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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
<p>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 <em>Calandrella</em>, with the description of a range-restricted African relic taxon" by Stervander <em>et al</em>. </p> <p>For details of samples/sequences/leaves, please refer to Appendix A of the above manuscript. </p> <p><strong>Phylogenetic analyses</strong></p> <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> <p><strong>Species delimitation</strong></p> <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>
FIG. 1. — Areas VI-V-VI in Redescription of two overlooked species of the Perinereis nuntia complex and morphological delimitation of P. nuntia (Savigny in Lamarck, 1818) from the Red Sea (Annelida, Nereididae)
FIG. 1. — Areas VI-V-VI patterns of the pharynx shaped by the ridges and furrows: A-C, Perinereis latipalpa (Schmarda, 1861) n. comb. with a λ-shaped pattern; D-F, Perinereis nuntia (Savigny in Lamarck, 1818) with a χ-shaped pattern; G-I, Perinereis larentukana (Grube in Peters, 1881) n. comb. with a υ-shaped pattern; J-L, Perinereis shikueii Glasby & Hsieh, 2006 with a ɔc-shaped pattern; A, D, G, J, dorsal portion of oral ring; B, E, H, K, same with a slightly irregular line drawings on the shape formed by AVI-V-VI pattern; C, F, I, L, symmetrical line drawings of the AVI-V-VI patterns. Scale bars: 1 mm. J, K, after Glasby & Hsieh (2006).
FIG. 4 in Redescription of two overlooked species of the Perinereis nuntia complex and morphological delimitation of P. nuntia (Savigny in Lamarck, 1818) from the Red Sea (Annelida, Nereididae)
FIG. 4. — Perinereis latipalpa (Schmarda, 1861) n. comb. lectotype (NMHW 769a): A-F, parapodia, anterior view (numbers refer the chaetiger); A, B, with bent dorsal cirri; E, black arrowheads, points used for measuring entire length of distal lobe of dorsal ligule; white, same but for proximal lobe; F, with incomplete dorsal cirri; black arrowheads, central glandular patch; white, proximal patch; G, H, approach of notopodial homogomph spinigers (chaet. 39 and 60, respectively) (arrows point thick, separated teeth); I, Heterogomph spiniger (chaet. 60); inset: proximal teeth; J, neuropodial heterogomph falciger, supracicular (chaet. 60); K, same, subacicular (chaet. 60); black arrowheads, points used for measuring length of blade of the proximal end (a); white, same but for distal end (b); L, same, subacicular (chaet. 119), black arrowheads, points used for measuring length of the serrated region; white, same but for entire length of blade. Scale bars: A-F, 0.5 mm; G-L, 15 µm.
FIG. 8 in Redescription of two overlooked species of the Perinereis nuntia complex and morphological delimitation of P. nuntia (Savigny in Lamarck, 1818) from the Red Sea (Annelida, Nereididae)
FIG. 8. — Perinereis larentukana (Grube in Peters, 1881) n. comb., syntypes (ZMB 863): A-D, I-K, from best-preserved specimen; E-H, L, from complete specimen; A, anterior region, dorsal view; B, prostomium, dorsal view (arrow points nuchal organ); C, left jaw, dorsal (left) and ventral (right) views; D, same, zoom-in, ventral view (arrows point canals); E, maxillary ring of pharynx, frontal view; F, oral ring, frontal view; G, same, dorsal view (arrow points distal portion of λ-shaped pattern); H, same, ventral view; I, approach of notopodial homogomph spiniger (chaet. 10) (arrow points slender, evenly spaced teeth); J, neuropodial heterogomph falciger, supracicular (chaet. 10); M, same, subacicular (chaet.10); L, posterior region, dorsal view. Scale bars: A, 3 mm; B, H, L, 1 mm; C, E-G, 0.5 mm; D, 0.1 mm; I-L, 15 µm.
FIG. 9 in Redescription of two overlooked species of the Perinereis nuntia complex and morphological delimitation of P. nuntia (Savigny in Lamarck, 1818) from the Red Sea (Annelida, Nereididae)
FIG. 9. — Perinereis larentukana (Grube in Peters, 1881) n. comb. best-preserved syntype (ZMB 863): A-F, parapodia, anterior view (numbers refer the chaetiger); F, with bent ventral cirri. Scale bars: 0.5 mm.
