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opencc-by-3.0Nov 2017View details →

Fig. 3 in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia

Fig. 3. Posterior estimates of divergence time of 24 taxa on the phylogenetic tree. Blue bars depict the 95% highest posterior density (HPD). Estimations were performed with MCMCTree using the independent rate model.

opencc-by-3.0Nov 2017View details →

Fig. 1. Bayesian majority rule consensus tree reconstructed for 90 in Phylogenetic analysis and systematic position of two new species of the ant genus Crematogaster (Hymenoptera, Formicidae) from Southeast Asia

Fig. 1. Bayesian majority rule consensus tree reconstructed for 90 taxa using five genes (ArgK, CAD, LWRh, Top1, Wg) in a MrBayes analysis. Above node numbers indicate posterior probability. Data were partitioned by PartitionFinder v.1.1.1 and analyzed using a best fit model for each gene and codon position, with 10 million generations and a burn-in of 25 %. Area enclosed by dashed lines is enlarged on Fig. 2.

opencc-by-3.0Oct 2012View details →

Fig. 2. Phylogenetic tree constructed with 57 in A review of Bennelongia De Deckker & McKenzie, 1981 (Crustacea, Ostracoda) species from eastern Australia with the description of three new species

Fig. 2. Phylogenetic tree constructed with 57 novel COI sequences of Bennelongia, 26 published Bennelongia sequences and one Heterocypris spec. as outgroup (sequence names are given in brackets at the end of species names). This tree represents two trees of identical topology inferred by ML and BI. Bootstrap values (for 1000 bootstrap replicates) from ML analyses and Bayesian posterior probabilities (ranging from 0 to 1) are shown for each node (in the format: 'Bootstrap Support/Posterior Probability'). Branch lengths are proportional to the genetic distance scale at the bottom left. Clades with published sequences have been collapsed; the number of sequences in these clades is included in brackets after the species name. Nodes with less than 50% bootstrap support and a posterior probability of less than 0.5 have been collapsed. The tree shows six strongly supported clades that correspond to the species presented in this study.

opencc-by-4.0May 2020View details →

Genetic data and underlying taxa and GenBank sources of diatoms used in phylogenetic analysis for the diatom genus Nupela

Supplementary material for the manuscript: Kulikovskiy M., Maltsev Y., Glushchenko A., Gusev E., Kapustin D., Kuznetsova I., Kociolek J.P. Preliminary molecular phylogeny of the diatom genus Nupela with the description of a new species and consideration of the interrelationships of taxa in the suborder Neidiineae D.G. Mann sensu E.J. Cox. Fottea Molecular investigation of diatom genera Nupela and Brachysira is conducted using strains from Indonesia and Vietnam. New species from the genus Nupela indonesica sp. nov. is described using combined approach. Nupela lesothensis (Schoeman) Lange-Bertalot is investigated using molecular data too. Phylogenetic analysis shows that Nupela and Brachysira are not closest genera. Morphology of Nupela and it differences from Brachysira is discussed. The genus Nupela is differs from all other diatom taxa by having coalescent hymenes ouside of areolae but not inside. Facultative development of raphe between different Nupela species is discussed. SUPPLEMENT S1. Taxa and DNA sequence data used in phylogenetic analysis. SUPPLEMENT S2. Final alignment of 2-gene DNA sequence data used for phylogenetic analysis in FASTA format. SUPPLEMENT S3. Maximum Likelihood tree of Nupela species (indicated in bold) constructed from a concatenated alignment of 163 partial rbcL and partial 18S rDNA sequences of 1806 characters. Values near the horizontal lines (slash) are bootstrap support from RAxML analyses (<50 are not shown). Species from the centric diatoms were used as an outgroup. Families indicated according COX (2015).

opencc-zeroJun 2020View details →

FIG. 7 in Description of a new species of Cynodictis Bravard & Pomel, 1850 (Carnivora, Mammalia) from the Quercy Phosphorites with comments on the use of skull morphology for phylogenetics

FIG. 7. — Cranium of Cynodictis lacustris Gervais, 1852 (MNHN.F.Qu1903-20) in dorsal view (A), lateral view (B) and ventral view (C). Abbreviations: bo, basioccipital; bs, basisphenoid; ce, carnassial embrasure pit; csm, crista supramastoideus; eo, exoccipital; fm, foramen magnum; fr, frontal; M1, upper first molar; mp, mastoid process; mx, maxillary; nc, nuchal crest; oc, occipital condyle; pa, parietal; pal, palatine; pop, postorbital process of frontal; pp, paroccipital process; pr, promontorium of petrosal; ps, presphenoid; pt, pterygoid; ptp, posttympanic process of squamosal; rt, foramen for ramus temporalis; sc, sagittal crest; tc, temporal crest. Scale bar: 10 mm.

opencc-by-4.0Jun 2020View details →

Neighbor-joining phylogenetic tree based on 16S rRNA sequences.

