313 a

Onychophora, or velvet worms, are a key group for understanding ecdysozoan evolution. It comprises two families: Peripatopsidae, largely of Austral distribution, and Peripatidae, which is circumtropical. The interrelationships between the members of Peripatidae present many taxonomic issues exacerbated in the radiation of the Neotropical species or Neopatida. To understand the phylogeny of Neopatida, and to test the information of such morphological characters, we gathered novel molecular and morphological datasets focusing on Neotropical specimens. Our data were analysed using a combination of parsimony and maximum likelihood for the individual and combined molecular and morphological datasets. An analysis of morphology alone was inconclusive, supporting the notion that morphological characters used in peripatid taxonomy have little power to resolve phylogenetic relationships among higher taxa in Neopatida. However, the analyses of molecular or combined data show a split of the Neotropical species into two clades, which we use to reassign genera. Epiperipatus, as currently understood, is non-monophyletic, because it includes species of monotypic genera. To avoid paraphyly of Epiperipatus, the following new combinations are proposed: Epiperipatus bouvieri (Fuhrmann, 1913), Epiperipatus hitoyensis (Oliveira et al., 2012a), Epiperipatus solorzanoi (Morera-Brenes & Monge-Nájera, 2010) and Epiperipatus sucuriuensis (Oliveira et al., 2015).

10abiogeography10acaraïbes onychophorans10aconserved morphology10aEpiperipatus10amorphology10aNeopatida10aNew World10aPeripatidae10aSouth America10asystematics1 aCosta, Cristiano, Sampaio1 aGiribet, Gonzalo1 aPinto-Da-Rocha, Ricardo uhttps://academic.oup.com/zoolinnean/advance-article/doi/10.1093/zoolinnean/zlaa100/595994301539nas a2200157 4500008004100000022001400041245012600055210006900181260001500250300000800265490000700273520101200280100002101292700002101313856004701334 2010 eng d a1445-522600a'Moa's Ark' or 'Goodbye Gondwana': is the origin of New Zealand's terrestrial invertebrate fauna ancient, recent or both?0 aMoas Ark or Goodbye Gondwana is the origin of New Zealands terre c17/05/2010 a1-80 v243 a

Evaluating the hypothesis of New Zealand’s total submersion during the Oligocene requires the strictest tests, including sound phylogenetic data and dating of phylogenies. Although New Zealand has been traditionally considered to host ancient biota that originated by vicariance after it separated from Australia ~80 Mya, the ancient origins of its biota have been recently questioned, with some authors even suggesting that all current land organisms had to arrive to the islands after it re-emerged from the ocean 22 million years ago. Here we examine examples of short-range endemic soil-dwelling invertebrates and find compelling evidence that at least some of them are the result of old lineages that diversified in New Zealand before the hypothesised submersion event 22 million year ago. We conclude that New Zealand indeed has old lineages as well as recently diversified lineages and compare this situation with that of other more stable areas of the Neotropics.

1 aGiribet, Gonzalo1 aBoyer, Sarah, L. uhttp://www.publish.csiro.au/?paper=IS1000902264nas a2200241 4500008004100000022001400041245009100055210006900146260001500215300001200230490000700242520154600249653001701795653002601812653001701838653002401855653001601879653002401895653000801919100002701927700002101954856004701975 2004 eng d a1445-522600aMolecular phylogeny of Australasian anopsobiine centipedes (Chilopoda: Lithobiomorpha)0 aMolecular phylogeny of Australasian anopsobiine centipedes Chilo c18/06/2004 a235-2490 v183 a

Species assigned to the anopsobiine centipede genera Anopsobius Silvestri, 1899, and Dichelobius Attems, 1911, are widely distributed on fragments of the Gondwanan supercontinent, including temperate and tropical Australia, New Zealand, New Caledonia, the Cape region of South Africa, and southern South America. Phylogenetic relationships between Australasian and other Gondwanan Anopsobiinae are inferred based on parsimony and maximum likelihood analyses (via direct optimisation) of sequence data for five markers: nuclear ribosomal 18S rRNA and 28S rRNA, mitochondrial ribosomal 12S rRNA and 16S RNA, and the mitochondrial protein-coding cytochrome c oxidase subunit I. New molecular data are added for Anopsobius from South Africa and New Zealand, Dichelobius from New Caledonia, and a new species from Queensland, Australia, Dichelobius etnaensis, sp. nov. The new species is based on distinctive morphological and molecular data. The molecular phylogenies indicate that antennal segmentation in the Anopsobiinae is a more reliable taxonomic character than is spiracle distribution. The former character divides the Gondwanan clade into a 17-segmented group (Dichelobius) and a 15-segmented group (Anopsobius). Confinement of the spiracles to segments 3, 10 and 12 has at least two origins in the Gondwanan clade. The area cladogram for Dichelobius (Queensland (Western Australia + New Caledonia)) suggests a relictual distribution pruned by extinction.

