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I hope I didn't forget anything! Thank you! If anyone can find better pictures where we can see the Earth and the line that separates night from day, that would be great. Mateussf talk , 3 December UTC. I want a video or perhaps a photo of fluorine gas reacting with something. There is nothing PD or even that I can think of as an easy donation. Looking for something like in the videos below. Will go into a Wiki Featured Article Candidate. Either someone to make it for us or who has it.

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See also w:Category:Wikipedia requested photographs of biology. More pictures of cinnamon and fawn cats Some good blue tabby cats who are not ticked tabby Abyssinians Pedigreed cats in the colors caramel, lilac based caramel, fawn based caramel and apricot I found no pictures at all Some more rare color combinations like chocolate silver tabby.

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We sampled specimens from species of the moth family Noctuidae from seven locations in Tibet Fig. Samplings were performed with traditional light trap methods collecting moths overnight, typically, in a relatively short time period of some two weeks Aug. These specimens represented 68 species and 45 genera Appendix S6 ; no specific permits were required for the described field studies, the locations are not privately-owned or protected in any way, and the field studies did not involve endangered or protected species. Three species eight specimens from the family Pyralididae [91] were included as outgroup taxa when inferring phylogenetic trees.

Specimens were identified by one of us, an expert lepidopterist in East Asia H. Decisions on species status were based exclusively on morphological evidence, with male genital characters further examined when necessary Appendix S7. DNA samples were prepared from individual insects by extraction of total DNA from animals either frozen or preserved in ethanol. The amplification reaction was performed in a total volume of , including buffer, 2. Sequencing was performed with an ABI sequencer. Samples were collected from seven locations from West to East in Tibet, representing different ecological conditions.

The resulting alignment of bp contained no gaps and all sequences could be correctly translated into amino acids. To infer phylogenetic relationships among these species, we performed a neighbor-joining analysis [37] using MEGA 4. A search using nearest-neighbor interchange was conducted to gain a preliminary estimate of the phylogeny.

We then conducted a search using subtree pruning and regrafting to estimate the maximum-likelihood tree. The K2P substitution model was used [16] , [17]. Branch support values were estimated using bootstrap replicates. All other parameters were set to their default values.

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The distance between intraspecific and interspecific variation the DNA barcode gap is an important quantity in DNA barcoding practice. A large DNA barcode gap makes it easy to distinguish among species, whereas small or negative barcoding gaps tend to blur species boundaries and hamper species assignation.

To explore intraspecific and interspecific variation in noctuid moths, we performed an analysis of DNA barcode gaps using a custom Perl script [41]. Given the large number of indices, it is often difficult to decide which is the best method of measuring diversity [1] , [3] — [8] , [67]. In this study, we use the following criteria to choose diversity measures: discriminant ability, sensitivity to sample size, what component of diversity is being measured, and whether or not the index is widely used.

Six diversity indices were selected: the Shannon index, the exponential of Shannon index, the Simpson index, the transformed Simpson index, the Brillouin index, and the log series, index [1] , [3] — [8] , [67]. The most widely used measures of diversity are the information theory indices, which treat the diversity in a natural system in a similar way to the information contained in a message. It is calculated using the equation:. The quantity is the proportion of individuals found in the th species. The probability that any two individuals, randomly drawn from an infinitely large community, belong to different species is Simpson :.

As increases, diversity decreases and so the Simpson index is usually expressed as:. The Shannon index and the Simpson index, which have moderate discriminant ability and moderate sensitivity to sample size, are commonly used in ecological studies [] — []. The exponential of the Shannon index is given by. We also used the log series index, , owing to its good discriminant ability and because it is not unduly influenced by sample size [1] , [8] , [67].

The log series takes the form:. The index can be obtained from the equation:. For a community with a very large number of hyperdiverse taxa, such as arthropods, investigations of species diversity are usually hindered by the difficulty of identifying species by traditional morphological means alone. DNA-based species identification [16] , [17] provides an alternative method for assessment of species diversity. The commonly used barcoding gene, COI , was sequenced for all samples.

Their species identities were assessed by matching their COI barcodes against a reference barcode library. Generally, species in a community are not necessarily closely phylogenetically related, but they are ecologically related, due to the broad taxon coverage and filtering of environmental factors for a community. Therefore, instead of using phylogeny-based DNA barcoding methods, a non-tree-based Bayesian approach, which takes advantages of both Bayesian theory and bioinformatics, was used to infer species identity via COI barcoding Fig.

The dual-vector curve DV-Curve was proposed by Zhang [] as a two-dimensional graphical representation for visualizing and analysing DNA sequences Fig. It is able to represent DNA sequences without degeneracy and loss of information. Let us consider a DNA sequence consisting of n nucleotide sites. Let be the point of the DV-Curve, where is the start point.

The DV-Curve is uniquely determined by the following formula [] :. The value [] is calculated as follows:. To get equation 14 , we need to assign , , , and to basic Dual-Vectors in 4! The vector is further used as the input for the Bayes prior attributes.


