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Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon

This deposition contains the phylogenetic and species delimitation data for the manuscript "Molecular species delimitation of larks (Aves: Alaudidae), and integrative taxonomy of the genus Calandrella, with the description of a range-restricted African relic taxon" by Stervander et al.  For details of samples/sequences/leaves, please refer to Appendix A of the above manuscript.   Phylogenetic analyses <ol> <li>Fasta sequence alignment of cytochrome b for the lark family and outgroups: Alaudidae_cytb_extended_200316.fa</li> <li>BEAST v. 2.6.1 input file: Alaudidae_cytb_HKYGI_BDrelLN_modOp2003_20M1K.xml</li> <li>BEAST v. 2.6.1 output log file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.log</li> <li>BEAST v. 2.6.1 output (raw) trees file: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K.trees</li> <li>TreeAnnotator maximum credibility clade tree based on BEAST v. 2.6.1 output, newick format: Alaudidae_cytb_HKYGI_BDrelLN_modOp_20M1K_c40Mbi5.mccmed.nwk</li> </ol> Species delimitation <ol> <li>Input tree, manipulated to remove negative branch lengths (replaced by 0) and tips/leafs that are single representatives of a species, based on current taxonomy (IOC v. 10.2), newick format: Alaudidae_cytb_HKYGI_BDrelLN_c40Mbi5_mccmed_nonNeg_multiSeq_ingroup_remDuplicate.nwk</li> <li>mPTP text output of the multi-rate species delimitation, containing command for run and species delimitation results: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.txt</li> <li>mPTP likelihood log of the multi-rate species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.out.txt</li> <li>mPTP output tree in SVG format, with support values for species delimitation: Alaudidae200316_cytb_HKYGI_BDrelLN_c40Mbi5_remDuplCaboweni201007_mccmed_delim_varRate_10M_minbrAUTO.1602073064.combined.svg</li> </ol>

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Fig. 2 in Integrative taxonomy reveals two new cryptic species of Hyphessobrycon Durbin, 1908 (Teleostei: Characidae) from the Maracaçumé and middle Tocantins River basins, Eastern Amazon region

Fig. 2. Hyphessobrycon frickei Guimarães, Brito, Bragança, Katz & Ottoni sp. nov. (CICCAA 02388), 17.7 mm SL; jaw suspensory. A. Premaxillary. B. Maxilla. C. Dentary. Scale bar: 1 mm

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Fig. 8 in Integrative taxonomy reveals two new cryptic species of Hyphessobrycon Durbin, 1908 (Teleostei: Characidae) from the Maracaçumé and middle Tocantins River basins, Eastern Amazon region

Fig. 8. Topology of the ultrametric tree performed in BEAST ver. 1.8.4 including unique haplotypes summarizing the results of GMYC, bPTP and ABGD. Numbers above and below branches are posterior probability values. The star indicates the Hyphessobrycon copelandi clade.

opencc-zeroDec 2016View details →

FIGURE 3 Halosaurus ovenii from the northeastern Atlantic Ocean, MHNUSC 25010 - 2, 578 in Halosaur fishes (Notacanthiformes: Halosauridae) from Atlantic Spanish waters according to integrative taxonomy

FIGURE 3 Halosaurus ovenii from the northeastern Atlantic Ocean, MHNUSC 25010 - 2, 578 mm total length.

Fig. 15 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species

Fig. 15. Differences in the posterior part of the surstylus among species of the M. avidus complex. A. UPGMA phenogram constructed using squared Mahalanobis distances. B. Thin-plate spline deformation grids showing overall shape differences between analysed species.

Fig. 14 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species

Fig. 14. Differences in the posterior part of the surstylus among species of the M. avidus complex. A. Scatter plot of individual scores of CV1 vs CV2. B. Scatter plot of individual scores of CV2 vs CV3.

Fig. 11 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species

Fig. 11. UPGMA phenogram constructed using the squared Mahalanobis distances of wing shape for species of the M. avidus complex.

Fig. 12 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species

Fig. 12. Thin-plate spline deformation grids showing wing shape differences between analysed species. Differences between the species have been exaggerated five-fold to make them more visible.

Fig. 10 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species

Fig. 10. Differences in wing shape among species of the M. avidus complex. A. Scatter plot of individual scores of CV1 vs CV2. B. Scatter plot of individual scores of CV2 vs CV3.

Fig. 9 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species

Fig. 9. UPGMA tree based on pairwise genetic distances for four species from the Merodon avidus complex.

Fig. 8 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species

Fig. 8. Median-joining network of the mtDNA 5'-end of the COI gene. Circle sizes are proportional to haplotype frequencies. Each branch represents one mutational step; if more than one mutational step is present, it is denoted by the given number.

