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opencc-by-4.0Aug 2020View details →

Fig. 54 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)

Fig. 54. Maximum likelihood tree inferred from CO1 gene of species of Loxosceles Heineken & Lowe, 1832 from Mexico. Colors of branches and bars indicate different species. Numbers above bars represent the delimitation methods: 1 = morphology (M); 2 = neighbor joining (NJ); 3 = ABGD with initial partitions (IP); 4–6 = ABGD with recursive partitions (RP); 7 = GMYC yule analysis; 8 = GMYC coalescent analysis; 9 = bPTP with ML; 10 = bPTP with IB. Numbers below bars represent species recovered for each delimitation method. Red numbers on branches correspond to Bayesian posterior probabilities, black numbers are bootstrap support values from the ML analysis.

Fig. 7 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 7. Anaplecta cruciata Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Tegmina. F. Tegmina vein. G. Maxillary palp. H. Front femur, ventral view. I. Wings. J. Supra-anal plate, dorsal view. K. Subgenital plate, ventral view. L. Hook, ventral view. M. Left phallomere, ventral view. N. Right phallomere, ventral view. Scale bars: A–C = 1 mm; D–F, I–K = 0.5 mm; G–H = 0.2 mm; L–N = 0.25 mm.

Fig. 5 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 5. Anaplecta strigata Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Tegmina. F. Tegmina vein. G. Maxillary palp. H. Front femur, ventral view. I. Wings. J. Supra-anal plate, dorsal view. K. Subgenital plate, ventral view. L. Hook, ventral view. M. Left phallomere, ventral view. N. Right phallomere, ventral view. Scale bars: A–B = 2 mm; C, E–F, I = 1 mm; D, G–H, J–K, M–N = 0.5 mm; L = 0.25 mm.

Fig. 10. A–B, E in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 10. A–B, E. Anaplecta omei Bey-Bienko, 1958. A. Habitus, dorsal view. B. Habitus, ventral view. E. Supra-anal plate, dorsal view. – C–D. Anaplecta basalis Bey-Bienko, 1969. C. Habitus, dorsal view. D. Habitus, ventral view. – F–I. Comparison of R1 of A. corneola Deng & Che sp. nov. from different localities. F. Guangdong Prov., Zhaoqing City (ZQ). G. Hainan Prov., Ledong County, Mt. Jianfengling (JFL1). H. Hunan Prov., Chenzhou City, Yizhang County, Mangshan National Forest Park (MS). I. Fujian Prov., Wuyishan City, (WY). Scale bars: A–B = 2 mm; C–D = 1 mm; E = 0.5 mm; F–I = 0.25 mm.

Fig. 4 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 4. Anaplecta arcuata Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Maxillary palp. F. Front femur, ventral view. G. Tegmina. H. Wings. I. Supra-anal plate, dorsal view. J. Subgenital plate, ventral view. K. Hook, ventral view. L. Left phallomere, ventral view. Scale bars: A–B, G–H = 2 mm; C = 1 mm; D–F, I–J = 0.5 mm; K–L = 0.1 mm.

Fig. 1 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 1. Maximum-likelihood (ML) tree derived from COI gene analysis following GTR GAMMA model with 1000 bootstrap replicates. Colored bars in red refer to the morphospecies, those in blue to MOTUs in ABGD and those in purple to MOTUs in GMYC.

Fig. 6 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 6. Anaplecta furcata Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Tegmina. F. Tegmina vein. G. Maxillary palp. H. Front femur, ventral view. I. Wings. J. Supra-anal plate, dorsal view. K. Supra-anal plate. L. Subgenital plate, ventral view. M. Hook, ventral view. N. Left and right phallomere, ventral view. Scale bars: A–B = 1 mm; C–F, H–N = 0.5 mm; G = 0.25 mm.

Fig. 3 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 3. Anaplecta staminiformis Deng & Che sp. nov. A–M. Holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Maxillary palp. F. Front femur, ventral view. G. Tegmina. H. Wings. I. Supra-anal plate, dorsal view. J. Subgenital plate, ventral view. K. Hook, ventral view. L. Left phallomere, ventral view. M. Right phallomere, ventral view. – N–P. Paratype, ♂, samples from LMS (SWU). N. Hook, ventral view. O. Left phallomere, ventral view. P. Right phallomere, ventral view. Scale bars: A–B, G–H = 2 mm; C, E–F = 1 mm; D, I–J, L–M, O–P = 0.5 mm; K, N = 0.25 mm.

opencc-zeroDec 2020View details →

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Anatomical partitioning has little influence in topologies from Bayesian phylogenetic analyses of morphological data

