Out of the darkness - a new genus of Paederinae from the Neotropics (Coleoptera: Staphylinidae) and its phylogenetic position

The new genus Kellochloa is proposed, on the basis of morphological and molecular characters, to include two North American species of Panicum s.l., previously classified in sect. Verrucosa: P.brachyanthum and P. verrucosum. Both species are annual, with decumbent culms branching divaricately at the lower nodes, and erect culms with terminal and axillary inflorescences. The spikelets are pilose, with lower glume 1/6 to 1/4 the length of the spikelet, upper glume and lower lemma subequal, 3–5-nerved, the lower anthecium reduced to the lower lemma, and upper anthecium indurate, with bicellular microhairs and simple papillae evenly distributed all over the lemma and palea. Molecular phylogenetic studies, analyzing plastid ndhF and rpoA sequences, confirmed that these morphological characters are differential. The phylogenetic position and taxonomic features of the new genus are established and compared with Panicum s.str. and other taxa of the Sacciolepis–Trichanthecium clade. Full synonymies and descriptions, a distribution map, illustrations of both species, and a key are provided. Two new combinations are proposed. In addition, four African ungrouped species of Panicum s.l. were, for the first time, included in the phylogenetic analysis to analyze their relationship with the new genus and its positions in the Sacciolepis–Trichanthecium clade.

Mushroom corals are reef corals of the family Fungiidae, which live in the tropical and subtropical Indo-Pacific region. Recently, most species of this family have been revised taxonomically based on morphological and molecular analyses. However, the phylogenetic position of Cycloseris hexagonalis ( Milne Edwards and Haime, 1848 ) has not been analyzed and remains unclear. This species is believed to show allometric growth by changing its corallum shape from hexagonal in juveniles to irregularly circular with an undulated corallum margin in mature individuals. However, these morphological changes have not been monitored and their genetic basis has not been confirmed. In the present study morphological and molecular phylogenetic analyses were performed to evaluate the identity of the morpho-types in C. hexagonalis and to clarify the phylogenetic and taxonomic position of the species. In the morphological analysis, we used 20 specimens of C. hexagonalis collected from around Iriomote Island, Okinawa, Japan, and identified four morphotypes. Moreover, the molecular phylogenetic analyses using mitochondrial COI and nuclear ITS markers showed that all morpho-types of C. hexagonalis together form an independent clade, indicating that they are all conspecific. Molecular phylogenetic comparison between this species and other fungiids revealed that the clade of C. hexagonalis is clearly distant from the Cycloseris clade as well as from clades representing other genera in the Fungiidae. Considering these data, we establish a monotypic new genus, Sinuorota, to accommodate C. hexagonalis.

Endemism and diversification in freshwater insects of Madagascar revealed by coalescent and phylogenetic analysis of museum and field collections

Quantifying species-richness patterns along geographical gradients (typically latitude and elevation) has a long history in ecology and can be based on more-or-less complete censuses from a specified area (plot sampling), selective collection within a specified area (e.g. museum collections), or general information about species distributions (e.g. observations of extremes along the gradient, distribution maps). All these approaches require complete sampling to give the true richness in an area, but the richness pattern (i.e., the relative changes in richness along the gradient) may be estimated without complete sampling, although equal sampling between areas is necessary. This is relatively easy to do for fine-scale plot sampling, but rarely easy for other types of data. For data extracted from museum collections, a correct perception of the species richness pattern therefore depends on post-sampling treatment of data. Two commonly applied techniques for quantifying species richness patterns with these types of data are discussed, namely interpolation of species ranges and rarefaction. Such treatment may correct for unequal sampling in some instances, but may in other cases introduce artificial patterns. With incomplete sampling interpolation introduces an artificial humped pattern and rarefaction requires similar species abundance distributions to make unbiased comparisons among samples. One must therefore be cautious when applying these methods for estimating species richness patterns along geographical gradients.

