Find research datasets worth reusing

opencc-zeroJul 2019View details →

Data from: The bivalved arthropod Tuzoia from the Balang Formation (Cambrian Stage 4) of Guizhou, China, and new observations on comparative species

Tuzoia is a large, bivalved Cambrian arthropod having a widespread distribution in shallow-shelf to deeper marine Lagerstätten; stratigraphically it ranges from Cambrian Series 2 through the Miaolingian Series. In the present study, three species are recognized from relatively deep-water deposits of the Balang Formation (Cambrian Stage 4) of Guizhou, South China: Tuzoia sinensis Pan, 1957, T. bispinosa Yuan et Zhao, 1999 and T. lazizhaiensis sp. nov. The new species is unique in having 6-10 small marginal spines on the dorsal margin, an inflated anterior margin with 3 short, closely spaced marginal spines. These remains, which usually occur as disarticulated valves, are inferred to be parautochthonous. One new specimen of T. lazizhaiensis shows a stalked eye and antenna. New Tuzoia material from the Kaili Biota (Cambrian: Wuliuan Stage) of Guizhou, and from the Guanshan Biota (Cambrian Stage 4) of Yunnan, China, provide additional comparative information about the genus. Some new specimens of T. bispinosa from the Kaili Biota provide information on valve morphology and palaeoecology. One specimen of T. sinensis from the Guanshan Biota provides information on the appendages, and one specimen of T. tylodesa, from the Guanshan Biota adds provides information on the trunk and appendages.

Data from: A new mesophotic goby, Palatogobius incendius (Teleostei: Gobiidae), and the first record of invasive lionfish preying on undescribed biodiversity

A new species of deep-reef fish in the goby genus Palatogobius is described from recent submersible collections off Curaçao and Dominica. Video footage of schools of this species reveal predation by the invasive Indo-Pacific lionfish (Pterois spp.), the first record of undescribed fauna potentially being eaten by lionfish outside of its native range. We present molecular phylogenetic data for all valid species of Palatogobius and related genera, as well as a taxonomic key to the species of Palatogobius and a generic key to Palatogobius and related genera in the western Atlantic. Lastly, we discuss ecological and behavioral aspects of some deep-reef fishes in light of potential threats from invasive lionfish.

Data from: Complete species phylogeny of the marine midge Pontomyia (Diptera: Chironomidae) reveals a cosmopolitan species and a new synonym

Pontomyia (Diptera: Chironomidae) is an exclusively marine and flightless insect genus with four described species from the Indo-Pacific and one undescribed taxon known only by its larvae, pupal skins and females from the western Atlantic. A previous study of relationships among three of the Indo-Pacific species reported each of them to be monophyletic, with high genetic diversity within P. natans Edwards, the type species, and P. pacifica Tokunaga. The evolutionary affinities of the Australian endemic P. cottoni Womersley that resembles P. natans, as well as the putative Atlantic species are hitherto undetermined. A complete molecular phylogeny of the genus based on two nuclear and two mitochondrial DNA markers indicates that P. cottoni and a Puerto Rican (Atlantic) larval population are nested within the P. natans clade. Furthermore, P. natans and P. cottoni are inseparable in all morphological characters used previously to distinguish them. Therefore, we synonymize P. cottoni with P. natans, syn. nov., whose known range now encompasses all three ocean basins after including the Puerto Rican population. This distribution warrants further investigation into the life history of Pontomyia, a midge with one of the shortest known adult lifespans among insects.

opencc-zeroDec 2015View details →

Data from: Xianella: a new mat-forming calcified cyanobacterium from the Middle–Late Ordovician of North China

Xianella hongii gen. et sp. nov. is described from the Middle–Late Ordovician of Shaanxi, China and interpreted as a calcified cyanobacterial sheath. Xianella filaments formed cable-like strands that constructed thick fenestral layers. The specimens occur in metre-sized limestone blocks, possibly derived from local collapse of a reefal platform margin. In combination with micrite, some of which is intraclastic and peloidal, Xianella created thick and extensive stacks of layered calcified fenestral fabric that appear to be synsedimentarily calcified open-frame mat deposits. The fenestrae range from small, laminose and very irregular, to large equidimensional areas ~2 cm across. Fenestrae with rounded outlines resemble primary gas bubbles observed in present-day microbial mats. These delicate fabrics are comparable in structure and quality of preservation with those of some Proterozoic silicified stromatolitic mats.