10aAnopsobiinae10aantennal segmentation10abiogeography10adirect optimisation10aHenicopidae10amolecular phylogeny10aPOY1 aEdgecombe, Gregory, D.1 aGiribet, Gonzalo uhttp://www.publish.csiro.au/?paper=IS0303302025nas a2200217 4500008004100000022001400041245017900055210006900234260001500303300001400318490000700332520127800339653001701617653001301634653002401647100001601671700003101687700002101718700002101739856004701760 2018 eng d a1445-522600aCryptic speciation in a biodiversity hotspot: multilocus molecular data reveal new velvet worm species from Western Australia (Onychophora: Peripatopsidae: Kumbadjena)0 aCryptic speciation in a biodiversity hotspot multilocus molecula c27/11/2018 a1249-12640 v323 a

There is a yet uncovered multitude of species to be found among Western Australian Onychophora. Kumbadjena, one of the two genera that reside in this region, has been previously suggested to house an extensive species complex. Morphology alone has not been able to elucidate the diversity in this genus and has instead muddled species delineations. Topologies and species delimitation analyses resulting from the sequences of two mitochondrial ribosomal markers (12S rRNA and 16S rRNA), one nuclear ribosomal marker (18S rRNA), and one mitochondrial protein-coding gene (cytochrome c oxidase subunit I) are indicative of several undescribed species. Fixed diagnostic nucleotide changes in the highly conserved sequences of 18S rRNA warrant distinction of three new species of Kumbadjena: K. toolbrunupensis, sp. nov., K. karricola, sp. nov., and K. extrema, sp. nov. The geographic distributions of the proposed species suggest that Kumbadjena is another example of short-range endemism, a common occurrence in the flora and fauna of the region. The extensive biodiversity and endemism in the region necessitates conservation to preserve the species and processes that promote speciation harboured by Western Australia.

10aconservation10aendemism10amolecular diagnosis1 aSato, Shoyo1 aBuckman-Young, Rebecca, S.1 aHarvey, Mark, S.1 aGiribet, Gonzalo uhttp://www.publish.csiro.au/?paper=IS1802402407nas a2200241 4500008004100000022001400041245016400055210006900219260001500288300001200303490000700315520161200322653002501934653000901959653001701968653001801985653001902003100002402022700002702046700002402073700002102097856004702118 2011 eng d a1445-522600aResolving the phylogenetic position of enigmatic New Guinea and Seychelles Scutigeromorpha (Chilopoda): a molecular and morphological assessment of Ballonemini0 aResolving the phylogenetic position of enigmatic New Guinea and  c29/04/2011 a539-5590 v243 a

Recent phylogenetic analyses of scutigeromorph centipedes omitted New Guinea endemics for lack of modern data, either from morphology or molecular sequences. Among these is the tribe Ballonemini, originally established for Ballonema Verhoeff, 1904, and Parascutigera Verhoeff, 1904, based on similar tergal prominences. Subsequent systematic revision led to their separation into different subfamilies. Combined analyses of morphology and sequence data including Ballonema gracilipes Verhoeff, 1904, resolve Ballonema either in a grade of Scutigerinae or as sister to all other Scutigerinae + Thereuoneminae. Confocal laser scanning microscopy (CLSM) of the types of B. gracilipes demonstrates the utility of this technique for non-destructive imaging of historical museum material at a resolution comparable to scanning electron microscopy. A possible record of Ballonema in the Seychelles is dismissed; a collection from Silhouette samples a member of Thereuoneminae described as Seychellonema gerlachi, gen. nov. sp. nov. Morphological data, analysed with sequence data for other Scutigeromorpha, ally Seychellonema with the Oriental–Australian genus Thereuopoda Verhoeff, 1904, but it displays a novel patterning of its tergal spinula and tarsal papillae. The phylogenetic analyses include sequence data for African Pselliodidae, corroborating a sister group relationship to remaining Scutigeromorpha and generating a more stable result than in earlier analyses using only Neotropical species.

