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opencc-zeroDec 2018View details →

Data from: Old World and New World Phasmatodea: phylogenomics resolve the evolutionary history of stick and leaf insects

Phasmatodea comprises over 3,000 extant species and stands out as one of the last remaining insect orders for which a robust, higher-level phylogenetic hypothesis is lacking. New research suggests that the extant diversity is the result of a surprisingly recent and rapid radiation that has been difficult to resolve with standard Sanger sequence data. In order to resolve the early branching events of stick and leaf insects, we analyzed transcriptomes from 61 species, including 38 Phasmatodea species comprising all major clades and 23 outgroup taxa, including all other Polyneoptera orders. Using a custom-made ortholog set based on reference genomes from four species, we identified on average 2,274 orthologous genes in the sequenced transcriptomes. We generated various sub-alignments and performed maximum-likelihood analyses on several representative datasets to evaluate the effect of missing data and matrix composition on our phylogenetic estimates. Based on our new data, we are able to reliably resolve the deeper nodes between the principal lineages of extant Phasmatodea. Among Euphasmatodea, we provide strong evidence for a basal dichotomy of Aschiphasmatodea and all remaining euphasmatodeans, the Neophasmatodea. Within the latter clade, we recovered a previously unrecognized major New World and Old World lineage, for which we introduce the new names Oriophasmata tax. nov. ("Eastern phasmids") and Occidophasmata tax. nov. ("Western phasmids"). Occidophasmata comprise Diapheromerinae, Pseudophasmatinae, and Agathemera, whereas all remaining lineages form the Oriophasmata, including Heteropterygidae, Phylliinae, Bacillus, Lonchodidae (Necrosciinae + Lonchodinae), Clitumninae, Cladomorphinae, and Lanceocercata. We furthermore performed a divergence time analysis and reconstructed the historical biogeography for stick and leaf insects. Phasmatodea either originated in Southeast Asia or in the New World. Our results suggest that the extant distribution of Phasmatodea is largely the result of dispersal events in a recently and rapidly diversified insect lineage rather than the result of vicariant processes.

opencc-by-4.0May 2020View details →

New understanding of the spatiotemporal lightning activity over the Tibetan Plateau based on WWLLN data

The submitted data are associated with the figures in the paper titled "New understanding of the spatiotemporal lightning activity over the Tibetan Plateau based on WWLLN data". The following is the abstract of this paper.   The spatiotemporal distribution of the lightning activity over the Tibetan Plateau (TP) has been previously studied based on data from the Lightning Imaging Sensor (LIS) aboard the polar-orbit Tropical Rainfall Measuring Mission satellite. In this study, using lightning data from the World Wide Lightning Location Network (WWLLN), we reinvestigated the lightning activity over the TP and found that the geographic and seasonal lightning distributions suggested by the WWLLN are somewhat different from those obtained from the LIS. In particular, 1) while the LIS indicates strong lightning activity over the northeastern TP, the WWLLN indicates relatively weak lightning activity over the region; 2) the WWLLN indicates the existence of a center with relatively frequent lightning activity over the south-by-west TP, which is not indicated by the LIS; furthermore, 3) the WWLLN indicates the most frequent lightning in August and September, while the LIS suggests July and June. The black body temperature data from the Fengyun-2E geostationary satellite (as a proxy of deep convection), thunderstorm day data, and local cloud-to-ground lightning data strongly support the lightning spatiotemporal distribution patterns suggested by the WWLLN. The difference between the WWLLN and LIS data is attributed to their very different sample numbers and observation methods, and the situation that lightning tends to occur in the lower part of TP thunderstorms. Owing to the time-continuous nature, the WWLLN data were also used to obtain the ten-day distributions of lightning in space and time and the diurnal variation of lightning. This study may further elucidate our knowledge of the lightning activity over the TP.

Data from: A strong east-west Mediterranean divergence supports a new phylogeographic history of the carob tree (Ceratonia siliqua, Leguminosae) and multiple domestications from native populations