Simple SummaryConservation of insects requires a reliable knowledge of their distribution. Such knowledge is hard to obtain in many cases, due to lack of human power and funding for extensive surveys. Three ways out of this problem have been suggested: (1) data already available in museum collections, (2) data already available in the entomological literature and (3) use of citizen science projects as a cheap, efficient way to survey extensive territories. We assessed the contribution of each of these sources of information in delineating the Spanish distribution of the European stag beetle. Although citizen science quickly contributed more grid cells than the other sources, some grid cells were uniquely contributed by museum and publication data. Thus, the three sources of information need to be combined when targeting endangered species in a broad, heterogenous, sparsely populated territory such as Spain.Reliable distribution maps are in the basis of insect conservation, but detailed chorological information is lacking for many insects of conservation concern (the Wallacean shortfall). Museum collections, entomological publications and citizen science projects can contribute to solve this Wallacean shortfall. Their relative contribution to the knowledge on the distribution of threatened insects has been scarcely explored, but it is important given that each of these three sources of information has its own biases and costs. Here we explore the contribution of museum data, entomological publications and citizen science in delineating the distribution of the European stag beetle in Spain. Citizen science contributed the highest number of records and grid cells occupied, as well as the highest number of grid cells not contributed by any other information source (unique grid cells). Nevertheless, both museum data and publications contributed almost 25% of all unique grid cells. Furthermore, the relative contribution of each source of information differed in importance among Spanish provinces. Given the pros and cons of museum data, publications and citizen science, we advise their combined use in cases, such as the European stag beetle in Spain, in which a broad, heterogeneous, sparsely populated territory has to be prospected.

The spider genus Ianduba is known from seven species, all restricted to the Brazilian Atlantic rainforest, a biodiversity hotspot. The genitalic morphology of these spiders is rather peculiar and they have been considered incertae sedis in Corinnidae. We present novel morphological data for the genus, including scanning electronic microscopy images for several somatic and genitalic features, and test their phylogenetic position by including one Ianduba species in a large morphological matrix of dionychan spiders. Our results suggest that Ianduba is a true corinnid, possibly belonging in a clade sister to Corinninae. Furthermore, we here describe eight new species of the genus: I. acaraje sp.n. (Bahia), I. apururuca sp.n. (Minas Gerais to Espírito Santo), I. capixaba sp.n. (Espírito Santo), I. dabadu sp.n. (Espírito Santo), I. beaga sp.n. (Minas Gerais), I. benjori sp.n. (Rio de Janeiro), I. liberta sp.n. (Minas Gerais) and I. angeloi sp.n. (Minas Gerais to São Paulo). Six of the new species seem to be closely related to I. varia, previously considered an aberrant species. Thus, we divide the genus into two morphological groups. All species from the varia group (except for I. varia, which is synanthropic in southeastern Brazil) appear to be restricted, or more common, at altitudes of at least 800 m above sea level. We argue that unsampled montane rainforest areas from southeastern Brazil are likely to yield new records or even undescribed species of Ianduba, and that montane species are likely to be under threat of extinction. New records for previously known species are provided, the female of I. caxixe Bonaldo, 1997 is described and illustrated for the first time, and distribution maps and an identification key for the fifteen known species are provided.

Natural history museum collections represent a vast source of ancient and historical DNA samples from extinct taxa that can be utilized by high-throughput sequencing tools to reveal novel genetic and phylogenetic information about them. Here, we report on the successful sequencing of complete mitochondrial genome sequences (mitogenomes) from eleven extinct bird species, using de novo assembly of short sequences derived from toepad samples of degraded DNA from museum specimens. For two species (the Passenger Pigeon Ectopistes migratorius and the South Island Piopio Turnagra capensis), whole mitogenomes were already available from recent studies, whereas for five others (the Great Auk Pinguinis impennis, the Imperial Woodpecker Campehilus imperialis, the Huia Heteralocha acutirostris, the Kauai Oo Moho braccathus and the South Island Kokako Callaeas cinereus), there were partial mitochondrial sequences available for comparison. For all seven species, we found sequence similarities of >98%. For the remaining four species (the Kamao Myadestes myadestinus, the Paradise Parrot Psephotellus pulcherrimus, the Ou Psittirostra psittacea and the Lesser Akialoa Akialoa obscura), there was no sequence information available for comparison, so we conducted blast searches and phylogenetic analyses to determine their phylogenetic positions and identify their closest extant relatives. These mitogenomes will be valuable for future analyses of avian phylogenetics and illustrate the importance of museum collections as repositories for genomics resources.

