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Displaying 19 of 19 results for "DGCR2"
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Title Date Issued Date Released Description
Data from: Altered breeding biology of the European blackbird under artificial light at night
04-05-2017 04-21-2017
Artificial light at night (LAN) has become a stressor of global extent. Previous work has highlighted the high potential of LAN to interfere with annual and diel rhythms of seasonal organisms as well as to affect interactions at the community level. However, our understanding how LAN induced alterations of activity and breeding cycles affect the reproductive outcome and fitness of the birds is still limited. Here, we focus on the effects of night time illumination on the breeding biology of urban European blackbirds (Turdus merula). Our results indicate that blackbirds prefer illuminated nest sites and advance their date of clutch initiation by 6 days per 1 lux of night time illumination. Furthermore, daily nest survival rates increased with increasing LAN although this effect was most pronounced for the transition from dark to slightly illuminated sites. We suggest that blackbirds breeding under low artificial night light conditions benefit from the LAN-avoidance of their major predators (nocturnal) whereas predominant predators of blackbirds nesting in the city centre are diurnal and are, thus, not affected by LAN. Hence, it seems likely that both direct effects of LAN on the timing of reproduction as well as indirect effects on interspecific interactions might contribute to the observed changes in the breeding biology of European blackbirds.This study emphasizes the diverse ecological effects of the night time illumination which are – in its complexity – still poorly understood.
Onset of activity
10-30-2013 11-01-2013
Dataframe for the analyses of the onset of activity data
Offset of activity
10-30-2013 11-01-2013
Dataframe for the analyses of the offset of activity
raw activity
10-30-2013 11-01-2013
n/a
Supplementary Table 1
06-10-2016 08-30-2016
Completeness scores of main skeletal sections. Abbreviations: Bol: Bolosauria; Lan: Lanthanosuchoidea; Mes: Mesosauridae; Mil: Millerosauria; Nyc: Nycteroleteroidea; Par: Pareiasauria; Pro: Procolophonoidea. SCM and CCMa columns are the main values (same as in table 4).
Statistical models
10-30-2013 11-01-2013
R script used to run all statistical models included in the manuscript
Authors' Note for Agić et al. JoP
02-13-2015 03-12-2015
Note on the new age constraints on the Ruyang Formation, published in Lan et al. 2014 (Precambrian Research) after the submission and acceptance of this manuscript.
Apoptosis
12-02-2015 02-17-2016
MB= mushroom bodies, AL= antennal lobes, OL = optic lobes, CC= central complex, SEZ= subesophageal zone RCB= remainder of the central brain. Brain region cells reflects the number of cells per brain region based on a subset of sampled brains (see methods for details). Proportion X (followed by brain region) reflects the amount of that brain region available for counting. Brain region prop indicates the proportion of apoptotic cells of each region scaled by the number of cells per region and the proportion of that region sampled. Brain region prop + 0.001 adds a constant for non-zero values. Log brain region prop are the log transformed values of brain region prop +0.001.
Spruce distribution and climate data
01-28-2016 01-28-2016
Spruce distribution and climate data (LAN, latitude; LON, longitude; AL, altitude) and climatic variables for the 10 spruce taxa. MAT, mean annual air temperature; TCM, mean temperature of the coldest month; TWM, mean temperature of the warmest month; GDD5, growing degree days on a 5˚ C basis; GDD0, growing degree days on a 0˚ C basis; MAP, mean annual precipitation; AET, actual evapotranspiration; PET, potential evapotranspiration; α (AET/PET), aridity index.
