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... To abide by the independence principle, we prefer the "reductive coding" approach rather than "composite coding", as suggested by Wilkinson (1995), but not go to the extreme that binary absence/presence coding be finally reached as advocated by Pleijel (1995). In fact, linear and branching multistate transformation series as proposed by Wiley et al. (1991) are equally well applicable as binary coding, depending on circumstances. Only when covariation of characters can be positively assumed, "composite coding" can be allowed. ...
... For example, the particularly long labial border of the M1 in Ballusia orientalis is such an autapomorphy. 3) Contrary to the common tendency to prefer the maximally connected (= unordered) characters in cladistic analysis, Slowinski (1993) strongly advocated that "multistate characters are treated as minimally connected (= ordered linear and branching transformation series of Wiley et al. [1991]) whenever reasonable." Slowinski's suggestion is adopted here in view of the fact that the evolutionary history (polarity and additive steps) of the multistate characters used in our matrix is fairly well known in ursid animals. ...
... Accordingly, additive coding assumption is used here for most of the linear multistate characters. 4) While dealing with the complex "branching transformation series," instead of using nonadditive binary coding or mixed coding as suggested by Wiley et al. (1991), we employ the "reductive coding" approach to partition composite character into smaller binary or linear transformation series according to the diverging evolutionany directions of the character (see characters 7-13 in Appendix 2). However, there is the possibility of producing "inapplicable" states alternatively in one of the two transformation series. ...
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An almost complete Ursavus skull in association with its mandible is described. The skull was recently found from upper part of Liushu Formation in Linxia Basin. Its stratigraphic level and geologic age are correlated to the late Bahean ALMA/S, ~8 Ma. It represents a new species, here named Ursavus tedfordi. Cladistic analysis is conducted using the TNT software, based on a matrix of 11 taxa and 37 characters. The tree 5 of the 8 most parsimonious trees is chosen as the most reliable to reflect the phylogenetic history of the ursid clade. As the tree 5 shows, after divergence from the Oligocene-Early Miocene hemicyonids (Cephalogale), the ursid clade first yielded two stem-taxa: Ballusia elmensis and B. orientalis, the latter of which being an aberrant branch. Then, two major subclades emerged: one comprising Kretzoiarctos, Agriarctos and Ailurarctos, the other containing all Ursavus species and their descendants including all living bears (excluding Ailuropoda). Kretzoiarctos may not be the direct ancestral form of the giant panda as Abella and colleagues (2012) suggested, but the ancestral form of the lineage of Indarctos (+Agriotherium ?). Among the numerous Ursavus species, U. tedfordi is the most advanced and closest related to the living bears (excluding Ailuropoda) in morphology, however, might belong to a side-branch, judging by the autapomorphies possessed by it.
... To abide by the independence principle, we prefer the "reductive coding" approach rather than "composite coding", as suggested by Wilkinson (1995), but not go to the extreme that binary absence/presence coding be finally reached as advocated by Pleijel (1995). In fact, linear and branching multistate transformation series as proposed by Wiley et al. (1991) are equally well applicable as binary coding, depending on circumstances. Only when covariation of characters can be positively assumed, "composite coding" can be allowed. ...
... For example, the particularly long labial border of the M1 in Ballusia orientalis is such an autapomorphy. 3) Contrary to the common tendency to prefer the maximally connected (= unordered) characters in cladistic analysis, Slowinski (1993) strongly advocated that "multistate characters are treated as minimally connected (= ordered linear and branching transformation series of Wiley et al. [1991]) whenever reasonable." Slowinski's suggestion is adopted here in view of the fact that the evolutionary history (polarity and additive steps) of the multistate characters used in our matrix is fairly well known in ursid animals. ...
... Accordingly, additive coding assumption is used here for most of the linear multistate characters. 4) While dealing with the complex "branching transformation series," instead of using nonadditive binary coding or mixed coding as suggested by Wiley et al. (1991), we employ the "reductive coding" approach to partition composite character into smaller binary or linear transformation series according to the diverging evolutionany directions of the character (see characters 7-13 in Appendix 2). However, there is the possibility of producing "inapplicable" states alternatively in one of the two transformation series. ...