10aBallonema gracilipes10aCLSM10aScutigeridae10aSphendononema10aThereuoneminae1 aButler, Aodhán, D.1 aEdgecombe, Gregory, D.1 aBall, Alexander, D.1 aGiribet, Gonzalo uhttp://www.publish.csiro.au/?paper=IS1003702416nas a2200229 4500008004100000022001400041245014100055210006900196260001500265300000900280490000700289520169400296653001701990653001902007653001302026653002402039653001402063653001402077100002702091700002102118856004702139 2008 eng d a1445-522600aA New Zealand species of the trans-Tasman centipede order Craterostigmomorpha (Arthropoda: Chilopoda) corroborated by molecular evidence0 aNew Zealand species of the transTasman centipede order Craterost c18/03/2008 a1-150 v223 a

Craterostigmus tasmanianus Pocock, 1902, is the sole species in the centipede order Craterostigmomorpha and the focus of much phylogenetic research in Chilopoda. Originally named from Tasmania, Craterostigmus from New Zealand was first considered conspecific with Tasmanian samples based on external morphology, though recent anatomical studies have argued for a deep divergence between New Zealand and Tasmanian Craterostigmus, and a high-ranking taxonomic separation has been advocated. Unambiguous diagnostic nucleotide characters in nuclear ribosomal 18S and 28S rRNA genes as well as in the mitochondrial 16S rRNA, together with the significantly smaller size of New Zealand individuals, the arrangement of supernumerary Malpighian tubules, and patterns in leg spinosity, permit distinction of a New Zealand species, Craterostigmus crabilli, sp. nov. In addition, phylogenetic analysis of four markers (the aforementioned markers plus cytochrome c oxidase subunit I) suggests differentiation of C. tasmanianus from the New Zealand specimens. Combination of the nuclear ribosomal genes and mitochondrial 16S rRNA and COI sequences retrieves a geographic pattern within C. crabilli, sp. nov. in which geographic proximity is decoupled from closest affinities, although the 16S rRNA dataset alone shows more geographic structure. The genetic pattern observed, where among species diversity (for both mitochondrial markers) is equivalent to, or greater than, the within species diversity, is not consistent with a recent long-distance dispersal event, and a relictual Gondwanan distribution is the most plausible alternative.

10abiogeography10aCraterostigmus10aGondwana10amolecular diagnosis10aTasmantia10aZealandia1 aEdgecombe, Gregory, D.1 aGiribet, Gonzalo uhttp://www.publish.csiro.au/?paper=IS0703601642nas a2200253 4500008004100000022001400041245016400055210006900219260001500288300000900303490000800312520082800320653001401148653001601162653001301178653002201191653001501213653001901228653001901247653001301266100002701279700002101306856006101327 2003 eng d a1175-532600aA new blind Lamyctes (Chilopoda: Lithobiomorpha) from Tasmania with an analysis of molecular sequence data for the Lamyctes-Henicops Group0 anew blind iLamyctesi Chilopoda Lithobiomorpha from Tasmania with c05/03/2003 a1-230 v1523 a

The cosmopolitan, parthenogenetic centipede Lamyctes coeculus (Brölemann, 1889), type species of Lamyctinus Silvestri, 1909, occurs in New South Wales and Lord Howe Island, Australia, the former genetically identical to specimens from Tucumán, Argentina. Parsimony analysis of complete sequences of 18S rRNA and fragments of 28S rRNA, 16S rRNA, and cytochrome c oxidase subunit I for the Lamyctes-Henicops group suggests that loss of ocelli in Lamyctes coeculus has an independent origin from blindness in Lamyctes hellyeri n. sp. from northern Tasmania. Lamyctinus is nested within Lamyctes Meinert, 1868, its senior synonym. Lamyctes hellyeri is known exclusively from females in gardens, and is probably introduced to Tasmania.

