A new species of Lepidodactylus (Squamata: Gekkonidae) from Umboi Island, Papua New Guinea.

We describe a new species of Lepidodactylus from Umboi Island, just to the west of New Britain. It is a member of the Lepidodactylus guppyi Group and can be distinguished from all other Melanesian Lepidodactylus by aspects of digital scalation, digital webbing, enlarged femoral/precloacal scales, and color pattern. It is genetically distinct from its closest congeners, and genetic and morphological data indicate that the new species is most similar among named species to Lepidodactylus guppyi from the Solomon Islands, but it diverged from this species and other close relatives approximately 8 MYA or longer at a time prior to the existence of the island that it now occupies. The new species is known from only three individuals collected on a single tree, and efforts to find more animals in what seemed good habitat nearby were unsuccessful. This duplicates the pattern of apparent rarity seen for many Lepidodactylus species. Sufficient habitat exists on Umboi Island for arboreal geckos, suggesting that the species is not actually endangered but is ecologically cryptic. However, lack of needed information leads us to assess this species' conservation status as Data Deficient.

Changes in Biomass and Diversity of Soil Macrofauna along a Climatic Gradient in European Boreal Forests.

Latitudinal gradients allow insights into the factors that shape ecosystem structure and delimit ecosystem processes, particularly climate. We asked whether the biomass and diversity of soil macrofauna in boreal forests change systematically along a latitudinal gradient spanning from 60° N to 69° N. Invertebrates (3697 individuals) were extracted from 400 soil samples (20 × 20 cm, 30 cm depth) collected at ten sites in 2015-2016 and then weighed and identified. We discovered 265 species living in soil and on the soil surface; their average density was 0.486 g d·w·m-2. The species-level diversity decreased from low to high latitudes. The biomass of soil macrofauna showed no latitudinal changes in early summer but decreased towards the north in late summer. This variation among study sites was associated with the decrease in mean annual temperature by ca 5 °C and with variation in fine root biomass. The biomass of herbivores and fungivores decreased towards the north, whereas the biomass of detritivores and predators showed no significant latitudinal changes. This variation in latitudinal biomass patterns among the soil macrofauna feeding guilds suggests that these guilds may respond differently to climate change, with poorly understood consequences for ecosystem structure and functions.

Phylogeny of Lithobiidae Newport, 1844, with emphasis on the megadiverse genus Lithobius Leach, 1814 (Myriapoda, Chilopoda).

Phylogenetic analyses based on molecular and morphological data were conducted to shed light on relationships within the mostly Palaearctic/Oriental centipede family Lithobiidae, with a particular focus on the Palaearctic genus Lithobius Leach, 1814 (Lithobiidae, Lithobiomorpha), which contains >500 species and subspecies. Previous studies based on morphological data resolved Lithobius as nonmonophyletic, but molecular-based phylogenetic analyses have until now sampled few species. To elucidate species inter-relationships of the genus, test the validity of its classification into subgenera, and infer its relationships with other Lithobiidae, we obtained molecular data (nuclear markers: 18S rRNA, 28S rRNA; mitochondrial markers: 16S rRNA, COI) and 61 morphological characters for 44 species of Lithobius representing four of its eight subgenera and nine other representatives of Lithobiidae. The data were analyzed phylogenetically using maximum-likelihood, parsimony and Bayesian inference. This study suggests that (i) a close relationship between L. giganteus and the pterygotergine Disphaerobius loricatus highlighted in recent morphological analyses is also strongly supported by molecular data, and Pterygoterginae is formally synonymized with Lithobiinae; (ii) the Oriental/Australian genus Australobius is consistently resolved as sister group to all other sampled Lithobiidae by the molecular and combined data; (iii) the subfamily Ethopolyinae may be paraphyletic; (iv) the genus Lithobius is nonmonophyletic; (v) the subgenera Lithobius, Sigibius and Monotarsobius are nonmonophyletic and should not be used in future taxonomic studies; and (vi) there are instances of cryptic species and cases in which subspecies should be elevated to full species status, as identified for some European taxa within Lithobius.

The millipede family Polyxenidae (Diplopoda, Polyxenida) in the faunas of the Crimean Peninsula and Caucasus, with notes on other European Polyxenidae.

