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Text-fig. 10. Phylogenetic relationships of Miocene hyaenodonts (for definitions of character states see Table 2). The data matrix was compiled in MacClade 4.05 and run in PAUP 4.0b10 (Macintosh version). We chose Cimolestes magnus CLEMENS et RUSSELL, 1965, (additional data from Lillegraven 1969), as the outgroup. The unordered and unweighted analysis produced 16 trees. a: Majority-rule consensus. b: Strict consensus. Consistency index (CI): 0.5882; Homoplasy index (HI): 0.4118; Retention index (RI): 0.7742. in New Hyaenodonts (Ferae, Mammalia) From The Early Miocene Of Napak (Uganda), Koru (Kenya) And Grillental (Namibia)
Text-fig. 10. Phylogenetic relationships of Miocene hyaenodonts (for definitions of character states see Table 2). The data matrix was compiled in MacClade 4.05 and run in PAUP 4.0b10 (Macintosh version). We chose Cimolestes magnus CLEMENS et RUSSELL, 1965, (additional data from Lillegraven 1969), as the outgroup. The unordered and unweighted analysis produced 16 trees. a: Majority-rule consensus. b: Strict consensus. Consistency index (CI): 0.5882; Homoplasy index (HI): 0.4118; Retention index (RI): 0.7742.
FIG. 3 in Phylogenetic analysis of the red algal tribe Ceramieae reveals multiple morphological homoplasies but defines new genera
FIG. 3. — Phylogenetic reconstruction of the red algal tribe Ceramieae C.Agardh ex Greville inferred with an integrative approach based on rbcL gene and morphological characters. The tree is the majority rule consensus tree resulting from Bayesian analysis. Values at the nodes represent posterior probability and bootstrap values for ML; supports <0.65 (PP) and 75 (BP) are not shown. Sequences generated in this study are in bold. Abbreviations: AU, Australia; BE, Bermuda; BR, Brazil; NS CA, Nova Scotia, Canada; CL, Chile; DA, Dutch Antilles;DE, Denmark; EN, England; FR, France; FR PO, French Polynesia; GB TR, British Overseas Territory of Tristan da Cunha; GE, Germany; IR, Ireland; IT, Italy; JA, Japan; JM, Jamaica; KO, South Korea; MO, Morocco; MX, Mexico; BC MX, Baja California, Mexico; NA, Namibia; NO, Norway; NZ, New Zealand; PE, Peru; PR, Puerto Rico; SA, South Africa; SP, Spain; TW, Taiwan; AK US, Alaska; CA US, California; FL US, Florida; HI US, Hawaii; MA US, Massachusetts; OR US, Oregon; RI US, Rhode Island; WA US, Washington; WA, Wales. Symbol: *, full support.
FIG. 1 in Phylogenetic analysis of the red algal tribe Ceramieae reveals multiple morphological homoplasies but defines new genera
FIG. 1. — Diagnostic morphological features of the tribe Ceramieae:A, Ceramium pallidum (Kützing) Maggs & Hommersand;B, carposporophyte,Pseudoceramium oliveirarum Barros-Barreto, Maggs & M.A.Jaramillo, gen. nov., sp. nov.; C, tetrasporophyte, Centroceras gasparrinii (Meneghini) Kützing; D, male plant showing spermatangia, Corallophila atlantica (A.B.Joly & Ugadim) R.E.Norris; E, acropetal cells, Yoneshiguea compta (Børgesen) Barros-Barreto, Maggs & M.A.Jaramillo, comb. nov.; F, three cortical initial cells, Gayliella dawsonii (A.B.Joly) Barros-Barreto & F.P.Gomes; G, three cortical initial cells and two descending filaments, Centroceras gasparrinii; H, four cortical initial cells, Stirkia fujiana (Barros-Barreto & Maggs) Barros-Barreto & Maggs, comb. nov.; I, four cortical initial cells and descending filaments, Corallophila atlantica; J, five cortical initials including three descending filaments, Ceramium secundatum Lyngbye; K, Yoneshiguea affinis (Setchell & Gardner) Barros-Barreto, Maggs & M.A.Jaramillo, comb. nov. without descending filaments; L, one descending filament per periaxial cell, Gayliella dawsonii (A.B.Joly) Barros-Barreto & F.P.Gomes; M, two descending filaments, Stirkia fujiana (Barros-Barreto & Maggs) Barros-Barreto & Maggs, comb. nov.; N, five cortical initial cells, the fifth one over the periaxial cell, Stirkia codicola (J.Agardh) Barros-Barreto & Maggs, comb. nov.; O, transverse section showing four periaxial cells, Yoneshiguea compta (Børgesen) Barros-Barreto, Maggs & M.A.Jaramillo, comb. nov.; P, transverse section showing six periaxial cells,Stirkia brasiliensis (A.B.Joly) Barros-Barreto & Maggs, comb. nov.; Q, transverse section showing nine periaxial cells, Ceramieae sp. 5; R, transverse section showing 14 periaxial cells, Centroceras gasparrinii. Abbreviations: a1, first acropetal cell; a2, second acropetal cell; b1, first basipetal cell; b2, second basipetal cell; b3, third basipetal cell; p, periaxial cell. Scale bars: B, 500 μm; C, D, 200 μm; K, L, M, O-R, 100 μm.