Data from: An unusual new species of Bidens (Asteraceae, Coreopsideae) with its phylogenetic position and taxonomic notes

An unusual new species of Bidens (Asteraceae) from Brazil is described and its placement within the genus is elucidated by phylogenetic analysis of ITS sequences. The new species, described as Bidens campanulata , is distinct in the genus based on its broadly campanulate corolla limb with long lobes, an extremely reduced involucre (shorter than the flower length), and the absence of awns on the pappus. This study presents a taxonomic treatment of the species of Bidens with discoid capitula endemic to the Brazilian Cerrado, including a key to the species, typification, and information on conservation status.

opencc-zeroDec 2011View details →

Data from: Occurrence of the isopod Archaeoniscus coreaensis new species from the Lower Cretaceous Jinju Formation, Korea

The fossil isopod crustacean genus Archaeoniscus has been known to occur in England, France and Germany during the Upper Jurassic, and in Mexico and Egypt during the Lower Cretaceous. The morphology of this genus is unique in having dorsoventrally compressed body, the cephalon set deeply into the first pereionite, pleon as wide as pereion, and a broad semicircular pleotelson. These features have resulted in placing the classification of the genus in the monotypic family Archaeoniscidae. However, due to the lack of detailed morphological data, suprafamilial classification of this genus has remained unclear, as well as its ecology and lifestyle. Here we report Archaeoniscus coreaensis n. sp. from the Jinju Formation, Gyeongsang Basin, Korea. The occurrence of Archaeoniscus in the East Asia implies that the genus may have had a worldwide distribution. The Gyeongsang Basin was a Cretaceous backarc basin, which consists of exclusively non-marine sedimentary sequences. The occurrence of this genus, therefore, indicates that Archaeoniscus successfully adapted to a freshwater ecosystem as well. Detailed anatomy including antennulae, antennae, pereiopods, and uropods was observed from well-preserved multiple specimens, which allows better understanding of the morphology of Archaeoniscus. The axial structure in the posterior part of the body, which was previously interpreted as a unique brood pouch characterizing the family, turned out to be a remnant of the hindgut. Females of all isopods and most of the members of the superorder Peracarida have a thoracic ventral brood pouch, modified from the thoracic coxal endites. Based on the morphology of the largely unmodified ambulatory pereiopods of A. coreaensis, the possibility of Archaeoniscus being ectoparasitic is discounted. Instead, the flattened body and the form of limbs of A. coreaensis would have been suitable for a benthic lifestyle.

opencc-zeroDec 2015View details →

Data from: New information on Titanichthys (Placodermi: Arthrodira) from the Cleveland shale (upper devonian) of Ohio, USA

The placoderm (Titanichthys) from the Late Devonian (Famennian) is based on incomplete and fragmentary specimens that have hindered understanding of its overall anatomy and phylogenetic relationships. A new, nearly complete, articulated specimen from the Upper Devonian Cleveland Shale provides new information about the previously undescribed rostral, postmarginal, postsuborbital, submarginal, posterior superognathal plates, and the nasal capsule. A revised diagnosis is provided for the genus. Three new diagnostic characters are identified including a transversely elliptical rostral plate that does not contact adjacent plates, a reduced posterior superognathal, and a median dorsal plate that inserts into the posterior dorsal lateral plate. The first comprehensive phylogenetic analysis of (Titanichthys) indicates that the genus is a basal aspinothoracid arthrodire closely related to the enigmatic taxa (Bungartius) and (Tafilalichthys).