FIG. 7 in Redescription of two overlooked species of the Perinereis nuntia complex and morphological delimitation of P. nuntia (Savigny in Lamarck, 1818) from the Red Sea (Annelida, Nereididae)
FIG. 7. — Perinereis latipalpa (Schmarda, 1861) n. comb.: A-E, topotype of Perinereis namibia Wilson & Glasby, 1993, n. syn. (ZMB 4109b): A, maxillary ring of pharynx, frontal view; B, oral ring of pharynx, dorsal view (arrow points distal portion of λ-shaped pattern); C, same, ventral view; D, parapodium 74, anterior view; E, approach to homogomph spinigers (chaet. 74), notopodial (left), neuropodial supracicular (right) (arrows point thickened, separated teeth). F-K, Perinereis vallata (Grube & Kröyer in Grube, 1858), non-type (ZMB 3666); F, approach to neuropodial supracicular homogomph spiniger (chaet. 76) (arrow points barely thickened, evenly spaced teeth); G, anterior region, dorsal view; H, maxillary ring, frontal view (arrows point merged paragnaths); I, oral ring, dorsal view (arrow points distal portion of χ-shaped pattern); J, pharynx, ventral view; K, same, lateral view. Scale bars: A, D, H, 0.5 mm; B, C, G, I-K, 1 mm; E, F, 15 µm.
FIG. 5 in Redescription of two overlooked species of the Perinereis nuntia complex and morphological delimitation of P. nuntia (Savigny in Lamarck, 1818) from the Red Sea (Annelida, Nereididae)
FIG. 5. — Perinereis latipalpa (Schmarda, 1861) n. comb., holotype of Neanthes latipalpa Kinberg, 1865 n. syn. (SMNH 37900): A, anterior region, dorsal view; B, pharynx, dorsal view (arrow points proximal overlap of areas V and VI); C, oral ring of pharynx, lateral view; D, same, ventral view; E, posterior region, ventral view; F-I, parapodia, anterior view (numbers refer the chaetiger); J, approach of notopodial homogomph spinigers (chaet. 45) (arrows point thicker, separated teeth); K, neuropodial heterogomph falciger, subacicular (chaet. 45); L, permanent microscope slide, mounted 27th parapodia (SMNH 37900, housed at the NHMUK). Scale bars: A, 2 mm; B-E, 1 mm; F-H, 0.5 mm; I, 0.3 mm; J, K, 15 µm.
FIG. 3 in Redescription of two overlooked species of the Perinereis nuntia complex and morphological delimitation of P. nuntia (Savigny in Lamarck, 1818) from the Red Sea (Annelida, Nereididae)
FIG. 3. — Perinereis latipalpa (Schmarda, 1861) n. comb: A, recent (above) and older (below) labels of the jars containing paralectotype materials at the Natural History Museum, Vienna (NMHW 771); B, C, lectotype (NMHW 769a); D-I, Paralectotype (NMHW 771); B, anterior region, dorsal view; C, posterior region, dorsal view; D, pharynx, anterior view (arrow points distal portion of λ-shaped pattern); E, same, ventral view; F, same, dorsal view; inset: entire λ-shaped pattern (arrow points proximal overlap of areas V and VI); G, same, lateral view (arrow points narrow gap); H, left jaw, dorsal (left) and ventral (right) views; I, same, zoom-in, ventral view (arrow: canals). Scale bars: B, C, 3 mm; D-G, 2 mm; H, 1 mm; I, 0.5 mm.
FIG. 2 in Redescription of two overlooked species of the Perinereis nuntia complex and morphological delimitation of P. nuntia (Savigny in Lamarck, 1818) from the Red Sea (Annelida, Nereididae)
FIG. 2. — Perinereis nuntia (Savigny in Lamarck, 1818), topotypes (ZMB 4019-Q): A, F, I-P, from complete specimen; B-E, G, from incomplete specimen; A, anterior region, dorsal view; inset: left nuchal organ; B, right jaw, ventral (left) and dorsal (right) views; C, same, close up of pulp cavity, ventral view (arrow points canal); D, maxillary ring of pharynx, ventral view; E, pharynx, lateral view; F, oral ring of pharynx, dorsal view; black arrowhead, distal portion of χ-shaped pattern; white arrowhead, proximal portion of χ-shaped pattern; black arrow, pointing anterior region; G, pharynx, ventral view; H-K, parapodia, anterior view (numbers refer the chaetiger); L, neuropodial homogomph spiniger, supracicular (chaet. 64); M, heterogomph spiniger, subacicular (chaet. 24); N, heterogomph falciger, supracicular (chaet. 24); O, same, subacicular (chaet. 119); P, posterior region, dorsal view. Scale bars: A, 3 mm; B, D-G, P, 1 mm; C, 0.2 mm; H-K, 0.5 mm; L-O, 15 µm.
