Find research datasets worth reusing

FIGURE 4 in Rumen ciliates (Alveolata, Ciliophora) associated with goats: checklist, geographic distribution, host specificity, phylogeny and molecular dating

FIGURE 4. Interaction network between ciliate protozoa species associated with goats and other hosts. The bars in grey and black represent some hosts that associate with ciliates and the ciliate protozoa species, respectively. The colored arrows (ranging from black to red) represent the associations between hosts and ciliate species. The size of the grey and black bars represents the hosts and ciliate species with greater or lower association, respectively (Dogiel 1928; Dehority 1974; Vasily & Mitchell 1974; Wilkinson & Van Hoven 1976; Kleynhans & Hoven 1976; Van Hoven et al. 1979; Dehority 1987; Towne et al. 1988; Dehority 1995; Selim et al. 1996; Dehority 1997; Wright & Lynn 1997; Selim et al. 1999; Dehority et al. 1999; Franzolin & Dehority 1999; Su et al. 2000; Imai et al. 2004; Talar et al. 2004; De la Fuente et al. 2006; Obanda et al. 2008; Del Valle et al. 2008; Martinele & D'Agosto 2008; Mishima et al. 2009; Booyse & Dehority 2012; Baraka 2012; Booyse et al. 2014; Booyse et al. 2015; Cerón Cucchi et al. 2016; Cedrola et al. 2016; Cedrola et al. 2017; Kimura et al. 2017; Gürelli 2017; Gürelli 2018; Cedrola et al. 2018).

FIGURE 5 in Rumen ciliates (Alveolata, Ciliophora) associated with goats: checklist, geographic distribution, host specificity, phylogeny and molecular dating

FIGURE 5. Phylogenetic tree obtained through Maximum Likelihood representing evolutionary relationships of some species of ciliates, based on 18S rDNA sequences. The red color represents species observed in studies with rumen samples from goats. Subclass Haptoria was chosen as outgroup. The values in each node of the tree mean, respectively: Maximum Likelihood (ML) bootstrap and Bayesian inference (BI) values of posterior probability. Scale bar represents 3 substitutions per 100 nucleotide positions.

FIGURE 2 in Rumen ciliates (Alveolata, Ciliophora) associated with goats: checklist, geographic distribution, host specificity, phylogeny and molecular dating

FIGURE 2. Schematic representation of the association of ciliate protozoa genera and the host species of the Caprinae subfamily. The numbers around the circle represent the number of times a genus has been observed in a host. The colors red, pink, caramel and dark orange of the bars represent, respectively, the hosts Capra hircus, Rupicapra rupicapra, Capra pyrenaica, and Capra ibex, and the genera associated with them. The lines within the circle indicate the association between host species and the genera.

FIGURE 3 in Rumen ciliates (Alveolata, Ciliophora) associated with goats: checklist, geographic distribution, host specificity, phylogeny and molecular dating

FIGURE 3. Geographic and quantitative distribution of the ciliate protozoa species associated with goats. Some regions in the map (Spain, former Czechoslovakia, Italy, South Korea and Japan), were amplified for better visualization of the geographic boarders (Lubinsky 1955; Christl 1958; Imai et al. 1978; Lee 1979; Crha et al. 1985; Fernandez-Galiano & Campos 1992; Ito et al. 1995; Gurung et al. 2002; Göçmen & Atatur 2002; Göçmen et al. 2002; Mermer et al. 2003; Rastgeld & Göçmen 2003; Göçmen & Rastgeldi 2004; Talar et al. 2004; Göçmen et al. 2005; Göçmen & Karaoðlu 2005; De la Fuente et al. 2006; Mermer et al. 2006; Göçmen & Sezgin 2006; De la Fuente et al. 2009; Baraka 2012; Gürelli 2014; Gürelli et al. 2016; Mohamed 2017).

FIGURE 1 in Rumen ciliates (Alveolata, Ciliophora) associated with goats: checklist, geographic distribution, host specificity, phylogeny and molecular dating

FIGURE 1. Schematic drawings of the rumen ciliate species described in goats (Christl 1958; Fernandez-Galiano & Campos 1992; Göçmen & Rastgeldi 2004; Göçmen et al. 2005). A. Entodinium alpinum; B. Entodinium ibicis; C. Entodinium couturier; D. Entodinium wertheimi; E. Entodinium salmani; F. Ophryoscolex monoacanthus. G-H: frequent species in observations of caprine rumen samples; G. Isotricha prostoma; H. Dasytricha ruminantium; I. Entodinium dubardi; J. Entodinium caudatum; K. Entodinium exiguum; L. Entodinium minimum; M. Entodinium simplex; N. Entodinium longinucleatum; O. Epidinium ecaudatum. Abbreviations: ACZ, adoral ciliary zone; CV, contractile vacuole; CS, caudal spine; Ma, macronucleus; Mi, micronucleus; Ve, vestibulum; Sk, skeletal plate. Scale bar:10μm.

Figure 1 in Total-evidence dating and morphological partitioning: a novel approach to understand the phylogeny and biogeography of augochlorine bees (Hymenoptera: Apoidea)

Figure 1. Bayesian consensus tree from morphological data with homoplasy criterion partitioning for Augochlorini bees. Node numbers represent the posterior probabilities. Genus groups coloured as in Figure 2. Red font indicates fossil species.