10aChilopoda10aHenicopidae10aLamyctes10aLamyctes hellyeri10aLamyctinus10aLithobiomorpha10amolecular data10aTaxonomy1 aEdgecombe, Gregory, D.1 aGiribet, Gonzalo uhttps://biotaxa.org/Zootaxa/article/view/zootaxa.152.1.102210nas a2200289 4500008004100000022001400041245009900055210006900154260001600223300001400239490000800253520132700261653005001588653001801638653001401656653001201670653001601682653002301698653001701721100002501738700002701763700002501790700002301815700001801838700002101856856004301877 2016 eng d a1744-741000aCarboniferous Onychophora from Montceau-les-Mines, France, and onychophoran terrestrialization0 aCarboniferous Onychophora from MontceaulesMines France and onych cJan-09-2016 a179 - 1900 v1353 a

The geological age of the onychophoran crown-group, and when the group came onto land, have been sources of debate. Although stem-group Onychophora have been identified from as early as the Cambrian, the sparse record of terrestrial taxa from before the Cretaceous is subject to contradictory interpretations. A Late Carboniferous species from the Mazon Creek biota of the USA, Helenodora inopinata, originally interpreted as a crown-group onychophoran, has recently been allied to early Cambrian stem-group taxa. Here we describe a fossil species from the Late Carboniferous Montceau-les-Mines Lagerstätte, France, informally referred to as an onychophoran for more than 30 years. The onychophoran affinities of Antennipatus montceauensis gen. nov., sp. nov. are indicated by the form of the trunk plicae and the shape and spacing of their papillae, details of antennal annuli, and the presence of putative slime papillae. The poor preservation of several key systematic characters for extant Onychophora, however, prohibits the precise placement of the Carboniferous fossil in the stem or crown of the two extant families, or the onychophoran stem-group as a whole. Nevertheless, A. montceauensis is the most compelling candidate to date for a terrestrial Paleozoic onychophoran.

10aAntennipatus montceauensis gen. nov. sp. nov.10aCarboniferous10aEcdysozoa10afossils10aOnychophora10aTerrestrialization10avelvet worms1 aGarwood, Russell, J.1 aEdgecombe, Gregory, D.1 aCharbonnier, Sylvain1 aChabard, Dominique1 aSotty, Daniel1 aGiribet, Gonzalo uhttp://doi.wiley.com/10.1111/ivb.1213002336nas a2200325 4500008004100000020001400041245009000055210006900145260000900214300001600223490000700239520129900246653001401545653001301559653001701572653002101589653001401610653003101624653001801655100002101673700002801694700001901722700001801741700002101759700002501780700002901805700002701834700002101861856012801882 2014 eng d a0737-403800aEvaluating Topological Conflict in Centipede Phylogeny Using Transcriptomic Data Sets0 aEvaluating Topological Conflict in Centipede Phylogeny Using Tra c2014 a1500 - 15130 v313 a

Relationships between the five extant orders of centipedes have been considered solved based on morphology. Phylogenies based on samples of up to a few dozen genes have largely been congruent with the morphological tree apart from an alternative placement of one order, the relictual Craterostigmomorpha, consisting of two species in Tasmania and New Zealand. To address this incongruence, novel transcriptomic data were generated to sample all five orders of centipedes and also used as a test case for studying gene-tree incongruence. Maximum likelihood and Bayesian mixture model analyses of a data set composed of 1,934 orthologs with 45% missing data, as well as the 389 orthologs in the least saturated, stationary quartile, retrieve strong support for a sister-group relationship between Craterostigmomorpha and all other pleurostigmophoran centipedes, of which the latter group is newly named Amalpighiata. The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, such as maternal brood care, but accords with patterns of first appearances in the fossil record.

10aChilopoda10aIllumina10aincongruence10amolecular dating10aMyriapoda10anext-generation sequencing10aphylogenomics1 aFernández, Rosa1 aLaumer, Christopher, E.1 aVahtera, Varpu1 aLibro, Silvia1 aKaluziak, Stefan1 aSharma, Prashant, P.1 aPérez-Porro, Alicia, R.1 aEdgecombe, Gregory, D.1 aGiribet, Gonzalo uhttps://myriatrix.myspecies.info/content/evaluating-topological-conflict-centipede-phylogeny-using-transcriptomic-data-sets03989nas a2200229 4500008004100000245012700041210006900168260000900237300001400246490000700260520315300267653009303420100002103513700003103534700003003565700002303595700002503618700002903643700002303672700002803695856003603723 2018 eng d00aThe ‘Peripatos’ in Eurogondwana? – Lack of evidence that south-east Asian onychophorans walked through Europe0 aiPeripatosi in Eurogondwana Lack of evidence that southeast Asia c2018 a842 - 8650 v323 a

