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FIG. 4 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 4. Anterior orbital region of Caluromysiops irrupta (A, AMNH 208101) and Trichosurus vulpecula (B, AMNH 65543). Alternative states for characters 8, 10, 13, and 14 (see main text for descriptions of these characters and character states) are illustrated as follows: Caluromysiops 8(0) 10(0[but note that C. irrupta is polymorphic for this character]), 13(0), 14(0); Trichosurus vulpecula 8(1), 10(1), 13(1), 14(1). Abbreviations: dlf, dorsal lacrimal foramen; fro, frontal; jug, jugal; lac, lacrimal; lf, lacrimal foramen; lt, lacrimal tubercle; max, maxillary; mf, maxillary foramen; nas, nasal; pal, palatine; vlf, ventral lacrimal foramen. Specimens are not drawn to the same scale.
FIG. 13 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 13. Occlusal views of right deciduous third upper premolars (dP3) of Dromiciops gliroides (A, FMNH 127415), Sminthopsis crassicaudata (B, AMNH 196686), and Echymipera kalubu (C, AMNH 221654). Alternative states of character 120 (see main text for description of this character and character states) are illustrated as follows: Dromiciops 120(0); Sminthopsis 120(1); Echymipera: 120(2). Note the obvious wear facet on the postmetacrista of dP3 in S. crassicaudata, indicating that this tooth is occlusally functional.
FIG. 12 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 12. Occipital views of Lestodelphys halli (A, UWZM 22422), Metachirus nudicaudatus (B, AMNH 267009), and Trichosurus vulpecula (C, AMNH 65557). Alternative states of characters 32, 90, 91, 93, and 95 (see main text for descriptions of these characters and character states) are illustrated as follows: Lestodelphys: 32(0), 90(0), 91(1), 93(1), 95(0); Metachirus: 32(1[but note that the modal condition for M. nudicaudatus is 0]), 90(0), 91(0), 93(2), 95(1); Trichosurus vulpecula: 32(-), 90(1), 91(0), 93(2), 95(0). Abbreviations: exo, exoccipital (yellow, coossified with basioccipital); fm, foramen magnum; mas, mastoid exposure of pars canalicularis of petrosal (blue, coossified with pars cochlearis); mf, mastoid fenestra; par, parietal (purple); pp, paroccipital process (of exoccipital); so, supraoccipital; sq, squamosal (orange). Specimens are not drawn to the same scale.
FIG. 11 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 11. Occiput of Echymipera kalubu (AMNH 192168) illustrating the mature peramelemorphian morphology (a conspecific juvenile is shown in fig. 6C). States for characters 25 and 89 (see main text for descriptions of these characters and character states) are illustrated as follows: 25(1), 89(1). Abbreviations: exo, exoccipital; ju, jugal; ls, lambdoid sesamoid; mas, mastoid; par, parietal; so, supraocciptal; sq, squamosal.
FIG. 2 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 2. Left lateral cranial and mandibular views of Marmosa murina showing principal osteological features mentioned in the text. Abbreviations: als, alisphenoid; ap, angular process; atp, alisphenoid tympanic process; conp, condylar process; corp, coronoid process; ect, ectotympanic; exo, exoccipital; fpj, frontal process of jugal; fr, foramen rotundum; fro, frontal; hpp, hamular process of pterygoid; iof, infraorbital foramen; ip, interparietal (coossified with supraoccipital); jug, jugal; lac, lacrimal; lc, lambdoid crest; lf, lacrimal foramina; maf, masseteric fossa; mas, mastoid exposure of pars canalicularis (of petrosal); max, maxillary; mef, mental foramina; nas, nasal; pal, palatine; par, parietal; pcf, paracanine fossa; pco, pars cochlearis (of petrosal); pop, postorbital process; pre, premaxillary; rmf, retromolar fossa; sq, squamosal; ssf, subsquamosal foramen; sup, supraoccipital (coossified with interparietal); zps, zygomatic process of squamosal.
FIG. 1 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 1. Dorsal and ventral cranial views of Marmosa murina showing principal osteological features mentioned in the text. Abbreviations: als, alisphenoid (coossified with basisphenoid); atp, alisphenoid tympanic process; bo, basioccipital (coossified with exoccipitals); bs, basisphenoid (coossified with alisphenoid); cc, carotid canal; ect, ectotympanic; fm, foramen magnum; fpj, frontal process of jugal; fro, frontal; gf, glenoid fossa; gpa, glenoid process of alisphenoid; ip, interparietal; jug, jugal; lac, lacrimal; max, maxillary; mp, mastoid process (of petrosal); nas, nasal; occ, occipital condyle (of exoccipital); of, orbital fossa; pal, palatine; par, parietal; pcf, paracanine fossa; pogp, postglenoid process (of squamosal); pop, postorbital process; pre(ap), premaxillary (alveolar process); pre(fp), premaxillary (facial process); prgp, preglenoid process (of jugal); pro, promontorium (of petrosal); ps, presphenoid; pt, pterygoid; rtp, rostral tympanic process (of petrosal); sq, squamosal; tcf, transverse canal foramen; tf, temporal fossa; za, zygomatic arch.
