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FIGURE. DnaSP DNA polymorphism analysis - Nucleotide variability (Pi) comparison between Strobilanthes lupulina and S. glandulata. The window length and step size were set to 600bp and 200bp respectively. The most varying regions and the commonly used barcoding regions are listed against the base-pair differences found. in Strobilanthes glandulata (Acanthaceae), a new species from Sri Lanka based on the morphological and molecular evidences
FIGURE. DnaSP DNA polymorphism analysis - Nucleotide variability (Pi) comparison between Strobilanthes lupulina and S. glandulata. The window length and step size were set to 600bp and 200bp respectively. The most varying regions and the commonly used barcoding regions are listed against the base-pair differences found.
Data from: Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding
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Data from: Identification of Swedish mosquitoes based on molecular barcoding of the COI gene and SNP analysis
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Fig. 1 in Molecular authentication of Pargo fillets Lutjanus purpureus (Perciformes: Lutjanidae) by DNA barcoding reveals commercial fraud
Fig. 1. Neighbor-joining (NJ) tree constructed from a 600-bp of the COI gene, showing two clades, which indicates the presence of two species among the fillets labeled as "Pargo"; the nucleotide divergence between the species (the value of 8.7%) is indicated above the outermost node. Within parentheses the frequency of each haplotype is described and the replacement rate present in the fillets is shown in plot to the right.
Figure 9 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 9 Morphometric relationships and fecundity characteristics of Macropodia czernjawskii. a. Relationships between carapace width (CW) and the geometric mean of chela length, height and thickness (ChGM). b. Relationships between CW and decimal logarithm of the number of developing eggs (I or II stage of development) on pleopods (F). For statistical data see Table 2.
Figure 7 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 7 Macropodia czernjawskii. a. Right chela, male, CW 11.0 (ZMMU Ma 3547); b. Right chela, male. CW 6.0 mm (ZMMU Ma 3544) c. Malformed right chela, male, CW 8.0 mm (ZMMU Ma 3543); d, e. Same specimen as c. dactylus and propodus of P 5. Scale bars: 1 mm (a–c, e), 0.5 mm (d).
Figure 6 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 6 Macropodia czernjawskii. a. Anterior part of the body with basal antennal segment (ZMMU Ma 3543); b. Anterior part of the body with basal antennal segments, male (ZMMU Ma 3547). c. Male pleon (ZMMU Ma 3547); d. Female sterno-pleonal cavity with exposed genital segment (ZMMU Ma 3538). Scale bar: 1 mm.
Figure 5 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 5 Macropodia czernjawskii, photographs in natural coloration. a. male (ZMMU Ma 3547), dorsal view. b. Same specimen as a. ventral view. c. female ov (ZMMU Ma 3542), dorsal view. d. Same specimen as c. ventral view. Scale bar: 10 mm. Photographs by SE Anosov.
Figure 4 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 4 Macropodia czernjawskii (a, b. possible paralectotype ZIN-RAS 1609; c, d.ZIN-RAS 35102) and Macropodia longirostris (JC Fabricius, 1775) (e.SMF 3752). a. Right cheliped, ventral view. b. Right cheliped, dorsal view. c. Cphalothorax, dorsal view. d. Cephalothorax, ventral view. e. Cephalothorax, dorsal view. Scale bar: 10 mm.
Figure 3 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 3 Comparison of Macropodia czernjawskii (a–d. possible paralectotype, male, ZIN-RAS 88750) to Macropodia tenuirostris (Leach, 1814) (a'–d'. male, SMF 3749) and Macropodia rostrata (Linnaeus, 1761) (a''–d''.SMF 40660). a. Dorsal view. b. Lateral view. c. Anterior part of the body, with antennules, basal antennal segments, and epistome, ventral view. d. Dactylus of pereopod 5. Scale bars: 10 mm (a–a''–b–b''), 1 mm (c–c''–d–d'').
Figure 2 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 2 Macropodia czernjawskii (Brandt, 1880), female lectotype (ZIN-RAS 88751). a. Dorsal view. b. Ventral view. c. Lateral view. Scale bar: 5 mm.
Figure 8 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 8 Macropodia czernjawskii. Male (ZMMU Ma 3543), right gonopod . a. Pleonal view. b. Sternal view. Scale bar: 1 mm.
Figure 12 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 12 Phylogenetic relationships of Macropodia spp. based on partial sequence of the COI gene, obtained using Bayesian inference. Tips of the tree colored according to their morphological identification. Numbers above the branches are the posterior probabilities.