Aim: Phylogeography of fruit trees is challenging due to the recurrent exchanges between domesticated and wild populations. Here we tested the eastern refugium hypothesis (ERH) for the carob tree, Ceratonia siliqua, which supports its natural and domestication origins in the Eastern Mediterranean and a feral origin in the West. Location: Mediterranean basin Taxon: Ceratonia siliqua L., Leguminosae Methods: Divergence time of the divergence between the carob tree and its sister species (C. oreothauma) was estimated based on two nuclear and one plastid sequences. Variation from four plastid regions and 17 nuclear microsatellite loci were used to decipher genetic structure in the carob tree and to test coalescent-based models by an Approximate Bayesian Computation (ABC) approach. We assessed our hypotheses by examining palaeobotanical records and hindcasting the past distribution of the carob tree at the Mid-Holocene, Last Glacial Maximum (LGM) and Last Interglacial (LIG) using species distribution modelling (SDM). Results: The split between C. oreothauma and C. siliqua was estimated at 6.4 Ma, and a first divergence within C. siliqua at 1.3 Ma. After a presence since the Oligocene, Ceratonia was found in the Western and the Eastern Mediterranean in the fossil records during the Pleistocene. Plastid and nuclear markers, characterized by low allelic richness, revealed a strong west-east genetic structuring. Approximate Bayesian computation (ABC) analyses rejected the ERH. Main conclusions: Our study supports a severe population decline during LIG. The strong west-east divergence and the occurrence of four lineages within C. siliqua provided support for a new hypothesis of multiple domestications of the carob tree from native populations throughout the Mediterranean basin.

FIGURE 4 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data

FIGURE 4 Scale detail of C. tatama n. sp. IMCN 8924, Paratype, 36.3 mm LS, white arrows show the rounded point characteristic in the lateral line

FIGURE 2 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data

FIGURE 2 Ultrametric tree using BEAST representing the phylogenetic relationships of the genus Characidium using COI sequences. Branch lengths were adjusted to a strict molecular clock. The black bars represent the UTOs obtained with the ABGD, GMYC and bPTP molecular delimitation methods and the majority consensus. Green dots posterior probability (>0.95)

FIGURE 1 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data

FIGURE 1 Distribution map of the Characidium genus in the trans- Andean and cis-Andean regions of Colombia. Black triangle (HT)/yellow cicle, C. tatama n. sp.; red triangle (HT)/orange circle, C. dule n. sp.; red diamond, C. caucanum; red circle, C. phoxocephalum; white red mark (HT)/ purple circle, C. chancoense; white circle, C. cf. boavistae; blue diamond, C. cf. zebra; red-black star (HT)/grey circle, C. santcjohanni; HT, holotype

FIGURE 3 C. tatama n in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data

FIGURE 3 C. tatama n. sp., Holotype, IMCN 8925, 38.1 mm LS, Colombia, Chocó, San José Del Palmar. Scale bar = 1 cm

FIGURE 7 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data

FIGURE 7 Detail of the composition of spots in C. dule n. sp. IMCN 8929, Paratype 38.24 mm LS, arrows show the detail. Scale bar = 1 cm

Data from: An enigmatic new ungulate-like mammal from the early Eocene of India

We report on a new genus and species of herbivorous mammal, Pahelia mysteriosa, from the early Eocene Cambay Shale Formation, Tadkeshwar Lignite Mine, Gujarat, India. The new taxon, approximately the size of a small phenacodontid (e.g., Ectocion parvus), is represented by three mandibular fragments, the most complete of which documents nearly the entire symphysis and mandibular body plus P3-M3. Pahelia has incipiently selenolophodont molars with strong exodaenodonty, absent paraconids, weak but distinct entolophids, and prominent ectostylids. Molar size increases distally, but M3 does not develop a prominent third lobe. Premolars are simple, with prominent protoconids and short talonids but little development of other trigonid cusps. The mandibular symphysis is strongly fused, and there is an enlarged alveolus for an anterior tooth. The combination of features present in the new taxon does not closely match that of any known mammal, but there are some similarities to a diversity of ungulates from Africa, Asia, Europe, and North America. Preserved morphology is insufficient to confidently assess the affinities of the new taxon, but a link to Quettacyonidae, also endemic to the Indian subcontinent, is morphologically and biogeographically plausible. If this scenario is correct, it suggests that P. mysteriosa could be a part of the endemic mammalian fauna of India prior to its initial faunal contact with Asia.

Data from: New taxa of Rhododendron tschonoskii alliance (Ericaceae) from East Asia

Three new taxa, Rhododendron sohayakiense Y. Watan. & T. Yukawa (Ericaceae), and its two varieties, var. kiusianum Y. Watan., T. Yukawa & T. Minamitani and var. koreanum Y. Watan. & T. Yukawa are described and illustrated from Japan and South Korea. They can be distinguished each other and from the other members of the R. tschonoskii alliance, i.e. R. tschonoskii, R. tetramerum, R. trinerve and R. tsusiophyllum, by the combination of leaf size, leaf morphologies including lateral nerves on abaxial leaf surface, corolla morphologies including number of corolla lobes, style length and anther form. Phylogenetic inferences based on chloroplast DNA and genome-wide sequences revealed that each of the three new taxa is monophyletic and they further form a clade. Distributions of the three taxa are also clearly separated each other and also from the other members of the R. tschonoskii alliance.