Supplementary Figure (S1): Bayesian 50% majority rule phylogram of 16S ribosomal RNA region showing the phylogenetic relationships among the bacterial isolates in our study. The newly generated sequences are preceded by red circle. The GenBank sequences are preceded by blue squares. The GenBank accession number appears after the species name. Numbers above the branches represent Bayesian posterior probabilities (≥ 0.90), and the maximum parsimony bootstrap support values are given below the branches (≥70%). The out group used for tree construction preceded by empty circle.

opencc-zeroJun 2020View details →

FIG. 2 in Description of a new species of Cynodictis Bravard & Pomel, 1850 (Carnivora, Mammalia) from the Quercy Phosphorites with comments on the use of skull morphology for phylogenetics

FIG. 2. — Cranium of Cynodictis peignei n. sp. (snout – MNHN.F.Qu9007; neurocranium – MNHN.F.Qu9008) in dorsal view (A), lateral view (B) and ventral view (C). Abbreviations: bo, basioccipital; bs, basisphenoid; C, upper canine; ce, carnassial embrasure pit; csm, crista supramastoideus; eo, exoccipital; fm, foramen magnum; fr, frontal; gf, glenoid fossa; I3, upper third incisor; inf, incisive foramen; iof, infraorbital foramen; ju, jugal; lac, lacrimal; lacf, lacrimal foramen; mp, mastoid process; mpfr, maxillary process of frontal; mx, maxillary; mxt, maxillary tuberosity; na, nasal; nc, nuchal crest; np, nasal process of nasal; oc, occipital condyle; P1, upper first premolar; P2, upper second premolar; P3, upper third premolar; P4, upper ultimate premolar; pa, parietal; pal, palatine; pdp, posterodorsal process of premaxillary; pgp, postglenoid process; pmx, premaxillary; pop, postorbital process of frontal; pp, paroccipital process; pr, promontorium of petrosal; ptp, posttympanic process of squamosal; rt, foramen for ramus temporalis; sc, sagittal crest; sq, squamosal; zpmx, zygomatic process of maxillary; zpsq, zygomatic process of squamosal. Scale bar: 10 mm.

Fig. 55. One ofthreetreesfromtotalevidenceanalysiswith POYof 92-taxondatasetusing 2 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)

Fig. 55. One ofthreetreesfromtotalevidenceanalysiswith POYof 92-taxondatasetusing 2: 2 indel ⁄ transition–transversioncostratio, whichhad the lowest MRI value. Bremer support values are shown.

Fig. 53 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)

Fig. 53. One of six trees from total evidence analysis with POY of 92-taxon data set using 1: 1 indel ⁄ transition–transversion cost ratio. (d) Non-homoplasious; (s) homoplasious.

Figs 45–48. 45. Oneoftwotreesderivedfromanalysisofcombinedmoleculardatawith 1 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)

Figs 45–48. 45. Oneoftwotreesderivedfromanalysisofcombinedmoleculardatawith 1: 1 indel ⁄ transition–transversioncostratio. 46. Singletree derivedfromanalysisofcombinedmoleculardatawith 2: 2 indel ⁄ transition–transversioncostratio. 47. Singletreederivedfromanalysisof ~500 bp of 16S rRNAdatausing 1: 1 indel ⁄ transition–transversioncost ratio. 48. Singletreederivedfromanalysis of ~1800 bpof 18S rRNAusing 1: 1 indel ⁄ transition–transversioncostratio.

Fig. 43 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)

Fig. 43. Strict consensus of three trees derived from successive weighting of the results shown in Fig. 42. (d) Non-homoplasious; (s) homoplasious.

Figs 16–24. 16 in Phylogenetic relationships of family groups in Pentatomoidea based on morphology and DNA sequences (Insecta: Heteroptera)

Figs 16–24. 16. Saileriola sandakanensis (Saileriolidae). Coxae of middle and hind legs more distant from each other. 17a. Cydnus aterrimus (Cydnidae): hind tibiae, posterior view; 17b. Dallasiellus dilatipes (Cydnidae): fore tibiae, anterior view. 18. Ruckesona vitrella (Saileriolidae). Abdominal trichobothria. 19. Serbana borneensis (Phloeidae). Abdominal trichobothria. 20. Atarsocoris sp. (Cydnidae). Abdominal trichobothria. 21. Edessa sp. (Pentatomidae). Abdominal spiracles well removed from lateral margins of sternum. 22. Phloea subquadrata (Phloeidae). Male abdominal segment VIII with spiracles. 23. Tessaratoma papillosa (Tessaratomidae). Spiracles on second segment totally exposed and far removed from lateral margins of sternum. 24. Ruckesona vitrella (Saileriolidae), female. Sternite VII split on the midline.