Morphological data is a fundamental source of evidence to reconstruct the Tree of Life, and Bayesian phylogenetic methods are increasingly being used for this task, along with, or instead of, traditional parsimony approaches. Bayesian phylogenetic analyses require the use of proper evolutionary models and their performance have been intensively studied in the past few years, with significant improvements to our knowledge regarding their performance. Notwithstanding, it was only recently that partitioned models for morphology received attention in studies of empirical data, but a systematic evaluation of its performances using simulations was never performed. Here we evaluate the influence of partitioned models defined by anatomical criterion in the precision and accuracy of consensus tree topologies, evaluating the possible negative effects of under and overpartitioning. For that, we analysed datasets simulated using parameters and properties of two empirical datasets, using Bayesian phylogenetic analyses in MrBayes. Additionally, we reanalysed 32 empirical datasets for diverse groups of vertebrates, applying unpartitioned and partitioned models. We found that in general, partitioning by anatomy has little to no influences in the performance of Bayesian phylogenetic methods in respect to the metrics studied here, with analyses under alternative partitioning schemes presenting very similar tree precision and accuracy. We discuss the possible reasons for the disagreement between the results obtained here and previous studies for empirical morphological data, and with empirical and simulation studies of molecular data, discussing the adequacy of anatomical partitioning relative to alternative methods to partition morphological datasets and how morphological and molecular partitioning are related.

opencc-by-4.0Nov 2020View details →

Replication R code and data for "Geometric morphometric investigation of craniofacial morphological change in domesticated silver foxes"

This repository holds various files and R code used in the publication of the manuscript entitled "Geometric morphometric investigation of craniofacial morphological change in domesticated silver foxes". Data files include: The 3D landmark coordinates of each individual specimen (Fox_data_Morphologika.txt), the linear measurement data associated with those foxes (fox_linear_volume_data.csv), and replication data measurements.  The following files include the R code used to perform the analyses contained within the paper: 1_Procrustes_analysis - details the Geometric morphometrics analyses performed 2_linear_models - details the model specification for the GLS models employed in the paper 3_graph_code - contains R script for the creation of the graphs displayed in the paper 4_repeatability_script - contains R code that details the statistical calculations made with the repeatability measurements indicated above.

opencc-by-4.0Jun 2021View details →

Data for: Faster rates of molecular sequence evolution in reproduction-related genes and in species with hypodermic sperm morphologies

This repository contains a record of analysis scripts and sequence alignments used for the analyses presented in the manuscript. Some of the R scripts depend on supplementary tables associated with the manuscript.

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Data from: Genetic and morphological evidence of a geographically widespread hybrid zone between two crocodile species, Crocodylus acutus and Crocodylus moreletii

Hybrid zones represent natural laboratories to study gene flow, divergence and the nature of species boundaries between closely related taxa. We evaluated the level and extent of hybridization between Crocodylus moreletii and C. acutus using genetic and morphological data on 300 crocodiles from 65 localities. To our knowledge, this is the first genetic study that includes the entire historic range and sympatric zone of the two species. Contrary to expectations, Bayesian admixture proportions and maximum likelihood estimates of hybrid indexes revealed that most sampled crocodiles were admixed and that the hybrid zone is geographically extensive, extending well beyond their historical region of sympatry. We identified a few geographically isolated, non-admixed populations of both parental species. Hybrids do not appear to be F1s or recent backcrosses, but rather are more likely later-generation hybrids, suggesting that hybridization has been going on for several to many generations and is mostly the result of natural processes. C. moreletii is not the sister species of C. acutus, suggesting that the hybrid zone formed from secondary contact rather than primary divergence. Non-admixed individuals from the two species were distinguishable based on morphological characters, whereas hybrids had a complex mosaic of morphological characters that hinders identification in the wild. Very few non-admixed C. acutus and C. moreletii populations exist in the wild. Consequently, the last non-admixed C. moreletii populations have become critically endangered. Indeed, not only the parental species but also the naturally occurring hybrids should be considered for their potential conservation value.

opencc-zeroDec 2015View details →

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Comparative data for dance fly eye morphology and female ornamentation

These data were collected as part of a comparative study of the relationship between female ornamentation and sexual dimorphism in eye morphology. Data come from specimens collected in the field in Scotland near Loch Lomond in the summers of 2009, 2010, and 2011 as well as the summer of 2012 near Glen Williams in Ontario, Canada. The repository contains raw image files including information on magnifications at which these were taken, excel spreadsheets of morphological measurements taken from these images, a dataset from search of Collin's (1961) key to the Empidinae for reports of sexual dimorphism and exaggerations of male eye morphology, and an Rnotebook file detailing the analytical steps taken.

