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64 results for “molecular dating”
Data from: Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: analysis of mtDNA data
Phylogenetic relationships among 41 species of salmonid fish and some aspects of their diversification-time history were studied using the GenBank and original mtDNA data. The position of the root of the Salmonidae phylogenetic tree was uncertain. Among the possible variants, the most reasonable seems to be that in which thymallins are grouped into the same clade as coregonins and the lineage of salmonins occupied a basal position relative to this clade. The genera of Salmoninae formed two distinct clades, i.e., (Brachymystax, Hucho) and (Salmo, Parahucho, (Salvelinus, (Parasalmo, Oncorhynchus)). Furthermore, the genera Parasalmo and Oncorhynchus were reciprocally monophyletic. The congruence of Salmonidae phylogenetic trees obtained using different types of phylogenetic markers is discussed. According to Bayesian dating, ancestral lineages of salmonids and their sister esocoids diverged about 106 million years ago. Sometime after, probably 100–70 million years ago, the salmonid-specific whole genome duplication took place. The divergence of salmonid lineages on the genus level occurred much later, within the time interval of 42–20 million years ago. The main wave of the diversification of salmonids at the species level occurred during the last 12 million years. The possible effect of genome duplication on the Salmonidae diversification pattern is discussed.
The 'Evil Tribe' spreads across the land: A dated molecular phylogeny provides insight into dispersal, expansion, and biogeographic relationships within one of the largest tribes of the sunflower family (Vernonieae: Compositae)
<p><strong>Premise:</strong> With over 1500 species, the globally distributed Vernonieae is one of the most successful members of the Compositae. However, due to its morphological complexity and limited geographic representation in previous studies, subtribal and biogeographic relationships are unclear. Here new DNA sequence data spanning the geographical range of the tribe provides a taxonomically robust time-calibrated phylogeny, an estimation of migration pathways and timing of important biogeographical events and allows inference of environmental factors that have contributed to the success of the Vernonieae worldwide.</p> <p><strong>Methods: </strong>Phylogenetic relationships were estimated for 368 taxa representing all Vernonieae subtribes. Molecular clock and ancestral range estimation analyses provide a framework for inference of the tribe's biogeographic history.</p> <p><strong>Results:</strong> Relationships among the subtribes were established. We confirmed that the Moquinieae are nested in Vernonieae, determined the correct placement of several<br> problematic taxa, and conducted the first model-based assessment of the biogeographical history of the tribe. The . Vernonieae were estimated to have evolved ~50 Ma ago. Africa was the first center of diversity, from which a single dispersal event established the monophyletic New World lineage. Long-distance dispersal from Africa and Brazil established the tribe on five continents and Oceania.</p> <p><strong>Conclusions:</strong> Moquinieae are nested in Vernonieae. The New World lineage is monophyletic, but Old World taxa are not. New subtribal taxonomies are needed. Long-distance dispersal from Africa beginning 45 Ma was key to establishing the tribe's near-global distribution. Migration corridors created by volcanic mountain chains and iron-rich soils in Africa and the Americas promoted radiation and range expansion.</p>
FIGURE 6 in Rumen ciliates (Alveolata, Ciliophora) associated with goats: checklist, geographic distribution, host specificity, phylogeny and molecular dating
FIGURE 6. Dated phylogeny obtained through Maximum Likelihood for endosymbiont ciliates of the Trichostomatia subclass. The red vertical line represents the radiation period of the Caprinae subfamily (Ropiquet & Hassanin 2005 a, b). The green circles represent the nodes and the possible period in millions of years of diversification of the Isotrichidae (4.3–15.5) and Ophryoscolecidae (1.0–5.7) families. My—Millions of years.
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.
Fig. 4 in A dated molecular perspective of eucalypt taxonomy, evolution and diversification
Fig. 4. Bayesian analysis using the concatenated dataset of internal transcribed spacer (ITS), external transcribed spacer (ETS), matK and psbA–trnH, labelled with the informal higher-level groups mesicalypts (3 genera) and newcalypt (1 genus), the eucalypt genus Angophora, and all eucalypt subgenera as classified by Nicolle (2015b). Numbers at nodes in the larger phylogeny represent the penalised-likelihood estimated age. Numbers after each name in the inset box represent the number of terminals in the clade and numbers at nodes represent the posterior probability in the Bayesian analysis. Ma represents millions of years as returned for each penalised-likelihood dating analysis (a summary of estimated ages is provided in Table 2).