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Where is the th species in the community, is an unknown sample with a DNA sequence, is the probability of a sample belonging to. To explore the effect of reference library size on the assessment of species diversity, we randomly selected as the reference library different scales of the reference database, including , , , , , , and of the whole dataset. These are subsequently referred to as 01 ref, 03 ref, and so on. The full reference library comprises the barcoded and morphologically identified specimens. Once species identities were inferred with barcoding-based methods, species diversity indices were calculated following equations 1 — 6 and 9.

We computed species diversity for each of seven communities in Tibet, and for the whole Tibetan community. All of these calculations were performed with 30 random replications. The differences in species diversity among different communities were statistically examined via a permutation test with replications. Likewise, the permutation test was also applied to assess the differences in species diversities between morphology-based and barcoding-based methods.

To investigate further the relationship between TM- and DB-based species diversities, we additionally performed a correlation analysis between these two types of measurement for all six diversity indices. In this species are plotted in sequence from most to least abundant along the horizontal axis, with abundances displayed on the y axis [67].

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One of the advantages of a rank-abundance curve is the clearly display of contrasting patterns of species richness and their relative abundances, compared with the inefficient presentation of a histogram [67] , []. By plotting the relative abundance of species against their rank in abundance, we can readily gain information about the diversity of species within a community. We investigated whether DB-based rank-abundance curves could serve as an effective surrogate for TM-based rank-abundance ones.

Therefore, we computed both TM- and DB-based rank-abundance plots, and further examined them with the Kolmogorov-Smirnov two-sample test []. To explore the relationship between species diversity and environmental factors, we examined 22 variables, including annual mean temperatures, mean diurnal range, and precipitation of the driest quarter Appendix S8. Climate data are from the WorldClim dataset []. Both TM- and DNA-based indices of species diversity were calculated for the six species-diversity indices. Correlation analyses were performed between each species diversity index and each environmental factor.

Diversities of moth species between these two regions Shigatse, Gyantse, Lhasa, and Shannan in the west, and the remaining three communities in the east were further compared for the six diversity indices using a t-test. We also constructed rank-abundance plots and evaluated them with the Kolmogorov-Smirnov two-sample test for the two regions []. In our study of biodiversity assessment via DNA barcoding for a Tibetan moth community, we found that diversity measurements based on DNA barcoding are able to serve as good surrogates for morphology-based measures.

Compared with traditional morphology-based methods, a DNA barcode approach, along with appropriate analytical procedures as outlined here, is fast and convenient and can greatly reduce the time needed for specimen identification.

However, we note that our current method is subject to some limitations, for example, requiring a pre-defined reference library. We have not applied a method based solely on molecular operational taxonomic units, although such approaches have been successfully implemented elsewhere. In fact, barcoding has proven to be an excellent tool for biodiversity surveys where the studied taxa do not have a solid taxonomic foundation [].

However, an arbitrary threshold may be largely taxon-dependent [24] , [28] , [] , and was not applied in current study. Besides the threshold method, the generalized mixed Yule-coalescent GMYC model could be an alternaltive approach for species delimitation based on DNA sequences [21]. The GMYC method models branching events between species with a Yule model [] and branch events within species using a neutral coalescent model [].

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The method has potential for biodiversity assessments although empirical studies are desirable to examine its consistency with traditional morphspecies since splitting or lumping was often observed compared to traditional taxonomy. An artificial intelligence-based approach, such as BP-based species identification [26] , could be another choice for species identification, but was not applied to the current study due to its relatively slow training process during the construction of neural networks, making it impractical for the simulation study.

The development of fast algorithms of this method for large datasets is highly desirable. In addition, it is generally recognised that multiple markers, especially the inclusion of nuclear genes, would increase the accuracy of species delimitations, and therefore the accuracy of species diversity assessment. Howver, we only applied the standard COI barcode in assessments of species diversity because of the widespread generality of the commonly used primers [16] , [].

We applied a non-tree based Bayesian method for species identification before the calculation of diversity mainly because species in a community are not necessarily closely phylogenetically related, although they are ecologically related, due to the broad taxon coverage and filtering of environmental factors for a community. Tree-based methods, including Bayesian phylogenetic methods, are not always able to produce reliable assignments of specimens when taxon sampling is incomplete, as is the case here. In this study, we focus mainly on assessments of species diversity, not barcoding approaches, as the latter have been systematically evaluated with both simulated and empirical data [39] , [40] , [86] — [90] and are outside the scope of the present study.

This environmental factor might affect the survival of pupae by changing the moisture of the micro-environments, or by influencing the diversity of their host plants. Our results are supported by the significantly higher diversity in the drier eastern communities compared with the wetter western communities on the Tibetan Plateau, where dramatically different ecological landscapes are present.