Onychophorans, or velvet worms, are cryptic but extremely charismatic terrestrial invertebrates that have often been the subject of interesting biogeographic debate. Despite great interest, a well resolved and complete phylogeny of the group and a reliable chronogram have been elusive due to their broad geographic distribution, paucity of samples, and challenging molecular composition. Here we present a molecular phylogenetic analysis of Onychophora that includes previously unsampled and undersampled lineages and we analyse the expanded dataset using a series of nested taxon sets designed to increase the amount of information available for particular subclades. These include a dataset with outgroups, one restricted to the ingroup taxa, and three others for Peripatopsidae, Peripatidae and Neopatida (= the Neotropical Peripatidae). To explore competing biogeographic scenarios we generate a new time tree for Onychophora using the few available reliable fossils as calibration points. Comparing our results to those of Cyphophthalmi, we reconsider the hypothesis that velvet worms reached Southeast Asia via Eurogondwana, and conclude that a more likely scenario is that they reached Southeast Asia by rafting on the Sibumasu terrane. Our phylogenetic results support the reciprocal monophyly of both families as well as an early division between East and West Gondwana, also in both families, each beginning to diversify between the Permian and the Jurassic. Peripatopsidae clearly supports paraphyly of South Africa with respect to southern South America (Chile) and a sister group relationship of the Southeast Asian/New Guinean Paraperipatus to the Australian/New Zealand taxa. The latter includes a clade that divides between Western Australia and Eastern Australia and two sister clades of trans-Tasman species (one oviparous and one viviparous). This pattern clearly shows that oviparity is secondarily derived in velvet worms. Peripatidae finds a sister group relationship between the Southeast Asian Eoperipatus and the West Gondwanan clade, which divides into the African Mesoperipatus and Neopatida. The latter shows a well supported split between the Pacific Oroperipatus (although it is unclear whether they form one or two clades) and a sister clade that includes the members of the genera Peripatus, Epiperipatus, Macroperipatus and representatives of the monotypic genera Cerradopatus, Plicatoperipatus and Principapillatus. However, Peripatus, Epiperipatus and Macroperipatus are not monophyletic, and all the species from the monotypic genera are related to geographically close species. The same goes for the type species of Macroperipatus (from Trinidad, and sister group to other Trinidad and Tobago species of Epiperipatus) and Epiperipatus (from French Guiana, and related to other Guyana shield species of Epiperipatus and Peripatus). Geographic structure within Neopatida is largely obscured by an unresolved backbone, but many well supported instances of generic non-monophyly challenge the current taxonomic framework, which has often relied on anatomical characters that are untested phylogenetically.

