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134 results for “Total Evidence”
Data from: Total-evidence dating under the fossilized birth-death process
Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth-death (FBD) process, which has been used to model speciation, extinction and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of datasets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants and bees). Previous total-evidence dating analyses of this dataset were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push towards more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.
Data from: Total-evidence approach reveals an extinct lineage of Paederinae rove beetles from Cretaceous Burmese amber
The fossil record contains vital information about the evolution of lineages and is a source of data that cannot be reconciled in any other way than by the direct observation of morphologies. Total-evidence phylogenetic reconstruction is being increasingly used to assess the position of extinct taxa by incorporating morphological data from extinct and extant taxa together with molecular data from extant taxa in a united framework. Here we apply the method to two Cretaceous Burmese amber inclusions belonging to the rove beetle subfamily Paederinae. To perform the total evidence analysis, we constructed the first morphological matrix and the most comprehensive molecular dataset for the subfamily. Our analyses reveal an extinct lineage of Paederinae rove beetles with a suite of unique morphological characters, resulting in the description of a new genus: Diminudon gen. nov. and two new species: D. schomannae sp. nov. and D. kachinensis sp. nov. Simultaneously our analyses provide new insights into the evolution and classification of the entire subfamily. We also discuss the unusually small size of the newly described Paederinae, which may represent an additional case for miniaturization in the Cretaceous.
Figure 9 from: Pellegrini MOO, Horn CN, Almeida RF (2018) Total evidence phylogeny of Pontederiaceae (Commelinales) sheds light on the necessity of its recircumscription and synopsis of Pontederia L. PhytoKeys 108: 25-83. https://doi.org/10.3897/phytokeys.108.27652
Figure 9 PontederiaL.subg.Pontederia. A–C habit: A dense population of P.parviflora Alexander B population of P.ovalis Mart. ex Schult. & Schult.f. C habit of P.rotundifolia L.f. D–E petiolate leaves: D blade of P.rotundifoliaE blade of P.parvifloraF–H inflorescences: F inflorescence of P.cordata L., showing flowers with two yellow nectar guides in the posterior perianth lobes G inflorescence of P.parviflora, showing flowers with a sole yellow nectar guide in the posterior perianth lobes H inflorescence of P.rotudifolia, showing a lilac-flowered form I oblique view of a flower of P.ovalisJ–K fruits: J detail of the apex of the infructescence of P.ovalis, showing the anthocarp with sinuate ridges K detail of an achene of P.cordata, showing the toothed ridges. A by C. Willig & L. Nusbaumer B, I, J by M.O.O. Pellegrini C by L.O.A. Teixeira, D, H by R. Aguilar E by M.R. Engels F by Ashitaka-f Studio G by M.V. Lameiras and K by A. Haines.
Figure 6 from: Pellegrini MOO, Horn CN, Almeida RF (2018) Total evidence phylogeny of Pontederiaceae (Commelinales) sheds light on the necessity of its recircumscription and synopsis of Pontederia L. PhytoKeys 108: 25-83. https://doi.org/10.3897/phytokeys.108.27652
Figure 6 Pontederiasubg.Monochoria (C.Presl) M.Pell. & C.N.Horn. A–B habit: A paludal habit of P.australasica (Ridl.) M.Pell. & C.N.Horn B paludal habit of P.cyanea (F.Muell.) M.Pell. & C.N.Horn C ligule of P.vaginalis Burm.f., showing the truncate apex D–E petiolate leaf-blades: D blade of P.cyanea, showing the lack of a posterior division E blade of P.vaginalis, showing the presence of a posterior division F–G inflorescences: F inflorescence of P.australasica, showing the developed main axis G inflorescence of P.plantaginea Roxb., showing the contracted main axis H front view of a flower of P.korsakowii (Regel & Maack) M.Pell. & C.N.Horn I–J inflorescences at post-anthesis: I erect inflorescence of P.hastata L. bearing flowers at post-anthesis J infructescence of P.hastata, showing the deflexed posture and the elongated pedicels K sections of immature capsules of P.vaginalis, showing developing seeds. A, F by M. Barritt B by R. Cumming C, E, K by P.B. Pelser & J.F. Barcelona D by A. & S. Pearson G by D. Valke H by Ashitaka-f Studio and I & J by Cerlin Ng.
Figure 3 from: Pellegrini MOO, Horn CN, Almeida RF (2018) Total evidence phylogeny of Pontederiaceae (Commelinales) sheds light on the necessity of its recircumscription and synopsis of Pontederia L. PhytoKeys 108: 25-83. https://doi.org/10.3897/phytokeys.108.27652
Figure 3 Majority-rule tree recovered for the parsimony and Bayesian analysis of the combined morphological + plastid dataset. Yellow: Philydraceae. Orange: Haemodoraceae. Blue: Heterantheras.l. Pink: Pontederias.l.