The Polyxenidae in the fauna of the Crimeo-Caucasian region is represented by four species: Polyxenus lagurus (Linnaeus, 1758) (= P. lagurus caucasicus Lignau, 1924, syn. n.), Propolyxenus argentifer (Verhoeff, 1921) comb. n. (= P. trivittatus Verhoeff, 1941, = P. sokolowi Lignau, 1924, both syn. n.), a new species, Polyxenus lankaranensis sp. n., and an undescribed Polyxenus sp. The distributions of all these species in the region concerned are mapped, based on old and new records. A molecular phylogeny based on COI sequences is used to study the relationship within and among the genera Polyxenus and Propolyxenus from Western Europe to the southern Caucasus. The results highlight the presence of a number of undescribed species of Polyxenus across this region.

An overview of the extant genera and subgenera of the order Scolopendromorpha (Chilopoda): a new identification key and updated diagnoses.

The extant genera and subgenera of the order Scolopendromorpha are critically reviewed and provided with updated diagnoses and a new identification key; the most recent revisions of scolopendromorph genera are concisely summarised. Rhoda Meinert, 1886 and Cryptops (Chromatanops) Verhoeff, 1906 are suggested to be a junior synonyms of Scolopendropsis Brandt, 1841 and Cryptops (Cryptops) Leach, 1814, respectively. The subgeneric status is formally fixed for Cryptops (Paracryptops) Pocock, 1891 and Cormocephalus (Campylostigmus) Ribaut, 1923; the taxonomic status of the former genus Kanparka Waldock Edgecombe, 2012 is discussed. As a result of synonymies, the number of scolopendromorph genera and subgenera is currently 37. The formal status of the former tribes Scolopendrini Leach, 1814, Asanadini Verhoeff, 1907 and Arrhabdotini Attems, 1930 is briefly discussed; the presence of the sexual dimorphism among the taxa of generic level is overviewed.

Taxonomy of Micronesian monitors (Reptilia: Squamata: Varanus): endemic status of new species argues for caution in pursuing eradication plans.

In the light of recent phylogenetic studies, we re-assess the taxonomy and biogeography of the Varanus populations distributed in the Micronesian islands of Palau, the Western Carolines and the Marianas. Whether these populations are of natural origin or human introductions has long been contentious, but no study has fully resolved that question. Here, we present molecular and morphological evidence that monitor lizards of the Varanus indicus Group reached both Palau and the Mariana Islands sometime in the late Pleistocene and subsequently differentiated into two separate species endemic to each geographical region. One species is confined to the Mariana Islands, and for these populations, we revalidate the name V. tsukamotoi Kishida, 1929. The other species has a disjunct distribution in Palau, the Western Carolines and Sarigan Island in the Northern Marianas and is herein described as V. bennetti sp. nov. Both species are most closely allied to each other, V. lirungensis and V. rainerguentheri, suggesting that colonization of Micronesia took place from the Moluccas. We discuss the biogeographic distributions of both species in the light of the likely colonization mechanism and previous arguments for human introduction, and we argue that bounties for Palauan populations are ill-advised and plans for eradication of some other populations must first demonstrate that they are, in fact, introduced and not native.

Five million years in the darkness: A new troglomorphic species of Cryptops Leach, 1814 (Chilopoda, Scolopendromorpha) from Movile Cave, Romania.

A new species of Cryptops Leach, 1814, C. speleorex sp. nov., is described from Movile Cave, Dobrogea, Romania. The cave is remarkable for its unique ecosystem entirely dependent on methane- and sulfur-oxidising bacteria. Until now, the cave was thought to be inhabited by the epigean species C. anomalans, which is widespread in Europe. Despite its resemblance to C. anomalans, the new species is well-defined morphologically and molecularly based on two mitochondrial (cytochrome c oxidase subunit I COI and 16S rDNA) and one nuclear (28S rDNA) markers. Cryptops speleorex sp. nov. shows a number of troglomorphic traits such as a generally large body and elongated appendages and spiracles, higher number of coxal pores and saw teeth on the tibia of the ultimate leg. With this record, the number of endemic species known from the Movile Cave reaches 35, which ranks it as one of the most species-rich caves in the world.

Effects of reindeer grazing and recovery after cessation of grazing on the ground-dwelling spider assemblage in Finnish Lapland.