Fig. 3. Maximum likelihood-2 in A dated molecular perspective of eucalypt taxonomy, evolution and diversification
Fig. 3. Maximum likelihood-2 (ML-2) analysis using the concatenated dataset of internal transcribed spacer (ITS), external transcribed spacer (ETS), matK and psbA–trnH, labelled with the informal higher-level groups mesicalypts (3 genera) and newcalypt (1 genus), the eucalypt genus Angophora, and all eucalypt subgenera as classified by Nicolle (2015b). Numbers at nodes in the larger phylogeny represent the penalised-likelihood estimated age. Numbers after each name in the inset box represent the number of terminals in the clade and numbers at nodes represent the bootstrap value in the ML analysis. Ma represents millions of years as returned for each penalised-likelihood dating analysis (a summary of estimated ages is provided in Table 2).
Fig. 2. Maximum likelihood-1 in A dated molecular perspective of eucalypt taxonomy, evolution and diversification
Fig. 2. Maximum likelihood-1 (ML-1) analysis using the concatenated dataset of internal transcribed spacer (ITS), external transcribed spacer (ETS), matK and psbA–trnH, labelled with the informal higher-level groups mesicalypts (3 genera) and newcalypt (1 genus), the eucalypt genus Angophora, and all eucalypt subgenera as classified by Nicolle (2015b). Numbers at nodes in the larger phylogeny represent the penalised-likelihood estimated age. The numbers after each name in the inset box represent the number of terminals in the clade and numbers at nodes represent the bootstrap value in the ML analysis. Ma represents millions of years as returned for each penalised-likelihood dating analysis (a summary of estimated ages is provided in Table 2).
FIGURE 1 in Fossil calibration dates for molecular phylogenetic analysis of snakes 1: Serpentes, Alethinophidia, Boidae, Pythonidae
FIGURE 1. Time-calibrated phylogeny of Serpentes based on Pyron et al. (2013) and Reynolds et al. (2014). Numbers represent calibrated nodes in text. Fossil taxa are the calibration points for their respective nodes. Thickened bars represent well-sampled, taxonomically resolved stratigraphic distributions for the sister taxa to Pan-Serpentes and snake lineages whose first occurrences are determined by older sister taxa. Thin bars represent estimated stratigraphic distributions for taxa with poorly resolved fossil records, or no published fossil record (names in grey). "Scolecophidia" represents a paraphyletic grade with respect to Alethinophidia (see text).
FIGURE 1 in Fossil calibration dates for molecular phylogenetic analysis of snakes 2: Caenophidia, Colubroidea, Elapoidea, Colubridae
FIGURE 1. Phylogeny of Caenophidia from Pyron et al. (2013a) temporally calibrated on minimum ages reported here. Taxon names in grey have not been described in the fossil record. Taxon names in black have been described from fossils. See Holman (2000) and Szyndlar (2012) for records. Taxa labeled with two identifiers represent the most inclusive clades subtended by those identifiers following Pyron et al. (2013a).
Figure 3 in Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences
Figure 3. Posterior probability distributions for mean rates of evolution estimated from the combined data under a partitioned analysis for the mitochondrial (A) and nuclear genes (B). The middle line of each box plot represents mean rates and the top and bottom lines indicate the 95% credibility intervals. CMOS; MXRA-5.
Figure 2 in Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences
Figure 2. Age posterior probability distributions for each of the Eulaemus crown groups. Vertical black line represents the Miocene-Pliocene boundary (5.33 Mya).
Figure 1 in Molecular dating and diversification of the South American lizard genus Liolaemus (subgenus Eulaemus) based on nuclear and mitochondrial DNA sequences
Figure 1. Fifty per cent majority rule phylogram from the partitioned BEAST analyses of the combined data set (cytochrome b, 12S, CMOS, and MXRA5). Numbers above and below the nodes represent posterior probability values and mean estimates of divergence dates (in millions of years), respectively.
Data from: Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating
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Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)
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The 'Evil Tribe' spreads across the land: A dated molecular phylogeny provides insight into dispersal, expansion, and biogeographic relationships within one of the largest tribes of the sunflower family (Vernonieae: Compositae)
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Data from: Phylogeny of salmonids (Salmoniformes: Salmonidae) and its molecular dating: analysis of nuclear RAG1 gene
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