FIG. 6 in Redescription of two overlooked species of the Perinereis nuntia complex and morphological delimitation of P. nuntia (Savigny in Lamarck, 1818) from the Red Sea (Annelida, Nereididae)
FIG. 6. — Perinereis latipalpa (Schmarda, 1861) n. comb., syntypes of Neanthes latipalpa typica Willey, 1904 n. syn. (NHMUK 1911.2.1.23-26); A, anterior region, dorsal view; B, same, ventral view; C, right jaw, ventral view (arrows point canals); D, maxillary ring of pharynx, ventral view; E, oral ring of pharynx, ventral view (arrow points distal portion of λ-shaped pattern); F, posterior region, dorsal view; G-J, parapodia, anterior view (numbers refer the chaetiger); K, approach of notopodial homogomph spiniger (chaet. 41) (arrow points thicker, separated teeth); L, neuropodial heterogomph falciger, supracicular (chaet. 41); M, same, subacicular (chaet. 41); N, permanent microscope slide with mounted 8th, 33rd and 73rd parapodia (NHMUK 1911.2.1.23-26a); O, same, 28th parapodia (NHMUK 1911.2.1.23-26b). Scale bars: A, B, F, 1 mm; C, 0.2 mm; D, E, G-J, 0.5 mm; K-M, 15 µm.
Fig. 1. Merodon aureus Fabricius, 1805 in An assessment of new character in hoverfly species delimitation using linear and geometric morphometrics - genus Merodon Meigen, 1803 (Diptera: Syrphidae) as a case study
Fig. 1. Merodon aureus Fabricius, 1805, ♂, right wing with the character used in linear morphometric: a = intersection of R4+5 with r-m vein; b = intersection of R4+5 vein with a line drawn in the middle between a and c; c = the intersection of R4+5 with M1 vein; D = the angle formed by the lines that connect a, b and c.
Fig. 4 in An assessment of new character in hoverfly species delimitation using linear and geometric morphometrics - genus Merodon Meigen, 1803 (Diptera: Syrphidae) as a case study
Fig. 4. Results of the geometric morphometric wing shape analysis of species of the Merodon aureus complex. A. Scatter plot of individual scores showing R4+5 vein shape variability. B. Scatter plot of individual scores showing wing shape variability from Vujić et al. (2020c). C. Scatter plot of individual scores showing semilandmark R4+5 vein shape and landmark wing shape variability D. Superimposed outline drawings showing R4+5 vein shape differences among investigated species.
Fig. 5 in An assessment of new character in hoverfly species delimitation using linear and geometric morphometrics - genus Merodon Meigen, 1803 (Diptera: Syrphidae) as a case study
Fig. 5. Results of the geometric morphometric wing shape analysis of males of the Merodon natans group. A. Scatter plot of individual scores showing the R4+5 vein shape variability. B. Scatter plot of individual scores showing the wing shape variability from Vujić et al. (2021c). C. Scatter plot of individual scores showing the semilandmark R4+5 vein shape and landmark wing shape variability D. Superimposed outline drawings showing R4+5 vein shape differences among males of the investigated species.
Fig. 3. Box plot showing a in An assessment of new character in hoverfly species delimitation using linear and geometric morphometrics - genus Merodon Meigen, 1803 (Diptera: Syrphidae) as a case study
Fig. 3. Box plot showing a comparison of the angle at the intersection of the R4+5 vein and the middle
Fig. 2. Merodon aureus Fabricius, 1805 in An assessment of new character in hoverfly species delimitation using linear and geometric morphometrics - genus Merodon Meigen, 1803 (Diptera: Syrphidae) as a case study
Fig. 2. Merodon aureus Fabricius, 1805, ♂, right wing with the location of 20 semilandmarks selected for geometric morphometric analysis.
Fig. 3. Box plot showing a in An assessment of new character in hoverfly species delimitation using linear and geometric morphometrics - genus Merodon Meigen, 1803 (Diptera: Syrphidae) as a case study
Fig. 3. Box plot showing a comparison of the angle at the intersection of the R4+5 vein and the middle line for all species used in the analysis.