The effect of reindeer Rangifer tarandus L. grazing on the ground-dwelling spider assemblage in Northern Finland was studied. Changes in species richness, abundance and evenness of spider assemblages were analyzed in relation to changes in vegetation and environmental factors in long term grazed and ungrazed sites as well as sites that had recently switched from grazed to ungrazed and vice versa. Grazing was found to have a significant impact on height and biomass of lichens and other ground vegetation. However, it seemed not to have an impact on the total abundance of spiders. This is likely caused by opposing family and species level responses of spiders to the grazing regime. Lycosid numbers were highest in grazed and linyphiid numbers in ungrazed areas. Lycosidae species richness was highest in ungrazed areas whereas Linyphiidae richness showed no response to grazing. Four Linyphiidae, one Thomisidae and one Lycosidae species showed strong preference for specific treatments. Sites that had recovered from grazing for nine years and the sites that were grazed for the last nine years but were previously ungrazed resembled the long term grazed sites. The results emphasize the importance of reindeer as a modifier of boreal forest ecosystems but the impact of reindeer grazing on spiders seems to be family and species specific. The sites with reversed grazing treatment demonstrate that recovery from strong grazing pressure at these high latitudes is a slow process whereas reindeer can rapidly change the conditions in previously ungrazed sites similar to long term heavily grazed conditions.

Species limits and phylogeography of Newportia (Scolopendromorpha) and implications for widespread morphospecies.

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 Newportia (Newportia) stolli (Pocock, 1896) and Newportia (Newportia) 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. Newportia (Newportia) stolli is paraphyletic with respect to Newportia (Newportia) 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 "Newportia (Newportia) stolli" from Brazil are not closely allied to those from the Mesomerican type area. The widespread morphospecies Newportia (Newportia) 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 Newportia (Newportia) 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 may be 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).

Nine genera of Eucnemidae (Coleoptera) new to Peru, with a key to Peruvian genera.

Thirteen genera of Eucnemidae containing forty species were collected from the Iquitos region in Peru. Nine of the genera are new to the country: Rhagomicrus Fleutiaux, 1902, Adelorhagus Horn, 1890, Adelothyreus Chevrolat, 1867, Microrhagus Dejean, 1833, Dyscharachthis Blackburn, 1900, Heterotaxis Bonvouloir, 1871, Spinifornax Fleutiaux, 1926, Serrifornax Fleutiaux, 1926 and Maelodrus Fleutiaux, 1928. The previous eucnemid record from Peru contained eleven species in ten genera. Only one of the forty species caught, Entomophthalmusamericanus Bonvouloir, was previously known and described from the country. Dyscharachthis, Maelodrus and Adelorhagus are recorded from South America for the first time. Many of the collected species seem to favor white-sand forest as their habitat. Possible reasons for this are discussed. A list of eucnemids from Peru is included, containing taxa already recorded from the country and also taxa that are likely to occur there. A key to the Peruvian genera is included.

Unveiling of a cryptic Dicranomyia (Idiopyga) from northern Finland using integrative approach (Diptera, Limoniidae).

The subgenus Idiopyga Savchenko, 1987 is a northern hemisphere group of short-palped crane flies (Diptera, Limoniidae). In the current article we describe a new species, Dicranomyia (I.) boreobaltica Salmela sp.n., and redescribe the male and female post-abdomen of a closely related species, D. (I.) intricata Alexander. A standard DNA barcoding fragment of 5' region of the cytochrome c oxidase I (COI) gene of the new species is presented, whilst the K2P minimum distances between the new species and 10 other species of the subgenus were found to range from 5.1 to 15.7 % (mean 11.2 %). Phylogenetic analyses (parsimony and maximum likelihood) based on COI sequences support the identity of the new species and its close relationship with D. (I.) intricata and D. (I.) esbeni (Nielsen). The new species is known from the northern Baltic area of Finland. The new species has been mostly collected from Baltic coastal meadows but an additional relict population is known from a calcareous rich fen that was estimated to have been at sea level circa 600-700 years ago. Dicranomyia (I.) intricata (syn. D.suecica Nielsen) is a Holarctic species, occurring in the north boreal and subarctic vegetation zones in Fennoscandia.

First molecular data and the phylogenetic position of the millipede-like centipede Edentistoma octosulcatum Tömösváry, 1882 (Chilopoda: Scolopendromorpha: Scolopendridae).

