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- Werdelin, Lars, et al.
(författare)
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A comparison of two methods to study correlated discrete characters on phylogenetic trees
- 1996
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Ingår i: Cladistics. - 0748-3007 .- 1096-0031. ; 11, s. 265-277
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Tidskriftsartikel (refereegranskat)abstract
- We use a simulation approach to study two methods proposed for the analysis of correlated discrete characters on cladograms, the concentrated changes test (CCT) and the contingent states test (CST). Both of these consider the case where there is an independent and a dependent character and assign probabilities to various events in the dependent character given one or the other state of the independent character. The CCT gives different results for symmetric and asymmetric cladograms. In the latter case, the proportion of branches reconstructed as having the derived state has less influence on the resulting probabilities. The CST is only sensitive to the proportion of derived branches, regardless of whether the tree is symmetric or asymmetric. The CCT calculates probabilities by considering character state reconstructions which are not allowed by parsimony algorithms, thereby increasing the probability of rejecting a true null hypothesis (type I error rate). We discuss some alternative questions that could be studied using these tests and also derive equations for calculating the number of possible events in the dependent character for unresolved parts of the phylogeny.
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- Bjorklund, M
(författare)
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Are third positions really that bad? A test using vertebrate cytochrome b
- 1999
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Ingår i: CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY. - : ACADEMIC PRESS LTD. - 0748-3007. ; 15:2, s. 191-197
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In the analysis of coding DNA sequences for phylogenetic purposes 3rd positions are commonly downweighted, or excluded, and 2nd positions are likewise given high weight. The basis of this is a belief that the larger numbers of 3rd position substitutions i
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- Bremer, B
(författare)
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Combined and separate analyses of morphological and molecular data in the plant family Rubiaceae
- 1996
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Ingår i: CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY. - : ACADEMIC PRESS LTD. - 0748-3007. ; 12:1, s. 21-40
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The Rubiaceae are one of the largest of the families of angiosperms, with over 10000 species. The tribal and subfamilial classification is provisional due to the lack of phylogenetic hypotheses. The present study of the Rubiaceae is based on 33 genera and
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- Pleijel, Fredrik, 1955, et al.
(författare)
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Position and delineation of Chrysopetalidae and Hesionidae (Annelida, polychaeta, Phyllodocida)
- 1998
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Ingår i: Cladistics-the International Journal of the Willi Hennig Society. - 0748-3007. ; 14:2, s. 129-150
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies suggest that the polychaete taxa Hesionidae and Chrysopetalidae may not represent separate groups, that Pilargidae constitute a subgroup within Hesionidae, and that Hesionides and Microphthalmus are highly derived hesionids. Phylogenetic systematic analyses of Phyllodocida and the subgroup Nereidiformia are presented in order to clarify the position and delineation of these taxa. The phyllodicida analysis includes 18 families representing the majority of the taxa in the group, is rooted with Onuphidae, and is based on 42 absent/ present coded morphological characters, obtained mainly from literature. All 69 resulting shortest trees include the clade (Chrysopetalidae, Nereididae, Hesionidae), but with either Syllidae, Nautiliniellidae, Pilargidae or (Aphroditiformia, Pisionidae) as sister. In- and outgroup taxon selection for the Nereidiformia study is dictated by the outcome of Phyllodocida analysis, with scores based on examined species of two chrysopetalids, four hesionids, one nereid, one pilargid, one pisionid, one syllid, plus the putative hesionids Hesionides arenaria and Microphthalmus sp. It is based on 46 absent/present coded morphological characters. Two equally parsimonious trees indicate that chrysopetalids and hesionids are well delineated, that pilargids and hesionids are non-overlapping, and that Microphthalmus and Hesionides are not hesionids. (C) 1998 The Willi Hennig Society.
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- Ronquist, F
(författare)
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Fast Fitch-parsimony algorithms for large data sets
- 1998
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Ingår i: CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY. - : ACADEMIC PRESS LTD. - 0748-3007. ; 14:4, s. 387-400
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The speed of analytical algorithms becomes increasingly important as systematists accumulate larger data sets. In this paper I discuss several time-saving modifications to published Fitch-parsimony tree search algorithms, including shortcuts that allow ra
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- Ronquist, F
(författare)
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Three-dimensional cost-matrix optimization and maximum cospeciation
- 1998
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Ingår i: CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY. - : ACADEMIC PRESS LTD. - 0748-3007. ; 14:2, s. 167-172
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In recent years, event-based approaches have been gaining ground in coevolutionary and biogeographical inference. Unlike pattern-based methods, event-based protocols deal directly with evolutionary events, such as dispersals and host switches. Three proto
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