Data from: Testing the scaling effects and mechanisms of N-induced biodiversity loss: evidence from a decade-long grassland experiment
03-10-2015 03-10-2016
Although extensive studies demonstrate that nitrogen (N) enrichment frequently reduces plant diversity within small quadrats (0.5 –4 m2), only a few studies have evaluated N effects on biodiversity across different spatial scales. We conducted the first experimental test of the scale dependence of N effects on species richness from a 10-year N treatment (1.75- 28 g N m−2 yr−1) in a typical steppe. We used species area relationship (SAR) to analyze the scale dependence of species loss with power model S = cAz (S is species number, A is area, c is intercept, and z is slope). Absolute species loss decreased at sampling area > 8 m2. Proportional species loss (compared to control) decreased and critical threshold (Ncrit) for biodiversity losses increased with sampling areas. These scale dependences were quantified as increasing slope (z-value) of SAR with N addition. Through SAR decomposition, we found that this overall positive effect was in response to positive effects of changes to the species abundance distribution over negative effects of overall species richness losses. Synthesis. As nitrogen (N) enrichment typically occurs at scales much larger than individual plots, understanding how N enrichment affects the scaling patterns of biodiversity is necessary for biodiversity conservation and ecosystem management in response to anthropogenic N deposition.
Data from: Ontogeny of the articulated yiliangellinine trilobite Zhangshania typica from the lower Cambrian (Series 2, Stage 3) of southern China
11-28-2016 01-06-2017
New discoveries of the early Cambrian yiliangellinine trilobite Zhangshania typica Li and Zhang in Kunming preserve almost all instars from early postembryonic (protaspid) to mature (holaspid) phases in articulated state, in addition to mature specimens with antennae bearing paired spines on the basal articles. The ontogenetic series shows protarthrous development with some, but likely not all, early holaspid instars expressing additional pygidial segments, gradual rearward migration of the location of the longest pleural spines on the trunk segments, and striking positive allometry of the genal spines. It also reveals Parazhangshania sichuanensis Li and Zhang, 1990 to be the holaspid stage 3 of Z. typica, and therefore its junior synonym. This new find in the Hongjingshao Formation provides species-based regional correlation across the South China block and Z. typica may provide an important biostratigraphic marker for the base of the traditional Tsanglangpuan Stage.
Data from: Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes
04-03-2017 04-06-2017
Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialised macrobenthos such as mussels. But lack of genome information hinders understanding of the adaptation of these animals to such inhospitable environment. Here we report the genomes of a deep-sea vent/seep mussel Bathymodiolus platifrons and a shallow-water mussel Modiolus philippinarum. Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilising protein structures and removing toxic substances from the cells, are greatly expanded in B. platifrons, indicating adaptation to extreme environmental conditions. The B. platifrons innate immune system is considerably more complex than that of other lophotrochozoan species including M. philippinarum, with significant expansion and high expression of gene families related to immune recognition, endocytosis and caspase-mediated apoptosis in the gill, revealing presumed genetic adaptation of the deep-sea mussel to the presence of its chemoautotrophic endosymbionts. A follow-up metaproteomic analysis of the gill of B. platifrons found methanotrophy, assimilatory sulfate reduction, and ammonia metabolic pathways in the symbionts, providing energy and nutrients to allow the host to thrive. Our study of the genomic composition allowing symbiosis in extremophile molluscs gives wider insights into the mechanisms of symbiosis in other organisms such as deep-sea tubeworms and giant clams.
Data from: Two novel genera and one new species of treefrog (Anura: Rhacophoridae) highlight cryptic diversity in the Western Ghats of India
04-17-2013 04-17-2013
Amphibian diversity in the Western Ghats-Sri Lanka biodiversity hotspot is extremely high, especially for such a geo-graphically restricted area. Frogs in particular dominate these assemblages, and the family Rhacophoridae is chief among these, with hundreds of endemic species. These taxa continue to be described at a rapid pace, and several groups have recently been found to represent unique evolutionary clades at the genus level. Here, we report DNA sequences, larval and breeding data for two species of rhacophorid treefrog (Polypedates bijui and a new, hitherto undescribed species). Re-markably, they represent unique, independent clades which form successive sister groups to the Pseudophilautus (Sri Lan-ka) + Raorchestes (India, China & Indochina) clades. We place these species into two new genera (Beddomixalus gen. nov. and Mercurana gen. nov.). Both of these genera exhibit a distinct reproductive mode among Rhacophoridae of pen-insular India and Sri Lanka, with explosive breeding and semiterrestrial, unprotected, non-pigmented eggs oviposited in seasonal swamp pools, which hatch into exotrophic, free-living aquatic tadpoles. Relationships and representation of re-productive modes in sister taxa within the larger clade into which these novel genera are placed, is also discussed. These results suggest that more undescribed taxa may remain to be discovered in South Asia, and the crucial importance of con-serving remaining viable habitats.