BackgroundThe colubrid snakes of the genus Rhynchocalamus are seldom studied and knowledge of their ecology and life history is scarce. Three species of Rhynchocalamus are currently recognized, R. satunini (from Turkey eastwards to Iran), R. arabicus (Yemen and Oman), and R. melanocephalus (from the Sinai Peninsula northwards to Turkey). All are slender, secretive, mainly nocturnal and rare fossorial snakes. This comprehensive study is the first to sample all known Rhynchocalamus species in order to review the intra-generic phylogenetic relationships and historical biogeography of the genus.MethodsWe revised the systematics of Rhynchocalamus using an integrative approach and evaluated its phylogeography. The phylogenetic position within the Colubridae and the phylogenetic relationships within the genus were inferred using 29 individuals belonging to the three known species, with additional sampling of two other closely-related genera, Muhtarophis and Lytorhynchus. We analysed three mitochondrial (12S, 16S, cytb) and one nuclear (c-mos) gene fragments. Phylogenetic trees were reconstructed using maximum likelihood and Bayesian inference methods; the latter method also used to provide the first time-calibrated molecular phylogeny of the genus. We generated a nuclear network and carried out a topology test and species delimitation analysis. Morphological comparisons were used to differentiate among species and to describe a new species from Israel. The studied material was comprised of 108 alcohol-preserved specimens, 15 photographs, and data from the literature for the examination of 17 mensural, 14 meristic, and two categorical characters.ResultsThe molecular results support Rhynchocalamus as monophyletic, and as having split from its sister genus Lytorhynchus during the Late Oligocene. The three recognized species of Rhynchocalamus comprise four independently evolving groups. The molecular results reveal that the genus began to diverge during the Middle Miocene. We revealed that the best-studied species, R. melanocephalus, is paraphyletic. A population, formally ascribed to this species, from the Negev Mountain area in southern Israel is phylogenetically closer to R. arabicus from Oman than to the northern populations of the species from Israel, Syria and Turkey. Herein we describe this population as a new species: Rhynchocalamus dayanaesp. nov.DiscussionWe identify four species within Rhynchocalamus: R. satunini, R. arabicus, R. melanocephalus, and R. dayanaesp. nov., the latter, to the best of our knowledge, is endemic to southern Israel. The onset of Rhynchocalamus diversification is very old and estimated to have occurred during the Middle Miocene, possibly originating in the Levant region. Radiation probably resulted from vicariance and dispersal events caused by continuous geological instability, sea-level fluctuations and climatic changes within the Levant region.

Phylogeny of Spinicaudata (Branchiopoda, Crustacea) based on three molecular markers – An Australian origin for Limnadopsis

The small Neotropical papilionoid legume genus Sigmoidotropis (nine species) has been described only relatively recently as the result of the taxonomic rearrangement of the genus Vigna (subtribe Phaseolinae), based on phylogenetic analyses of DNA sequence data. Here, we formally propose a new lianescent species of Sigmoidotropis that occurs disjunctly in enclaves of moist forest of mountainous regions surrounded by dry vegetation at three different localities in the Brazilian states of Bahia and Minas Gerais. Its phylogenetic position and morphological affinities with other genera of Phaseolinae were evaluated by Bayesian inference and maximum likelihood analyses, using sequence data from the nuclear ITS/5.8S and plastid trnK/matK. To better understand this new species’ widely disjunct distribution and a possible connection between its populations in the past, an environmental niche modelling (ENM) analysis was performed. The phylogenetic analyses revealed that Sigmoidotropis appears closest to the genera Ancistrotropis and Delgadoana, together forming the Sigmoid‐keel clade. The new species proposed here is strongly recovered within Sigmoidotropis, being most closely related to S. ekmaniana, S. elegans, and S. megatyla. The ENM indicated changes in the potential distribution of the new species over different climatic periods, with expansion during colder periods and contraction during warmer periods, leading to possible relictual populations in moist forest enclaves. A description of the new species Sigmoidotropis maculata is presented, along with illustrations, a distribution map, taxonomic comments, and conservation status assessment.