opencc-by-4.0Sep 2015View details →

Figure 1. Bayesian phylogenetic tree inferred from the 640 in Two new Geoplaninae species (Platyhelminthes: Continenticola) from Southern Brazil based on an integrative taxonomic approach

Figure 1. Bayesian phylogenetic tree inferred from the 640-bp of cytochrome c oxidase subunit I gene under GTR + I + G model of sequence evolution. The two new species are highlighted in light grey (Cratera ochra sp. nov.) and dark grey (Obama maculipunctata sp. nov.). Values indicate support for each node according to the maximum posterior probabilities>70% and bootstrap support values> 70%, respectively.

opencc-by-4.0Aug 2020View details →

Phylogenetic signal in phonotactics: Supplementary materials

Data, code and results for the paper Phylogenetic signal in phonotactics (<a href="https://doi.org/10.1075/dia.20004.mac">Macklin-Cordes, Bowern & Round, 2021</a>). Information and usage instructions are found in the readme.txt file and Section S3 of the paper's Supplementary Information.

opencc-by-4.0Aug 2020View details →

Fig. 23. Phylogenetic hypothesis for the Halopterididae Millard, 1962 in Plumularioid hydroids (Cnidaria: Hydrozoa) from off New Caledonia collected during KANACONO and KANADEEP expeditions of the French Tropical Deep-Sea Benthos Program

Fig. 23. Phylogenetic hypothesis for the Halopterididae Millard, 1962. The species discussed in this study is highlighted in yellow, and the newly-produced sequence is in bold. Numbers at nodes represent BPP and BS, respectively, and are shown only when both BPP Ż 0.9 and BS Ż 75.

Fig. 7. Potamonautes choloensis Chace, 1953 in Phylogenetics of the freshwater crab (Potamonautes MacLeay, 1838) fauna from 'sky islands' in Mozambique with the description of a new species (Brachyura: Potamoidea: Potamonautidae)

Fig. 7. Potamonautes choloensis Chace, 1953 (SAM A46802). A. Left gonopod 1, anterior view. B. Left gonopod 1, posterior view. C. Left gonopod 2, anterior view. Scale bar = 10 mm.

Fig. 8 in Phylogenetics of the freshwater crab (Potamonautes MacLeay, 1838) fauna from 'sky islands' in Mozambique with the description of a new species (Brachyura: Potamoidea: Potamonautidae)

Fig. 8. Map showing the distribution of all the known and some as yet undescribed freshwater crab species from the 'sky islands' of Malawi, Mozambique and Zimbabwe. Two new freshwater species not yet described are listed as undescribed sp. 1 and 2 respectively.

Fig. 5. A in Phylogenetics of the freshwater crab (Potamonautes MacLeay, 1838) fauna from 'sky islands' in Mozambique with the description of a new species (Brachyura: Potamoidea: Potamonautidae)

Fig. 5. A. Primary rainforest habitat where Potamonautes licoensis sp. nov. occurs. B. Live colour of P. licoensis sp. nov upon collection. Photographs by J. Bayliss.

Fig. 6. Potamonautes choloensis Chace, 1953 in Phylogenetics of the freshwater crab (Potamonautes MacLeay, 1838) fauna from 'sky islands' in Mozambique with the description of a new species (Brachyura: Potamoidea: Potamonautidae)

Fig. 6. Potamonautes choloensis Chace, 1953 (SAM A46802). A. Entire animal, dorsal aspect. B. Entire animal, ventral aspect. C. Cephalothorax, frontal aspect. Scale bar = 10 mm.

Fig. 1. A in Phylogenetics of the freshwater crab (Potamonautes MacLeay, 1838) fauna from 'sky islands' in Mozambique with the description of a new species (Brachyura: Potamoidea: Potamonautidae)

Fig. 1. A Bayesian Inference phylogram and divergence time estimation for the three mtDNA loci (12S rRNA +16S rRNA + COI) for the eastern and southern African freshwater crab genus Potamonautes MacLeay, 1838, with outgroups removed. Bootstrap values> 75% are indicated below each node while posterior probability values> 0.95 pP are shown above each node by an asterisk (*). Where no asterisk is present no support for a node was obtained. Blue polygons on branches indicates species present, on Mozambique 'sky islands'.