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Figure 5 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)

Figure 5. Fossil-calibrated ultrametric chronogram of the Unionidae calculated under a lognormal relaxed clock model and a Yule process speciation implemented in BEAST v.1.10.1 and obtained for the complete F-type mitogenome data set. The newly sequenced tribe-level taxa are coloured red. An outgroup sample (Margaritiferidae) has been removed for better visualization (but see original BEAST tree in Supporting Information, Fig. S1A). Bars indicate 95% confidence intervals of the estimated divergence times between lineages (Mya). Black numbers near nodes are mean ages (Mya). Colour labels indicate the F-mtDNA gene order (UF1, UF2, and UF3). Stratigraphic chart according to the International Commission on Stratigraphy v.2018/08 (www.stratigraphy.org). Abbreviations: J, Jurassic; K, Cretaceous; N, Neogene; Pg, Palaeogene; Q, Quaternary.

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Fig. 3 in Multigene fossil-calibrated analysis of the African lampeyes (Cyprinodontoidei: Procatopodidae) reveals an early Oligocene origin and Neogene diversification driven by palaeogeographic and palaeoclimatic events

Fig. 3 Phylogenetic relationships between African lampeyes genera as depicted in Huber (1999) and Ghedotti (2000)

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Fig. 1 Phylogenetic relationships among 36 in Multigene fossil-calibrated analysis of the African lampeyes (Cyprinodontoidei: Procatopodidae) reveals an early Oligocene origin and Neogene diversification driven by palaeogeographic and palaeoclimatic events

Fig. 1 Phylogenetic relationships among 36 species of Procatopodidae, including all genera but Aapticheilichthys, inferred by using partial sequences of the nuclear-encoded genes GLYT1, ENC1, RAG1, MYH6, and SREB2, a total of 5009 bp. Numbers left to the bar indicate posterior probability values and in the right are bootstrap support values taken from the maximum likelihood analysis. Asterisk means maximum values. The green dot next to species name refers to species occurring in rainforests, red dot refers to species occurring in savannahs, green/red dot refer to

opennotspecifiedJun 2012View details →

Fig. 2 in Divergence time estimation in Cichorieae (Asteraceae) using a fossil-calibrated relaxed molecular clock

Fig. 2 Chronogram of Cichorieae produced by the program BEAST based on ITS1 and ITS2 sequences (unconstrained topology; maximum clade credibility tree with mean node heights obtained by stem group node calibration). Posterior probabilities of nodes are shown

FIGURE 3 in Five well-supported fossil calibrations within the "Waterbird" assemblage (Tetrapoda, Aves)

FIGURE 3. Alternative phylogenetic tree based on the osteological analysis of Smith (2010) showing the family-level relationships (with silhouettes of representatives within each family) within the waterbird assemblage, with five fossil calibrations (Table 1) included. Groups color-coded by membership in traditional avian orders: Pelecaniformes (green), Ciconiiformes (orange), Procellariiformes (blue), Sphenisciformes (brown), Podicipediformes (gold), Gaviiformes (purple). Stratigraphy and associated ages from Cohen et al. (2013; see also Walker et al., 2013). Branches (internodes) outside of fossil calibrations are set to a unit length to make topological relationships clear, and are not intended to represent actual divergence times. Nodes that are numbered correspond to fossil calibrations described in the text. Asterisk next to Waimanu manneringi references a vetted calibration from Ksepka and Clarke (2015). Abbreviations: E, Early. M, Middle. L, Late.

FIGURE 2 in Five well-supported fossil calibrations within the "Waterbird" assemblage (Tetrapoda, Aves)

FIGURE 2. Preferred phylogenetic tree based on the phylogenomic analysis of Hackett et al. (2008) showing the family-level relationships (with silhouettes of representatives within each family) within the waterbird assemblage, with five fossil calibrations (Table 1) included. Groups color-coded by membership in traditional avian orders: Pelecaniformes (green), Ciconiiformes (orange), Procellariiformes (blue), Sphenisciformes (brown), Podicipediformes (gold), Gaviiformes (purple). Stratigraphy and associated ages from Cohen et al. (2013; see also Walker et al., 2013). Branches (internodes) outside of fossil calibrations are set to a unit length to make topological relationships clear, and are not intended to represent actual divergence times. Double hash marks indicate that the clade containing Phaethon, Podiceps, and Phoenicopterus is actually recovered as distantly related to the waterbird clade (i.e., it is not its sister-taxon). Nodes that are numbered correspond to fossil calibrations described in the text. Asterisk next to Waimanu manneringi references a vetted calibration from Ksepka and Clarke (2015). Abbreviations: E, Early. M, Middle. L, Late.