FIGURE S3 in Phylogenetic analysis of the red algal tribe Ceramieae reveals multiple morphological homoplasies but defines new genera
FIGURE S3. — Reconstructed phylogeny of Ceramieae based on concatenated rbcL, LSU and COI-5P gene sequences. Majority rule consensus tree resulting from Bayesian analysis. Values at the nodes represent posterior probability and bootstrap values for ML, support lower than 0.70 (PP) and 75 (BP) are not shown. Sequences generated in this study are in bold. Abbreviations: See Figure 3. Symbol: *, full support.
FIG. 2 in Phylogenetic analysis of the red algal tribe Ceramieae reveals multiple morphological homoplasies but defines new genera
FIG. 2. — Phylogenetic reconstruction of the red algal tribe Ceramieae C.Agardh ex Greville inferred from rbcL gene sequences showing genera. The tree is the majority rule consensus tree resulting from Bayesian analysis. Values at the nodes represent posterior probability and bootstrap values for ML, support lower than 0.70 (PP) and 75 (BP) are not shown. Symbol: *, full support.
FIGURE S5 in Phylogenetic analysis of the red algal tribe Ceramieae reveals multiple morphological homoplasies but defines new genera
FIGURE S5. — Bayesian tree inferred from COI-5P sequences. The trees are the majority rule consensus tree resulting from Bayesian analysis. Values at the nodes represent posterior probability and bootstrap values for ML, support lower than 0.70 (PP) and 75 (BP) are not shown. Sequences generated in this study are in bold. Abbreviations: See Figure 3. Symbol: *, full support.
FIGURE S2 in Phylogenetic analysis of the red algal tribe Ceramieae reveals multiple morphological homoplasies but defines new genera
FIGURE S2. — Phylogenetic reconstruction of the red algal tribe Ceramieae inferred from rbcL gene sequences (Part 2). The tree is the majority rule consensus tree resulting from Bayesian analysis. Values at the nodes represent posterior probability and bootstrap values for ML, support lower than 0.70 (PP) and 75 (BP) are not shown. Sequences generated in this study are in bold. Abbreviations: See Figure 3. Symbol: *, full support.
FIGURE S1 in Phylogenetic analysis of the red algal tribe Ceramieae reveals multiple morphological homoplasies but defines new genera
FIGURE S1. — Phylogenetic reconstruction of the red algal tribe Ceramieae inferred from rbcL gene sequences (Part 1). The tree is the majority rule consensus tree resulting from Bayesian analysis. Values at the nodes represent posterior probability and bootstrap values for ML, support lower than 0.70 (PP) and 75 (BP) are not shown. Sequences generated in this study are in bold. Abbreviations: See Figure 3. Symbol: *, full support.
FIGURE S4 in Phylogenetic analysis of the red algal tribe Ceramieae reveals multiple morphological homoplasies but defines new genera
FIGURE S4. — Bayesian tree inferred from partial LSU gene. The trees are the majority rule consensus tree resulting from Bayesian analysis. Values at the nodes represent posterior probability and bootstrap values for ML, support lower than 0.70 (PP) and 75 (BP) are not shown. Sequences generated in this study are in bold. Abbreviations: See Figure 3. Symbol: *, full support.
Fig. 1. Phylogenetic relationships of species of Eusurbus and Zentamyia. Tree generated from morpho- logical phylogenetic analysis, unambiguous apomorphies mapped on branches, black circles indicate non- homoplasious changes.
Fig. 1. Phylogenetic relationships of species of Eusurbus and Zentamyia. Tree generated from morpho- logical phylogenetic analysis, unambiguous apomorphies mapped on branches, black circles indicate non- homoplasious changes.