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An almost complete Ursavus skull in association with its mandible is described. The skull was recently found from upper part of Liushu Formation in Linxia Basin. Its stratigraphic level and geologic age are correlated to the late Bahean ALMA/S, ~8 Ma. It represents a new species, here named Ursavus tedfordi. Cladistic analysis is conducted using the TNT software, based on a matrix of 11 taxa and 37 characters. The tree 5 of the 8 most parsimonious trees is chosen as the most reliable to reflect the phylogenetic history of the ursid clade. As the tree 5 shows, after divergence from the Oligocene-Early Miocene hemicyonids (Cephalogale), the ursid clade first yielded two stem-taxa: Ballusia elmensis and B. orientalis, the latter of which being an aberrant branch. Then, two major subclades emerged: one comprising Kretzoiarctos, Agriarctos and Ailurarctos, the other containing all Ursavus species and their descendants including all living bears (excluding Ailuropoda). Kretzoiarctos may not be the direct ancestral form of the giant panda as Abella and colleagues (2012) suggested, but the ancestral form of the lineage of Indarctos (+Agriotherium ?). Among the numerous Ursavus species, U. tedfordi is the most advanced and closest related to the living bears (excluding Ailuropoda) in morphology, however, might belong to a side-branch, judging by the autapomorphies possessed by it.
... Vezda) was examined to produce the final data matrix. A set of 49 characters was extracted, with most characters coded in binary fashion (Wiley et al., 1991; Poe and Wiens, 2000; Lücking et al., 2005), except for quantitative features for which unordered multistate characters were defined (Table 3). Gaps were treated either as additional character (for inapplicable data) or as missing data (in case of taxa for which information on apothecia or pycnidia was unavailable). ...
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A treatment of filamentous and crustose species of the lichen genus Coenogonium in Costa Rica is presented, reporting a total of 48 taxa, including seven of unresolved taxonomic status. Eight species and one form are described as new to science: C. aciculatum Lücking & Aptroot sp. nov., C. barbatum Lücking, Aptroot & Umaña sp. nov., C. byssothallinum Aptroot & Lücking sp. nov., C. kalbii Aptroot, Lücking & Umaña sp. nov., C. luteocitrinum Rivas Plata, Lücking & Umaña sp. nov., C. magdalenae Rivas Plata, Lücking & Lizano sp. nov., C. saepincola Aptroot, Sipman & Lücking sp. nov., C. siquirrense f. denticulatum Rivas Plata & Lücking f. nov., C. strigosum Rivas Plata, Lücking & Chaves sp. nov. The following new combinations and nomenclatural novelties are introduced: C. antonianum Lücking, Aptroot & Sipman nom. nov., C. atroluteum (Vain.) Lücking, Aptroot & Sipman comb. nov., C. bacilliferum (Malme) Lücking, Aptroot & Sipman comb. nov., C. degeneri (Kalb & Vezda) Kalb & Lücking comb. nov., C. eximium (Vezda) Kalb & Lücking comb. nov., C. frederici (Kalb) Kalb & Lücking comb. nov., C. isidiatum (G. Thor & Vezda) Lücking, Aptroot & Sipman comb. nov., C. isidiigerum (Vezda & Osorio) Lücking, Aptroot & Sipman comb. nov., C. isidiosum (Breuss) Rivas Plata, Lücking, Umana & Chaves comb. nov., C. luteolum (Kalb) Kalb & Lücking comb. nov., C. nepalense (G. Thor & Vezda) Lücking, Aptroot & Sipman comb. nov., C. perminutum (Malme) Lücking, Aptroot & Sipman comb. et stat. nov., C. persistens (Malme) Lücking, Aptroot & Sipman comb. et stat. nov., C. pertenue (Stirt.) Kalb & Lücking comb. nov., C. pocsii (Vezda & Farkas) Lücking, Aptroot & Sipman comb. nov., C. pusillum (Mont.) Lücking, Aptroot & Sipman comb. nov., C. pyrophthalmum (Mont.) Lücking, Aptroot & Sipman comb. nov., C. stenosporum (Malme) Lücking, Aptroot & Sipman comb. nov., C. stramineum (Aptroot & Seaward) Lücking, Aptroot & Sipman comb. nov., C. subdentatum (Vezda & G. Thor) Rivas Plata, Lücking, Umana & Chaves comb. nov., C. subdilutum (Malme) Lücking, Aptroot & Sipman comb. nov., C. subfallaciosum (Vezda & Farkas) Lücking, Aptroot & Sipman comb. nov., C. subsquamosum (Aptroot & Seaward) Lücking, Aptroot & Sipman comb. nov., C. tavaresianum (Vezda) Lücking, Aptroot & Sipman comb. nov., and C. weberi (Vezda) Lücking, Aptroot & Sipman comb. nov. Coenogonium complexum Nyl. is established as a synonym of C. tuckermanii. Ten species are new records for Costa Rica. A phenotype-based cladistic analysis of 54 taxa using 49 characters supports merging Dimerella with Coenogonium and suggests polyphyletic origin of species with filamentous thallus structure. As additional result of our studies, we present a world-wide working key to the 82 accepted species of Coenogonium and an updated checklist including the status of 186 further names in Coenogonium and its twelve generic synonyms Biatorinopsis, Byssiplaca, Coenogoniomycella, Coenogoniomyces, Coenomycogonium, Didymopycnomyces, Dimerella, Flabellomyces, Holocoenis, Lecaniopsis, Microphiale, and Mycocoenogonium.
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Fossil odontocete cetaceans of the genus Kentriodon are small delphinoid of the extinct family Kentriodontidae. This genus has been previously reported from the Middle Miocene Rosarito Beach Formation in the area of La Misión in Baja California, México; however, the systematics of the specimens have not been described previously. The species from this deposit is here named Kentriodon diusinus, new species, and is based on cranial and postcranial material. This species belongs in the subfamily Kentriodontinae, and it is the first described species of Kentriodontidae from México. A computer-assisted phylogenetic analysis using the software PAUP* (Phylogeneic Analysis Using Parsimony and other methods) shows that K. diusinus is most closely related to Kentriodon obscurus, which is known only from the Sharktooth Hill Local Fauna, derived from the Round Mountain Silt, in Kern County, central California, USA than any of the other species assigned to the genus Kentriodon.
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Phymaturus comprises 44 species mainly distributed along the south-west of South America on both sides of the Andes. In this study we present a phylogenetic analysis of Phymaturus of the palluma group, one of its two large clades, including almost all described species. This analysis duplicates the number of in-group taxa compared with previous contributions. We performed a total-evidence analysis, combining molecular and morphological characters: sequencing fragments of cytochome b (cytb), 12S, and ND4, for all terminals; describing 45 new morphological characters; and incorporating all DNA sequences available from GenBank. Separate analyses of morphology and DNA partitions are presented and discussed in detail. Seven subclades are recognized here. We named three new subclades and redefined another, found to be paraphyletic. In order to recognize lineages within the traditional Phymaturus palluma group we proposed to treat it as a natural group, containing within it the ranks of clade, subclade, and lineages, respectively. The palluma group is composed by the vociferator and the bibronii clades. The vociferator clade, composed of Chilean and Argentinean species, would be the most basal in the group. Within the bibronii clade, the roigorum subclade includes the Phymaturus verdugo lineage, whereas the mallimaccii subclade would consist of 13 terminal taxa, for which three Chilean species have been added. In this study, morphological apomorphies are identified for all clades and the evolution of ‘male head melanism’ is discussed. © 2015 The Linnean Society of London
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The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.