Data from: Population genetic structure and connectivity of deep-sea stony corals (Order Scleractinia) in the New Zealand region: implications for the conservation and management of Vulnerable Marine Ecosystems

Deep-sea stony corals, which can be fragile, long-lived, late to mature and habitat-forming, are defined as vulnerable marine ecosystem indicator taxa. Under United Nations resolutions these corals require protection from human disturbance such as fishing. To better understand the vulnerability of stony corals (Goniocorella dumosa, Madrepora oculata, Solenosmilia variabilis) to disturbance within the New Zealand region, and to guide marine protected area design, genetic structure and connectivity were determined using microsatellite loci and DNA sequencing. Analyses compared population genetic differentiation between two biogeographic provinces, amongst three sub-regions (north-central-south), and amongst geomorphic features. Extensive population genetic differentiation was revealed by microsatellite variation, whilst DNA sequencing revealed very little differentiation. For G. dumosa, genetic differentiation existed amongst regions and geomorphic features, but not between provinces. For M. oculata, only a north-central-south regional structure was observed. For S. variabilis, genetic differentiation was observed between provinces, amongst regions and amongst geomorphic features. Populations on the Kermadec Ridge were genetically different from Chatham Rise populations in all three species. A significant isolation-by-depth pattern was observed for both marker types in G. dumosa, and also in ITS of M. oculata. An isolation-by-distance pattern was revealed for microsatellite variation in S. variabilis. Medium to high levels of self-recruitment were detected in all geomorphic populations, and rates and routes of genetic connectivity were species-specific. These patterns of population genetic structure and connectivity at a range of spatial scales indicate that flexible spatial management approaches are required for the conservation of deep-sea corals around New Zealand.

opencc-zeroDec 2011View details →

Data from: Paternity assignment and demographic closure in the New Zealand southern right whale

The identification and characterisation of reproductively isolated subpopulations or 'stocks' is essential for effective conservation and management decisions. This can be difficult in vagile marine species like marine mammals. We used paternity assignment and 'gametic recapture' to examine the reproductive autonomy of southern right whales (Eubalaena australis) on their New Zealand (NZ) calving grounds. We derived DNA profiles for 34 mother-calf pairs from skin biopsy samples, using sex-specific markers, 13 microsatellite loci and mtDNA haplotypes. We constructed DNA profiles for 314 adult males, representing 30% of the census male abundance of the NZ stock, previously estimated from genotypic mark-recapture modelling to be 1085 (95% CL 855, 1416). Under the hypothesis of demographic closure and the assumption of equal reproductive success among males, we predict: (1) the proportion of paternities assigned will reflect the proportion of the male population sampled and (2) the gametic mark-recapture (GMR) estimate of male abundance will be equivalent to the census male estimate for the NZ stock. Consistent with these predictions, we found that the proportion of assigned paternities equalled the proportion of the census male population size sampled. Using the sample of males as the initial capture, and paternity assignment as the recapture, the GMR estimate of male abundance was 1001 (95% CL 542, 1469), similar to the male census estimate. These findings suggest that right whales returning to the NZ calving ground are reproductively autonomous on a generational timescale, as well as isolated by maternal fidelity on an evolutionary timescale, from others in the Indo-Pacific region.

opencc-zeroDec 2010View details →

Data from: A new pliosaurid (Sauropterygia, Plesiosauria) from the Oxford Clay Formation (Middle Jurassic, Callovian) of England: evidence for a gracile, longirostrine grade of Early–Middle Jurassic pliosaurids

A partial skeleton from the Sigiloceras enodatum ammonite Subzone (early Callovian, Middle Jurassic) of the Oxford Clay Formation of Quest Pit, near Stewartby, Bedfordshire, UK respresents one of the basalmost Middle Jurassic pliosaurids. Marmornectes candrewi gen. et sp. nov. possesses seven autapomorphies and a longirostrine snout. Reassessment of pliosauroid relationships demonstrates that Thalassiodracon hawkinsii, Hauffiosaurus spp. and Attenborosaurus conybeari are successively more derived basal representatives of Pliosauridae. This indicates that a longirostrine snout was acquired among Early Jurassic pliosaurids (such as Hauffiosaurus), but that these early taxa had a small body size, long neck, and gracile skull and limb bones relative to the contemporaneous rhomaleosaurids, which were robust, large-bodied macropredators. The pliosaurid lineage only acquired its 'characteristic' large size, robust skull and short neck in the late Middle Jurassic after the extinction of Rhomaleosauridae.

