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7 results for “molecular clock dating”
FIGURE 2 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 2 Opening of Tasman Sea; Pal., Paleocene; P, Pliocene; Pe, Pelomedusa; Pel, Pelusios; Pelt, Peltocephalus; (cont.) Ph, Phrynops; Pl, Platemys; Ple, Pleurodira; Po, Podocnemis; Ps, Pseudemydura; Q, Quaternary; R, Rheodytes; Rh, Rhinemys. *, constrained nodes based on the TE MP topology; †, extinct taxa; ↑, origin of total groups Pan-Chelidae and Pan-Pelomedusioides. Downloaded from Brill.com10/07/2022 07:36:56PM via free access
FIGURE 3 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 3 Comparison of the three dating analyses performed in this study (simplified trees). Node number as in table 2. Abbreviations of analyses as in table 1. Abbreviations of geological events as in fig. 2. Abbrevia- tions of genera as in figs. 1 and 2. * constrained nodes based on the MP topologies; ↑, origin of total groups Pan-Chelidae and Pan- Pelomedusioides.
FIGURE 4 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 4 Comparison of dates produced by the three analyses of this study and four previous molecular clock studies. Abbreviations: Dea (2011), Dornburg et al. (2011); Jea (2013), Joyce et al. (2013); Pea (2017), Pereira et al. (2017); TS-M TD, This study morphological tip-dating; TS- ND, This study node-dating; TS-TE TD, This study total-evidence tip- dating; R&DF (2016), Rodrigues & Diniz-Filho (2016). Node numbers as in table 2.
Data from: Inflation of molecular clock rates and dates: molecular phylogenetics, biogeography, and diversification of a global cicada radiation from Australasia (Hemiptera: Cicadidae: Cicadettini)
Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1α intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from (1) an extrapolated EF-1α exon clock derived from COI-calibrated analysis within the largest New Zealand subclade, (2) post-hoc scaling of the tribe-level chronogram using results from subclade analyses, and (3) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera.
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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FIGURE 2 in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 2 Total-evidence dated Bayesian tree. Numbers in nodes are posterior probabilities. Red taxa denote the stem group. Red stars show different possible positions of the Early Cretaceous Australian pan- chelid turtles described by Smith (2010) (see Discussion). Concepts and bars in blue are taken from Vlachos et al. (2018). Abbreviations: A, Acanthochelys; BGBU, Beginning of Gondwana breakup; BODP, Beginning of the opening of the Drake Passage; C, Chelus; Ch, Chelodina; Che, Chelidae; Che. +SAec, Chelidae + South American extinct chelids; E, Erymnochelys; EECO, Early Eocene Climatic Optimum; El, Elseya; Elu, Elusor; Em, Emydura; EODP, End of the opening of the Drake Passage; F, Flavemys; H, Hydromedusa; M, Mesoclemmys; My, Myuchelys; Mya, Million years ago; DownloadedOlig., from Brill Oligocene.com; 10/07 OTS/, 2022 → 07:36:56PM via free access
FIGURE 1 Maximum Parsimony phylogenetic analyses. A in Dating the origin and diversiFIcation of Pan-Chelidae (Testudines, Pleurodira) under multiple molecular clock approaches
FIGURE 1 Maximum Parsimony phylogenetic analyses. A: Morphological phylogeny. B: Molecular phylogeny. C: Total-evidence phylogeny. Bootstrap supports are coded in grayscale. Australasian species are shown in red; South American species are shown in green. Abbreviations: A, Acanthochelys; B, Bonapartemys; Ch, Chelodina; El, Elseya; H, Hydromedusa; L, Lomalatachelys; M, Mesoclemmys; Me, Mendozachelys; My, Myuchelys; Pa, Palaeophrynops; Ph, Phrynops; Pl, Platemys; Pr, Prochelidella; Ps, Pseudemydura; Ri, Rionegrochelys; Y, Yaminuechelys. †, extinct taxa.
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