However, owing to the lack of historical climate records in the sampling sites under investigation, the climate elements considered, such as monthly precipitation and mean, minimum, and maximum temperature, were all derived from the WorldClim dataset [] , which has been commonly used in ecological studies, but is restricted to records from the — period.

However, this is unlikely to significantly affect our basic conclusions, because the assemblage of species for a certain community is not a consequence of short time interactions between species and environments, and among species but a long-term adaption to certain habitats. In the future, biodiversity assessments may be further accelerated by meta-barcoding [] ; meta-barcoding of bulked arthropod samples has recently been shown to provide good estimates of within and between community diversity []. Whether the preference is for the sequencing of bulked or individual specimens, it is abundantly clear that DNA barcode-based biodiversity assessments are very effective and efficient alternatives to more time-consuming morphological-based measures that require considerable taxonomic expertise.

Comparison of tree topology between NJ and ML trees. The nodes in green on the tree indicate shared nodes between two trees, nodes in dark grey are nodes present on the NJ tree, but not on the ML tree. Permutation tests for TM and DB-based species diverisities, and diversities for each community. Correlation analysis between TM and DB-based species diversities for six different diversity indices. The effect of different reference database sizes on the estimation of species diversity.

Sample localities in Tibet, geographical coordinates and sequences used for Noctuidae moth species. Species identification based on traditional morphology. Some pictures of moths used in this study; b. Female genitalia, example 1; c. Male genitalia, example 2. We gratefully acknowledge the constructive comments of Academic Editor, Dr. Alex Smith, and two anonymous referees on an earlier version of the manuscript.


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  7. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. National Center for Biotechnology Information , U. PLoS One. Published online May Ho , 4 Robert D. Simon Y. Robert D. Alex Smith, Editor. Author information Article notes Copyright and License information Disclaimer. Ward, has no competing interests. Received Dec 20; Accepted Apr This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

    This article has been cited by other articles in PMC. Appendix S4: The effect of different reference database sizes on the estimation of species diversity. Appendix S5: diversity among different communities. Appendix S6: Sample localities in Tibet, geographical coordinates and sequences used for Noctuidae moth species. Appendix S7: Species identification based on traditional morphology. Appendix S8: Twenty two environmental variables used in this study. Abstract With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this.

    Introduction The quantification of species diversity, and understanding the processes that drive variation in diversity across space and time, form the basis of some of the most fundamental questions in ecology and evolutionary biology. Open in a separate window. Figure 1. Figure 2. Species diversities of Tibetan moth species Noctuidae for each community, calculated using different diversity indices. Figure 3.

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    Rank-abundance curves of each community based on DNA barcoding DB with different reference database a—c or traditional morphology TM d. Figure 4. Correlations between species diversity and environmental factors. Figure 5. Sampling sites in the Qinghai-Tibetan Plateau in China. Species Diversity Analysis Traditional morphology-based method Given the large number of indices, it is often difficult to decide which is the best method of measuring diversity [1] , [3] — [8] , [67]. DNA barcoding-based method For a community with a very large number of hyperdiverse taxa, such as arthropods, investigations of species diversity are usually hindered by the difficulty of identifying species by traditional morphological means alone.

    Figure 6. Species identity inferred via DNA barcoding for a community with a Bayesian method.

    Discussion and Conclusions In our study of biodiversity assessment via DNA barcoding for a Tibetan moth community, we found that diversity measurements based on DNA barcoding are able to serve as good surrogates for morphology-based measures. PDF Click here for additional data file.

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    XLS Click here for additional data file. Appendix S4 The effect of different reference database sizes on the estimation of species diversity. Appendix S5 diversity among different communities. Appendix S6 Sample localities in Tibet, geographical coordinates and sequences used for Noctuidae moth species. Appendix S7 Species identification based on traditional morphology. JPG Click here for additional data file. Appendix S8 Twenty two environmental variables used in this study. Acknowledgments We gratefully acknowledge the constructive comments of Academic Editor, Dr.

    References 1. Princeton University Press, 1st edition, Cabaret J, Schmidt E Species diversity of nematode communities in the digestive tract of domestic ruminants: multivariate versus univariate estimations. Parasitol Res 87 : —6. Jost L Entropy and diversity. Oikos : — Jost L Partitioning diversity into independent alpha and beta components. Ecology 88 : — Jost L Gst and its relatives do not measure differentiation. Mol Ecol 17 : — Ecol Econ 68 : — Divers Distrib 16 : 65— Magurran A Measuring Biological Diversity.

    Blaxter M, Floyd R Molecular taxonomics for biodiversity surveys : already a reality. May R How many species are there on earth? Science : — Abdo Z, Golding GB A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups. Syst Biol 56 : 44— Proc Biol Sci : — Nature : Proc Biol Sci Suppl 1S96—9. Marshall E Taxonomy.

    Will DNA bar codes breathe life into classification? Science : BMC Genomics 9 : Syst Biol 58 : — Syst Biol 55 : —