10abiogeography, Neopatida, Onychophora, Peripatidae, Peripatopsidae, Peripatus, phylogeny.1 aGiribet, Gonzalo1 aBuckman-Young, Rebecca, S.1 aCosta, Cristiano, Sampaio1 aBaker, Caitlin, M.1 aBenavides, Ligia, R.1 aBranstetter, Michael, G.1 aDaniels, Savel, R.1 aPinto-Da-Rocha, Ricardo uhttps://doi.org/10.1071/IS1800702335nas a2200181 4500008004100000245011400041210006900155520165000224653001401874653001401888653001501902653001401917653002301931100001901954700002701973700002102000856013202021 2013 eng d00aPhylogenetics of scolopendromorph centipedes: Can denser taxon sampling improve an artificial classification?0 aPhylogenetics of scolopendromorph centipedes Can denser taxon sa3 aPrevious phylogenetic analyses of the centipede order Scolopendromorpha indicated a fundamental division into blind and ocellate clades. These analyses corroborated the monophyly of most families and tribes but suggested that several species-rich, cosmopolitan genera in traditional and current classifications are polyphyletic. Denser taxon sampling is applied to a dataset of 122 morphological characters and sequences for four nuclear and mitochondrial loci. Phylogenetic analyses including 98 species and subspecies of Scolopendromorpha employ parsimony under dynamic and static homology schemes as well as maximum likelihood and Bayesian inference of multiple sequence alignments. The monotypic Australian genera Notiasemus and Kanparka nest within Cormocephalus and Scolopendra, respectively, and the New Caledonian Campylostigmus is likewise a clade within Cormocephalus. New World Scolopendra are more closely related to Hemiscolopendra and Arthrorhabdus than to Scolopendra s.s., which is instead closely allied to Asanada; the tribe Asanadini nests within Scolopendrini for molecular and combined datasets. The generic classification of Otostigmini has a poor fit to phylogenetic relationships, although nodal support within this tribe is weak. New synonymies are proposed for Ectonocryptopinae Shelley & Mercurio, 2005 (≤ Newportiinae Pocock, 1896), Asanadini Verhoeff, 1907 (≤ Scolopendrini Leach, 1814), and Kanparka Waldock & Edgecombe, 2012 (≤ Scolopendra Linnaeus, 1758). Scolopendrid systematics largely depicts incongruence between phylogeny and classification rather than between morphology and molecules. © 2013 CSIRO.10aChilopoda10amolecules10amorphology10aphylogeny10aScolopendromorpha.1 aVahtera, Varpu1 aEdgecombe, Gregory, D.1 aGiribet, Gonzalo uhttps://myriatrix.myspecies.info/content/phylogenetics-scolopendromorph-centipedes-can-denser-taxon-sampling-improve-artificial03944nas a2200301 4500008004100000245014700041210006900188490000600257520291700263653001303180653001503193653001303208653001303221653001303234653003103247653001303278653001403291100001603305700002603321700002503347700001603372700002903388700001903417700002703436700002503463700002103488856013303509 2012 eng d00aComparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa0 aComparative description of ten transcriptomes of newly sequenced0 v93 aIntroduction: Traditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. Here we provide a comparative analysis of de novo assembled transcriptomic data for ten non-model species of previously understudied animal taxa.Results: cDNA libraries of ten species belonging to five animal phyla (2 Annelida [including Sipuncula], 2 Arthropoda, 2 Mollusca, 2 Nemertea, and 2 Porifera) were sequenced in different batches with an Illumina Genome Analyzer II (read length 100 or 150 bp), rendering between ca. 25 and 52 million reads per species. Read thinning, trimming, and de novo assembly were performed under different parameters to optimize output. Between 67,423 and 207,559 contigs were obtained across the ten species, post-optimization. Of those, 9,069 to 25,681 contigs retrieved blast hits against the NCBI non-redundant database, and approximately 50% of these were assigned with Gene Ontology terms, covering all major categories, and with similar percentages in all species. Local blasts against our datasets, using selected genes from major signaling pathways and housekeeping genes, revealed high efficiency in gene recovery compared to available genomes of closely related species. Intriguingly, our transcriptomic datasets detected multiple paralogues in all phyla and in nearly all gene pathways, including housekeeping genes that are traditionally used in phylogenetic applications for their purported single-copy nature.Conclusions: We generated the first study of comparative transcriptomics across multiple animal phyla (comparing two species per phylum in most cases), established the first Illumina-based transcriptomic datasets for sponge, nemertean, and sipunculan species, and generated a tractable catalogue of annotated genes (or gene fragments) and protein families for ten newly sequenced non-model organisms, some of commercial importance (i.e., Octopus vulgaris). These comprehensive sets of genes can be readily used for phylogenetic analysis, gene expression profiling, developmental analysis, and can also be a powerful resource for gene discovery. The characterization of the transcriptomes of such a diverse array of animal species permitted the comparison of sequencing depth, functional annotation, and efficiency of genomic sampling using the same pipelines, which proved to be similar for all considered species. In addition, the datasets revealed their potential as a resource for paralogue detection, a recurrent concern in various aspects of biological inquiry, including phylogenetics, molecular evolution, development, and cellular biochemistry. © 2012 Riesgo et al.; licensee BioMed Central Ltd.10aAnnelida10aArthropoda10aIllumina10aMollusca10aNemertea10anext-generation sequencing10aPorifera10aSipuncula1 aRiesgo, Ana1 aAndrade, Sónia, C.S.1 aSharma, Prashant, P.1 aNovo, Marta1 aPérez-Porro, Alicia, R.1 aVahtera, Varpu1 aGonzález, Vanessa, L.1 aKawauchi, Gisele, Y.1 aGiribet, Gonzalo uhttps://myriatrix.myspecies.info/content/comparative-description-ten-transcriptomes-newly-sequenced-invertebrates-and-efficiency02884nas a2200193 4500008004100000245012400041210006900165490000900234520215600243653001502399653001702414653001402431653002302445100002702468700001902495700002102514700002002535856013502555 2015 eng d00aSpecies limits and phylogeography of Newportia (Scolopendromorpha) and implications for widespread morphospecies0 aSpecies limits and phylogeography of iNewportiai Scolopendromorp0 v20153 a