FIG. 18 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 18. Occlusal views of upper molars of Hypsiprymnodon moschatus (A, AMNH 160120 [right M1]), Caenolestes fuliginosus (B, BMNH 1954.295 [left M2, reversed]), and Acrobates pygmaeus (C, AMNH 37185 [right M2]). General features of upper molar crown morphology discussed in the text are illustrated, as are characters 132, 133, 136, 137, 140, 141, 143, 144, 145, and 146 (see main text for description of these characters and character states), as follows: Hypsiprymnodon moschatus 132(-), 133(0), 136(2), 137(1), 140(-), 141(0), 143(1), 144(1), 145(-), 146(-); Caenolestes 132(-), 133(1), 136(2), 137(-[but note that some Caenolestes specimens retain a paracone and can be scored as 1]), 140(-), 141(0), 143(1), 144(0), 145(-), 146(-); Acrobates 132(-), 133(1), 136(2), 137(-), 140(-), 141(0), 143(1), 144(0), 145(-), 146(-). Abbreviations: mec, metacone; nci, neomorphic cingulum; pac, paracone; stB, stylar cusp B; stD, stylar cusp D. Teeth are not shown to the same scale.
FIG. 17 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 17. Occlusal views of left upper molars of Distoechurus pennatus (A, AMNH 104058 [M1]), Hypsiprymnodon moschatus (B, AMNH 160120 [M2]), Trichosurus vulpecula (C, AMNH 65547 [M2]), and Lagostrophus fasciatus (D, AMNH 155105 [M2]). General features of upper molar crown morphology discussed in the text are illustrated, as are characters 132, 133, 136, 137, 140, 141, 143, 144, 145, and 146 (see main text for description of these characters and character states), as follows: Distoechurus 132(-), 133(1), 136(2), 137(-), 140(-), 141(0), 143(1), 144(1), 145(0), 146(0); Hypsiprymnodon moschatus 132(-), 133(0), 136(2), 137(-[but note that this can be scored in lightly worn specimens of H. moschatus; see fig. 18A]), (140(-), 141(0), 143(1), 144(1), 145(-), 146(-); Trichosurus vulpecula 132(-), 133(0), 136(2), 137(-), 140(-), 141(0), 143(1), 144(1), 145(0), 146(0); Lagostrophus 132(-), 133(0), 136(2), 137(-), 140(-), 141(0), 143(1), 144(2), 145(1), 146(1). Note that in the illustrated specimen of D. pennatus the neomorphic labial cingulum is restricted to the region between the major labial cusps, but in other specimens it extends along the entire labial margin of the upper molars. Abbreviations: mec, metacone; mecl, metaconule; mel, metaloph; prc, protocone; prl, protoloph; stB, stylar cusp B; stD, stylar cusp D; urcr, urocrista. Teeth are not drawn to the same scale.
FIG. 6 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 6. Posterior braincase of Dromiciops gliroides (A, UWBM 78641), Marmosa murina (B, AMNH 266418), and Echymipera kalubu (C, AMNH 190977). Alternative states for characters 30 and 31 (see main text for descriptions of these characters and character states) are illustrated as follows: Dromiciops 30(1), 31(0); Marmosa 30(1), 31(1); Echymipera 30(0), 31(-). Note that the incompletely mineralized lambdoid sesamoids (see Character 89) have fallen away in this juvenile specimen of Echymipera (the mature morphology is illustrated in fig. 11), fully exposing the parietal-supraoccipital suture. Abbreviations: exo, exoccipital; ip, interparietal; mas, mastoid; mf, mastoid fenestra; par, parietal; so, supraocciptal; sq, squamosal; ssf, subsquamosal foramen. Specimens are not drawn to the same scale.
FIG. 5 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 5. Posterior orbital region of Potorous tridactylus (A, AMNH 65293) and Perameles gunnii (B, MVZ 127070). Alternative states for characters 15–17 (see main text for descriptions of these characters and character states) are illustrated as follows: Potorous 15(0), 16(1), 17(1); Perameles 15(1), 16(0), 17(0). Abbreviations: als, alisphenoid; atp, alisphenoid tympanic process; for, foramen rotundum; fro, frontal; jug, jugal; lac, lacrimal; max, maxillary; os, orbitosphenoid; pal, palatine; plpf, posterolateral palatal foramen; pt, pterygoid; sf, sphenorbital fissure; sq, squamosal. Specimens are not drawn to the same scale.