Figure 2 from: Pellegrini MOO, Horn CN, Almeida RF (2018) Total evidence phylogeny of Pontederiaceae (Commelinales) sheds light on the necessity of its recircumscription and synopsis of Pontederia L. PhytoKeys 108: 25-83. https://doi.org/10.3897/phytokeys.108.27652
Figure 2 Majority-rule tree recovered for the morphological and plastid datasets. Morphology: bootstrap support values are depicted over the branches, while Bremer Index support values are depicted under the branches. Plastid: posterior probability values are depicted over the branches. Yellow: Philydraceae. Orange: Haemodoraceae. Blue: Heterantheras.l. Pink: Pontederias.l.
Figure 1 from: Pellegrini MOO, Horn CN, Almeida RF (2018) Total evidence phylogeny of Pontederiaceae (Commelinales) sheds light on the necessity of its recircumscription and synopsis of Pontederia L. PhytoKeys 108: 25-83. https://doi.org/10.3897/phytokeys.108.27652
Figure 1 Strict consensus tree (length=209 steps; CI=0.5913; RI=0.8618) recovered by the morphological dataset, showing the character state optimisations at each node of the cladogram, represented by circles. In each circle, the numbers above and below represent the character and character state numbers, respectively (as presented in Suppl. material 1).
Figure 8 from: Pellegrini MOO, Horn CN, Almeida RF (2018) Total evidence phylogeny of Pontederiaceae (Commelinales) sheds light on the necessity of its recircumscription and synopsis of Pontederia L. PhytoKeys 108: 25-83. https://doi.org/10.3897/phytokeys.108.27652
Figure 8 Pontederiasubg.Eichhornia (Kunth) M.Pell. & C.N.Horn. A–B habit: A habit of P.heterosperma (Alexander) M.Pell. & C.N.Horn, showing the emerged petiolate leaves B habit of P.diversifolia (Vahl) M.Pell. & C.N.Horn, showing the floating petiolate leaves C–F inflorescence: C 2–3-flowered inflorescences of P.diversifolia, showing the flowers with a yellow nectar guide in the posterior perianth lobes D 1-flowered inflorescence of P.natans P.Beauv., showing the lack of a nectar guide E inflorescence of P.heterosperma, showing the lack of nectar guides in the posterior perianth lobes F morphological variation of inflorescences and perianth colour of P.azurea Sw G front view of a flower of P.azurea H front view of a flower of P.natans. A, B by O. Gaubert C by A.S. Castro D by P. Birnbaum E by H. Medeiros F by L.O.A. Teixeira G by M.O.O. Pellegrini and I by T.C. Buruwate.
Figure 5 from: Pellegrini MOO, Horn CN, Almeida RF (2018) Total evidence phylogeny of Pontederiaceae (Commelinales) sheds light on the necessity of its recircumscription and synopsis of Pontederia L. PhytoKeys 108: 25-83. https://doi.org/10.3897/phytokeys.108.27652
Figure 5 Pontederiasubg.Cabanisia (Klotzsch ex Schltdl.) M.Pell. & C.N.Horn. A habit B–C inflorescence: B young inflorescence, showing the inflated leaf-sheath and flat basal bract with caudate apex C mature inflorescence showing the pedunculate cincinni with elongate internodes D detail of a cincinni, showing (from left to right) an immature floral bud, a pre-anthesis floral bud and a post-anthesis flower E front view of a flower F detail of an immature capsule, showing the ridged anthocarp. All photos of P.paniculata Spreng.; A by C. Willig & L. Nusbaumer, remaining photos by M.O.O. Pellegrini.
Figure 4 from: Pellegrini MOO, Horn CN, Almeida RF (2018) Total evidence phylogeny of Pontederiaceae (Commelinales) sheds light on the necessity of its recircumscription and synopsis of Pontederia L. PhytoKeys 108: 25-83. https://doi.org/10.3897/phytokeys.108.27652
Figure 4 Heteranthera Ruiz & Pav. A–D habit: A emerged and flowering population of H.gardneri (Hook.f.) M.Pell. during the dry season B floating specimen of H.reniformis Ruiz & Pav. C emergent habit with floating and emerged leaves of H.rotundifolia (Kunth) Griseb. D habit of H.dubia (Jacq.) MacMill., showing the persistent sessile leaves E petiolate leaf of H.pumila M.Pell. & C.N.Horn, showing the lack of a pulvinus F Ligule and inflorescence of H.pumilaG–J flowers: G pseudanthium of H.gardneriHH.reniformisIH.rotundifoliaJH.zosterifolia Mart. A by A.P. Fontana B, H by C.N. Horn C, I by A. Popovkin D by S.R. Turner E, F by M.O.O. Pellegrini G by C.P. Bove and J by S.S. Oliveira.
