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The Compleat Cladist
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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. ...
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. ...
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). ...
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.
... Lieberman (1997Lieberman ( , 2002a tested this proposition in greater detail using a phylogenetic paleobiogeographic approach to analyze trilobites, the most diverse and abundant Early Cambrian animals. These analyses used a modified version of Brooks Parsimony Analysis (BPA); BPA is described in detail by Brooks (1985), Wiley (1988), Funk and Brooks (1990), McLennan (1991, 2002), and Wiley et al. (1991), while the modified version of BPA is described in detail by Lieberman and Eldredge (1996) and Lieberman (1997Lieberman ( , 2000. In essence, the modified version of BPA works by taking the phylogenies of organisms, converting these to area cladograms by substituting the species name with its geographic distribution, and then coding this information into two data matrices: one designed to retrieve congruent episodes of vicariance and one designed to retrieve congruent episodes of geo-dispersal. ...
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.
Phylogenetic relationships of important trichothecene-producing strains originally identified as Fusarium nivale Fn-2, Fn-3 and Fn-2B and F. episphaeria Fn-M were investigated within the Gibberella lineage of Fusarium using nucleotide characters obtained by sequencing polymerase chain reaction (PCR) DNA amplified from the following 4 loci: nuclear 28S ribosomal DNA, nuclear ribosomal internal transcribed spacer (ITS) region, mitochondrial small subunit (mtSSU) ribosomal DNA, and β-tubulin gene exons and introns. Parsimony analysis of the individual and combined data sets indicate that Fn-2, Fn-3, Fn-2B, and Fn-M represent an undescribed species of Fusarium. Bootstrap and decay analysis identified a clade containing F. sambucinum and several other diacetoxyscipenol (DAS) and/or T-2 trichothecene-producing species as a sister to Fusarium sp. n. The outgroup species used to root the tree, by contrast, produce a different set of mycotoxins that include deoxynivalenol and zearalenone. These results emphasize the importance of investigating the evolution of Fusarium toxins the contex of a robust species-level phylogeny.
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
The variation in microscopic characters of plumulaceous feathers is well known to be useful as an aid in species identifications. However, until now, the phylogenetic significance of these characters has not been thoroughly investigated. In the first part of this study, electron and light microscopy were used to examine the range of variation in downy feather characters of more than 145 species of shorebirds (Charadriiformes) and outgroup taxa. The major results of Part 1 demonstrate that similarities and differences exist in the microscopic features within this order, that different downy types (true down vs. contour feather down) of the same individual may have different microscopic structures, that some shorebirds have villi (previously unknown on the barbule bases of this group), and 38 microscopic feather characters are deemed useful for phylogenetic study. In Part 2, parsimony analysis was used to assess the phylogenetic value of these characters by comparing feather results to hypotheses based on osteological data and traditional classification. Three different taxa lists are analyzed using the computer software PAUP, Star (*) version. Although initial analyses of 111 taxa and 38 feather characters found more than 10,000 equally parsimonious trees, the analyses provided evidence that feather characters were tracking some natural groupings in this order. Additional analyses on two smaller sets of taxa used feather characters alone (38 characters), osteological characters alone (68 characters), and a combination of both character types to search for shortest trees. The final reduced-taxa analysis shows that feather character tree statistics and character indices are comparable to those of skeletal characters. Incongruence in tree topologies is noted in the placement of plovers with sandpipers according to feather characters. Indices of total-evidence trees for 154 shortest trees are higher than either of the data sets alone. Convergence in microscopic feather characters of loons and auks has been documented here for the first time and a functional hypothesis for nodal morphology is proposed. In this study of Charadriiformes, microscopic feather characters prove to be comparable to osteological characters in tracking phylogeny. However, better results are achieved when the data sets are combined. These results support the utility of microscopic feather characters in phylogenetic studies and in microscopic identification of avian species from fragmentary evidence.
Phylogenetic relationships among ascomycetous truffles and the true and false morels were examined by using sequences from two nuclear encoded ribosomal DNA genes. The data consist of 18S rDNA and partial 28S rDNA sequences for 29 taxa. Individual and combined data sets were analyzed by maximum parsimony (MP), neighbor-joining (NJ) and maximum likelihood (ML) methods. Parsimony analysis of the combined data set, which contained 3 published 18S sequences and consisted of 2358 nucleotide characters, yielded a single most parsimonious tree of 1728 steps. The results indicate that the hypogeous ascomycetous truffle and trufflelike taxa studied represent at least 5 independent lineages within the Pezizales. Results also suggest that several epigeous and most hypogeous taxa have been misplaced taxonomically. Bootstrap analyses show strong support for a Tuberaceae-Helvellaceae clade which is a monophyletic sister group of a Morchellaceae-Discinaceae clade. Rhizina is a sister group to both of these clades in the MP and ML trees while in the NJ tree it is a sister of the Morchellaceae-Discinaceae clade. MP, ML, and NJ tree topologies indicate that Rhizina should be removed from the Helvellaceae and classified in a monotypic family, the Rhizinaceae. A phylogenetically-based classification for these fungi is proposed together with emendations of 4 families.
Paleontology has undergone a renaissance in the past 50 years, expanding from an empirical field focused on stratigraphic context to the theoretically grounded discipline of paleobiology. This transformation has been propelled by conceptual advances in two broadly construed areas, evolution and paleoecology. Phylogenetic systematic has revised our understanding of the evolutionary relationships among organisms. New understanding of tempo and mode in evolution, evolutionary hierarchies, the role of mass extinctions and recoveries, and developmental evolution has led to unexpected insights on evolutionary processes. Within paleoecology, taphonomy has led to greater understanding of the nature of the fossil record. Evolutionary paleoecologists have unearthed temporal and spatial patterns, at various scales, in diversity and community organization and have investigated the processes responsible for them. Other advances in paleoecology involve trace fossils; paleobiogeography; novel uses of fossils in understanding the environment; and the new discipline of conservation paleobiology. New concepts have been furthered by incorporating tools from other disciplines, including quantitative analytical methods, biostratigraphic innovations, geochemical and molecular tools, and advanced microscopy techniques. Fueling these advances are fossil discoveries revealing previously unknown Archean-Proterozoic worlds, detailed accounts of the explosion of life in the Cambrian, and fl oras and faunas yielding surprising and unexpected insights into the origins and evolution of important plant and animal groups.
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.