Edentistoma octosulcatum Tömösváry, 1882, is a rare, superficially millipede-like centipede known only from Borneo and the Philippines. It is unique within the order Scolopendromorpha for its slow gait, robust tergites, and highly modified gizzard and mandible morphology. Not much is known about the biology of the species but it has been speculated to be arboreal with a possibly vegetarian diet. Until now its phylogenetic position within the subfamily Otostigminae has been based only on morphological characters, being variably ranked as a monotypic tribe (Arrhabdotini) or classified with the Southeast Asian genus Sterropristes Attems, 1934. The first molecular data for E. octosulcatum sourced from a newly collected specimen from Sarawak were analysed with and without morphology. Parsimony analysis of 122 morphological characters together with two nuclear and two mitochondrial loci resolves Edentistoma as sister group to three Indo-Australian species of Rhysida, this clade in turn grouping with Ethmostigmus, whereas maximum likelihood and parsimony analyses of the molecular data on their own ally Edentistoma with species of Otostigmus. A position of Edentistoma within Otostigmini (rather than being its sister group as predicted by the Arrhabdotini hypothesis) is consistently retrieved under different analytical conditions, but support values within the subfamily remain low for most nodes. The species exhibits strong pushing behaviour, suggestive of burrowing habits. Evidence against a suggested vegetarian diet is provided by observation of E. octosulcatum feeding on millipedes in the genus Trachelomegalus.

Evaluating topological conflict in centipede phylogeny using transcriptomic data sets.

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.

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa.

INTRODUCTION: 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.

Evolution of blindness in scolopendromorph centipedes (Chilopoda: Scolopendromorpha): insight from an expanded sampling of molecular data.

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. 4.5 kb 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. © The Willi Hennig Society 2011.

Running W ILD: the case for exploring mixed parameter sets in sensitivity analysis.

The robustness of clades to parameter variation may be a desirable quality or even a goal in phylogenetic analyses. Sensitivity analyses used to assess clade stability have invoked the incongruence length difference (ILD or W ILD) metric, a measure of congruence among datasets, to compare a series of most-parsimonious results from re-running analyses under different analytical conditions. It is also common practice to select a single "optimal" parameter set that minimizes W ILD across all parameter sets. However, the divergent molecular evolution of ribosomal genes and protein-encoding genes-specifically the bias against transversion events in coding genes of conserved function-suggests that deployment of multiple parameter sets could outperform the use of a single parameter set applied to all molecules. We explored congruence in five published datasets by including mixed parameter sets in our sensitivity analysis. In four cases, mixed parameter sets outperformed the previously reported, single optimal parameter set. Conversely, multiple parameter sets did not outperform a single optimal parameter set in a case in which actual strong topological conflict exists between data partitions. Exploration of mixed parameter sets may prove useful when combining ribosomal and protein-encoding genes, due to the relatively higher frequency of single- and double-base pair indel events in the former, and the relatively lower frequency of transversions in the latter. © The Willi Hennig Society 2010.

Phylogeny of the Thylacosterninae (Coleoptera, Elateridae).

The phylogeny of the Elateridae subfamily Thylacosterninae was studied using morphological characters and mitochondrial 16S rDNA sequences. Five monophyletic groups were recovered: the Asian Cussolenis, the American Pterotarsus, Balgus and Thylacosternus, and the African "Cussolenis", which is described here as Lumumbaia new genus Muona & Vahtera (type-species Cussolenis attenuatus Fleutiaux, 1925). The following new combinations are made: Lumumbaia africanus (Fleutiaux, 1897) [Soleniscus], Lumumbaia praeustus (Fleutiaux, 1926) [Cussolenis], Lumumbaia nigripes (Fleutiaux, 1926) [Cussolenis], Lumumbaia robustus (Fleutiaux, 1925) [Cussolenis], Lumumbaia attenuatus (Fleutiaux, 1925) [Cussolenis] and Lumumbaia notabilis (Fleutiaux, 1926) [Cussolenis]. A key to the genera of the subfamily is provided. The data were efficient in recovering generic limits within the group. At species level the mitochondrial 16S rDNA data seemed to work unpredictably, either agreeing or not with traditional species-level limits based on male genitalia and body structure. The evolution of bioluminescence is optimized as a feature originating in the ancestors of clicking elateroids. © The Willi Hennig Society 2009.