Data from: A revision of African helmeted terrapins (Testudines: Pelomedusidae: Pelomedusa), with descriptions of six new species

Using nearly range-wide sampling, we analyze up to 1848 bp of mitochondrial DNA of 183 helmeted terrapins and identify a minimum of 12 deeply divergent species-level clades. Uncorrected p distances of these clades equal or clearly exceed those between the currently recognized species of Pelusios, the genus most closely related to Pelomedusa. We correlate genetic discontinuities of Pelomedusa with data on morphology and endoparasites and describe six new Pelomedusa species. Moreover, we restrict the name Pelomedusa subrufa (Bonnaterre, 1789) to one genetic lineage and resurrect three further species from its synonymy, namely P. galeata (Schoepff, 1792), P. gehafie (Rüppell, 1835), and P. olivacea (Schweigger, 1812). In addition to these ten Pelomedusa species, we identify two further clades from Cameroon and Sudan with similar levels of genetic divergence that remain unnamed candidate species. We also note that some problematical terrapins from South Africa and Somalia may represent two additional candidate species. Some of the Pelomedusa species are morphologically distinctive, whilst others can only be identified by molecular markers and are therefore morphologically cryptic taxa.

Data from: Systematic and historical biogeography of the Bryconidae (Ostariophysi: Characiformes) suggesting a new rearrangement of its genera and an old origin of Mesoamerican ichthyofauna

Recent molecular hypotheses suggest that some traditional suprageneric taxa of Characiformes require revision, as they may not constitute monophyletic groups. This is the case for the Bryconidae. Various studies have proposed that this family (considered a subfamily by some authors) may be composed of different genera. However, until now, no phylogenetic study of all putative genera has been conducted. In the present study, we analyzed 27 species (46 specimens) of all currently recognized genera of the Bryconidae (ingroup) and 208 species representing all other families and most genera of the Characiformes (outgroup). Five genes were sequenced: 16SrRNA, Cytochrome b, recombination activating gene 1 and 2 and myosin heavy chain 6 cardiac muscle. The final matrix contained 4699 bp and was analyzed by maximum likelihood, maximum parsimony and Bayesian analyses. The results show that the Bryconidae, composed of Brycon, Chilobrycon, Henochilus and Salminus, is monophyletic and is the sister group of Gasteropelecidae + Triportheidae. However, the genus Brycon is polyphyletic. Fossil studies suggest that the family originated approximately 33 million years ago (Ma) and that one of the two main lineages persisted only in trans-Andean rivers, including Central American rivers, suggesting a much older origin of Mesoamerican ichthyofauna than previously accepted. Bryconidae is composed by five main clades, including the genera Brycon, Chilobrycon, Henochilus and Salminus, but a taxonomic review of these groups is needed. Our results points to a possible ancient invasion of Central America, dating about 17.4+/-8 Ma (late Oligocene/late Miocene), to explain the occurrence of Brycon in Central America.

opencc-zeroDec 2010View details →

Data from: A passerine bird's evolution corroborates the geologic history of the island of New Guinea