Figure 7 from: Pellegrini MOO, Horn CN, Almeida RF (2018) Total evidence phylogeny of Pontederiaceae (Commelinales) sheds light on the necessity of its recircumscription and synopsis of Pontederia L. PhytoKeys 108: 25-83. https://doi.org/10.3897/phytokeys.108.27652
Figure 7 Pontederiasubg.Oshunae M.Pell. & C.N.Horn. A–B habit: A dense population of the pink-flowered form B detail of a population, showing the free-floating rosettes, stolons and inflated petioles C–D petiolate leaves: C blade D detail of a young leaf showing its blade enclosing the inflated petiole of the presiding leaf E–G inflorescence: E young inflorescence of a lilac-flowered form F inflorescence of a lilac-flowered form at anthesis G inflorescence of a pink-flowered form at anthesis H–J flowers: H oblique view of a lilac flower I detail of the nectar guide J detail of the androecium and gynoecium showing the glandular hairs. All photos of P.crassipes Mart.; A by C. Willig & L. Nusbaumer B by O. Gaubert C by K. Pritchard & S.A. Harris, D–F, H–I by R. Aguilar and G by M.O.O. Pellegrini.
FIG. 5 in Evolution In The Genus Rhinella: A Total Evidence Phylogenetic Analysis Of Neotropical True Toads (Anura: Bufonidae)
FIG. 5. Skulls (ventral view) showing the anterior margin of cultriform process of the parasphenoid (in gray): A, Rhinella marina KU 152914 (char. 23.0); B, Nannophryne cophotis KU 218525 (char. 23.1); C, R . festae USNM 167168 (char. 23.2); D, R . cristinae ICN 26233 (char. 23.3). Panels redrawn from Pramuk, 2006 (A, B); Trueb, 1971(C) and Vélez-R. and Ruiz-C., 2002 (D).
Figure 4 from: Carpenter J, Kojima J, Villemant C (2013) Phylogeny of hornets: a total evidence approach (Hymenoptera, Vespidae, Vespinae, Vespa). Journal of Hymenoptera Research 32: 1-15. https://doi.org/10.3897/jhr.32.4685
Figure 4 - Support tree for the relationships within the genus Vespa based on a combined analysis. Support tree based on 45 morphological characters and six genes. Black nodes indicate clades supported by morphological characters. Absence of mark on nodes indicates clades diagnosed by molecular data only. Supports for nodes are given in GC-values.
Figure 3 from: Carpenter J, Kojima J, Villemant C (2013) Phylogeny of hornets: a total evidence approach (Hymenoptera, Vespidae, Vespinae, Vespa). Journal of Hymenoptera Research 32: 1-15. https://doi.org/10.3897/jhr.32.4685
Figure 3 - Support tree for the relationships among 13 Vespa species based on the six genes. Supports for nodes are given in GC-values. Grey rectangles show the molecular markers available for each species.
Figure 2 from: Carpenter J, Kojima J, Villemant C (2013) Phylogeny of hornets: a total evidence approach (Hymenoptera, Vespidae, Vespinae, Vespa). Journal of Hymenoptera Research 32: 1-15. https://doi.org/10.3897/jhr.32.4685
Figure 2 - Support tree for relationships among the 22 Vespa species based on 45 morphological characters.Supports for nodes are given in GC-values (see text for explanation) when they are greater than zero.
Figure 1 from: Carpenter J, Kojima J, Villemant C (2013) Phylogeny of hornets: a total evidence approach (Hymenoptera, Vespidae, Vespinae, Vespa). Journal of Hymenoptera Research 32: 1-15. https://doi.org/10.3897/jhr.32.4685
Figure 1 - Phylogeny of the genus Vespa after Archer (1994a: figure 8).Tree updated for the current classification (Nguyen et al. 2006). The species groups discussed in this paper are as follows: 1 crabro 2 tropica 3 affinis 4 bicolor sensu Archer (1994b).
Data from: Total-evidence dating under the fossilized birth-death process
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Data from: Total-evidence approach reveals an extinct lineage of Paederinae rove beetles from Cretaceous Burmese amber
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Data from: Multiple morphological clocks and total-evidence tip-dating in mammals
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Data from: Bayesian total-evidence dating reveals the recent crown radiation of penguins
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