FIG. 7 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 7. Palatal morphology of Thylamys venustus (AMNH 261254) illustrating nomenclature for fenestrae, foramina, and other features described in the text (reproduced from Voss and Jansa, 2003: fig. 5; 2009: fig. 14). Dental loci (I1–M4) provide convenient landmarks for defining the size and position of palatal structures. Abbreviations: if, incisive foramen; m, maxillary fenestra; mp, maxillopalatine fenestra; p, palatine fenestra; plpf, posterolateral palatal foramen.
FIG. 8 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 8. Postpalatal region of Caluromys philander (A, AMNH 267002), Dromiciops gliroides (B, UWBM 78641), Dactylonax palpator (C, AMNH 191042), and Potorous tridactylus (D, AMNH 66168). Alternative states for characters 43 and 45–50 (see main text for descriptions of these characters and character states) are illustrated as follows: Caluromys 43(0), 45(0), 46(0), 47(1; but note that C. philander is polymorphic for this character), 48(0), 49(0), 50(0); Dromiciops 43(1), 45(1), 46(3), 47(0), 48(1), 49(0), 50(0); Dactylonax 43(1), 45(1), 46(2), 47(1), 48(0), 49(0), 50(1); Potorous 43(-), 45(2), 46(1; but note that the modal condition for P. tridactylus is 0), 47(1), 48(0), 49(1), 50(0). Abbreviations: als, alisphenoid (purple, coossified with basisphenoid); apf, anterior pterygoid foramen; atp, alisphenoid tympanic process; bk, basisphenoid keel; bs, basisphenoid (purple, coossified with alisphenoid); cc, carotid canals; ecr, ectopterygoid crest; fo, foramen ovale; pal, palatine (green); plfp, posterolateral palatal foramen; ps, presphenoid (blue); pt, pterygoid (yellow); ptf, pterygoid fossa; tcf, transverse canal foramen; v, vomer (orange). Specimens are not drawn to the same scale.
FRONTISPIECE. The honey opossum (Tarsipes rostratus, illustrated by Gould, 1863) has aptly been described as "a paragon of autapomorphic specialization" (Aplin and Archer, 1987). in Craniodental Morphology And Phylogeny Of Marsupials
FRONTISPIECE. The honey opossum (Tarsipes rostratus, illustrated by Gould, 1863) has aptly been described as "a paragon of autapomorphic specialization" (Aplin and Archer, 1987).
FIG. 15 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 15. Occlusal views of left upper second molars (M2) of Metachirus nudicaudatus (A, AMNH 266453), Caenolestes fuliginosus (B, UMMZ 155575), Echimipera kalubu (C, AMNH 221654), and Notoryctes typhlops (D, AMNH 198651). General features of upper molar crown morphology discussed in the text are illustrated, as are characters 132, 133, 136, 137, 140, 141, 143, and 144 (see main text for description of these characters and character states), as follows: Metachirus 132(1), 133(0), 136(0), 137(1), 140(3), 141(0), 143(0), 144(0); Caenolestes 132(-), 133(1), 136(2), 137(-), 140(-), 141(0), 143(1), 144(0); Echimipera 132(1), 133(0), 136(0), 137(1), 140(4), 141(0), 143(1), 144(0); Notoryctes 132(1), 133(0), 136(0), 137(2), 140(-), 141(0), 143(0), 144(0). Note, however, that some C. fuliginosus specimens retain a paracone and can be scored as 137(1). Abbreviations: alci, anterolabial cingulum; ccr, centrocrista; mec, metacone; mecl, metaconule; nci, neomorphic cingulum; pac, paracone; prc, protocone; stB, stylar cusp B; stD, stylar cusp D. Teeth are not drawn to the same scale.