Fig. 7 in An assessment of new character in hoverfly species delimitation using linear and geometric morphometrics - genus Merodon Meigen, 1803 (Diptera: Syrphidae) as a case study
Fig. 7. Results of the geometric morphometric wing shape analysis of males of the Merodon clavipes and pruni groups. A–B. Scatter plot of individual scores showing the R4+5 vein shape variability. C–D. Scatter plot of individual scores showing the wing shape variability from Vujić et al. (in prep.). E–F. Scatter plot of individual scores showing the semilandmark R4+5 vein shape and landmark wing shape variability. G–H. Superimposed outline drawings showing the R4+5 vein shape differences between the males of the investigated species.
Fig. 6 in An assessment of new character in hoverfly species delimitation using linear and geometric morphometrics - genus Merodon Meigen, 1803 (Diptera: Syrphidae) as a case study
Fig. 6. Results of the geometric morphometric wing shape analysis of females of the Merodon natans group. A. Scatter plot of individual scores showing the R4+5 vein shape variability. B. Scatter plot of individual scores showing wing the shape variability from Vujić et al. (2021c). C. Scatter plot of individual scores showing the semilandmark R4+5 vein shape and landmark wing shape variability D. Superimposed outline drawings showing the R4+5 vein shape differences among females of the investigated species.
Metazoa-level USCOs as markers in species delimitation and classification
<p><span>Metazoa-level<strong> </strong>Universal Single-Copy Orthologs (USCOs) are universally applicable markers for DNA taxonomy in animals which can replace or supplement single-gene barcoding. While Metazoa-level USCOs from target enrichment data were shown to reliably distinguish species, it remains to be tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome, and hence can facilitate detection of past hybridization events. Besides, unlinked loci are a principal assumption in coalescent-based species delimitation approaches. 239 chromosome-level genomes were analyzed to show that Metazoa-level<strong> </strong>USCOs are a representative sample of a genome: in terms of distances to each other on a chromosome, but also over the chromosomes, they are almost as evenly distributed as protein-coding genes in general are. We tested the suitability of Metazoa-level USCOs extracted from genomes for species delimitation and phylogeny in four case studies: <em>Anopheles</em> mosquitos, <em>Drosophila</em> fruit flies, <em>Heliconius </em>butterflies, and Darwin's finches. In almost all instances USCOs allowed delineating species and yielded phylogenies that correspond to those generated from whole genome data.<strong> </strong>Our results show<strong> </strong>that USCO genes can be considered as genetically unlinked for practical purposes and representative for an entire metazoan genome. Our phylogenetic analyses demonstrate that USCOs may complement single-gene barcoding and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and at times impact taxonomic conclusions. However, we expect this problem to become less severe as the size of genome reference libraries and their sampling of organismic lineages is rapidly increasing.</span></p>
Data for: Morphological species delimitation in the Western Pond Turtle (Actinemys): Can machine learning methods aid in cryptic species identification?
<p>As the discovery of cryptic species has increased in frequency, there has been interest in whether geometric morphometric data can detect fine-scale patterns of variation that can be used to morphologically diagnose such species. We used a combination of geometric morphometric data and an ensemble of five supervised machine learning methods to investigate whether plastron shape can differentiate two putative cryptic turtle species, <em>Actinemys marmorata</em> and <em>Actinemys pallida</em>. <em>Actinemys</em> has been the focus of considerable research due to its biogeographic distribution and conservation status. Despite this work, reliable morphological diagnoses for its two species are still lacking. We validated our approach on two datasets, one consisting of eight morphologically disparate emydid species, and the other consisting of two subspecies of <em>Trachemys</em> (<em>T. scripta scripta</em>, <em>T. scripta elegans</em>). The validation tests returned near-perfect classification rates, demonstrating that plastron shape is an effective means for distinguishing taxonomic groups of emydids via machine learning methods. By contrast, the same methods did not return high classification rates for a set of alternative phylogeographic and morphological binning schemes in <em>Actinemys</em>. All classification hypotheses performed poorly relative to the validation datasets and no single hypothesis was unequivocally supported for <em>Actinemys</em>. Two hypotheses had machine learning performance that was marginally better than our remaining hypotheses. In both cases, those hypotheses favored a two-species split between <em>A. marmorata</em> and <em>A. pallida</em> specimens, lending tentative morphological support to the hypothesis of two <em>Actinemys</em> species. However, the machine learning results also underscore that <em>Actinemys</em> as a whole have lower levels of plastral variation than other turtles within Emydidae, but the reason for this morphological conservatism is unclear.</p>
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