FIGURE 1 in Five well-supported fossil calibrations within the "Waterbird" assemblage (Tetrapoda, Aves)

FIGURE 1. Specimens representative of two taxa that provide fossil calibrations within the waterbird assemblage. 1, Limnofregata azygosternon (USNM 22753) from the early Eocene Green River Formation represents the sister taxon (with its congener Limnofregata hasegawai) to Fregata, and calibrates the node Fregatidae + Suloidea. 2, Rhynchaeites messelensis (SMF 218) from the middle Eocene of Messel. Together with other Messel Rhynchaeites messelensis specimens and Rhynchaeites sp. (MGUH 20288) from the early Eocene Fur Formation, these represent the sister taxon to Threskiornithidae, and MGUH 20288 calibrates the node uniting Threskiornithidae and its extant sister taxon. Scale bars equal 50 mm.

FIGURE 4 in Fossil calibrations for the cockroach phylogeny (Insecta, Dictyoptera, Blattodea), comments on the use of wings for their identification, and a redescription of the oldest Bla

FIGURE 4. "Gyna" obesa (Piton, 1940) with ventral perspective. 1, Illustration of holotype. Hashed line on pronotum denotes two possible paths delimiting the posterior margin of the pronotum. Broken lines elsewhere denote damage or incomplete preservation. Scale bar equals 10 mm. 2, Photo of holotype MNHN.F.R06689. Photo is a composite of two images taken with polarized lighting at different angles. Scale 10 mm total. 3, Higher magnification of posterior end showing stout, segmented cerci and details of abdominal termination. Scale 3 mm total.

FIGURE 1 in Fossil calibrations for the cockroach phylogeny (Insecta, Dictyoptera, Blattodea), comments on the use of wings for their identification, and a redescription of the oldest Bla

FIGURE 1. Cladogram of Blattodea phylogeny synthesized from eight previous studies (figure 2 in Maekawa et al., 2003; figure 4 in Klass and Meier, 2006; figure 1 in Inward et al., 2007; figure 3 in Pellens et al., 2007; figure 2 in Murienne, 2009; figure 2 in Djernaes et al., 2012; figure 3 in Djernaes et al., 2015; figures 4, 5, and 6 in Legendre et al., 2015). Support for a clade is represented by circles, each colored to indicate the studies in which that clade was recovered. Inward et al. (2007) and Pellens et al. (2007) do not report all support values for nodes on their trees so support from the topology of these studies may be over-represented here. The numbering next to Anaplectidae represents different possible positions of this group, or the potential that this group is polyphyletic. Legendre et al. (2015) supports Blattoidea and Blattoidea + Corydioidea but without Anaplectidae – 1, yet will still note their support for these clades with this one exception. Single terminals are shown for other taxa even though some may prove paraphyletic or polyphyletic with further study (e.g., Pseudophyllodromiinae and Epilamprinae). We did not find any reliably supported relationships within most of the Blaberidae, and thus its phylogeny is largely a polytomy. In some cases, a clade was recovered but the study had insufficient taxon sampling to support that clade (e.g., Maekawa et al., 2003 recovered Blattodea as monophyletic by necessity because it did not include Mantodea or other outgroup taxa).

FIGURE 3 in Fossil calibrations for the cockroach phylogeny (Insecta, Dictyoptera, Blattodea), comments on the use of wings for their identification, and a redescription of the oldest Bla

FIGURE 3. Illustrations of calibrating fossils. All illustrations reproduced with permission. Scale bars equal 1 mm. 1, Cretaholocompsa montsecana Martinez-Delclos, 1993 (in Martinez-Delclos, 1993, figure 8). 2, Cariblattoides labandeirai Vršanský, Vidlička, Čiampor, Jr. and Marsh 2012 (in Vršanský et al., 2012, figure 12). 3, Ectobius kohlsi Vršanský, Vidlička, and Labandeira 2014 (in Vršanský et al., 2014, figure 3).

