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32 results for “genetic species identification”
Figure 5 from: Li Y, Li H, Motokawa M, Wu Y, Harada M, Sun H, Mo X, Wang J, Li Y (2019) A revision of the geographical distributions of the shrews Crocidura tanakae and C. attenuata based on genetic species identification in the mainland of China. ZooKeys 869: 147-160. https://doi.org/10.3897/zookeys.869.33858
Figure 5 Comparison of teeth of Crocidura attenuata (left: S2576) and Crocidura tanakae (right: S2566) from Baoxing, Sichuan.
Figure 2 from: Li Y, Li H, Motokawa M, Wu Y, Harada M, Sun H, Mo X, Wang J, Li Y (2019) A revision of the geographical distributions of the shrews Crocidura tanakae and C. attenuata based on genetic species identification in the mainland of China. ZooKeys 869: 147-160. https://doi.org/10.3897/zookeys.869.33858
Figure 2 ML tree based on Cytb of Crocidura genus. Numbers above the branches represent bootstrap support (BS). The blue clade represents C. tanakae and orange clade represents C. attenuata.
Figure 4 from: Li Y, Li H, Motokawa M, Wu Y, Harada M, Sun H, Mo X, Wang J, Li Y (2019) A revision of the geographical distributions of the shrews Crocidura tanakae and C. attenuata based on genetic species identification in the mainland of China. ZooKeys 869: 147-160. https://doi.org/10.3897/zookeys.869.33858
Figure 4 Comparison of crania of Crocidura attenuata (S2576) and Crocidura tanakae (S2566) from Baoxing, Sichuan. Top row from left to right: dorsal views of the skulls of C. attenuata and C. tanakae (S2576 andS2566), ventral views of the skulls in the same order. Lower row: lateral view of skulls and mandibles from top to bottom of C. attenuata and C. tanakae (S2576 and S2566).
Figure 6 from: Li Y, Li H, Motokawa M, Wu Y, Harada M, Sun H, Mo X, Wang J, Li Y (2019) A revision of the geographical distributions of the shrews Crocidura tanakae and C. attenuata based on genetic species identification in the mainland of China. ZooKeys 869: 147-160. https://doi.org/10.3897/zookeys.869.33858
Figure 6 Scatter plot of C. attenuata (red) and C. tanakae (blue) sample distribution over PC1 and PC2 axes constructed based on external and skull morphological variables. Different symbols represent different populations. GD: Guangdong, FJ: Fujian, ZJ: Zhejiang, SCBX: Baoxing, Sichuan, HB: Hubei, SC: Sichuan, GX: Guangxi, AH: Anhui, HuN: Hunan, HN: Hainan, CQ: Chongqing, YN: Yunnan, JX: Jiangxi
Figure 3 from: Li Y, Li H, Motokawa M, Wu Y, Harada M, Sun H, Mo X, Wang J, Li Y (2019) A revision of the geographical distributions of the shrews Crocidura tanakae and C. attenuata based on genetic species identification in the mainland of China. ZooKeys 869: 147-160. https://doi.org/10.3897/zookeys.869.33858
Figure 3 Distributions of Crocidura attenuata and C. tanakae in the mainland of China,Laos and Vietnam. Black and white triangles represent the sampled sites of C. tanakae first presented in this study and in previous studies, respectively. White circles and squares represent the sampled sites of C. attenuata first presented in this study and in previous studies. Black triangles and white circles overlapped indicate sympatry sites.
Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
Data from: Genetic barcoding of dark-spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies
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Data from: Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: application to non-invasive sampling
Species identification through non-invasive sampling is increasingly used in animal conservation genetics, given that it obviates the need to handle free-living individuals. Non-invasive sampling is particularly valuable for elusive and small species such as rodents. Although rodents are not usually assumed to be the most obvious target for conservation, of the 21 species or near-species present in Iberia, three are considered endangered and declining while several others are poorly studied. Here we develop a genetic tool for identifying all rodent species in Iberia by non-invasive genetic sampling. To achieve this purpose we selected one mitochondrial gene (cytochrome b – cyt-b) and one nuclear gene (interphotoreceptor retinoid-binding protein – IRBP), which we first sequenced using tissue samples. Both genes allow for the phylogenetic distinction of all species except the sibling species Microtus lusitanicus and M. duodecimcostatus. Overall, cyt-b showed higher resolution than IRBP, revealing a clear barcoding gap. To allow these markers to be applied to non-invasive samples, we selected a short highly-diagnostic fragment from each gene, which we used to obtain sequences from faeces and bones from owl pellets. Amplification success for the cyt-b and IRBP fragment was 85% and 43% in faecal and 88% and 64% in owl-pellet DNA extractions, respectively. The method allows the unambiguous identification of the great majority of Iberian rodent species from non-invasive samples, with application in studies of distribution, spatial ecology and population dynamics, and for conservation.
Figure 1 from: Li Y, Li H, Motokawa M, Wu Y, Harada M, Sun H, Mo X, Wang J, Li Y (2019) A revision of the geographical distributions of the shrews Crocidura tanakae and C. attenuata based on genetic species identification in the mainland of China. ZooKeys 869: 147-160. https://doi.org/10.3897/zookeys.869.33858
Figure 1 Distributions of Crocidura attenuata and C. tanakae by the IUCN.
Data from: Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses
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Data from: Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: application to non-invasive sampling
Open the record for dataset details and reuse information.
Fig. 2 ITS phylogeny and genetic distances from the 13 in DNA barcoding of brown Parmeliae (Parmeliaceae) species: a molecular approach for accurate specimen identification, emphasizing species in Greenland
Fig. 2 ITS phylogeny and genetic distances from the 13 brown Pakmeliae species occurring in Greenland. a Cartoon representation of the maximum likelihood ITS topology obtained from 372 brown Pakmeliae specimens. Values at each node indicate non-parametric bootstrap support; only support values>50% are shown (complete ITS topology is shown in Supplementary Figure, S1). b Box plots of ITS genetic distances estimated for each species and all interspecific distances. 'CO' =Cetkakiella commixta; 'AG' =Melaielia agiata; 'HE' = M. hepatizoi; 'ST' = M. stygia; 'EL' = Melaiohalea elegaitula; 'EX' = M. exaspekatula; 'IN' = M. iifumata; 'OL' =M. olivacea; 'SE' =M. septeitkioialis; 'DI' =Moitaielia disjuicta; 'PA' = M.
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International Brain Laboratory public data
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OpenNeuro
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