New Guinea is a biologically diverse island, with a unique geologic history and topography that has likely played a role in the evolution of species. Few island-wide studies, however, have examined the phylogeographic history of lowland species. The objective of this study was to examine patterns of phylogeographic variation of a common and widespread New Guinean bird species (Colluricincla megarhyncha). Specifically, we test the mechanisms hypothesized to cause geographic and genetic variation (e.g., vicariance, isolation by distance and founder-effect with dispersal). To accomplish this, we surveyed three regions of the mitochondrial genome and a nuclear intron and assessed differences among 23 of the 30 described subspecies from throughout their range. We found support for eight highly divergent lineages within C. megarhyncha. Genetic lineages were found within continuous lowland habitat or on smaller islands, but all individuals within clades were not necessarily structured by predicted biogeographic barriers. There was some evidence of isolation by distance and potential founder-effects. Mitochondrial DNA sequence divergence among lineages was at a level often observed among different species or even genera of birds (5-11%), suggesting lineages within regions have been isolated for long periods of time. When topographical barriers were associated with divergence patterns, the estimated divergence date for the clade coincided with the estimated time of barrier formation. We also found that dispersal distance and range size are positively correlated across lineages. Evidence from this research suggests that different phylogeographic mechanisms concurrently structure lineages of C. megarhyncha and are not mutually exclusive. These lineages are a result of evolutionary forces acting at different temporal and spatial scales concordant with New Guinea's geological history.

Data from: Anchored hybrid enrichment provides new insights into the phylogeny and evolution of longhorned beetles (Cerambycidae)

Cerambycidae is a species-rich family of mostly wood-feeding (xylophagous) beetles containing nearly 35 000 known species. The higher-level phylogeny of Cerambycidae has never been robustly reconstructed using molecular phylogenetic data or a comprehensive sample of higher taxa, and its internal relationships and evolutionary history remain the subjects of ongoing debate. We reconstructed the higher-level phylogeny of Cerambycidae using phylogenomic data from 522 single copy nuclear genes, generated via anchored hybrid enrichment. Our taxon sample (31 Chrysomeloidea, four outgroup taxa: two Curculionoidea and two Cucujoidea) included exemplars of all families and 23 of 30 subfamilies of Chrysomeloidea (18 of 19 non-chrysomelid Chrysomeloidea), with a focus on the large family Cerambycidae. Our results reveal a monophyletic Cerambycidae s.s. in all but one analysis, and a polyphyletic Cerambycidae s.l. When monophyletic, Cerambycidae s.s. was sister to the family Disteniidae. Relationships among the subfamilies of Cerambycidae s.s. were also recovered with strong statistical support except for Cerambycinae being made paraphyletic by Dorcasomus Audinet-Serville (Dorcasominae) in the nucleotide (but not amino acid) trees. Most other chrysomeloid families represented by more than one terminal taxon – Chrysomelidae, Disteniidae, Vesperidae and Orsodacnidae – were monophyletic, but Megalopodidae was rendered paraphyletic by Cheloderus Gray (Oxypeltidae). Our study corroborates some relationships within Chrysomeloidea that were previously inferred from morphological data, while also reporting several novel relationships. The present work thus provides a robust framework for future, more deeply taxon-sampled, phylogenetic and evolutionary studies of the families and subfamilies of Cerambycidae s.l. and other Chrysomeloidea.

opencc-zeroDec 2017View details →

Data from: Testing the role of climate in speciation: new methods and applications to squamate reptiles (lizards and snakes)

Climate may play important roles in speciation, such as causing the range fragmentation that underlies allopatric speciation (through niche conservatism) or driving divergence of parapatric populations along climatic gradients (through niche divergence). Here, we developed new methods to test the frequency of climate niche conservatism and divergence in speciation, and applied it to species pairs of squamate reptiles (lizards and snakes). We used a large-scale phylogeny to identify 242 sister-species pairs for analysis. From these, we selected all terrestrial allopatric pairs with sufficient occurrence records (n=49 pairs) and inferred whether each originated via climatic niche conservatism or climatic niche divergence. Among the 242 pairs, allopatric pairs were most common (41.3%), rather than parapatric (19.4%), partially sympatric (17.7%), or fully sympatric species pairs (21.5%). Among the 49 selected allopatric pairs, most appeared to have originated via climatic niche divergence (61–76%, depending on the details of the methods). Surprisingly, we found greater climatic niche divergence between allopatric sister species than between parapatric pairs, even after correcting for geographic distance. We also found that niche divergence did not increase with time, further implicating niche divergence in driving lineage splitting. Overall, our results suggest that climatic niche divergence may often play an important role in allopatric speciation, and the methodology developed here can be used to address the generality of these findings in other organisms.

opencc-zeroDec 2018View details →

Data from: Determinants of elephant foraging behavior in a coupled human-natural system: is brown the new green?