The genus Newportia Gervais, 1847, includes some 60 nominal species distributed in the Caribbean islands and from Mexico to central South America. Modern keys to species and subspecies are available, greatly fa­cilitating identification, but some species are based on few specimens and have incomplete documentation of taxonomically-informative characters. In order to explore genetic variability and evolutionary relationships within geographically-widespread morphospecies, specimens of N. (N.) stolli (Pocock, 1896) and N. (N.) divergens Chamberlin, 1922, two nominal species distinguished principally by differences in suture patterns on T1, were sequenced for mitochondrial 16S rRNA and cytochrome c oxidase subunit I (COI) genes from populations in southern Mexico, Guatemala, Honduras and Brazil. N. (N.) stolli is paraphyletic with respect to N. (N.) divergens within a clade from Guatemala, Honduras, and Chiapas (Mexico), most trees being consistent with a single loss of a connection between the anterior transverse suture on T1, whereas specimens of “N. (N.) stolli” from Brazil are not closely allied to those from the Mesomerican type area. The widespread morphospecies N. (N.) monticola Pocock, 1890, was sequenced for the same loci from populations in Costa Rica, Colombia and Brazil, finding that specimens from these areas do not unite as a monophyletic group. Samples of N. (N.) oreina Chamberlin, 1915, from different regions of Mexico form geographic clusters that resolve as each other’s closest relatives. These results suggest that some widespread species of Newportia maybe taxa of convenience more so than natural groupings. In several cases geographic proximity fits the phylog­eny better than taxonomy, suggesting that non-monophyletic species do not result from use of inappropriate molecular markers. Molecular identification is possible for specimens missing taxonomically informative morphological characters, notably damaged specimens that lack the ultimate leg pair, a protocol that may also apply to other taxonomically difficult genera that are prone to damage (such as Cryptops).

10aNeotropics10aNewportiinae10aphylogeny10aScolopocryptopidae1 aEdgecombe, Gregory, D.1 aVahtera, Varpu1 aGiribet, Gonzalo1 aKaunisto, Pipsa uhttps://myriatrix.myspecies.info/content/species-limits-and-phylogeography-newportia-scolopendromorpha-and-implications-widespread02714nas a2200265 4500008004100000022001400041245019300055210006900248260001600317300001200333490000800345520181000353653001802163653001202181653002302193653002002216100002702236700001902263700002202282700001802304700001902322700002002341700002102361856006602382 2012 eng d a0024-408200aA scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: Synchrotron microtomography and phylogenetic placement using a combined morphological and molecular data set0 ascolopocryptopid centipede Chilopoda Scolopendromorpha from Mexi c 26/11/2012 a768-7860 v1663 a

The first scolopocryptopid centipede known from the fossil record is a specimen of the subfamily Scolopocryptopinae in Miocene amber from Chiapas, southern Mexico. It is described here as Scolopocryptops simojovelensis sp. nov., displaying a distinct combination of morphological characters compared to extant congeners. Anatomical details of the fossil specimen were acquired by non-invasive 3D synchrotron microtomography using X-ray phase contrast. The phylogenetic position of the new species is inferred based on a combination of morphological data with sequences for six genes (nuclear 18S and 28S rRNA, nuclear protein-coding histone H3, and mitochondrial 12S rRNA, 16S rRNA, and protein-coding cytochrome c oxidase subunit I) for extant Scolopendromorpha. The data set includes eight extant species of Scolopocryptops and Dinocryptops from North America, east Asia, and the Pacific, rooted with novel sequence data for other blind scolopendromorphs. The molecular and combined data sets, analysed in a parsimony/direct optimization framework, identified a stable pattern of two main clades within Scolopocryptopinae. North American and Asian species of Scolopocryptops are united as a clade supported by both morphological and molecular characters. Its sister group is a Neotropical clade in which the type species of Dinocryptops is nested within a paraphyletic assemblage of Scolopocryptops species; Dinocryptops is placed in synonymy with Scolopocryptops. The strength of support for the relationships of extant taxa from the molecular data allow the Chiapas fossil to be assigned with precision, despite ambiguity in the morphological data; the fossil is resolved as sister species to the extant Laurasian clade.