Fig. 6 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species

Fig. 6. Maximum parsimony strict consensus tree based on DNA barcode COI sequences. Length 136 steps, Consistency Index (CI) = 93, Retention Index (RI) = 95. Filled circles denote unique changes, open circles non-unique.

Fig. 4 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species

Fig. 4. Merodon megavidus Vujić & Radenković sp. nov., head, antero-lateral view. A. Ƌ. B. ♀. Scale bar = 1 mm.

Fig. 3. Hind leg, lateral view. A–B in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species

Fig. 3. Hind leg, lateral view. A–B. Merodon avidus (Rossi, 1790). A. Ƌ. B. ♀. — C–D. M. megavidus Vujić & Radenković sp. nov. C. Ƌ. D. ♀. Scale bar = 1 mm.

Fig. 2 in Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae) using integrative taxonomy, with the description of a new species

Fig. 2. Merodon megavidus Vujić & Radenković sp. nov., male genitalia. A. Epandrium, lateral view. B. Left surstylus, anterior view. C. Hypandrium, lateral view. Abbreviations: psl = posterior surstylus lobe; asl = anterior surstylus lobe; c = cercus; ae = aedeagus; ea = ejaculatory apodeme. Scale bar = 0.5 mm.

Fig. 21 in Integrative taxonomy supports two new species of Macrobiotus (Tardigrada: Eutardigrada: Macrobiotidae) allowing further discussion on the genus phylogeny

Fig. 21. Bayesian phylogenetic reconstruction of Superclade I of the family Macrobiotidae. Values at nodes are BI posterior probability supports, nodes with support <0.70 were collapsed whereas nodes with maximum support values (1.00) are not shown. Newly sequenced taxa are bolded and marked with red font. The scale bar represents substitutions per position.

Fig. 20 in Integrative taxonomy supports two new species of Macrobiotus (Tardigrada: Eutardigrada: Macrobiotidae) allowing further discussion on the genus phylogeny

Fig. 20. Macrobiotus mileri sp. nov., SEM images of eggs (ISEA PAS). A–B. Entire egg. C–F. Details of egg processes and the surface between them. Empty indented arrowheads indicate pores in center of terminal discs, filled flat arrowheads indicate small pores around bases of egg processes, filled indented arrowheads indicate thickenings around bases of egg processes. Scale bars in μm.

Fig. 19 in Integrative taxonomy supports two new species of Macrobiotus (Tardigrada: Eutardigrada: Macrobiotidae) allowing further discussion on the genus phylogeny

Fig. 19. Macrobiotus mileri sp. nov., PCM images of the eggs under ×1000 magnification (ISEA PAS). A–C. Egg surface. D–E. Midsections of egg processes. Empty indented arrowheads indicate pores / light-refracting dots in the center of the terminal discs, filled flat arrowheads indicate small pores around bases of the egg processes, filled indented arrowheads indicate dark thickenings around bases of the egg processes. Scale bars in μm.

Fig. 18 in Integrative taxonomy supports two new species of Macrobiotus (Tardigrada: Eutardigrada: Macrobiotidae) allowing further discussion on the genus phylogeny

Fig. 18. Macrobiotus mileri sp. nov., mouth opening and the oral cavity armature seen under SEM (paratypes, ISEA PAS). A–B. The mouth opening of a single paratype visible from lateral and frontal view respectively. C–D. The oral cavity armature of a single paratype seen under SEM from different angles, dorsal (C) and ventral (D) view, respectively. Empty arrows indicate cuticular pores, filled flat arrowheads indicate the first band of tenth, empty flat arrowheads indicate the second band of teeth, and filled indented arrowheads indicate the third band of teeth. Scale bars in μm.

Fig. 17 in Integrative taxonomy supports two new species of Macrobiotus (Tardigrada: Eutardigrada: Macrobiotidae) allowing further discussion on the genus phylogeny

Fig. 17. Macrobiotus mileri sp. nov., PCM images of the buccal apparatus (all from holotype, IL.001.11, ISEA PAS, forma aporata). A. An entire buccal apparatus. B–C. The oral cavity armature, dorsal and ventral teeth respectively. D–E. Placoid morphology, dorsal and ventral placoids, respectively. The filled flat arrowheads indicate the first band of teeth, the empty flat arrowheads indicate the second band of teeth, the filled indented arrowheads indicate the third band of teeth, and the empty indented arrowheads indicate central and subterminal constrictions in the first and second macroplacoid, respectively. Scale bars in μm.