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190 results for “molecular species delimitation”
Fig. 18 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 18. Phylogeny of the family Clevelandellidae Kidder, 1938 based on 18S rRNA gene sequences. Bootstrap values for maximum likelihood analyses performed in IQTrees and PhyML as well as posterior probabilities for Bayesian interference performed in MrBayes and Phycas were mapped onto the best scoring IQTree. Dashes indicate statistical support below 50%. Sequences obtained in this study are in bold face. Members of each morphospecies are marked by the same color, as shown in Fig. 17. For specimen codes and further details, see Table 6. The scale bar denotes six substitutions per one thousand nucleotide positions.
Fig. 14. Paraclevelandia brevis Kidder, 1937. Thai I in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 14. Paraclevelandia brevis Kidder, 1937. Thai I specimens (A–C, F–G) isolated from Panesthia angustipennis angustipennis (Illiger, 1801) and Vietnamese specimens (D–E) isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 from life (A–C) and after protargol impregnation (D–G). A. Ventral overview, showing the general body organization. Arrows mark the proximal end of the peristomial opening, black arrowheads denote the proximal end of the adoral zone of membranelles, white arrowheads denote the karyophore attached to the anterior body pole. B–C. Ciliary pattern of ventral and dorsal sides. Asterisks mark the position of the ciliary whorl (posterior suture). D–G. Ventral views of specimens with well-preserved body shape. Scale bars = 20 μm.
Fig. 13. Paraclevelandia brevis Kidder, 1937. Thai I in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 13. Paraclevelandia brevis Kidder, 1937. Thai I specimens isolated from Panesthia angustipennis angustipennis (Illiger, 1801) after protargol impregnation. A–J. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. Scale bar = 20 μm.
Fig. 4 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 4. Clevelandella hastula (Kidder, 1937). Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 from life (A) and after protargol impregnation (B–N). A. Ventral view of a representative specimen, length 90 μm. B–K. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. L. Semi-schematic diagram, showing the general body organization. M–N. Ciliary pattern of ventral and dorsal sides. Arrow marks the right suture and black arrowheads denote the position of the ciliary whorl (posterior suture). Scale bars = 30 μm.
Fig. 2 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 2. Clevelandella constricta (Kidder, 1937). Thai I specimens isolated from Panesthia angustipennis angustipennis (Illiger, 1801) after protargol impregnation. A–J. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. Scale bar = 50 μm.
Fig. 7 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 7. Clevelandella panesthiae (Kidder, 1937). Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 after protargol impregnation. A–D. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. Scale bar = 50 μm.
Fig. 17 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 17. Phylogeny of the order Clevelandellida de Puytorac & Grain, 1976 based on 18S rRNA gene sequences. Some metopids were used as outgroup. Bootstrap values for maximum likelihood analyses performed in IQTrees and PhyML as well as posterior probabilities for Bayesian interference performed in MrBayes and Phycas were mapped onto the best scoring IQTree. Dashes indicate statistical support below 50%, asterisks denote mismatch with the topology shown. Sequences obtained in this study are in bold face. Members of each morphospecies are marked by the same color, following the code in the inset. For specimen codes and further details, see Table 6. The scale bar denotes three substitutions per one hundred nucleotide positions.
Fig. 9 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 9. Clevelandella parapanesthiae (Kidder, 1937). Thai I specimens isolated from Panesthia angustipennis angustipennis (Illiger, 1801) from life (A) and after protargol impregnation (B–N). A. Ventral view of a representative specimen, length 90 μm. B–K. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. L. Semi-schematic diagram, showing the general body organization. M–N. Ciliary pattern of ventral and dorsal sides. Arrow marks the right suture, black arrowheads indicate the position of the ciliary whorl (posterior suture). Scale bars = 30 μm.
Fig. 12. Paraclevelandia brevis Kidder, 1937 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 12. Paraclevelandia brevis Kidder, 1937. Vietnamese specimens isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 from life (A) and after protargol impregnation (B–N). A. Ventral view of a representative specimen, length 50 μm. B–K. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. L. Semi-schematic diagram, showing the general body organization. M–N. Ciliary pattern of ventral and dorsal sides. Arrow marks the right suture, black arrowheads indicate the position of the ciliary whorl (posterior suture). Scale bars = 20 μm.
Fig. 6 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 6. Clevelandella panesthiae (Kidder, 1937). Thai I specimens isolated from Panesthia angustipennis angustipennis (Illiger, 1801) from life (A) and after protargol impregnation (B–N). A. Ventral view of a representative specimen, length 105 μm. B–K. Variability of body shape and size as well as of the nuclear (shaded grey) and oral (shaded yellow) apparatus. L. Semi-schematic diagram, showing the general body organization. M–N. Ciliary pattern of ventral and dorsal sides. Arrow marks the right suture, black arrowheads denote the position of the ciliary whorl (posterior suture). Scale bars = 50 μm.