10aChiapas amber10aMiocene10aScolopocryptopidae10aScolopocryptops1 aEdgecombe, Gregory, D.1 aVahtera, Varpu1 aStock, Stuart, R.1 aKallonen, Aki1 aXiao, Xianghui1 aRack, Alexander1 aGiribet, Gonzalo uhttps://academic.oup.com/zoolinnean/article/166/4/768/262705001904nas a2200205 4500008004100000245012300041210006900164260001500233300001200248490000800260520122300268653001501491653001401506653003301520653001401553100001901567700002701586700002101613856006401634 2012 eng d00aSpiracle structure in scolopendromorph centipedes (Chilopoda: Scolopendromorpha) and its contribution to phylogenetics0 aSpiracle structure in scolopendromorph centipedes Chilopoda Scol c28/04/2012 a225-2480 v1313 a

The spiracles of scolopendromorph centipedes have long been a source of systematic characters based on their segmental distribution and gross morphology, but microscopic investigations to date have documented only a small number of species. A scanning electron microscopic survey of 34 species that samples the major groups of Scolopendromorpha reveals variability in such features as the structure of the peritremal margin, specific kinds of sensilla and glandular pores on the peritrema, projections on the valves that subdivide the atrium (in Scolopendrinae), and the form of the trichomes around the tracheal openings. Adding new characters from the spiracles to recent morphological datasets for phylogenetic inference reinforces the monophyly of major groups of Scolopendridae and is particularly informative for relationships within Scolopendrini. A bowl-like atrium with the tracheae opening between humps in its floor is more widespread in Scolopendromorpha than previously reported. Shared presence of spiracle muscles in Cryptopidae and Scolopendrinae may reflect convergent evolution of a subatrial cavity in these groups rather than being an apomorphic character for Scolopendromorpha as a whole.

10aCladistics10aphylogeny10aScanning electron microscopy10aSpiracles1 aVahtera, Varpu1 aEdgecombe, Gregory, D.1 aGiribet, Gonzalo uhttps://link.springer.com/article/10.1007/s00435-012-0157-002485nas a2200169 4500008004100000022001400041245014200055210006900197260001500266300000900281490000700290520187300297100001902170700002702189700002102216856007802237 2011 eng d a1096-003100aEvolution of blindness in scolopendromorph centipedes (Chilopoda: Scolopendromorpha): Insight from an expanded sampling of molecular data0 aEvolution of blindness in scolopendromorph centipedes Chilopoda  c24/05/2011 a4-200 v283 a

Relative to its diversity (34 genera, 700 species), Scolopendromorpha has been undersampled in molecular phylogenetic analyses compared with the other chilopod orders. Previous analyses based on morphology have not resolved several key controversies in systematics and evolutionary morphology unambiguously. Here we apply new molecular and morphological data to scolopendromorph phylogenetics, with a focus on the evolution of blindness. The taxonomic sample includes 19 genera, many lacking previous molecular data, and diverse, cosmopolitan genera of Scolopendridae are sampled by multiple species. Phylogenetic analysis with Direct Optimization used 94 morphological characters and ca. 4.5kb of sequence data from two nuclear (18S and 28S rRNA) and two mitochondrial (16S rRNA and COI) loci. A single most-parsimonious cladogram selected after sensitivity analyses resolves Scolopendromorpha as monophyletic, and divides it into a blind clade of three families (Plutoniumidae, Cryptopidae, Scolopocryptopidae) and its ocellate sister group, Scolopendridae. Some species-rich, cosmopolitan genera (Cormocephalus, Otostigmus, Scolopendra) in Scolopendridae are non-monophyletic, and in several instances (e.g. New and Old World Scolopendra) relationships are more congruent with geographical distributions than with traditional classifications. The tribe Asanadini is particularly subject to parameter-sensitivity, nesting in the combined analysis within Scolopendrini but as sister to all other Scolopendrinae for molecular data alone. The total-evidence tree unambiguously optimizes trunk segmentation: a 23-segmented trunk has a single origin in the blind clade.

Publication date remark: The publication date in Myriatrix is Wiley's "first published" date of 24/05/2011 and not the issue publication date of 02/2012.

1 aVahtera, Varpu1 aEdgecombe, Gregory, D.1 aGiribet, Gonzalo uhttps://onlinelibrary.wiley.com/doi/full/10.1111/j.1096-0031.2011.00361.x