Data from: Protein-encoding ultraconserved elements provide a new phylogenomic perspective of Oestroidea flies (Diptera, Calyptratae)

The diverse superfamily Oestroidea with more than 15,000 known species includes among others, blow flies, flesh flies, bot flies, and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oestroidea lineages. Phylogenomic inferences derived from targeted enrichment of ultraconserved elements or UCEs have emerged as a promising method for resolving difficult phylogenetic problems at varying timescales. To reconstruct phylogenetic relationships among families of Oestroidea, we obtained UCE loci exclusively derived from the transcribed portion of the genome making them suitable for larger and more integrative phylogenomic studies using other genomic and transcriptomic resources. We analysed datasets containing 37–2,077 UCE loci from 98 representatives of all oestroid families (except Ulurumyiidae and Mystacinobiidae) and seven calyptrate outgroups, with a total concatenated aligned length between 10–550 Mb. About 35% of the sampled taxa consisted of museum specimens (2–92 years old), of which 85% resulted in successful UCE enrichment. Our maximum likelihood and coalescent-based analyses produced well-resolved and highly supported topologies. With the exception of Calliphoridae and Oestridae, all included families were recovered as monophyletic with the following conclusions: Oestroidea is monophyletic with Mesembrinellidae as sister to the remaining oestroid families; Oestridae is paraphyletic with respect to Sarcophagidae; Polleniidae is sister to Tachinidae; Rhinophoridae sister to (Luciliinae (Toxotarsinae (Melanomyinae + Calliphorinae))); Phumosiinae is sister to Chrysomyinae and Bengaliinae is sister to Rhiniidae. These results support the ranking of most calliphorid subfamilies as separate families.

opencc-zeroOct 2020View details →

Data from: A spectacular new species of Habenaria (Orchidaceae) from southern Brazilian Amazon

A new Habenaria species from the state of Mato Grosso is described and illustrated. Habenaria gracilisegmenta was discovered in campinarana sub-forest, in northern Mato Grosso state, on the southern edge of the Brazilian Amazon. The species is distinguished by its slender habit, few, delicate flowers, and very long, thin lateral segments of the petals and lip, and its morphological affinity with other Neotropical species is unclear. A molecular phylogenetic analysis revealed that the new species does not belong to any of the Neotropical subclades of the genus, constituting an additional lineage. The species is one of two of the genus endemic to the Brazilian Amazon, and considered threatened by the small number of known populations and restricted distribution.

Data from: Muilla lordsburgana (Asparagaceae: Brodiaeoideae), a new species found north of Lordsburg, southwestern New Mexico

Muilla lordsburgana P.J.Alexander sp. nov. is described from eastern Lordsburg Mesa in the northwestern fringe of the Chihuahuan Desert, southwestern New Mexico. It is very similar to Muilla coronata, a species known in the Mojave Desert of California and a small area of adjacent Nevada. Compared to Muilla coronata, the style and stigma combined are longer, the anthers are longer, the fruits are larger, and the seeds are larger. It has a short flowering period in March, and is difficult or impossible to find at other times of the year. It is narrowly distributed, limited to a band of deep, coarse, sandy soils derived primarily from granite. Several species that are otherwise uncommon in the area also occur in this habitat, including Logfia depressa, Pectocarya platycarpa, and Plagiobothrys arizonicus. Invasive species, especially Erodium cicutarium in the winter annual flora, are generally dominant. Muillla lordsburgana has probably been overlooked until now because it is not easy to observe and occurs in habitats that are not attractive to botanists.

opencc-zeroOct 2020View details →

Data from: Temporal dynamics of competitive fertilization in social groups of red junglefowl (Gallus gallus) shed new light on avian sperm competition

Studies of birds have made a fundamental contribution to elucidating sperm competition processes, experimentally demonstrating the role of individual mechanisms in competitive fertilisation. However, the relative importance of these mechanisms and the way in which they interact under natural conditions remain largely unexplored. Here, we conduct a detailed behavioural study of freely-mating replicate groups of red junglefowl, Gallus gallus, to predict the probability that competing males fertilise individual eggs over the course of 10-day trials. Remating frequently with a female and mating last increased a male's probability of fertilisation, but only for eggs ovulated in the last days of a trial. Conversely, older males, and those mating with more polyandrous females, had consistently lower fertilisation success. Similarly, resistance to a male's mating attempts, particularly by younger females, reduced fertilisation probability. After considering these factors, male social status, partner relatedness and the estimated state of a male extragonadal sperm reserves did not predict sperm competition outcomes. These results shed new light on sperm competition dynamics in taxa such as birds, with prolonged female sperm storage and staggered fertilisations.