Data from: Genotypic distribution and hepatic fibrosis among HIV/HCV co-infected individuals in Southern China: a retrospective cross-sectional study
09-30-2015 10-08-2015
Background: End-stage liver disease and hepatocellular carcinoma due to hepatitis C virus (HCV) co-infection are increasingly common causes of death among HIV-infected individuals. However, there are few clinical investigations of HIV/HCV co-infected individuals from low and middle-income nations. Here, we compare the epidemiology of HCV-infected and HIV/HCV co-infected individuals in Southern China and examine hepatic fibrosis scores in co-infected individuals. Methods: We conducted a retrospective cross-sectional study of treatment-naïve HIV/HCV co-infected and HCV mono-infected subjects. Bivariate and multivariate models were used to examine the association between demographics and HCV genotype. Among co-infected individuals, we also studied the relationship between fibrosis scores derived from non-invasive studies and HCV genotype. Results: Data were collected from 175 HCV-infected individuals, including 89 (51 %) HIV/HCV co-infected individuals. HIV/HCV co-infection was correlated with intravenous drug use (AOR 46.25, p < 0.001) and not completing high school (AOR 17.39, p < 0.001) in a multivariate model. HIV/HCV co-infected individuals were more likely to be infected with HCV genotype 6a (p < 0.0001) or 3a (p < 0.023), whereas increased fibrosis (FIB-4 score) was associated with HCV genotype 3a infection (β 2.18, p < 0.001). Discussion: Our results suggest that intravenous drug use is driving HIV/HCV co-infection in Southern China. While additional studies are needed, HCV genotype 6a is more common and genotype 3a appears to be associated with more severe hepatic fibrosis in co-infected individuals. Conclusions: Future HIV/HCV co-infection research in China should focus on at risk populations, HCV testing uptake, and genotype-specific treatment.
Data from: Soil acidification exerts a greater control on soil respiration than soil nitrogen availability in grasslands subjected to long-term nitrogen enrichment
07-23-2015 10-05-2015
Terrestrial ecosystems worldwide are receiving increasing amounts of biologically reactive nitrogen (N) as a consequence of anthropogenic activities. This intended or unintended fertilization can have a wide-range of impacts on biotic communities and hence on soil respiration. Reduction in below-ground carbon (C) allocation induced by high N availability has been assumed to be a major mechanism determining the effects of N enrichment on soil respiration. In addition to increasing available N, however, N enrichment causes soil acidification, which may also affect root and microbial activities. The relative importance of increased N availability vs. soil acidification on soil respiration in natural ecosystems experiencing N enrichment is unclear. We conducted a 12-yr N enrichment experiment and a 4-yr complementary acid addition experiment in a semi-arid Inner Mongolian grassland. We found that N enrichment had contrasting effects on root and microbial respiration. N enrichment significantly increased root biomass, root N content and specific root respiration, thereby promoting root respiration. In contrast, N enrichment significantly suppressed microbial respiration likely by reducing total microbial biomass and changing the microbial community composition. The effect on root activities was due to both soil acidity and increased available N, while the effect on microbes primarily stemmed from soil acidity, which was further confirmed by results from the acid addition experiment. Our results indicate that soil acidification exerts a greater control than soil N availability on soil respiration in grasslands experiencing long-term N enrichment. These findings suggest that N-induced soil acidification should be included in predicting terrestrial ecosystem C balance under future N deposition scenarios.