FIGURE 2 in Fossil calibrations for the cockroach phylogeny (Insecta, Dictyoptera, Blattodea), comments on the use of wings for their identification, and a redescription of the oldest Bla

FIGURE 2. Simplified topology of Blattodea with fossil calibrations. Tree topology is simplified from Figure 1. Fossils are shown in grey with dashed lines to represent uncertain position within containing clade. Red symbol indicates the nodes each fossil calibrates with roman numerals indicating the fossil that corresponds to each node calibration. The minimum dates for each of the calibration points are: i – 125.45 Ma; ii – 52 Ma; iii – 48.14 Ma; iv – 48.14 Ma. Corydiidae s.s. consists of Holocompsinae, Tiviinae, and Euthyrrhaphinae. Corydiidae s.l. consists of Corydiidae s.s., Latindiinae and Nocticolinae. Note that no Ectobiinae other than Ectobius have been used in molecular phylogenetic studies to date.

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 2 in Sixteen vetted fossil calibrations for divergence dating of Charadriiformes (Aves, Neognathae)

FIGURE 2. Phylogram of alcid relationships showing calibrated nodes 7-15 (modified from Smith, 2011a, figure 1.26). Numbered nodes in red correspond to the following calibrations: (8) divergence of Alcidae from Stercorariidae; (9) divergence of Aethiini from Fraterculini; (10) divergence of Fratercula arctica from Fratercula corniculata; (11) divergence of Cepphus carbo from Cepphus columba; (12) divergence of Synthliboramphus hypoleucus from Synliboramphus craveri;divergence of Synthliboramphus hypoleucus from Synthliboramphus craveri; (13) divergence of Brachyramphus marmoratus from Brachyramphus brevirostris; (14) divergence of Alle alle from Uria; (15) divergence of Uria lomvia from Uria aalge; (16) divergence of Alca torda from Pinguinus impennis.

FIGURE 14 in Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves

FIGURE 14. Stratigraphic distribution of fossil Upupiformes in the Paleogene. The minimum possible age of the calibrating specimen SMF-ME 1883a+b is presented, and midpoints of age ranges are shown for the ages of other Paleogene Upupiformes. The fossil record of Upupiformes is probably more complete than implied by the figure as several important specimens may belong to this clade await evaluation (see text).

FIGURE 11 in Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves

FIGURE 11. Phylogenetic tree showing position of Pulchrapollia gracilis, illustrating the divergence calibrated by NMH A6207. Placement of Pulchrapollia gracilis as a stem parrot is supported by multiple analyses (see text).

FIGURE 7 in Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves

FIGURE 7. Phylogenetic tree showing position of Scaniacypselus wardi, illustrating the divergence calibrated by NHMUKA5430.

FIGURE 2 in Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves

FIGURE 2. Stratigraphic distribution of fossil anatoids in the Paleogene. The minimum possible age of the calibrating specimen of Vegavis iaai is presented, and midpoints of age ranges are shown for the ages of other Paleogene anatoid specimens.

FIGURE 4 in Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves

FIGURE 4. Stratigraphic distribution of fossil Sphenisciformes in the Paleogene. The minimum possible age of the calibrating specimen of Waimanu manneringi is presented, and midpoints of age ranges are shown for the ages of other Paleogene penguin specimens.

FIGURE 1 in Sixteen vetted fossil calibrations for divergence dating of Charadriiformes (Aves, Neognathae)

FIGURE 1. Phylogram of charadriiform relationships showing calibrated nodes 1-7 (modified from Baker et al., 2007, figure 1). Numbered nodes in red correspond to the following calibrations: (1) divergence of Charadriiformes from its nearest outgroup; (2) divergence of Charadrii from other Charadriiformes; (3) divergence of Burhinidae from Chionis and Pluvianellus; (4) divergence of Jacanidae from other Scolopaci; (5) basal divergence among Calidridinae; (6) divergence of Turnicidae from Lari; (7) basal divergence of Laromorphae; (8) divergence of Alcidae from Stercorariidae.

FIGURE 1 in Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves

FIGURE 1. Phylogenetic tree showing the position of Vegavis iaai, illustrating the divergence calibrated by MLP 93-I-3-1.