opencc-zeroOct 2020View details →

Data from: Small Carbonaceous Fossils (SCFs) from North Greenland: new light on metazoan diversity in early Cambrian shelf environments

The Sirius Passet Lagerstätte of North Greenland provides one of the oldest records of soft-bodied metazoan-dominated ecosystems from within the early Cambrian. The Lagerstätte site itself is restricted to just a single ~1 km-long outcrop located offshore from the shelf margin, in an area that has been affected by metamorphic alteration during the Ellesmerian Orogeny (Devonian–Early Carboniferous). The recent recovery of Small Carbonaceous Fossils (SCFs) to the south in areas that have escaped the effects of this deformation has substantially expanded the known coverage of organic preservation into shallower-water depositional settings in this region. Here we describe additional SCF assemblages from the siliciclastic shelf succession of the Buen Formation (Cambrian Series 2, Stages 3-4; ∼ 515 Ma), expanding upon the previously documented SCF biota. Newly recovered material reveals a rich diversity of non-mineralizing metazoans, chiefly represented by arthropod remains. These include the filtering and grinding elements of a sophisticated crustacean feeding apparatus - the oldest crustacean remains reported to date - alongside an assortment of bradoriid sclerites, including almost complete, three-dimensional valves which tie-together a number of SCFs previously found in isolation. Other metazoan remains include various trilobite cuticles, diverse scalidophoran sclerites, and a range of metazoan fragments of uncertain affinities. This shallower-water assemblage differs substantially from the Sirius Passet biota, which is dominated by problematic euarthropod stem-group members and sponges. Though some of these discrepancies are attributable to taphonomic or temporal factors, these lateral variations in taxonomic composition also point to significant palaeoenvironmental and/or palaeoecological controls on early Cambrian metazoan communities.

opencc-by-4.0Nov 2020View details →

The new Garba Guracha palynological sequence: revision and data expansion

Dataset by Graciela Gil-Romera et al. submitted to "Palaeocology of Africa". dictionary.csv is the file containing information on how taxa are attibuted to different functional and bioclimatic types and pollen.csv contains all raw pollen data. Charcoal data presented in Fig3 can be downloaded from here: https://github.com/ggilromera/BaleFire The age-depth model has been built using the dates and code published here: https://link.springer.com/article/10.1007/s10933-020-00138-w#Sec36 And the raw and calibrated dated samples can be found in the supmat_bittner_etal_2020.docx file.

opencc-by-4.0Nov 2020View details →

The Baby Steps web-based program for wellbeing of new parents - main data file

Main data set from Baby Steps RCT

opencc-by-4.0Dec 2020View details →

Data for manuscript "The synergistic role of sulfuric acid, bases, and oxidized organics governing new-particle formation in Beijing"

Data for the manuscript "The synergistic role of sulfuric acid, bases, and oxidized organics governing new-particle formation in Beijing" submitted to Geophysical Research Letters

opencc-zeroDec 2020View details →

Data from: Biogeography and anthropogenic impact shape the success of invasive wasps on New Zealand's offshore islands

Aim The theory of island biogeography predicts that the susceptibility of an island to invasion is determined by its isolation and size. However, many island ecosystems have been intensely modified by humans. Here, we investigated the biogeographic, biotic and anthropogenic drivers of invasive social wasps on 36 offshore islands. Location Islands off the east coast of New Zealand's North Island. Taxa Vespula germanica (Fabricius, 1793), Vespula vulgaris (Linnaeus, 1758) and Polistes chinensis antennalis (Fabricius, 1793), Polistes humilis (Fabricius, 1781). Methods We used GIS software for in situ randomisation of plots on each island (36 islands, 409 plots) and conducted 5-minute wasp counts to estimate wasp abundance. Wasp abundance and canopy cover were recorded at each plot. Island isolation was measured using GIS software. Data on island size, human settlement and the presence of introduced rats (Rattus spp.) were collated from the literature and island managers. The number of boat docks per island was counted from satellite images. A generalised linear mixed effect model (GLMM) was fitted to identify drivers of Vespula and Polistes abundance on offshore islands. Results The abundance of Vespula was negatively correlated with island isolation and canopy cover, yet positively correlated with island size. Vespula were also more abundant on islands that have been settled by humans. The abundance of Polistes was negatively correlated with canopy cover. Finally, results did not support the notion that invasive wasps were associated with introduced rats on New Zealand's offshore islands. Conclusions Our findings highlight the importance of biogeographic factors, such as island size and isolation, for species invasions, and suggest that intact forest cover could contribute to biotic resistance to invasive wasps in island ecosystems. Studies of invasive species should consider the joint effects of biogeographic, biotic and anthropogenic factors to best inform conservation management.ealand's North Island.