Ampullariidae Gray, 1824, commonly known as apple snails, are a diverse and conspicuous element of freshwater molluscan faunas in tropical regions, with some 120 species in about ten genera. Some are economically important, e.g. as invasive species and crop pests. Systematic and phylogenetic knowledge of these limnic snails, however, is still unsatisfactory. To help in providing the foundation for a thorough taxonomic revision and phylogeny of the family, this paper lists the type material of Ampullariidae held by the Malacozoological Collection of the Natural History Museum, Berlin (ZMB). We document types of 46 described species-group taxa, of which 24 are from the Neotropics and 22 are from Africa, and designate 32 lectotypes. Among this material we have also identified type specimens that were hitherto unknown to be part of the collection, some of which were even assumed to be lost, and that were therefore not mentioned in the most recently published nomenclatural catalogue of the group. The taxa dealt with in the present article were described by, among others, E. von Martens (22 taxa), R. A. Philippi (10 taxa), F. H. Troschel (2 taxa), J. H. Jonas (2 taxa), J. Thiele (1 taxon), and W. Dunker (1 taxon). Where necessary, brief remarks are given on the taxonomy, systematics, type localities and distribution of the taxa.

Contamination and chimerism are perpetuating the legend of the snake-eating cow with twisted horns ( Pseudonovibos spiralis). A case study of the pitfalls of ancient DNA

We describe a new genus and species of Paederinae rove beetles, Ruptor cordatus gen. et sp. nov., which lives in the arboreal nests of the termite Labiotermes labralis (Holmgren, 1906) in the Amazon lowlands of Peru. The morphology of Ruptor gen. nov. is highly derived, apparently due to its close association with the termite host, and thus, morphologically, the genus cannot be classified further than Lathrobiini incertae sedis. In order to address the sister-group relationships of Ruptor gen. nov., we conducted a molecular phylogenetic analysis based on seven gene fragments. The analysis indeed resolved the genus as a member of the tribe Lathrobiini and placed it nested within the informal clade of ‘Medonina and allied taxa’. We provide a morphological comparison of the new genus with all known myrmeco- and termitophilous representatives of the subfamily, and to the extent possible, we illustrate other relevant and poorly known Neotropical Paederinae inquilines.

The Malabar trevally Carangoides malabaricus is a widely distributed inshore fish species and commercially important in some tropical regions. This study presented the complete mitochondrial genome of C. malabaricus as well as its phylogenetic position in Carangidae. The entire sequence was 16,561 bp in length, including the typical structure of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, 1 control regions and 1 L-strand replication origin. The arrangement of the genes was in line with other teleosts. The genome was composed of 29.6% C, 27.8% A, 26.2% T and 16.4% G, showing an obvious anti G bias. Phylogenetic analyses using the concatenated sequence of the protein-coding genes showed similar results in the Neighbour-Joining and Bayesian inference trees. Three clades were formed as Subfamilies Caranginae, Seriolinae and Trachinotinae in Carangidae based on the current dataset. C. malabaricus was most closely related to the species in the same genus.

The African genus Lygodactylus Gray, is composed of roughly 60 species of diurnal geckos that inhabit tropical and temperate Africa, Madagascar, and South America. In this study, we assessed the phylogenetic position of L. angularis , for which molecular data were so far lacking, by means of sequence analysis of the mitochondrial 16S rDNA gene . We also compared intraspecific vs. interspecific genetic divergences using an extended data set (34 species, 153 sequences), to determine whether a fragment of this gene can be useful for species identification and to reveal the possible existence of new cryptic species in the genus. The analysis placed L. angularis in a monophyletic group together with members of “ fischeri ” and “ picturatus ” groups. Nevertheless, the independence of the “ angularis ” lineage is supported by the high genetic divergence. Comparison of intraspecific vs. interspecific genetic distances highlights that, assuming an equal molecular rate of evolution among the studied species for the used gene, the threshold value useful for recognising a candidate new species can be tentatively placed at 7%. We identified four species that showed an intraspecific divergence higher than, or close to, the 7% threshold: L. capensis (8.7%), L. gutturalis (9.3%), L. madagascariensis (6.5%) and L. picturatus (8.1%). Moreover, two species, L. mombasicus and L. verticillatus, are paraphyletic in terms of gene genealogy. Thus, the study shows that a short fragment of the 16S rDNA gene can be an informative tool for species-level taxonomy in the genus Lygodactylus.