Data from: Soil acidification exerts a greater control on soil respiration than soil nitrogen availability in grasslands subjected to long-term nitrogen enrichment
07-23-2015 05-16-2017
Terrestrial ecosystems worldwide are receiving increasing amounts of biologically reactive nitrogen (N) as a consequence of anthropogenic activities. This intended or unintended fertilization can have a wide-range of impacts on biotic communities and hence on soil respiration. Reduction in below-ground carbon (C) allocation induced by high N availability has been assumed to be a major mechanism determining the effects of N enrichment on soil respiration. In addition to increasing available N, however, N enrichment causes soil acidification, which may also affect root and microbial activities. The relative importance of increased N availability vs. soil acidification on soil respiration in natural ecosystems experiencing N enrichment is unclear. We conducted a 12-year N enrichment experiment and a 4-year complementary acid addition experiment in a semi-arid Inner Mongolian grassland. We found that N enrichment had contrasting effects on root and microbial respiration. N enrichment significantly increased root biomass, root N content and specific root respiration, thereby promoting root respiration. In contrast, N enrichment significantly suppressed microbial respiration likely by reducing total microbial biomass and changing the microbial community composition. The effect on root activities was due to both soil acidity and increased available N, while the effect on microbes primarily stemmed from soil acidity, which was further confirmed by results from the acid addition experiment. Our results indicate that soil acidification exerts a greater control than soil N availability on soil respiration in grasslands experiencing long-term N enrichment. These findings suggest that N-induced soil acidification should be included in predicting terrestrial ecosystem C balance under future N deposition scenarios.
Species name and abundance in 15 forest dynamic plots
02-09-2012 06-09-2012
1.The data were used in paper "Xiangcheng Mi, Nathan G. Swenson, Renato Valencia, John Kress, David L. Erickson, álvaro J. Pérez, Haibao Ren, Sheng-Hsin Su, Nimal Gunatilleke, Savi Gunatilleke, Zhanqing Hao, Wanhui Ye, Min Cao, H S Suresh, H S Dattaraja, S Sukumar, Keping Ma. 2012. The contribution of rare species to community phylogenetic diversity across a global network of forest plots. American Naturalist (accepted for publication)." | 2. Data in each of 15 plots were provided with a "csv" file with plot name, and species name, genus,family and abundance and a species code were provided in each "csv" file. | 3. data sources: (1) data of Luquillo, Barro Colorado Island,La Planada, Yasuní,Huai Kha Khaeng, Mudumalai,Pasoh plots, are from "Smithsonian Institute Global Earth Observatories. URL http://www.sigeo.si.edu/." (2) data of Changbaishan plot from "Hao Z.Q., Li B.H., Zhang J., Wang X. G., Ye J., and Yao X. L., 2008. Broad-leaved Korean pine (Pinus koraiensis) mixed forest plot in Changbaishan (CBS) of China: community composition and structure. Chinese Journal of Plant Ecology, 32:238-250 (in Chinese with English abstract)"; (3) data of Gutianshan plot from "Legendre, P., X. Mi, H. Ren, K. Ma, M. Yu, I.-F. Sun, and F. He. 2009. Partitioning beta diversity in a subtropical broad-leaved forest of China. Ecology 90:663-674. Appendix A." (4) data of Dinghushan plot from "Wang, Z. G. 2007. Species diversity and mechanisms for maintenance of monsoon evergreen broadleaved forest in Dinghushan. Ph. D. Dissertation, South China Botanical Garden, Chinese Academy of Sciences. (In Chinese with English abstract)" (5) data of Xishuangbanna plot from "Cao, M., H. Zhu, H. Wang, G. Lan, Y. Hu, S. Zhou, X. Deng et al. 2008, Xishuangbanna tropical seasonal rainforest dynamics plot: Tree distribution maps, diameter tables and species documentation. Kunming, China, Yunnan Science and Technology Press." (6) data of Fushan plot from "Su, S.-H., C.-H. Chang-Yang, C.-L. Lu, C.-C. Tsui, T.-T. Lin, C.-L. Lin, W.-L. Chiou et al. 2007, Fushan subtropical forest dynamics plot: tree species characteristics and distribution patterns. Taipei, Taiwan Forestry Research Institute." (7) data of Palanan plot from "Co, L. L., V. L. James, D. A. Lagunzad, K. A. C. Pasion, H. T. Consunji, N. A. Bartolome, S. L. Yap et al. 2006, Forest trees of Palanan, Philippines: A study in population ecology. Quezon, Philipines, University of the Philippines-Diliman. " (8) data of Sinharaja plot from "Gunatilleke, C. V. S., I. A. U. N. G. A. U. K. Ethugala, and S. Esufali. 2004, Ecology of Sinharaja rain forest and the forest dynamics plot in Sri Lanka's Natural World Heritage site. Sri Landka, WHT Publications." (9) data of Lambir plot from "Lee, H. S., P. S. Ashton, T. YamaKura, S. Tan, S. J. Davies, A. Itoh, E. O. K. Chai et al. 2002, The 52-hectrare forest research plot at Lambir Hills, Sarawak, Malaysia: Tree distribution maps, diameter table and species documentation. Sarawak, Malaysia, Forest Department Sarawak & The Arnold Arboretum-CTFS Asia Program." | 4. Notice: the data of Yasuní plot used in paper were more precisely identified than different those in website of Smithsonian Institute Global Earth Observatories, but their results were very similar.