opencc-zeroApr 2020View details →

opencc-zeroDec 2004View details →

FIGURE 6 in Salamandridae) using molecular and morphological data. Revalidation of the taxon Pleurodeles nebulosus (Guichenot, 1850)

FIGURE 6. Ventral aspect of the skull of A. adult P. p o i re t i, BMNH 1920.1. 20.1383 (Bône) and B. adult P. nebulosus, BMNH 130 a (Algiers).

opencc-zeroDec 2004View details →

FIGURE 1 in Salamandridae) using molecular and morphological data. Revalidation of the taxon Pleurodeles nebulosus (Guichenot, 1850)

FIGURE 1. Map of North Africa showing localities of Pleurodeles used in the present study. See Table 1 and Fig. 5 for further details. The dashed line delimits the approximate distribution range of P. poireti. We refer to it in the text as the Edough Peninsula.

opencc-zeroDec 2004View details →

FIGURE 3 in Salamandridae) using molecular and morphological data. Revalidation of the taxon Pleurodeles nebulosus (Guichenot, 1850)

FIGURE 3. Photograph showing nine specimens of P. p i o i re t i (above) and four P. nebulosus (below). A 23 centimetres scale bar is shown on the lefthand side of the picture; black rectangles and intermediate white spaces all represent 1 cm. Numbers above the specimens refer to: 1. BMNH 1920.1. 20.1327. 2, largest specimen of P. p oireti included in the present study. Female from Bône (Annaba); 2. BMNH 1946.9. 6.77, male of P. poireti from Mount Edough; 3. BMNH 1946.9. 6.78, male of P. p o i re t i from Mount Edough; 4. BMNH 1946.9. 6.79, male of P. poireti from Mount Edough; 5. BMNH 1946.9. 6.80, male of P. p o i re t i from Mount Edough; 6. BMNH 1946.9. 6.81, male of P. p o i re t i from Mount Edough; 7. BMNH 1946.9. 6.79, male of P. poireti from Mount Edough; 8. MNHNP 4744, female, paralectotype of P. p o i re t i from Bône (Annaba); 9. MNHNP 4744 A, male, lectotype of P. p o i ret i from Bône (Annaba); 10. BMNH 1.1.3.1. a, largest specimen of P nebulosus recorded to date. Male from N. Africa; 11. BMNH 88.4. 9.3, female of P. nebulosus from Algiers; 12. BMNH 88.4. 4, male of P. nebulosus from Algiers; 13. MNHNP 1442, female, lectotype of P. nebulosus from Algiers.

FIGURE 30 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status

FIGURE 30. Bayesian tree (TPM 2 uf + G) for Aegla species based on partial fragment of 16 S. Node numbers represent posterior probabilities (values <50 % are not shown), and divergence time in millions of years (my); * indicates the calibration points to molecular clock. The clade C proposed by Pérez-Losada et al. (2004) is highlighted in grey. The basin and sub-basin origin of the discussed species in this study are shown after the specific names.

FIGURE 24. A – L in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status

FIGURE 24. A – L, proximal portion of fifth pereiopod showing coxa and sexual tube of long and narrow type. A – B, Aegla paulensis Schmitt, 1942 s. str., male topotype (MZUSP 34368). C – D, Aegla rosanae Campos Jr., 1998, male topotype (MZUSP 34369). E – F, Aegla vanini n. sp., male paratype (MZUSP 34372). G – H, Aegla japi n. sp., male paratype (MZUSP 34375). I – J, Aegla jaragua n. sp. male paratype (MZUSP 34378). K-L, Aegla jundiai n. sp., male paratype (MZUSP 13490). Bars: A – D, F – H, J = 200 µm; K, L = 100 µm; E, I = 500 µm.

FIGURE 8 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status

FIGURE 8. Types of Aegla Leach, 1820 male sexual tubes. A, long and narrow (A. lancinhas Bond-Buckup & Buckup in Santos et al., 2015, MZUSP 34403). B, short and wide (A. leptochela Bond-Buckup & Buckup, 1994, MZUSP 34491).

FIGURE 1 in Morphological and molecular data reveal the cryptic diversity among populations of Aegla paulensis (Decapoda, Anomura, Aeglidae), with descriptions of four new species and comments on dispersal routes and conservation status

FIGURE 1. Distribution of the species of Aegla in four main hydrographic basins of southern Brazil: Rio Grande, Rio Tietê (Upper Paraná system), Rio Paraíba do Sul and Ribeira de Iguape. Indications L 1 through L 7 refer to the locations mentioned under “ sampling area ” in the Material & Methods section.