1. Crop raiding by wildlife poses major threats to both wildlife conservation and human wellbeing in agro-ecosystems worldwide. These threats are particularly acute in many parts of Africa, where crop raiders include globally threatened megafauna such as elephants, and where smallholder agriculture is a primary source of human livelihood. One framework for understanding herbivore feeding behavior, the forage-maturation hypothesis, predicts that herbivores should align their movements with intermediate forage biomass (i.e., peak green-up); this phenomenon is known as "surfing the green wave." Crop-raiding elephants, however, often consume not just foliage, but also fruits and tubers (e.g., maize, potatoes), which generally mature after seasonal peaks in photosynthetic activity. Thus, although elephants have been reported to surf the green wave in natural habitats, they may utilize a different strategy in cultivated landscapes by selecting crops that are "browning down." 2. We sought to understand the factors that underpin movement of elephants into agricultural landscapes. 3. In Mozambique's Gorongosa National Park, we used movement data from GPS-collared elephants, together with precipitation records, remotely sensed estimates of landscape greenness (NDVI), DNA-based diet analysis, measurements of plant nutritional quality, and survey-based metrics of crop availability to understand spatiotemporal variation in elephant crop-raiding behavior. 4. Elephants tracked peak NDVI while foraging inside the Park. During the dry season, however, when NDVI within the Park declined and availability of mature crops was high, crop-raiding increased dramatically, and elephants consistently selected crop plants that were browning down while foraging in cultivated landscapes. Crops contained significantly higher digestible energy than wild food plants, but comparable (and sometimes lower) levels of digestible protein, suggesting that this foraging strategy maximized energy rather than protein intake. 5. Our study is the first to combine GPS tracking data with high-resolution diet analysis and community-based reporting of crop availability to reveal fine-scale plasticity in foraging behavior of elephants at the human-wildlife interface. Our results extend the forage-maturation hypothesis by showing that elephants surf waves of plant brown-down in cultivated landscapes. These findings can aid efforts to reduce human-elephant conflict by enabling wildlife managers to prioritize mitigation actions in time and space with limited resources.

Data from: Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys

Background: The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced.Results: Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age. Conclusions: This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys.

Data from: Pleurostylia serrulata and two allied new species from Africa are actually members of the new world Crossopetalum (Celastraceae)

Based on phylogenetic analyses using rDNA and plastid sequence data, and the examination of morphological characters, we infer that Pleurostylia, as currently delimited, is a polyphyletic group. Pleurostylia serrulata and two newly described species from Africa are part of the New World Crossopetalum lineage. By contrast, Pleurostylia s. s. consists of all remaining species, which form a clade nested within a primarily Malagasy lineage. We present preliminary evidence that Pleurostylia opposita, the most geographically widespread species in the entire Celastraceae family, may include cryptic species. Although molecular evidence supports the monophyly of Crossopetalum, this genus does not appear to be well defined by a single morphological synapomorphy, rather the following combination of character states is diagnostic: 4-merous flowers; stamens inserted in the sinuses of a ± 4-lobed intrastaminal floral disk; pistil (2- or) 4-locular with one atropous ovule per locule; stigma conspicuously (2-) 4-branched; drupe usually single seeded and asymmetric with an excentric style remnant; and seeds exarillate with ramified postchalazal bundles visible on the surface and with endosperm present. A taxonomic treatment of Crossopetalum in Africa is presented, in which the new combination Crossopetalum serrulatum is proposed and two new species, C. bokdamii and C. mossambicense , are described and their conservation status assessed.