Figure 10 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 10 Natural habitats of Macropodiz czernjawskii in the Black Sea. a, b. Male (ZMMU Ma 3549) in Cystoseira sp., on rock, Tuaphat coastal rock masif, near Gelendzhik. c. Male (ZMMU Ma 3547), on sand, of Blagoveschenskaya village, near Anapa. d. Specimen collected of Blagoveschensakya in aquarium, decorated with red algae after few days of keeping. e. A characteristic biotope of M. czernjawskii in Tuaphat. f. Biotope in Kazachya Cove, Crimean Peninsula where M. czernjawskii has been repeatedly observed. Photographs by SE Anosov.
Figure 1 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 1 Study area and the original records of Macropodia czernjawskii in the Black Sea presented in this study.
Figure 11 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Figure 11 Estimates of evolutionary divergence over sequence pairs within and between species of Macropodia (M. czernjawskii; M. rostrata – M. parva; M. tenuirostris – M. longipes; the latter two pairs and M. parva, M. rostrata – Macropodia sp. are indicated as "?", meaning their possible conspecificity); and between genera of Majoidea. The number of base substitutions per site from averaging over all sequence pairs between groups are shown. Analyses were conducted using the Kimura 2-parameter mode. For values of K2P see also Table 3.
Supplementary material 1 from: Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342
Table S1
Data from: DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples
Although species assignment of scats is important to study carnivoran biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here we evaluate the potential of two short mtDNA fragments (ATP6 [126 bp] and COI [187 bp]) to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences, and analyzed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters, uniqueness of haplotypes, or by reducing the geographic scope of the comparison. In silico comparative analyses were also performed with a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case-studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA, and allowed an assessment of prey-DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.
Data from: Delimiting species-poor datasets using single molecular markers: a study of barcode gaps, haplowebs and GMYC
Most single-locus molecular approaches to species delimitation available to date have been designed and tested on data sets comprising at least tens of species, whereas the opposite case (species-poor data sets for which the hypothesis that all individuals are conspecific cannot by rejected beforehand) has rarely been the focus of such attempts. Here we compare the performance of barcode gap detection, haplowebs and generalized mixed Yule–coalescent (GMYC) models to delineate chimpanzees and bonobos using nuclear sequence markers, then apply these single-locus species delimitation methods to data sets of one, three, or six species simulated under a wide range of population sizes, speciation rates, mutation rates and sampling efforts. Our results show that barcode gap detection and GMYC models are unable to delineate species properly in data sets composed of one or two species, two situations in which haplowebs outperform them. For data sets composed of three or six species, bGMYC and haplowebs outperform the single-threshold and multiple-threshold versions of GMYC, whereas a clear barcode gap is only observed when population sizes and speciation rates are both small. The latter conditions represent a "sweet spot" for molecular taxonomy where all the single-locus approaches tested work well; however, the performance of these methods decreases strongly when population sizes and speciation rates are high, suggesting that multilocus approaches may be necessary to tackle such cases.
Data from: Molecular diversity of Germany's freshwater fishes and lampreys assessed by DNA barcoding
This study represents the first comprehensive molecular assessment of freshwater fishes and lampreys from Germany. We analysed COI sequences for almost 80% of the species mentioned in the current German Red List. In total, 1056 DNA barcodes belonging to 92 species from all major drainages were used to (i) build a reliable DNA barcode reference library, (ii) test for phylogeographic patterns, (iii) check for the presence of barcode gaps between species and (iv) evaluate the performance of the barcode index number (BIN) system, available on the Barcode of Life Data Systems. For over 78% of all analysed species, DNA barcodes are a reliable means for identification, indicated by the presence of barcode gaps. An overlap between intra- and interspecific genetic distances was present in 19 species, six of which belong to the genus Coregonus. The Neighbour-Joining phenogram showed 60 nonoverlapping species clusters and three singleton species, which were related to 63 separate BIN numbers. Furthermore, Barbatula barbatula, Leucaspius delineatus, Phoxinus phoxinus and Squalius cephalus exhibited remarkable levels of cryptic diversity. In contrast, 11 clusters showed haplotype sharing, or low levels of divergence between species, hindering reliable identification. The analysis of our barcode library together with public data resulted in 89 BINs, of which 56% showed taxonomic conflicts. Most of these conflicts were caused by the use of synonymies, inadequate taxonomy or misidentifications. Moreover, our study increased the number of potential alien species in Germany from 14 to 21 and is therefore a valuable groundwork for further faunistic investigations.
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Allen Brain Atlas
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