FIG. 9 in Craniodental Morphology And Phylogeny Of Marsupials
FIG. 9. Ventral view of left ear region of Marmosa murina (A, AMNH 267368), Phascogale tapoatafa (B, AMNH 160267), and Petaurus breviceps (C, AMNH 154468; note that the pterygoid bone, which when intact extends posteriorly as far as the carotid canal in P. breviceps [char. 47], is missing in this specimen). Alternative states for characters 23, 55, 60, 68, 79, 84, and 87 (see main text for descriptions of these characters and character states) are illustrated as follows: Marmosa 23(1), 55(1), 60(0), 68(0), 79(0), 84(0), 87(0); Phascogale 23(1), 55(2), 60(0), 68(2), 79(3), 84(1), 87(0); Petaurus 23(0), 55(3), 60(2), 68(1[not visible on intact skulls]), 79(4), 84(1[not visible on intact skulls]), 87(1; not visible on intact skulls). Abbreviations: als, alisphenoid; atp, alisphenoid tympanic process; bo, basioccipital; bs, basisphenoid; cc, carotid canal; cf, condyloid foramen; ctp, caudal tympanic process (of pars canalicularis of petrosal); ect, ectotympanic; fgpn, foramen for greater petrosal nerve; fips, foramen for inferior petrosal sinus; gf, glenoid fossa; gpa, glenoid process of alisphenoid; hf, hypoglossal foramen; jf, jugular foramen; jug, jugal; mas, mastoid exposure of pars canalicularis of petrosal); mf, mastoid fenestra; oc, occipital condyle; pes, posterior epitympanic sinus (of squamosal); pfo, primary foramen ovale; pgf, postglenoid foramen; pogp, postglenoid process (of squamosal); pp, paroccipital process (of exoccipital); pro, promontorium (of pars cochlearis of petrosal); pt, pterygoid; ptps, postympanic process (of squamosal); rtp, rostral tympanic process (of pars cochlearis of petrosal); smf, stylomastoid foramen; smn, stylomastoid notch; sq, squamosal; ssf, subsquamosal foramen; tcf, transverse canal foramen. Specimens are not drawn to the same scale.
Fig. 79. Maximum likelihood phylogeny inferred with IQTREE ver. 2.1.2 in Integrating morphology with phylogenomics to describe four island endemic species of Temnothorax from Sicily and Malta (Hymenoptera, Formicidae)
Fig. 79. Maximum likelihood phylogeny inferred with IQTREE ver. 2.1.2. The major clades found in Prebus (2017) are highlighted, and the focal species of the current study (all within the 'Palearctic clade IV') are evidenced as in Figs 75–78. Maximum likelihood bootstrap support for all nodes are 100, except where indicated.
The shape of phylogenies under phase-type distributed times to speciation and extinction
<p>Phylogenetic trees describe relationships between extant species, but beyond that their shape and their relative branch lengths can provide information on broader evolutionary processes of speciation and extinction. However, currently, many of the most widely used macro-evolutionary models make predictions about the shapes of phylogenetic trees that differ considerably from what is observed in empirical phylogenies. Here, we propose a flexible and biologically plausible macroevolutionary model for phylogenetic trees where times to speciation or extinction events are drawn from a Coxian phase-type (PH) distribution. First, we show that different choices of parameters in our model lead to a range of tree balances as measured by Aldous' $\beta$ statistic. In particular, we demonstrate that it is possible to find parameters that correspond well to empirical tree balance. Next, we provide a natural extension of the $\beta$ statistic to sets of trees. This extension produces less biased estimates of $\beta$ compared to using the median $\beta$ values from individual trees. Furthermore, we derive a likelihood expression for the probability of observing an edge-weighted tree under a model with speciation but no extinction. Finally, we illustrate the application of our model by performing both absolute and relative goodness-of-fit tests for two large empirical phylogenies (squamates and angiosperms) that compare models with Coxian PH distributed times to speciation with models that assume exponential or Weibull distributed waiting times. In our numerical analysis, we found that, in most cases, models assuming a Coxian PH distribution provided the best fit.</p>
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 mitochondrial genomes generated in this study. The dataset was supplemented with Thyropygus sp. and Abacion magnum as outgroups, derived from GenBank. GenBank accession numbers are provided in parentheses. Blue bars indicate the 95% highest probability density intervals for node ages. Age estimation for lineage divergence was based on a general arthropod mitochondrial DNA substitution rate and should be considered with caution. *Thyropygus sp. (red font) is very likely to be a misidentification; for more information, see the Discussion.
Data from: Bratzel et al. (2022) Target-enrichment sequencing reveals for the first time a well-resolved phylogeny of the core Bromelioideae (Bromeliaceae). Taxon
<p>DNA sequence alignments used for phylogenetic analyses in Bratzel et al. (2022) Target-enrichment sequencing reveals for the first time a well-resolved phylogeny of the core Bromelioideae (Bromeliaceae). Taxon.</p>
Fig. 4 in New insights into the phylogeny and relationships within the worldwide genus Riccardia (Aneuraceae, Marchantiophytina)
Fig. 4. Afroriccardia comosa (Steph.) Reeb & Gradst. comb. nov. A. Habit of the thallus, Wigginton U5039a, Reeb & Andriamanantena CR13Z28. B. Ventral face showing the wide insertion of rhizoids, DeLisle 220. C. Cross section of main axis showing variability in the thickening of cell walls, Reeb & Andriamanantena CR13Z28, holotype G0045027. D. Cross section of ultimate branch, holotype G0045027. E. Detail of female branch with dense cluster of rhizoids, holotype G0045027. Scale bars: A–B = 1 mm; C = 100 µm.
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Allen Brain Atlas
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