| 1. |
- Härlin, Mikael
(författare)
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On the relationship between content, ancestor, and ancestry in phylogenetic nomenclature
- 2003
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Ingår i: Cladistics. - 0748-3007 .- 1096-0031. ; 19:2, s. 144-147
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Tidskriftsartikel (refereegranskat)abstract
- In this paper I draw attention to the concepts of content and ancestry in phylogenetic nomenclature. I argue that these concepts are tightly linked and that they cannot be separated as suggested by Bryant and Cantino [Biol. Rev. 77 (2002) 39] in their recent response to a critique of phylogenetic nomenclature. In addition, I argue that the basic assumption in phylogenetic nomenclature that a taxon-name always refers to the same ancestor or ancestry is questionable.
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| 2. |
- Härlin, Mikael
(författare)
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Taxon names as paradigms : the structure of nomenclatural revolutions
- 2003
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Ingår i: Cladistics. - 0748-3007 .- 1096-0031. ; 19:2, s. 138-143
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Tidskriftsartikel (refereegranskat)abstract
- In the present paper I argue that the two systems of phylogenetic nomenclature hitherto proposed represent, in a generalized sense, two different philosophies for how science develops and progresses. The phylogenetic system of definition. initially proposed by de Queiroz and Gauthier [Syst. Zool. 39 (1990) 307], and later labeled PSD, is typically Popperian in the 'sense that science progresses toward truth by An accumulation of knowledge. Phylogenetic definitions of taxon names are assumed to adapt automatically to each new hypothesis of phylogeny, thereby reflecting better and better hypotheses. The phylogenetic system of reference proposed by Harlin [Zool. Scr. 27 (1998a) 381], on the other hand, is more Kuhnian, because it is built on the idea that successive hypotheses are incommensurable (and thus not cumulative) and that taxon names might be equalled with low-level paradigms.
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| 3. |
- Rousset, V., et al.
(författare)
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The phylogenetic position of Siboglinidae (Annelida) inferred from 18S rRNA, 28S rRNA and morphological data
- 2004
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Ingår i: Cladistics. - : Wiley. - 0748-3007 .- 1096-0031. ; 20:6, s. 518-533
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Tidskriftsartikel (refereegranskat)abstract
- We assess the phylogenetic position of Siboglinidae (previously known as the phyla Pogonophora and Vestimentifera, but now referred to Annelida) in parsimony analyses of 1100 bp from 18S rRNA, 320 bp from the D1 region of 28S rRNA, and 107 morphological characters, totaling 667 parsimony informative characters. The 34 terminal taxa, apart from six siboglinids, include polychaete members of Sabellida, Terbelliformia, Cirratuliformia and Spionida, plus two Aciculata polychaetes as outgroups. Our results contradict most recent hypotheses in showing a sistergroup relationship between Siboglinidae and Oweniidae, and in that the latter taxon is not a member of Sabellida. Furthermore, our results indicate that Sabellariidae is not closely related to Sabellida, that Serpulidae may be nested within Sabellidae. and that Alvinellidae is nested within Ampharetidae. (c) The Willi Hennig Society 2004.
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| 4. |
- Wallberg, Andreas, et al.
(författare)
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The phylogenetic position of the comb jellies (Ctenophora) and the importance of taxonomic sampling
- 2004
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Ingår i: Cladistics. - : Wiley. - 0748-3007 .- 1096-0031. ; 20:6, s. 558-578
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Tidskriftsartikel (refereegranskat)abstract
- The transition to a vermiform body shape is one of the most important events in animal evolution, having led to the impressive radiation of Bilateria. However, the sister group of Bilateria has remained obscure. Cladistic analyses of morphology indicate that Ctenophora is the sister group of Bilateria. Previous analyses of SSU rRNA sequences have yielded conflicting results; in many studies Ctenophora forms the sister group of Cnidaria + Bilateria, but in others the ctenophores group with poriferans. Here we re-examine the SSU sequence by analyzing a dataset with 528 metazoan + outgroup sequences, including almost 120 poriferan and diploblast sequences. We use parsimony ratchet and jackknife methods, as well as Bayesian methods, to analyze the data. The results indicate strong phylogenetic signals for a cnidarian + bilaterian group and for the comb jellies to have branched off early within a group uniting all epithelial animals [(Ct,(Cn,Bi))]. We demonstrate the importance of inclusive taxonomic coverage of ribosomal sequences for resolving this problematic part of the metazoan tree: topological stability increases dramatically with the addition of taxa, and the jackknife frequencies of the internal nodes uniting the lineages [(Cn,Bi) and ((Ct,(Cn,Bi))] also increase. We consider the reconstructed topology to represent the current best hypothesis of the interrelationships of these old lineages. Some morphological features supporting alternative hypotheses are discussed in the light of this result.