Fig. 8 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 8. Clevelandella panesthiae (Kidder, 1937). Vietnamese specimens (A, E–G) isolated from Panesthia angustipennis cognata Bey-Bienko, 1969 and Thai I specimens (B–D) isolated from Panesthia angustipennis angustipennis (Illiger, 1801) from life (A, E–G) and after protargol impregnation (B–D). A–D. Ventral view of specimens with well-preserved body shape. Arrow marks the proximal end of the peristomial opening, black arrowheads denote the proximal end of the adoral zone of membranelles, white arrowheads mark the karyophore fibers attaching to the left and right body margins. E. Ventral view, showing the general body organization. F–G. Ciliary pattern of ventral and dorsal sides. Asterisks mark the position of the ciliary whorl (posterior suture), white double arrowhead denotes the right suture. Scale bars = 50 μm.
Fig. 16 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 16. Ordination analyses of 94 specimens of six clevelandellid morphospecies based on morphometric data (A) and cell shape information (B). A. Multidimensional scaling of the Gower's similarity matrix. B. Principal component analysis of the Fourier coefficients. Eigenvalues of the first two ordination axes are λ1= 0.723 and λ2= 0.135, explaining 85.8% of the total variation. The morphometric and geometrical data delimit the clevelandellid morphospecies consistently and unambiguously, i.e., each clevelandellid morphospecies forms a homogeneous cluster that is well isolated from all other morphospecies analyzed. Members of each morphospecies are highlighted by the same color as in Fig. 15.
Fig. 15 in Morphological versus molecular delimitation of ciliate species: a case study of the family Clevelandellidae (Protista, Ciliophora, Armophorea)
Fig. 15. Cluster analyses of 94 specimens of six clevelandellid morphospecies based on morphometric data (A) and the cell shape information (B). A. Weighted average linkage clustering method in a combination with Gower's similarity index. B. Ward's D2 clustering method in a combination with the Manhattan city block distance. The morphometric and geometrical data delimit the clevelandellid morphospecies consistently and unambiguously, i.e., each clevelandellid morphospecies forms a homogeneous cluster that is well isolated from all other morphospecies analyzed. Since both techniques are phenetic, their results refer only to the similarity of the analyzed morphospecies in phenotypic space and not to their relatedness. Members of each morphospecies are highlighted by the same color.
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.
Supplementary material 1 from: Han W, Qiu L, Zhu J, Wang Z-Q, Che Y-L (2022) Exploring the diversity of Eupolyphaga Chopard, 1929 (Blattodea, Corydioidea): species delimitation based on morphology and molecular analysis. ZooKeys 1120: 67-94. https://doi.org/10.3897/zookeys.1120.87483
Table S1
Fig. 3 in Molecular Phylogenetic Analysis and Species Delimitation in the Pine Needle-feeding Aphid Genus Essigella (Hemiptera, Sternorrhyncha, Aphididae)
Fig. 3. Essigella specific differences in intron region 4 of EF-1α.
Supplementary material 1 from: Ottoni FP, Mattos JLO, Katz AM, Bragança PHN (2019) Phylogeny and species delimitation based on molecular approaches on the species of the Australoheros autrani group (Teleostei, Cichlidae), with biogeographic comments. Zoosystematics and Evolution 95(1): 49-64. https://doi.org/10.3897/zse.95.31658
: Data type: Adobe PDF file
Figure 4 from: Ottoni FP, Mattos JLO, Katz AM, Bragança PHN (2019) Phylogeny and species delimitation based on molecular approaches on the species of the Australoheros autrani group (Teleostei, Cichlidae), with biogeographic comments. Zoosystematics and Evolution 95(1): 49-64. https://doi.org/10.3897/zse.95.31658
Figure 4 Time-scaled phylogeny obtained from the Bayesian analysis in BEAST. Values above nodes are mean average ages of the nodes, followed below blue bars representing the 95% highest posterior densities intervals for estimated ages; numbers indicated by arrows are the posterior probability obtained from the Bayesian analysis in MrBayes followed by the node number, corresponding to the node numbers of the Figure 2 and Box 1. PP means posterior probability.
Figure 3 from: Ottoni FP, Mattos JLO, Katz AM, Bragança PHN (2019) Phylogeny and species delimitation based on molecular approaches on the species of the Australoheros autrani group (Teleostei, Cichlidae), with biogeographic comments. Zoosystematics and Evolution 95(1): 49-64. https://doi.org/10.3897/zse.95.31658
Figure 3 Species delimitation tree generated by the Bayesian Poisson Tree Processes (bPTP) model, using a fragment of the mitochondrial gene CYTB. Black lines indicate branching processes among species, red lines indicate branching processes within species. Species of the A.autrani species group delimited through bPTP are indicated with grey bars.
Figure 2 from: Ottoni FP, Mattos JLO, Katz AM, Bragança PHN (2019) Phylogeny and species delimitation based on molecular approaches on the species of the Australoheros autrani group (Teleostei, Cichlidae), with biogeographic comments. Zoosystematics and Evolution 95(1): 49-64. https://doi.org/10.3897/zse.95.31658
Figure 2 Phylogenetic haplotype tree based on Bayesian Inference (BI). Numbers above branches are posterior probability values, and below branches are numbered nodes which represent the combination of nucleotide substitution which define the species (in CBB) or clades. The nucleotide substitutions (CBB) can be checked in box1. Posterior probability value supporting the Australoherosautrani group is indicated in blue, as well as, the three clades herein proposed within this species group are indicated in green. Species of the in-group delimited though the tree based method (WP) are indicated with red bars, as well as, the species of the in-group delimited by nucleotide substitution method (CBB) have their nodes marked in red.
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