Functional assessment of morphological homoplasy in stem-gnathostomes
<p>The Osteostraci and Galeaspida are stem gnathostomes, occupying a key phylogenetic position for resolving the nature of the jawless ancestor from which jawed vertebrates evolved more than 400 million years ago. Both groups are characterized by the presence of rigid headshields that share a number of common morphological traits, in some cases hindering the resolution of their interrelationships and the exact nature of their affinities with jawed vertebrates. Here, we explore the morphological and functional diversity of osteostracan and galeaspid headshields using an innovative approach that combines geometric morphometrics and computational fluid dynamics, thereby constraining the underlying factors that promoted the evolution of their similar morphologies and informing on the ecological scenario under which jawed vertebrates emerged. Phylomorphospace, Mantel analysis and Stayton metrics demonstrate a high degree of homoplasy. Computational fluid dynamics reveals similar hydrodynamic performance among morphologically convergent species, indicating the independent acquisition of the same morphofunctional traits and, potentially, equivalent lifestyles. This confirms that a number of the characters typically used to infer the evolutionary relationships among galeaspids, osteostracans and jawed vertebrates are convergent in nature, potentially obscuring understanding of the assembly of the gnathostome bodyplan. Ultimately, our results reveal that while the jawless relatives of the earliest jawed vertebrates were ecologically diverse, widespread convergence on the same hydrodynamic adaptations suggests they had reached the limits of their potential ecological diversity – overcome by jawed vertebrates and their later innovations.</p>
Data from: Whole-genome phylogenetic reconstruction as a powerful tool to reveal homoplasy and ancient rapid radiation in waterflea evolution
<p>The Supplementary Material (and text) to Van Damme et al., contains 10 Supplementary Figures (Figs S1-S10), 5 Supplementary Tables (Tables S1-S5), Supplementary Materials and Methods (ST1), Supplementary Discussion (ST2) and a complete reference list to the manuscript and supplement (Supplementary References SR1). All Supplementary material and text have been peer-reviewed as part of the manuscript. The supplementary discussion provides an additional framework including the importance of the findings of the phylogenomic study for the interpretation of evolution in the Cladocera.</p>
Functional assessment of morphological homoplasy in stem-gnathostomes
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Data from: Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae)
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Data from: Whole-genome phylogenetic reconstruction as a powerful tool to reveal homoplasy and ancient rapid radiation in waterflea evolution
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FIGURE 12 in A phylogeny and classification of the Talitroidea (Amphipoda, Senticaudata) based on interpretation of morphological synapomorphies and homoplasies
FIGURE 12. Indian Ocean. # indicates terrestrial. + indicates coastal. Red indicates Protorchestoidae taxa. Blue indicates Talitroidae taxa.
FIGURE 9 in A phylogeny and classification of the Talitroidea (Amphipoda, Senticaudata) based on interpretation of morphological synapomorphies and homoplasies
FIGURE 9. South Atlantic Ocean. # indicates terrestrial. + indicates coastal. Red indicates Protorchestoidae taxa. Blue indicates Talitroidae taxa.
FIGURE 8 in A phylogeny and classification of the Talitroidea (Amphipoda, Senticaudata) based on interpretation of morphological synapomorphies and homoplasies
FIGURE 8. North Atlantic Ocean. # indicates terrestrial. + indicates coastal. Blue indicates Talitroidae taxa.
FIGURE 7 in A phylogeny and classification of the Talitroidea (Amphipoda, Senticaudata) based on interpretation of morphological synapomorphies and homoplasies
FIGURE 7. Cladogram of relationships in the Talitroidea. Significant synapomorphies are indicated (see table 1).
FIGURE 6. Epimera 1–3. 38.2 in A phylogeny and classification of the Talitroidea (Amphipoda, Senticaudata) based on interpretation of morphological synapomorphies and homoplasies
FIGURE 6. Epimera 1–3. 38.2 with slits (after Lowry & Myers 2013). Uropod 1 peduncle 39.1 with distolateral robust seta (after Friend 1987). Uropods 1 and 2 rami. 40.2 dorsally flattened (after Lowry & Baldanzi 2016). Uropod 2 exopod 43.2 with apical spear-shaped setae (after Momtazi et al. 2017); Telson. 48.1 tapering distally (after Duncan 1994); 48.2 rounded distally (after Friend 1987); 48.3 subrectangular (after Hurley 1957); 49.2 with apical robust setae only (after Duncan 1994, Hurley 1957); 49.3 with apical and marginal robust setae (after Friend 1987).
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