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| 5. |
- Ast, Jennifer C
(författare)
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Mitochondrial DNA evidence and evolution in Varanoidea (Squamata)
- 2001
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Ingår i: Cladistics. - : Wiley. - 0748-3007 .- 1096-0031. ; 17:3, s. 211-226
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Tidskriftsartikel (refereegranskat)abstract
- Varanoidea is a monophyletic group of anguimorph lizards, comprising the New World helodermatids, the Bornean earless monitor Lanthanotus borneensis, and the Old World monitors (Varanus). I use mitochondrial DNA sequences and extensive taxonomic sampling to test alternative hypotheses of varanoid relationships. The most parsimonious hypothesis confirms the monophyly of Varanoidea (Heloderma, Lanthanotus, and Varanus) and Varanus, as well as the sister-taxon relationship of Varanus and Lanthanotus. The relationships among Varanus species differ in several respects from previous hypotheses. Three major lineages are recognized within Varanus: an African clade basal to the rest of the group, an Indo-Asian clade, and an Indo-Australian clade. Within the last lineage, the endemic Australian dwarf monitors (Odatria) form a clade sister to the large Australian monitors (the gouldii group). Tests of the effects of rate heterogeneity and homoplasy demonstrate that putative process partitions of data are largely congruent with one another and contribute positive support to the overall hypothesis.
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| 6. |
- Swenson, Ulf, et al.
(författare)
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Nothofagus biogeography revisited with special emphasis on the enigmatic distribution of subgenus Brassospora in New Caledonia
- 2001
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Ingår i: Cladistics. - 0748-3007 .- 1096-0031. ; 17:1, s. 28-47
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Tidskriftsartikel (refereegranskat)abstract
- Dispersals versus vicariance events and the presence of subgenus Brassospora in New Caledonia are two riddles of Nothofagus biogeography, a genus also distributed in New Guinea, New Zealand, South America, Southeast Australia, and Tasmania, Within a cladistic framework using the software COMPONENT 2.0, we demonstrate that most parsimonious area cladograms (areagrams) sensu cladistic biogeography need not always be the most plausible explanation nor reflect alternative geological hypotheses, The most parsimonious Nothofagus history sensu historical biogeography is reconstructed where a minimum of dispersed taxa is hypothesized and vicariance events are identified. A fully resolved well-established Nothofagus phylogeny was reconciled with three geological hypotheses (geograms) of East Gondwana break-up: (a) the conventional view (b) an Australian-New Caledonian relationship, and (c) a biotic interchange between New Guinea and New Caledonia. Fossils determined to subgenus were optimized to the predicted lineages in the reconciled tree. Due to extensive extinctions, a maximum of three vicariance events are inferred, all being basal in the subgenera, an indication of subgeneric diversification prior to the break-up of Gondwana. Two taxa, N. gunnii and N. menziesii, are hypothesized as being long-distance dispersed, The most parsimonious solution suggests a close relationship between New Guinea and New Caledonia, supporting a Brassospora colonization route, but this hypothesis fails to predict numerous extinct lineages observed in the fossil record and thus must be rejected. The traditional break-up sequence of Gondwana is not the most parsimonious solution, indicating one incongruent node, but causes no overall incongruence with the fossil record, Considering all parameters, the occurrence of Brassospora in New Caledonia is most parsimoniously explained as a single colonization event from New Zealand where the subgenus subsequently went extinct in the Pliocene.
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| 9. |
- Stenroos, S, et al.
(författare)
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Phylogeny of the genus Cladonia s.lat. (Cladoniaceae, Ascomycetes) inferred from molecular, morphological, and chemical data
- 2002
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Ingår i: Cladistics. - 1096-0031. ; 18:3, s. 237-278
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Forskningsöversikt (refereegranskat)abstract
- Phylogenetic relationships within the genus Cladonia, including Cladina (Cladoniaceae, Lecanoromycetes), were reconstructed based upon simultaneous analyses of DNA sequences and morphological and chemical data. We used sequences from the internal transcribed spacer 1 (ITS1), the 5.8 rDNA gene, and the internal transcribed spacer 2 (ITS2) of the nuclear rDNA gene cluster, and partial sequences from the protein-coding beta-tubulin gene. The analyses included 235 specimens of 168 taxa representing all currently recognized sections of Cladonia and Cladina and the outgroup genera Cladia, Pycnothelia, and Rainalea. Analyses were performed using optimization alignment with three different parameter values. The results of all analyses support the inclusion of Cladina in Cladonia. The current sectional division of Cladonia was not supported, and a new provisional classification for the genus is proposed.
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