Data from: Individual-based measurements of light intensity provide new insights into the effects of artificial light at night on daily rhythms of urban-dwelling songbirds
10-30-2013 04-17-2014
1. The growing interest in the effects of light pollution on daily and seasonal cycles of animals has led to a boost of research in recent years. In birds, it has been hypothesized that artificial light at night can affect daily aspects of behaviour, but one caveat is the lack of knowledge about the light intensity that wild animals, such as birds, are exposed to during the night. 2. Organisms have naturally evolved daily rhythms to adapt to the 24-h cycle of day and night, thus, it is important to investigate the potential shifts in daily cycles due to global anthropogenic processes such as urbanization. 3. We captured adult male European blackbirds (Turdus merula) in one rural forest and two urban sites differing in the degree of anthropogenic disturbance. We tagged these birds with light loggers and simultaneously recorded changes in activity status (active/non-active) through an automated telemetry system. We first analysed the relationship between light at night, weather conditions and date with daily activity onset and end. We then compared activity, light at night exposure and noise levels between weekdays and weekends. 4. Onset of daily activity was significantly advanced in both urban sites compared to the rural population, while end of daily activity did not vary either among sites. Birds exposed to higher amounts of light in the late night showed earlier onset of activity in the morning, but light at night did not influence end of daily activity. Light exposure at night and onset/end of daily activity timing was not different between weekdays and weekends, but all noise variables were. A strong seasonal effect was detected in both urban and rural populations, such as birds tended to be active earlier in the morning and later in the evening (relative to civil twilight) in the early breeding season than at later stages. 5. Our results point at artificial light at night as a major driver of change in timing of daily activity. Future research should focus on the costs and benefits of altered daily rhythmicity in birds thriving in urban areas.
Data from: Early postembryonic to mature ontogeny of the oryctocephalid trilobite Duodingia duodingensis from the lower Cambrian (Series 2) of southern China
07-28-2015 12-10-2015
Many well-preserved, articulated exoskeletons recovered from the early Cambrian (Stage 3) Mingxinsi Formation in Weng'an, Guizhou Province, southern China, permit reconstruction of the early postembryonic to mature (i.e. protaspid to holaspid) ontogeny of the small oryctocephalid trilobite Duodingia duodingensis Chow. It is likely that the type material is a latest stage meraspis, and the species had nine thoracic segments in the holaspid phase rather than the eight suggested previously. The earliest holaspis is relatively small in size (about 3.00 mm in total length), and the succeeding instars show little size-related shape change. Striking changes take place in the morphology of the glabella during early ontogeny including forward extension of the axial furrows until they reach the anterior cephalic margin in meraspid degree 0iii, and narrowing of the glabellar mid-region. This is the first noneodiscid trilobite to show three developmental stages within meraspid degree 0. Documentation of ontogenetic changes demonstrates that both Duodingia hubeiensis and D. taihuensis are junior synonyms of D. duodingensis because they bear characters of particular ontogenetic stages of their senior synonym. The per-moult growth increment in D. duodingensis was apparently small in this small trilobite. The development of trunk segmentation during the meraspid phase is apparently more complex than in many other trilobites and could include multiple moults within individual meraspid degrees, intraspecific polymorphism in the pattern of segment release, or phenotypic variation among the population in the degree of segment expression. Fluctuations between accumulative moults, in which segments are added to the meraspid pygidium, and depletive moults, in which segments are released into the thorax, if confirmed, would suggest tight coordination between these different aspects of trunk segment development.