Figure 2 in Total-evidence dating and morphological partitioning: a novel approach to understand the phylogeny and biogeography of augochlorine bees (Hymenoptera: Apoidea)

Figure 2. Total-evidence time-calibrated consensus tree for Augochlorini bees. Bars represent the 95% Highest Posterior Density interval for node ages, node numbers represent the posterior probabilities. Genus groups coloured as in Figure 1. Absolute time scale presented in millions of years. Red font indicates fossil species.

opennotspecifiedSep 2024View details →

Figure 12. Tip-dated Bayesian phylogenetic analyses. A, unconstrained phylogeny using hypothesis 1 in A new dentition-based phylogeny of Litopterna (Mammalia: Placentalia) and 'archaic' South American ungulates

Figure 12. Tip-dated Bayesian phylogenetic analyses. A, unconstrained phylogeny using hypothesis 1 (H1) matrix. B, tip-dated topology constrained Bayesian phylogeny using hypothesis 1 (H1) matrix and constraining the node for the common ancestor of SANUs between the K/Pg boundary and the oldest age for the kollpaniines of Tiumpampa (66–65.075 Mya). The topological constraint in (B) was based on the topology of the undated Bayesian tree for H1. The trees in (A) and (B) represent a 50% majority rule in which tree support is indicated using Bayesian posterior probabilities in the nodes, and the node bars represent the 95% highest posterior density (HPD) for the estimated node ages. In (B), node support is only indicated for the node that was unconstrained (the undated tree presented a polytomy for that node). Litopterna is indicated with a star, but other nodes or tips of relevance are indicated in circles of different colours: blue, orders; black, families.

opencc-by-4.0Oct 2024View details →

European origins of Squamata supported by biogeographic analysis of fossil-tip-dated phylogenies using paleocontinental plate-tectonic models

<p>Attached are the full results for the biogeographic analyses, with all tips labeled with taxon names. In addiiton, we have included the code utilized for all three trees used.</p>

opennotspecifiedMay 2019View details →

FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com] in Contributions of biogeographical functions to species accumulation may change over time in refugial regions

FIG UR E 3 (a) Dated phylogeny of the genus Theodoxus constructed in BEAST based on COI, 16S and ATPα. Node labels denote divergence times in millions of years ago (Ma); node bars indicate the 95% credibility interval around these dates. Small squares at nodes indicate significant support of divergence events found with BEAST and other phylogenetic analyses (see Figures S2.1 and S2.2), as explained through the key. Where MOTUs (A–R) show conspecifics among a number of morphospecies, species names are given in order of their year of description. Morphospecies, incorporated from GenBank, where determination was potentially dubious are highlighted by an asterisk. Clades (C) and subclades (SC) are demarcated by dashed lines between MOTUs. (b) LTT plots indicating the build‐up of lineages in Theodoxus over geological time. Dashed lines surrounding the solid LTT lines indicate the 95% confidence intervals. Where intra‐ and interspecific diversity diverge, interspecific diversity is highlighted in blue and intraspecific diversity in red. Transitions in geological ages are highlighted by narrow grey lines, while the grey bar marks the period of pronounced glacial cycles (last 900 kyr) [Colour figure can be viewed at wileyonlinelibrary.com]

Figure 8 in Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models

Figure 8. Divergence ages (median and 95% HPD) for all dating models, shown for the main groups of Folivora of the present classification. Time scale in million years ago.

Figure 5 in Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models

Figure 5. Estimated rate multipliers for anatomical partitions in each model. Partition colours as in Figure 1.

Figure 2 in Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models

Figure 2. Diversity through time for sloth genera sampled and its association with geological epochs. Time scale in million years ago.

Figure 1 in Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models

Figure 1. Anatomical partitions and partitioning schemes. Coloured anatomical regions in the skeleton of Paramylodon harlani (modified from Stock, 1925) correspond to the maximally partitioned data subsets, as used in model A7, whereas their combinations into composite partitions used in schemes A1 to A6 are indicated by other colours in the table. UN, unpartitioned model.

Figure 4 in Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models

Figure 4. Selected trees, with node supports (Poisson boostrap and posterior probabilities), depicting the overall variation in topologies obtained. A, parsimony IW100. B, parsimony IW5. C, Bayesian UN_p. D, Bayesian IW100_e. All topologies and branch lengths for Bayesian trees are available in the Supporting Information (File S9).

Figure 3. A in Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models

Figure 3. A, marginal likelihoods of Bayesian models. B, normalized Robinson–Foulds (nRF) distances among topologies (with IW100_e used as reference). C, distribution of node supports, with posterior probabilities for Bayesian inferences and bootstrap values for maximum parsimony.

Figure 7 in Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models

Figure 7. Stratigraphic fit of maximum parsimony and Bayesian topologies evaluated with two metrics, considering fossil age intervals as known ranges or as stratigraphic uncertainty. A, stratigraphic consistency index (SCI). B, gap excess ratio (GER).

Figure 10 in Reassessing the phylogeny and divergence times of sloths (Mammalia: Pilosa: Folivora), exploring alternative morphological partitioning and dating models

Figure 10. Relative rates (median and 95% HPD) of speciation, extinction and fossilization obtained with a skyline fossilized birth-death process for seven consecutive time bins.